Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 101399
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:4713 original size:11 final size:11
Alignment explanation
Indices: 4697--4721 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4687 TGGTTTAGTG
4697 TTTTTTGAATT
1 TTTTTTGAATT
4708 TTTTTTGAATT
1 TTTTTTGAATT
4719 TTT
1 TTT
4722 CGTTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTGAATT
Left flanking sequence: Indices 4197 -- 4696
TCCAGATTTTGTTAATGTGATTTTTGTTGAATGGAGATCCTTTCACAAGAATGCATGGCTGTCTG
ACTAACACACACTGAGTTTCCATTATTTACCACAAACCCCTCCTGCGTCATTTTGTTTTCAAGGC
TCTACCCTTCCGGGTTATTGATTAAGTCGTAATAAATGACAAAAATTTTTTCCATAAGATTTGCT
AACTACGTACATAGATACGTAAGATCTTACTGTAAAACACAAGGAAAACATCAGCCAAACCAGAG
CGGTTGGAGGGAGAAGGCCGCCATAGGTAATGAAAGAGTATGAGGCATATAACGACGAGTTGCTA
GTGGGGTTGACCAAAGGGTAGCAGGAAATGGAACCCTGGTCTCTCACTCGTCGGGAGCATGTTAG
CCATTGACACTACCACCGAAATGGGCTCCCCCTCGGCAGTCGTCTCGTCCCCTTAGTTAATTATT
TTGGATTTTTTGTTTGTAGTGAAAGTCGGATTGTTTGGTTTAGTG
Right flanking sequence: Indices 4722 -- 5221
CGTTTTTTGGTCTCGAGACATCGATCATGCCATGCCCCTGCCCGTCTTGATGTATTCCAATTTGC
TCTTAATCCACTCCTAATAATACAACCAAAAGTTTGGACCTTCTTGAAGATATTGTAGGAAACCA
AGTCGGAACGAGTGCGTACTGTTGCCAGTCGCACGCTCCAGTCCTCGGGCGCCTAACCACTAGAT
GAGGATCGGAGTCATTATACAACAATATTGAGCTTGATAAGAAATGAAACAAAAAAAAATAAGTA
TTTAGTTAATTTTCGCGAAAAGTGAAAAAAAAAAAAAAAGTTGAAAAATTCTGCATTTGTCGTTG
TTGTGGAAGCAAGGTTGTTTCTCCAATCACGCGTGACGCAGTATGAGTTCGAATCGCACTAATGA
TGATTAACAATGGATAAGTGAACAATCTCTGATGTCAAACGACAATTTGATTAAGAAACCGCATG
CCTTCCTACTGATGAGCGATCAACGTTGATGCTCTACGTCTTTCA
Found at i:38036 original size:15 final size:15
Alignment explanation
Indices: 37982--38041 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
37972 CTTGACCACT
*
37982 GAGCAGCCCGCCCCC
1 GAGCAGCCCGCTCCC
37997 GAGCAGCCCGCTCCCTC
1 GAGCAGCCCGCT-CC-C
38014 G-GC--CCCTGCTCCC
1 GAGCAGCCC-GCTCCC
*
38027 GAGCAGCCTGCTCCC
1 GAGCAGCCCGCTCCC
38042 TCTTCTGCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 2 0.05
14 7 0.19
15 20 0.54
16 6 0.16
17 2 0.05
ACGTcount: A:0.10, C:0.55, G:0.25, T:0.10
Consensus pattern (15 bp):
GAGCAGCCCGCTCCC
Left flanking sequence: Indices 37482 -- 37981
ACTACCTAACGCCACAACTTAAAGCATATAAATATCATTAGCCCTGTCTCTATAATTTTCATCAC
TGTCTATCGCTTAAAATGAAGTTTTCTACCACTGCCGCTGCCCTCGCTATCGCCACCCCCGCTTT
GGCTCAGTACTCCAACGGCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTG
AGGACAACAAGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACC
GTGTACACCACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCC
CTCTGACGCTCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCT
CGTGCCACCCTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGAC
GTCGAGAACAAGACTGTGTACACCACTTACTGCCCCTTGACCACT
Right flanking sequence: Indices 38042 -- 38541
TCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCC
CGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCTGCCCCCACTGAGGCCGCCCCCGAGCAGC
CCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCTGCCCCCACTGAGGCCGCCCCCGAGCAG
CCCGCTCCCTCTTCCGCCGCCCCTGCCTCCGAGCAGCCCGCCCCTACTGAGGCTCCCGCCCCCAC
CACTCAGGAGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAAGGTTCCTACCATTGAGACCG
CCAACGGTGCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTGTCGCTTTCAACCTCTTGTAA
GTTGGGTGATTTCGTTATTTTCTAAATATTTCGGACTTTTAATACATTAATTTTGGGCTATACAA
TACCGGTTTTACAACCACCGTGCTTGTTTCCACTTGACTATTAAT
Found at i:38064 original size:36 final size:36
Alignment explanation
Indices: 37991--38281 Score: 350
Period size: 36 Copynumber: 8.6 Consensus size: 36
37981 TGAGCAGCCC
37991 GCCCCCGAGCAGCCCGCT--C-C--CT-CGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
* *
38021 GCTCCCGAGCAGCCTGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38057 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38093 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
* * *
38129 GCCCCCGAGCAGCCTGC-CCC-C-ACTGAGG--CC-
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38159 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
* * *
38195 GCCCCCGAGCAGCCTGC-CCC-C-ACTGAGG--CC-
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
* *
38225 GCCCCCGAGCAGCCCGCTCCCTCTTCCGCCGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
*
38261 GCCTCCGAGCAGCCCGC-CCCT
1 GCCCCCGAGCAGCCCGCTCCCT
38282 ACTGAGGCTC
Statistics
Matches: 224, Mismatches: 19, Indels: 31
0.82 0.07 0.11
Matches are distributed among these distances:
30 48 0.21
31 10 0.04
32 3 0.01
33 19 0.08
34 2 0.01
35 16 0.07
36 126 0.56
ACGTcount: A:0.08, C:0.56, G:0.23, T:0.14
Consensus pattern (36 bp):
GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
Left flanking sequence: Indices 37491 -- 37990
CGCCACAACTTAAAGCATATAAATATCATTAGCCCTGTCTCTATAATTTTCATCACTGTCTATCG
CTTAAAATGAAGTTTTCTACCACTGCCGCTGCCCTCGCTATCGCCACCCCCGCTTTGGCTCAGTA
CTCCAACGGCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTGAGGACAACA
AGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACCGTGTACACC
ACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCCCTCTGACGC
TCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCTCGTGCCACC
CTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGACGTCGAGAAC
AAGACTGTGTACACCACTTACTGCCCCTTGACCACTGAGCAGCCC
Right flanking sequence: Indices 38282 -- 38781
ACTGAGGCTCCCGCCCCCACCACTCAGGAGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAA
GGTTCCTACCATTGAGACCGCCAACGGTGCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTG
TCGCTTTCAACCTCTTGTAAGTTGGGTGATTTCGTTATTTTCTAAATATTTCGGACTTTTAATAC
ATTAATTTTGGGCTATACAATACCGGTTTTACAACCACCGTGCTTGTTTCCACTTGACTATTAAT
CAACAACGAATTTTCCCGCTCGGTTCCGAAGACGAAACATCTGAGTAACTTCAAAAACAGGGGCA
ATATAAGTAACGGTGGTGAAAGTATTGTAGTCTTAAAGTACCCAATTCCATTTTTTACCTAAAGA
