Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold68
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: 39187
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.24
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:257 original size:6 final size:6
Alignment explanation
Indices: 246--315 Score: 79
Period size: 6 Copynumber: 11.5 Consensus size: 6
236 CCCCTTTTCA
* * *
246 TTGGTG TTGGTG GTGTTG GT-GTG TTGGTG TTGGTGTG TTGGTG TTGGTG
1 TTGGTG TTGGTG TTGGTG TTGGTG TTGGTG TT-G-GTG TTGGTG TTGGTG
*
295 TTGTTG TTGGTG TTGGTG TTG
1 TTGGTG TTGGTG TTGGTG TTG
316 TTGCTGCTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
5 3 0.05
6 45 0.82
7 2 0.04
8 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (6 bp):
TTGGTG
Left flanking sequence: Indices 1 -- 245
TGTTACTGGTGGCGTCGCGACCCACCAGCTACGGGTCCTCGAACAGTCCTGACATGTGCAGTTGC
ACGCTTCTACTCGATGGCCGACGGGCCGGGAGGTAGGGGGTGCAATCTAGCGTCAGGATGGGCGG
TATCGCCACAGAACCATCCCGTGGTCGGCGCGGGGAGCTGCAAGCCTCTGGGCTTCGCTTCCTTT
GCCATATGGGAGACGATATTTGAAGTACTAGTGGTGCCACCCCCTTTTCA
Right flanking sequence: Indices 316 -- 815
TTGCTGCTGTTGTTAGGGTTGGATGCCAATGGCTCCTTTTCCCCCTGTTGGTGGTGTCAGTGGTG
CTCGATTCGATTCGTTGGATCGAGTGCCATTGGTGCCGTTTTTTCCCCCTGTTGGTGGTGCCATT
GGTATCCAATCCGGGTTTCTATAATTGTATAGTTAAGCACTGGGTGCGCCTTCGGGGTAGCCTGC
ATGAGCGGGCTACCCTGAAGCCGTACTGGGGGCTTATTGTAGTATATAGGATATATAGGATATAT
ACAGGTTCGCCATAATCAACGCTATCTACGGTACCAATAGTAAAGTCACGTGATATTTATCACAT
GTGTTGAGCCGCACTGCTGTATTAGGTCAGCTTAGGTCAGCTCGTAACGCGGTTATGTAATACTC
GTAACTCTAACAGAGAATATTATGTAATACATATTATACTCAAAGTCACGTGAAATGGTCACATG
ACTTACCAATAACAATCCTAGAGCGAAACACGTGACCTGCGTCAC
Found at i:275 original size:14 final size:14
Alignment explanation
Indices: 246--315 Score: 85
Period size: 14 Copynumber: 5.2 Consensus size: 14
236 CCCCTTTTCA
*
246 TTGGTGTTGGTGGTG
1 TTGGTG-TGTTGGTG
261 TTGGTGTGTTGGTG
1 TTGGTGTGTTGGTG
275 TTGGTGTGTTGGTG
1 TTGGTGTGTTGGTG
*
289 TT-G-GTGTTGTTG
1 TTGGTGTGTTGGTG
301 TT-G-GTGTTGGTG
1 TTGGTGTGTTGGTG
313 TTG
1 TTG
316 TTGCTGCTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
12 21 0.41
13 1 0.02
14 23 0.45
15 6 0.12
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (14 bp):
TTGGTGTGTTGGTG
Left flanking sequence: Indices 1 -- 245
TGTTACTGGTGGCGTCGCGACCCACCAGCTACGGGTCCTCGAACAGTCCTGACATGTGCAGTTGC
ACGCTTCTACTCGATGGCCGACGGGCCGGGAGGTAGGGGGTGCAATCTAGCGTCAGGATGGGCGG
