Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold38
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: 49614
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.24
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:425 original size:124 final size:123
Alignment explanation
Indices: 204--451 Score: 478
Period size: 124 Copynumber: 2.0 Consensus size: 123
194 TTGACCGGTA
*
204 AGACCATTACCCTCGAGGTTGAGTCCTCGGACACCATTGACAATGTCAAGTCCAAGATTCAGGAC
1 AGACCATTACCCTCGAGGTTGAGTCCTCGGACACCATTGACAACGTCAAGTCCAAGATTCAGGAC
269 AAGGAAGGTATCCCTCCGGACCAGCAGCGTCTTATCTTTGCTGGTAAGCAGTTGGAAG
66 AAGGAAGGTATCCCTCCGGACCAGCAGCGTCTTATCTTTGCTGGTAAGCAGTTGGAAG
327 ANGACCATTACCCTCGAGGTTGAGTCCTCGGACACCATTGACAACGTCAAGTCCAAGATTCAGGA
1 A-GACCATTACCCTCGAGGTTGAGTCCTCGGACACCATTGACAACGTCAAGTCCAAGATTCAGGA
392 CAAGGAAGGTATCCCTCCGGACCAGCAGCGTCTTATCTTTGCTGGTAAGCAGTTGGAAG
65 CAAGGAAGGTATCCCTCCGGACCAGCAGCGTCTTATCTTTGCTGGTAAGCAGTTGGAAG
451 A
1 A
452 TGGCAGAACC
Statistics
Matches: 123, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 1 0.01
124 122 0.99
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (123 bp):
AGACCATTACCCTCGAGGTTGAGTCCTCGGACACCATTGACAACGTCAAGTCCAAGATTCAGGAC
AAGGAAGGTATCCCTCCGGACCAGCAGCGTCTTATCTTTGCTGGTAAGCAGTTGGAAG
Left flanking sequence: Indices 1 -- 203
CTCGGACACCATTGACAATGTCAAGTCCAAGATTCAGGACAAGGAAGGTATCCCTCCGGACCAGC
AGCGTCTTATCTTTGCTGGTAAGCAGTTGGAAGACGGCAGAACCTTGTCCGACTACAACATCCAG
AAGGAGTCTACTCTTCACTTGGTGCTCAGATTGAGAGGTGGTATGCAGATTTTTGTCAAGACCTT
GACCGGTA
Right flanking sequence: Indices 452 -- 951
TGGCAGAACCTTGTCTGACTACAACATCCAGAAGGAGTCTACTCTTCACTTGGTGCTCAGATTGA
GAGGTGGCCAGTAAGGCCTCACCTCAGTATTTAGCTGAACTATTATGAATGTATGAGCTCGAGGT
AATCATGCGTAGTGATGGGATTAGTTTGTCGCCTGACTAATCCGATCGTTGTTCGAATACAACAA
TCATGTGCATTAAAAAAATAACCTGAAGCCTTTATATAAACCATTGCAAGAAGCATTAAACGTCT
AAATCCATGAACTGAAACAAAACCGACCCAAATACCAAACCTAATACGCCTCTTCCACCAATGTA
TCCAAATTGGCAACCAAAAGTTTTCCCTGTCGGGGCAAGTCCAAAGACTTTACGCCGAACCGAAG
GTCCTCTACAACCGTGGAAACATCATCCGCCTCAATGGAGGTACGCTTGAGGCCCGGGGTGCCCA
TATCAGAGCGGTAACGATGAATGTCAAGACGGTAAGTCTTCAACT
Found at i:6877 original size:18 final size:18
Alignment explanation
Indices: 6856--6891 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6846 CTTGGACTTA