TGCACTTGCTATTTACTCCTTGTATGTCATTCATCGGTTTTCGTGGTTTCGCCGCTTGAGATTTA
AATCATGCTCCAACAGCGTTAACACGCTGGGCAAATGCTTACTAT
Found at i:38127 original size:66 final size:65
Alignment explanation
Indices: 37990--38250 Score: 238
Period size: 66 Copynumber: 3.9 Consensus size: 65
37980 CTGAGCAGCC
* *
37990 CGCCCCCGAGCAGCCCGCT--CCCT-CGGCCCCTGCTCCCGAGCAGCCTGCTCCCTCTTCTGCGG
1 CGCCCCCGAGCAGCCCGCTCCCCCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGG
38052 CCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCT
1 ---C-GCCCCCGAGCAGCCCGCTCCC-C--CTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCT
38117 TCTGCGG
59 TCTGCGG
* *
38124 CCCCTGCCCCCGAGCAGCCTGC-CCCCACTGAGG--CC-GCCCCCGAGCAGCCCGCTCCCTCTTC
1 ---C-GCCCCCGAGCAGCCCGCTCCCC-CTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTC
38185 TGCGG
61 TGCGG
* *
38190 CCCCTGCCCCCGAGCAGCCTGC-CCCCACTGAGG--CC-GCCCCCGAGCAGCCCGCTCCCTCTTC
1 ---C-GCCCCCGAGCAGCCCGCTCCCC-CTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTC
38251 CGCCGCCCCT
Statistics
Matches: 184, Mismatches: 5, Indels: 13
0.91 0.02 0.06
Matches are distributed among these distances:
65 1 0.01
66 110 0.60
67 2 0.01
68 1 0.01
69 6 0.03
70 1 0.01
71 5 0.03
72 58 0.32
ACGTcount: A:0.08, C:0.55, G:0.23, T:0.14
Consensus pattern (65 bp):
CGCCCCCGAGCAGCCCGCTCCCCCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGG
Left flanking sequence: Indices 37490 -- 37989
ACGCCACAACTTAAAGCATATAAATATCATTAGCCCTGTCTCTATAATTTTCATCACTGTCTATC
GCTTAAAATGAAGTTTTCTACCACTGCCGCTGCCCTCGCTATCGCCACCCCCGCTTTGGCTCAGT
ACTCCAACGGCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTGAGGACAAC
AAGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACCGTGTACAC
CACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCCCTCTGACG
CTCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCTCGTGCCAC
CCTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGACGTCGAGAA
CAAGACTGTGTACACCACTTACTGCCCCTTGACCACTGAGCAGCC
Right flanking sequence: Indices 38251 -- 38750
CGCCGCCCCTGCCTCCGAGCAGCCCGCCCCTACTGAGGCTCCCGCCCCCACCACTCAGGAGGAGG
TCCCCTCCCCCACCCTCGCTGGCGAGTCCAAGGTTCCTACCATTGAGACCGCCAACGGTGCCGCT
CGTGCCATGCCCTTCGCTTTGGCCGGTGTTGTCGCTTTCAACCTCTTGTAAGTTGGGTGATTTCG
TTATTTTCTAAATATTTCGGACTTTTAATACATTAATTTTGGGCTATACAATACCGGTTTTACAA
CCACCGTGCTTGTTTCCACTTGACTATTAATCAACAACGAATTTTCCCGCTCGGTTCCGAAGACG
AAACATCTGAGTAACTTCAAAAACAGGGGCAATATAAGTAACGGTGGTGAAAGTATTGTAGTCTT
AAAGTACCCAATTCCATTTTTTACCTAAAGATGCACTTGCTATTTACTCCTTGTATGTCATTCAT
CGGTTTTCGTGGTTTCGCCGCTTGAGATTTAAATCATGCTCCAAC
Found at i:38167 original size:102 final size:101
Alignment explanation
Indices: 37991--38281 Score: 319
Period size: 102 Copynumber: 2.9 Consensus size: 101
37981 TGAGCAGCCC
* * *
37991 GCCCCCGAGCAGCCCGCTCCCTCGGCCCCTGCTCCCGAGCAGCCTGCTCCCTCTTCTGCGGCCCC