TATCGCCACAGAACCATCCCGTGGTCGGCGCGGGGAGCTGCAAGCCTCTGGGCTTCGCTTCCTTT
GCCATATGGGAGACGATATTTGAAGTACTAGTGGTGCCACCCCCTTTTCA
Right flanking sequence: Indices 316 -- 815
TTGCTGCTGTTGTTAGGGTTGGATGCCAATGGCTCCTTTTCCCCCTGTTGGTGGTGTCAGTGGTG
CTCGATTCGATTCGTTGGATCGAGTGCCATTGGTGCCGTTTTTTCCCCCTGTTGGTGGTGCCATT
GGTATCCAATCCGGGTTTCTATAATTGTATAGTTAAGCACTGGGTGCGCCTTCGGGGTAGCCTGC
ATGAGCGGGCTACCCTGAAGCCGTACTGGGGGCTTATTGTAGTATATAGGATATATAGGATATAT
ACAGGTTCGCCATAATCAACGCTATCTACGGTACCAATAGTAAAGTCACGTGATATTTATCACAT
GTGTTGAGCCGCACTGCTGTATTAGGTCAGCTTAGGTCAGCTCGTAACGCGGTTATGTAATACTC
GTAACTCTAACAGAGAATATTATGTAATACATATTATACTCAAAGTCACGTGAAATGGTCACATG
ACTTACCAATAACAATCCTAGAGCGAAACACGTGACCTGCGTCAC
Found at i:8675 original size:20 final size:20
Alignment explanation
Indices: 8611--8687 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
8601 GTGCCCGACA
*
8611 CGGACTCTATACAGCTCAGTG
1 CGGACTCTATACAGC-CAGCG
***
8632 CGGACTCTATACAAATAGTC-
1 CGGACTCTATACAGCCAG-CG
8652 CGGACTCTATACAGCCAGCG
1 CGGACTCTATACAGCCAGCG
8672 CGGACTCTATACAGCC
1 CGGACTCTATACAGCC
8688 GTTTATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 33 0.70
21 13 0.28
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (20 bp):
CGGACTCTATACAGCCAGCG
Left flanking sequence: Indices 8111 -- 8610
GTCTATCCCTGCGCCGGTCCCGATCTCAGTCTATATACGACAAAAGAAATGCTAGCGAGGGGGGG
AACATTCAAATCCAAGAAAAACCGCCGAGAGTAACGAGTTGAAACTGGGAAGGTAGTTGCGGGAG
ACCTTTCCCATCAAGGAGACCTTTCCCCGGTGTCGCTAGAGCGTTTCAAACAGCAGCCATCGCTT
CAGCCGTAGGAAAACCAATCCCGCAATGGTGGCAGGGTGCATAAATAATATTCGATGCCCAGGAA
AATTTTCACCTAGAGTCAAAATGAATTAGTAATGAGAGAGCAACAGAAGGTGGTGGGCAGCGGGG
AGAGCTAGGGTGAGCCAGTGTTGCGAGTGGCTTTCATTCAAGCCGGTTTGACCCCCTTTAGCTCG
AAAATCACTATAGCTAGAGGTCAGTGAGTTTCAGGTGGGTGGAAACGCACCCCCGAATAAGCCAT
ACATCGGACCGCCCGTCCGGATATGGGCGGAGGCGGTGCCCGACA
Right flanking sequence: Indices 8688 -- 9187
GTTTATTTTTAGTGGCAACCGTTGCGCTCATCCCAAACGGGTAATTTAGGCGTTTTTCCACCGTA
TTCGCTACGTGTAGATCCAAGAAAAAGCAACAACTTCTAGCGAAACAGCTAATGCCAGGGTGGCT
GATGACCCGGGGACCGATCTAGACTACAGCCGAACGTTTAAATAGTGGGGCGATCCCGTCAAATC
TCAATTTGACTGACGAATCGACTGATTTTGAGTCAATAATACCAACACGATGGTATTGACATAAT
ACCATCGTAATTATTTCCACTACAGAGTGGAGGAATCGCCCCATTTAGGTTCCCACGGATAATTG
CGAGTGTCTGAATGTGCTCCCGGAGAAGCCGTAAGCGATGAAGACCGCCTGGATCTTTGTTCGGA
CGCAGGTGGGAGTCAAGTGGGAGTCAAGTGGGAGTCAAATGGGAGTCATCATACCGGATATGTCT