6856 TTTCTCTCCTTCTTCTCC
1 TTTCTCTCCTTCTTCTCC
6874 TTTCTCTCCTTCTTCTCC
1 TTTCTCTCCTTCTTCTCC
6892 CGTTTCTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCTCTCCTTCTTCTCC
Left flanking sequence: Indices 6356 -- 6855
CGTTGAGCAAGGACTCAGAAATAGCTACCACCGAGGCCACGTGCTCGGCGGATGGCAAGTCAATG
TAGGCAAAACCCTTAATCTTTTTCTCCTTCTTAGGGATGTTGATTCTTGACATGTCCTCCTCGAC
TACACTAGGCTCCAACTCTGAGGTCTTGGCCACAATGAAACGAACGAGGTCGTCACGGGTGGTGT
CAAACGACATGTTTCCAATCCACACACCAAATGGGGACCGCTTGGGGGTCTCGGGCTCGGGCTCT
TTGCCGTCCTCGGTAAGCGGCTTAACCTTGGCCTGCTTACGCTCCAACTTGGCAAGATCAAGCTT
ACCCTTCTTCAACAAACGCTGTTGCTTCTTGTTCAACGCGGGCCCAGCGTTCAAGTCGATCTCAA
TTTCATCCGACAAGGCCTTGGTGGTCTCATGCTCCTCGTCGGCGTCGGCGTGCAGGTCCAAGGTG
GCCACTTCGGACTCCAGAGGCAACTCATCGACGTCCTTGGACTTA
Right flanking sequence: Indices 6892 -- 7391
CGTTTCTCACTCTTATCTTTACCCATGGCTCTATCTCTTGTCGCAGCACCTCCGATGAGATGAGT
CGCAGCGAGGTGCGCGGGCACACAACCGTATACATGATATCGTTTCCGAATTTAAAGAGGGCAGT
CTACACGCGTTAAGCTCGAAGAAATTATTCAGTACAAACTTCATTCATATTCAAAACAATAGTGT
CCCTTAGTGGGCGTGCCCGTCCAAAGGCTTGTGGTTGTGGCGTTCAAACTCCTCCGCCGTCACCT
GGATGTAGTCTGGGTCGTTCTTGTGACGCTCAAACTCCTCAGAAGTCACCTCTTCGTACACAGAA
AAGGTGTCGTACTCACCCAGCGACGCAGTGGAGATCGCCGACGACTGCTTACGAGCCAAAGCGCC
CGCGGGAACCGCGGGAACGACAGCGTCGTTGGGGGTAGCCGACTGCGACATCGACCGCTGCTTGG
CCGCGGACGACGCAGTGCGCACAGGCGCCTGCTTGCCGTCGTCCT
Found at i:9580 original size:21 final size:21
Alignment explanation
Indices: 9554--9594 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9544 GGTCGCAAGC
*
9554 TCCTCGGCCTTCTCCTCGGCG
1 TCCTCGGCCTTCACCTCGGCG
*
9575 TCCTCGGCCTTGACCTCGGC
1 TCCTCGGCCTTCACCTCGGC
9595 AGCAGCAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.46, G:0.24, T:0.27
Consensus pattern (21 bp):
TCCTCGGCCTTCACCTCGGCG
Left flanking sequence: Indices 9054 -- 9553
TTTTGCCCTCAAGCTTCTTGGTGAACTTGGCAAAGTCCAGACGCAACGACTGCTCGTGGCCCTTT
TGCTTGTTGGACAAGTCCAACTGGCGACGCGACTCGTCCTCCTCGCGGGTCTTGCCCACCGCGTC
GTTGATGTTGGCCAACACAGGCGCCACCCGCTTGGCGGCCATGTCCATCAAGTCCTGCTGCTTCA
TCTTGAGACCACCGCCCAAGTCGATCATGGCGTCGGGGTCGTCGGCAGTGCGAGTGGACAGCAGG
ATCCCCTGCTGCTGCAACTCCATGTACCGCTGGAGCAACGCCGGCTGGTCCTTGAACTGCTCGAG
GTTGGCGTCGGACTCGATCTTGGTGAACTTGTCGGCGGGATCGACGTGGAGGCCGTCCGTCGGCG
GCTCCTCCTTGATGCGCTGCTCGATGCCGTCAGTGGCGTCGCCCTCGACGTTGACAGCCTCGCCA
GCGGCGCCCAAGTCCGTCACAAGCTTTTCGCGCTCGGTCGCAAGC