1 GCCCCCGAGCAGCCCGCTCCCTCGGCCCCTGCCCCCGAGCAGCCTGCTCCCTCTACTGAGG-CCC
38056 TGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
65 TGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38093 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCTGC-CCC-C-ACTGA
1 GCCCCCGAGCAGCCCGCT--C-C--CT-CGGCCCCTGCCCCCGAGCAGCCTGCTCCCTCTACTGA
38155 GG-CC-GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
60 GGCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
* * * * * * * * *
38195 GCCCCCGAGCAGCCTGCCCCCACTGAG-GCC-GCCCCCGAGCAGCCCGCTCCCTCTTCCGCCGCC
1 GCCCCCGAGCAGCCCGCTCCCTC-G-GCCCCTGCCCCCGAGCAGCCTGCTCCCTCTACTG-AGGC
*
38258 CCTGCCTCCGAGCAGCCCGC-CCCT
63 CCTGCCCCCGAGCAGCCCGCTCCCT
38282 ACTGAGGCTC
Statistics
Matches: 162, Mismatches: 13, Indels: 29
0.79 0.06 0.14
Matches are distributed among these distances:
96 17 0.10
97 7 0.04
98 2 0.01
99 3 0.02
100 2 0.01
101 6 0.04
102 86 0.53
103 2 0.01
104 1 0.01
105 6 0.04
106 1 0.01
107 5 0.03
108 24 0.15
ACGTcount: A:0.08, C:0.56, G:0.23, T:0.14
Consensus pattern (101 bp):
GCCCCCGAGCAGCCCGCTCCCTCGGCCCCTGCCCCCGAGCAGCCTGCTCCCTCTACTGAGGCCCT
GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
Left flanking sequence: Indices 37491 -- 37990
CGCCACAACTTAAAGCATATAAATATCATTAGCCCTGTCTCTATAATTTTCATCACTGTCTATCG
CTTAAAATGAAGTTTTCTACCACTGCCGCTGCCCTCGCTATCGCCACCCCCGCTTTGGCTCAGTA
CTCCAACGGCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTGAGGACAACA
AGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACCGTGTACACC
ACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCCCTCTGACGC
TCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCTCGTGCCACC
CTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGACGTCGAGAAC
AAGACTGTGTACACCACTTACTGCCCCTTGACCACTGAGCAGCCC
Right flanking sequence: Indices 38282 -- 38781
ACTGAGGCTCCCGCCCCCACCACTCAGGAGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAA
GGTTCCTACCATTGAGACCGCCAACGGTGCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTG
TCGCTTTCAACCTCTTGTAAGTTGGGTGATTTCGTTATTTTCTAAATATTTCGGACTTTTAATAC
ATTAATTTTGGGCTATACAATACCGGTTTTACAACCACCGTGCTTGTTTCCACTTGACTATTAAT
CAACAACGAATTTTCCCGCTCGGTTCCGAAGACGAAACATCTGAGTAACTTCAAAAACAGGGGCA
ATATAAGTAACGGTGGTGAAAGTATTGTAGTCTTAAAGTACCCAATTCCATTTTTTACCTAAAGA
TGCACTTGCTATTTACTCCTTGTATGTCATTCATCGGTTTTCGTGGTTTCGCCGCTTGAGATTTA
AATCATGCTCCAACAGCGTTAACACGCTGGGCAAATGCTTACTAT
Found at i:38231 original size:30 final size:30
Alignment explanation
Indices: 38129--38238 Score: 139
Period size: 30 Copynumber: 3.5 Consensus size: 30
38119 TGCGGCCCCT
38129 GCCCCCGAGCAGCCTGCCCCCACTGAGGCC
1 GCCCCCGAGCAGCCTGCCCCCACTGAGGCC
* * *
38159 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCC
1 GCCCCCGAGCAGCCTGC-CCC-C-ACTGAGG--CC
38194 TGCCCCCGAGCAGCCTGCCCCCACTGAGGCC
1 -GCCCCCGAGCAGCCTGCCCCCACTGAGGCC
38225 GCCCCCGAGCAGCC
1 GCCCCCGAGCAGCC