CGGAGAATTATTGTCTTGCGAAACGCGGCATTACCTTGCTTTCAA
Found at i:9099 original size:11 final size:11
Alignment explanation
Indices: 9083--9125 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
9073 TCGGACGCAG
9083 GTGGGAGTCAA
1 GTGGGAGTCAA
9094 GTGGGAGTCAA
1 GTGGGAGTCAA
9105 GTGGGAGTCAA
1 GTGGGAGTCAA
*
9116 ATGGGAGTCA
1 GTGGGAGTCA
9126 TCATACCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.44, T:0.19
Consensus pattern (11 bp):
GTGGGAGTCAA
Left flanking sequence: Indices 8583 -- 9082
CGGATATGGGCGGAGGCGGTGCCCGACACGGACTCTATACAGCTCAGTGCGGACTCTATACAAAT
AGTCCGGACTCTATACAGCCAGCGCGGACTCTATACAGCCGTTTATTTTTAGTGGCAACCGTTGC
GCTCATCCCAAACGGGTAATTTAGGCGTTTTTCCACCGTATTCGCTACGTGTAGATCCAAGAAAA
AGCAACAACTTCTAGCGAAACAGCTAATGCCAGGGTGGCTGATGACCCGGGGACCGATCTAGACT
ACAGCCGAACGTTTAAATAGTGGGGCGATCCCGTCAAATCTCAATTTGACTGACGAATCGACTGA
TTTTGAGTCAATAATACCAACACGATGGTATTGACATAATACCATCGTAATTATTTCCACTACAG
AGTGGAGGAATCGCCCCATTTAGGTTCCCACGGATAATTGCGAGTGTCTGAATGTGCTCCCGGAG
AAGCCGTAAGCGATGAAGACCGCCTGGATCTTTGTTCGGACGCAG
Right flanking sequence: Indices 9126 -- 9625
TCATACCGGATATGTCTCGGAGAATTATTGTCTTGCGAAACGCGGCATTACCTTGCTTTCAAGAC
TAAGAATCATTACGGAATCATAACGTAGACAACATTTCAAAGAAGGGCCCACGGAATACGGCGGG
GTTTAGTGTTTGCATGAGGTGTTCGTTGTCTCAGGTGCTCGTTGCCTCGAGGCTTTCGGGATCAT
GCAATACGCGTCAGGGCTTTGGTCTAAGGCGTCCCTCAAAGGTTATACCCCACAAATGAGAAAGA
AATGTTCTATTCGGGGCGATTAGGCGAGCTTAAAGTCTCTGGGAATCTTGGCAATATGCTGATAG
GTGCACCCTGATACGCGTCGTGCCATCGACAAACTAGGAGGCGGTGTCTCTAGAGCTCGCACCTA
GAGGCAACACCCTACAACCGTCGTATTCTATCCAGCTCCTGCAATCATGTGTGAATTTTAACTTG
GTGTAAGGGTGCCAACTCGGAAGTCGCCGAGGTTGTAAATTGATA
Found at i:12495 original size:11 final size:11
Alignment explanation
Indices: 12479--12503 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12469 AGCCTATCAA
12479 ACAGATGTTTG
1 ACAGATGTTTG
12490 ACAGATGTTTG
1 ACAGATGTTTG
12501 ACA
1 ACA
12504 CAGGGGACAT
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:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (11 bp):
ACAGATGTTTG
Left flanking sequence: Indices 11979 -- 12478
TCAACGAAGTTGACATCCTTGGGCAGGAATTGCCAAACCACTAAAAAACGGCTTATATGCACTCC
TGCTACTGCCTAGTACGCCAATGCTTTGGAGAAAACCCGGGAAATCAACCTAAAACTCCATAAGC
GGTGGGTTCACAGTGGTAGTAGTGTGCTTTCATTGTTGATAGACACGTTTTTTCGTATTGCGCCT
CGCCAGGTAGTCAATCGGAGCCAAACTTCCAAGTAGGCTCGATCTGGGTGTTAGCATCAACGAAG