Right flanking sequence: Indices 9595 -- 10094
AGCAGCAGCCTTGTTGATGTGCTTCTCGACCTTGGGGTCCTCAGCAAGCTCCTCGAGCTTGGCCT
CCTCGGAGTCAGGCACCACCGAGTCGTCGGCGGTGTCCGCAGGCTCAGCGGACTCCGTGAGCTCG
GCGATGGCGACGGGCTGGGTGGCGTCAACGTCCGCGGCATCGGTCTCGGCGGCATCCTTGGCCTC
GAGCTCGGCGTCGGTCAACGGACGCTCCAGCTGGACGTCGTCGGCGTCGACAGCCGCGTCGCCAG
CGTCAGCGGCAGCGGTCTTGGGAGCAGCCTCCTCGGTGGTGGTACCGTCCTTCTTGGCGGCCGTG
GGCTTTTTGGCGCCCTTGATGTTCTGGTAGCCGCGGTTGCGGAAGCGCTCGGGCACCTGGATCGC
GTCCAACTTGTTCAGCTCCTTGAATTGCTGGTGCAAGTTGACCTTGGCCTTTTCGTCCTCGGCGT
TGCCGCCACGGAAAGGCGACTCCCACGCCTCGCCCTGCACCACCT
Found at i:49086 original size:36 final size:36
Alignment explanation
Indices: 49058--49286 Score: 395
Period size: 36 Copynumber: 6.4 Consensus size: 36
49048 ACCCCTGAGT
49058 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
1 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
* *
49094 CGCTGTCGAGTTCGTGTGAGACTCTGACCTCCAAGA
1 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
*
49130 CGCTGTCGAGTTCGTCTGAGACTCTGACCTCCAAGA
1 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
*
49166 CGCTGTCGAGTTCTTCTGAGACCCTGACCTCCAAGA
1 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
*
49202 CGCTGTCGAGTTCGTCTGAGACTCTGACCTCCAAGA
1 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
*
49238 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCGAGA
1 CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
*
49274 CGCTGTCGGGTTC
1 CGCTGTCGAGTTC
49287 TTCAGGTTCT
Statistics
Matches: 183, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 183 1.00
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.24
Consensus pattern (36 bp):
CGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAAGA
Left flanking sequence: Indices 48558 -- 49057
ATTGAGCTCCTCGTCGATGTCTTCAACAGCTTCCAGTTCGTCAGAATCCGAGACCTCGACCGAGT
CGTCTTCGTCCGAAAAGGAAAGCAGCACCTCAGAGCTTTCGTCCTGTCTTACAGTAACGATCACT
ACGGTAACCACTCCCGAGGTTTCGGTCCATGAGTCTACACTGTCAGAGTCCACACTCGAAACTTC
CTCGTCTGCGCTGACCACTGAGTCACTGACTTTGTCTAGTTCTCTGGTTTCTGAGTCGCAAGGAA
GTTCTTCATCGTCGCTGACTGAATCGAGCTCTCTGGCTACGGAGTCACTGGTCACTTCCACCACT
GCGACCTCTGAACTGAGTGCGTCCTCGTCTTCTACTTTAGAGTCGCTGACTGGCTCCCTGAGCCT
GGAGGTGTCAACTTCATCTACATCTGAAGAGCTGTGCATTACTACGACGACGACCACCGTCACTA