38239 CGCTCCCTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
30 30 0.44
31 5 0.07
32 1 0.01
33 10 0.15
34 1 0.01
35 5 0.07
36 16 0.24
ACGTcount: A:0.11, C:0.55, G:0.25, T:0.09
Consensus pattern (30 bp):
GCCCCCGAGCAGCCTGCCCCCACTGAGGCC
Left flanking sequence: Indices 37629 -- 38128
GCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTGAGGACAACAAGTGTAAC
GAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACCGTGTACACCACCTACTG
CCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCCCTCTGACGCTCCCGGCA
CTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCTCGTGCCACCCTGACAAG
CCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGACGTCGAGAACAAGACTGT
GTACACCACTTACTGCCCCTTGACCACTGAGCAGCCCGCCCCCGAGCAGCCCGCTCCCTCGGCCC
CTGCTCCCGAGCAGCCTGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCT
GCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
Right flanking sequence: Indices 38239 -- 38738
CGCTCCCTCTTCCGCCGCCCCTGCCTCCGAGCAGCCCGCCCCTACTGAGGCTCCCGCCCCCACCA
CTCAGGAGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAAGGTTCCTACCATTGAGACCGCC
AACGGTGCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTGTCGCTTTCAACCTCTTGTAAGT
TGGGTGATTTCGTTATTTTCTAAATATTTCGGACTTTTAATACATTAATTTTGGGCTATACAATA
CCGGTTTTACAACCACCGTGCTTGTTTCCACTTGACTATTAATCAACAACGAATTTTCCCGCTCG
GTTCCGAAGACGAAACATCTGAGTAACTTCAAAAACAGGGGCAATATAAGTAACGGTGGTGAAAG
TATTGTAGTCTTAAAGTACCCAATTCCATTTTTTACCTAAAGATGCACTTGCTATTTACTCCTTG
TATGTCATTCATCGGTTTTCGTGGTTTCGCCGCTTGAGATTTAAA
Found at i:38259 original size:66 final size:66
Alignment explanation
Indices: 38024--38289 Score: 397
Period size: 66 Copynumber: 3.9 Consensus size: 66
38014 GGCCCCTGCT
* * *
38024 CCCGAGCAGCCTGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGC
1 CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGC-CCC-C-ACTGAGG-
38089 CCCTGCC
62 -CC-GCC
*
38096 CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCTGCCCCCACTGAGGCCGC
1 CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCCCCCACTGAGGCCGC
38161 C
66 C
*
38162 CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCTGCCCCCACTGAGGCCGC
1 CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCCCCCACTGAGGCCGC
38227 C
66 C
* * * *
38228 CCCGAGCAGCCCGCTCCCTCTTCCGCCGCCCCTGCCTCCGAGCAGCCCGCCCCTACTGAGGC
1 CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCCCCCACTGAGGC
38290 TCCCGCCCCC
Statistics
Matches: 185, Mismatches: 9, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
66 126 0.68
67 2 0.01
69 5 0.03
70 1 0.01
71 3 0.02
72 48 0.26
ACGTcount: A:0.08, C:0.55, G:0.23, T:0.14
Consensus pattern (66 bp):
CCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCCCCCACTGAGGCCGC
C
Left flanking sequence: Indices 37524 -- 38023
CCTGTCTCTATAATTTTCATCACTGTCTATCGCTTAAAATGAAGTTTTCTACCACTGCCGCTGCC
CTCGCTATCGCCACCCCCGCTTTGGCTCAGTACTCCAACGGCACTGTCACTGATATCCACACCAC