CGCCAGCGTTTCCTGATTTTGGTGCTAGATCGAACACTGGAATTGTTTCACGATAAGTCTAGTGT
CTCTGATGCTAGATATTCGTTTTGAATGGGTGGTAGTAGTTCATGGTGTTTCAGTGGAGATCCTT
AATATTTTAAAGTCGCATGGCGCGTCTAACCGCTGCAGTCAACTAAAACGGGCGATCTGCAAATT
CTAGATGAAGTCACCACTCTCGGTAAAGGTTCGGTAGCCTATCAA
Right flanking sequence: Indices 12504 -- 13003
CAGGGGACATCTATTTCTCCTGTATTGTCCTTTAAAACGGTGATGCGAATTCATCAGTGCCAAAC
TGCCAATCGATACCACTCGATCAAATGCCTACTACATGTGTGCCATTCCCTGCTACCACTAGCTC
TTACAATTCCTTTTATTCCATATCCATTTTATCTCTTCTAACCGAAACCCAAGCAATTTTACCGA
TTCTCCGAATCAATCCATGACAAACAAGTCTTCCTTGGCCCGGCGGCCCAACGTGCCCAGCTGCG
ACCGTGACACCCGCCGCTTGAGCTCCTGCGGCGTCAAAATGGCATCGGAAAGCAGACCGGGAATG
CAGTCTTCAAAGTCCAGCGCGTTGCCGTCGTCGTCATCAATGATGGCCAACTCCGACACCCCCAC
CAGATCTAAGTAGGAGGTGGCAGCCAGCGATGTAGCCACCATAACAGCCTTGGACGACCCTGGCG
AGCCCAGAGCCGCCAGGTGGGGAGTCTCAAGAAAAACGTTGTTGG
Found at i:35730 original size:18 final size:18
Alignment explanation
Indices: 35707--35741 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35697 TGAGGACTTG
35707 AAGAAGTTGAACAAGAAC
1 AAGAAGTTGAACAAGAAC
*
35725 AAGAAGTTGATCAAGAA
1 AAGAAGTTGAACAAGAA
35742 GTTGGCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (18 bp):
AAGAAGTTGAACAAGAAC
Left flanking sequence: Indices 35207 -- 35706
TTACGCCACTAGCTGCTACGCTCTTCTAAGTTCGACGTTTCCACCACTTATTTTAGCAATTTAAC
CCCCTTACCCTGTGAATATTACCCGTTTTGTCATTCACGTGATTAGGGTTGTTAACCCTAGCATT
GTCTGCAGTCCGCTCCGATGGCGCAGACGCCCGGTGAAAAAAAAATCGTGCGGGAAGGGGTACCT
CTTTACCAAAGTTTTTACATTGGAAGACAAGTAACATGTCGAAATTGCCCAGCTCCGAGGTTCGC
GCCAAGGTCCAAGAGATCATCAAGTACTCTAAGGAGACCAAGCCTAGAAACTTTCTCGAGTCCAT
CGAGTTGCAGGCTTCGTTGAAGAACTACGACCCCCAGAGAGACAAGCGTTTCGCTGGTTCGTTGA
GACTTCCCGAGGTCCCCCGTCCCAACATGTCTATCTGCTTGTTTGGTGACGCTTTCGACGTTGAC
CGTGCCAAGTCTATTGGTATTGACGCCATGTCGGTTGAGGACTTG
Right flanking sequence: Indices 35742 -- 36241
GTTGGCCAAGAAGTACAACGCCTTCGTCGCTTCCGAGGTCTTGATTAAGCAGATCCCCCGTTTGT
TGGGTCCTGGTTTGTCCAAGGCTGGTAAGTTCCCCACCCCCGTGTCTCACAACGACGACTTGTAC
GGTAAGGTCCAGGACGTCAAGTCCACCATCAAGTTCCAGTTGAAGAAGGTCTTGTGTATGTCTGT
TGCCGTTGGTCACGTTGAGATGGAGGAGGACATTATCGTCAACCAGGTCTTGATGGCCGCTAACT
TCTTGGTTTCTTTGTTGAAGAAGAACTGGCAGAACGTTGGCGGTTTCGTTATCAAGTCGACCATG
GGTCCCCCCCAGAAGATCTACTAGATTTTCGGTTAATTTGTATAATAATAGGAACGTCATTAATC
ACGGATACACTGTAGAAAAATTTTCACGCGGAGATCAAAAGAGGGTGGAGGTGAGGGGATATGAG
AAGCCAAATAAAAGGTGAAAACTAATATAAATGCGGTAGATACTC
Done.