CACCTGAAGTTACCGTCTACGAATCGACAACTGTGACCCCTGAGT
Right flanking sequence: Indices 49287 -- 49614
TTCAGGTTCTGTGACTATTGAGTCACTGACAGGTTCCGAGTCTTCCACCTCTGCCTCGGAAGAGA
CACTGTCGAGTTTCTCTGAGACCGAATCTACCACTCAGACACGGTCTACGGAGATCCCTCCCCCT
ATTGTGACCTCCAACCCCCCGCCTACCAACCCTCCAGTGAGCCCGCCTCCTACCAACCCTCCGGT
GAGCCCACCTCCCACCAACCCTCCGGTGAGCCCGCCTCCCACCAACCCTCCGGTGAACCCTCCCA
CCAACCCTCCGGTGAACCCTCCCACCAACCCTCCGGTGAACCCTCCCACCAACCCTCCGGTGAAC
CCT
Found at i:49461 original size:24 final size:24
Alignment explanation
Indices: 49434--49613 Score: 180
Period size: 24 Copynumber: 7.1 Consensus size: 24
49424 CCTCCAACCC
* *
49434 CCCGCCTACCAACCCTCCAGTGAG
1 CCCGCCTACCAACCCTCCGGTGAA
*
49458 CCCGCCTCCTACCAACCCTCCGGTGAG
1 CCCG---CCTACCAACCCTCCGGTGAA
* *
49485 CCCACCTCCCACCAACCCTCCGGTGAG
1 CCCGCCT---ACCAACCCTCCGGTGAA
49512 CCCGCCTCCCACCAACCCTCCGGTGAA
1 CCCGCCT---ACCAACCCTCCGGTGAA
* *
49539 CCCTCCCACCAACCCTCCGGTGAA
1 CCCGCCTACCAACCCTCCGGTGAA
* *
49563 CCCTCCCACCAACCCTCCGGTGAA
1 CCCGCCTACCAACCCTCCGGTGAA
* *
49587 CCCTCCCACCAACCCTCCGGTGAA
1 CCCGCCTACCAACCCTCCGGTGAA
49611 CCC
1 CCC
49614 T
Statistics
Matches: 144, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
24 75 0.52
27 69 0.48
ACGTcount: A:0.19, C:0.54, G:0.14, T:0.12
Consensus pattern (24 bp):
CCCGCCTACCAACCCTCCGGTGAA
Left flanking sequence: Indices 48934 -- 49433
GGCTCCCTGAGCCTGGAGGTGTCAACTTCATCTACATCTGAAGAGCTGTGCATTACTACGACGAC
GACCACCGTCACTACACCTGAAGTTACCGTCTACGAATCGACAACTGTGACCCCTGAGTCGCTGT
CGAGTTCGTCTGAGACCCTGACCTCCAAGACGCTGTCGAGTTCGTGTGAGACTCTGACCTCCAAG
ACGCTGTCGAGTTCGTCTGAGACTCTGACCTCCAAGACGCTGTCGAGTTCTTCTGAGACCCTGAC
CTCCAAGACGCTGTCGAGTTCGTCTGAGACTCTGACCTCCAAGACGCTGTCGAGTTCGTCTGAGA
CCCTGACCTCCGAGACGCTGTCGGGTTCTTCAGGTTCTGTGACTATTGAGTCACTGACAGGTTCC
GAGTCTTCCACCTCTGCCTCGGAAGAGACACTGTCGAGTTTCTCTGAGACCGAATCTACCACTCA
GACACGGTCTACGGAGATCCCTCCCCCTATTGTGACCTCCAACCC
Right flanking sequence: Indices 49614 -- 49614
T
Found at i:49540 original size:12 final size:12
Alignment explanation
Indices: 49525--49614 Score: 72
Period size: 12 Copynumber: 7.5 Consensus size: 12
49515 GCCTCCCACC
49525 AACCCTCCGGTG
1 AACCCTCCGGTG
****
49537 AACCCTCCCACC
1 AACCCTCCGGTG
49549 AACCCTCCGGTG
1 AACCCTCCGGTG
****
49561 AACCCTCCCACC
1 AACCCTCCGGTG
49573 AACCCTCCGGTG