TGTTGTCACCATCACTTCTTGTGAGGACAACAAGTGTAACGAGACCCCCGTGACCACTGGTTACC
AGGTTGTCACTGAGGAGCACACCGTGTACACCACCTACTGCCCCTTGACTGATGAGAAGCCCGAG
GAGCCTACCCAGGCCCCCGCTCCCTCTGACGCTCCCGGCACTGAGACCGTGGTGAACCCCATTGA
CACCACCGTTGTCACTGTCACCTCGTGCCACCCTGACAAGCCTTGTGAGACTCAGGAGGTCACCA
CTGGTGTCATCACCTCTTACGACGTCGAGAACAAGACTGTGTACACCACTTACTGCCCCTTGACC
ACTGAGCAGCCCGCCCCCGAGCAGCCCGCTCCCTCGGCCCCTGCT
Right flanking sequence: Indices 38290 -- 38789
TCCCGCCCCCACCACTCAGGAGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAAGGTTCCTA
CCATTGAGACCGCCAACGGTGCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTGTCGCTTTC
AACCTCTTGTAAGTTGGGTGATTTCGTTATTTTCTAAATATTTCGGACTTTTAATACATTAATTT
TGGGCTATACAATACCGGTTTTACAACCACCGTGCTTGTTTCCACTTGACTATTAATCAACAACG
AATTTTCCCGCTCGGTTCCGAAGACGAAACATCTGAGTAACTTCAAAAACAGGGGCAATATAAGT
AACGGTGGTGAAAGTATTGTAGTCTTAAAGTACCCAATTCCATTTTTTACCTAAAGATGCACTTG
CTATTTACTCCTTGTATGTCATTCATCGGTTTTCGTGGTTTCGCCGCTTGAGATTTAAATCATGC
TCCAACAGCGTTAACACGCTGGGCAAATGCTTACTATTCTGCAGA
Found at i:39895 original size:15 final size:15
Alignment explanation
Indices: 39877--39914 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
39867 TTTACGCCGT
*
39877 CGTTCTCGTGGTGGA
1 CGTTCTCGTGGTAGA
*
39892 CGTTCTCATGGTAGA
1 CGTTCTCGTGGTAGA
39907 CGTTCTCG
1 CGTTCTCG
39915 CCATAGGCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.34
Consensus pattern (15 bp):
CGTTCTCGTGGTAGA
Left flanking sequence: Indices 39377 -- 39876
AAAGAGATGGAGTTTGTACGGCTCAACAAAAAATGGCCGCGACACCACGGGCACCCGGGCTTGAA
TCTGGCTGAGAATGTAGTATTCCCACTTCAGAGCCGGTTTCTCTATTTTCAACGCACCATAGGTG
CCATCCAAACACAGTTCAATCAAATAGACCACCCCGTAGCCCCCACGGCCCAACTCACTTTTGAT
CAGGTACAAGGAATCACCGCAAAAGTCGATAAGCAGCGCCAGCAGCGCCGGGGTGGGCTTTCCGA
GAAGAAACAAATTGACAAAGTTGCGGCTCCGGTTGATCGTTTTCGAGGAATGGTCGTAGAAACCC
TCGCAGGTCAGTGGACGCATGCTGAGCAACTGCTGGCTGCGCAGGGACAAGTCGGAGACATCGAC
GATGGCCACCTCTGCCAACGGCACCTCTGGATTCATGACAAACAGCAGAGAGTGTTCGGTGACAG
GCGTGACCTCAGACGTCAAGTTCGGGTTGTCGTCATTTACGCCGT
Right flanking sequence: Indices 39915 -- 40414
CCATAGGCGTAATCGCCGTAGGCGCTGTCGTTGTCGTGGTCGTTTTCGTGCGGTAGCCGCGGCAG
GGCTTGCTGGCCCGTGAGGGGGAGCTCAGTGACGTAGTCGGTGAAGTTGGTGAGAGTCGGTTGGT
AGGCTCCAGCAATGGCCAAGTCCTCCTCCTCAGAGTCGTGCAAATCGACCCCGACGTCGTACATT
CCCAACAATTCCTTCTTCGTGTCCTTGCCAAAGAACGTCGTGGTAGGCGACCCCGGCACACGCCC
TACCGACGGAGGCCGCAACGCCAATGGGTGGCTGTCGTCGCCGGAGAAGTTGTCGGGTATCGTGG
CCTGAGAAAGCTGCACGGGTTCGGGGTCTACGGGTGTTTCCTCGAGTGGTTTTCGTATGGTGGAA
GCGGCCTCTCTCGAGCTCAGAGGCTGGAGCCCGGCCTTTGGGTGCGCGTGGGTGGAAACGGTGGC
CAACAACAACTCCAACGAGCAAAGCTCTGTCGCGAAGCTCTTTTG
Found at i:41633 original size:14 final size:14
Alignment explanation
Indices: 41614--41660 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
41604 ACCGGGGATA
41614 TACCGCTAGTTATG
1 TACCGCTAGTTATG
41628 TACCGCTAGTTATG
1 TACCGCTAGTTATG
*
41642 TACCAG-TCGTTATG
1 TACC-GCTAGTTATG
41656 TACCG
1 TACCG
41661 GTCGTTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (14 bp):
TACCGCTAGTTATG
Left flanking sequence: Indices 41114 -- 41613
CCACTCCAACCACAACCGGACATAGCGGATGTCGTTGGCGTAGCTCTTGTCCTCCATAAAGTGCC
GGGTGGCCGTCTCCAAAACCTCGACAAGCTCGGGGTGTTTCAGGTTGTAGGCAAAAGTGGAGCGG
AGGGACGCGACGTAGTCGACAAACACCAGGAGCGGATCGTCCATCTCGTCGAGCCCCGCTAGTTG
CGCCTCAAAGTGGTCGCGGTCCCTGCGGGTGTCCTCGTCTAGATTCAGCCTCAGGCCCAAACGAA
GCAGTGCCGCTAGCTTTTTTAGCAGCCGCCCGCCTGCGACGGGCTGGATGTTCTCTTTGTGGTCC
TGGAATAGGGAGATATCGCTCATCCGACCCGATTGCGCACCGAGATCCGTGGTGTTTATCTTTGG
TGCGGACGCGCGCACACTACTGACGCGCTACGCGGTGGAAAAACGAGGTGCCATCACGAGGTTAT
GCTATTCGAAGATACTGATATTCGATGATACTAATACCGGGGATA
Right flanking sequence: Indices 41661 -- 42160
GTCGTTACAACTTGGGTGTGAGGCTCAACGATCTCAAGTGCTTGACGGCCTCCATGCCCAGCCCG
TACGAGAGCTCGTAGCCCATGCCACCCGCACCGTAGTTGTTGATGACATGGTTACGACGCCCAGG
GTGGTCCTGACAACGCTCGAGCAGAGTGTTCAAACCCCCTTCGCGAGCTGGTCTGAACCCGACGT
TGATGTTGACCACGTCAAACTCGCCGTTCCGCATCAACTCGGGGAACAACTTCGCGCCCCGGCGC
TTCAACGAGGCAGTGTCTTCGTCGCGCACCCCTCCGTAGGTGTCACGCACCTGCTTGGTGCCACC
CAAAATCATCCCTCCGTCAAGTGGACGCGGAATGCAAAATGTCCACATGCCATCTGCCAGCTGGT
GGGTCACGGTGGCGTCCGCGTACTTGTTGCCCGGGGGTGGGCGAATCAAGAGGGTCTGACCTCTG
ATGGGGTAGGACATCGGGTCATAGCCTCCGTCGTACTGCAAACCT
Found at i:41664 original size:14 final size:14
Alignment explanation
Indices: 41622--41667 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
41612 TATACCGCTA
* *
41622 GTTATGTACCGCTA
1 GTTATGTACCGGTC
*
41636 GTTATGTACCAGTC
1 GTTATGTACCGGTC
41650 GTTATGTACCGGTC
1 GTTATGTACCGGTC
41664 GTTA
1 GTTA
41668 CAACTTGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (14 bp):
GTTATGTACCGGTC
Left flanking sequence: Indices 41122 -- 41621
ACCACAACCGGACATAGCGGATGTCGTTGGCGTAGCTCTTGTCCTCCATAAAGTGCCGGGTGGCC
GTCTCCAAAACCTCGACAAGCTCGGGGTGTTTCAGGTTGTAGGCAAAAGTGGAGCGGAGGGACGC
GACGTAGTCGACAAACACCAGGAGCGGATCGTCCATCTCGTCGAGCCCCGCTAGTTGCGCCTCAA
AGTGGTCGCGGTCCCTGCGGGTGTCCTCGTCTAGATTCAGCCTCAGGCCCAAACGAAGCAGTGCC
GCTAGCTTTTTTAGCAGCCGCCCGCCTGCGACGGGCTGGATGTTCTCTTTGTGGTCCTGGAATAG
GGAGATATCGCTCATCCGACCCGATTGCGCACCGAGATCCGTGGTGTTTATCTTTGGTGCGGACG
CGCGCACACTACTGACGCGCTACGCGGTGGAAAAACGAGGTGCCATCACGAGGTTATGCTATTCG
AAGATACTGATATTCGATGATACTAATACCGGGGATATACCGCTA
Right flanking sequence: Indices 41668 -- 42167
CAACTTGGGTGTGAGGCTCAACGATCTCAAGTGCTTGACGGCCTCCATGCCCAGCCCGTACGAGA
GCTCGTAGCCCATGCCACCCGCACCGTAGTTGTTGATGACATGGTTACGACGCCCAGGGTGGTCC
TGACAACGCTCGAGCAGAGTGTTCAAACCCCCTTCGCGAGCTGGTCTGAACCCGACGTTGATGTT
GACCACGTCAAACTCGCCGTTCCGCATCAACTCGGGGAACAACTTCGCGCCCCGGCGCTTCAACG
AGGCAGTGTCTTCGTCGCGCACCCCTCCGTAGGTGTCACGCACCTGCTTGGTGCCACCCAAAATC
ATCCCTCCGTCAAGTGGACGCGGAATGCAAAATGTCCACATGCCATCTGCCAGCTGGTGGGTCAC
GGTGGCGTCCGCGTACTTGTTGCCCGGGGGTGGGCGAATCAAGAGGGTCTGACCTCTGATGGGGT
AGGACATCGGGTCATAGCCTCCGTCGTACTGCAAACCTTGACCCA
Done.