1 AACCCTCCGGTG
****
49585 AACCCTCCCACC
1 AACCCTCCGGTG
49597 AACCCTCCGGTG
1 AACCCTCCGGTG
49609 AACCCT
1 AACCCT
Statistics
Matches: 54, Mismatches: 24, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.21, C:0.52, G:0.13, T:0.13
Consensus pattern (12 bp):
AACCCTCCGGTG
Left flanking sequence: Indices 49025 -- 49524
CCGTCTACGAATCGACAACTGTGACCCCTGAGTCGCTGTCGAGTTCGTCTGAGACCCTGACCTCC
AAGACGCTGTCGAGTTCGTGTGAGACTCTGACCTCCAAGACGCTGTCGAGTTCGTCTGAGACTCT
GACCTCCAAGACGCTGTCGAGTTCTTCTGAGACCCTGACCTCCAAGACGCTGTCGAGTTCGTCTG
AGACTCTGACCTCCAAGACGCTGTCGAGTTCGTCTGAGACCCTGACCTCCGAGACGCTGTCGGGT
TCTTCAGGTTCTGTGACTATTGAGTCACTGACAGGTTCCGAGTCTTCCACCTCTGCCTCGGAAGA
GACACTGTCGAGTTTCTCTGAGACCGAATCTACCACTCAGACACGGTCTACGGAGATCCCTCCCC
CTATTGTGACCTCCAACCCCCCGCCTACCAACCCTCCAGTGAGCCCGCCTCCTACCAACCCTCCG
GTGAGCCCACCTCCCACCAACCCTCCGGTGAGCCCGCCTCCCACC
Right flanking sequence: None
Found at i:49614 original size:24 final size:24
Alignment explanation
Indices: 49462--49614 Score: 225
Period size: 24 Copynumber: 6.1 Consensus size: 24
49452 AGTGAGCCCG
* *
49462 CCTCCTACCAACCCTCCGGTGAGCCC
1 CCTCCCACCAACCCTCCGGTGA--AC
*
49488 ACCTCCCACCAACCCTCCGGTGAGCCC
1 -CCTCCCACCAACCCTCCGGTGA--AC
49515 GCCTCCCACCAACCCTCCGGTGAAC
1 -CCTCCCACCAACCCTCCGGTGAAC
49540 CCTCCCACCAACCCTCCGGTGAAC
1 CCTCCCACCAACCCTCCGGTGAAC
49564 CCTCCCACCAACCCTCCGGTGAAC
1 CCTCCCACCAACCCTCCGGTGAAC
49588 CCTCCCACCAACCCTCCGGTGAAC
1 CCTCCCACCAACCCTCCGGTGAAC
49612 CCT
1 CCT
Statistics
Matches: 123, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
24 75 0.61
25 1 0.01
27 47 0.38
ACGTcount: A:0.19, C:0.54, G:0.14, T:0.13
Consensus pattern (24 bp):
CCTCCCACCAACCCTCCGGTGAAC
Left flanking sequence: Indices 48962 -- 49461
CATCTACATCTGAAGAGCTGTGCATTACTACGACGACGACCACCGTCACTACACCTGAAGTTACC
GTCTACGAATCGACAACTGTGACCCCTGAGTCGCTGTCGAGTTCGTCTGAGACCCTGACCTCCAA
GACGCTGTCGAGTTCGTGTGAGACTCTGACCTCCAAGACGCTGTCGAGTTCGTCTGAGACTCTGA
CCTCCAAGACGCTGTCGAGTTCTTCTGAGACCCTGACCTCCAAGACGCTGTCGAGTTCGTCTGAG
ACTCTGACCTCCAAGACGCTGTCGAGTTCGTCTGAGACCCTGACCTCCGAGACGCTGTCGGGTTC
TTCAGGTTCTGTGACTATTGAGTCACTGACAGGTTCCGAGTCTTCCACCTCTGCCTCGGAAGAGA
CACTGTCGAGTTTCTCTGAGACCGAATCTACCACTCAGACACGGTCTACGGAGATCCCTCCCCCT
ATTGTGACCTCCAACCCCCCGCCTACCAACCCTCCAGTGAGCCCG
Right flanking sequence: None
Done.