Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold614
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27003
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:10269 original size:20 final size:20
Alignment explanation
Indices: 10240--10290 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
10230 ATTCACTTGT
*
10240 TATATCGATACATAAGTGAA
1 TATATCGATACATAAGTAAA
*
10260 TATATTGATACATAAGTAAA
1 TATATCGATACATAAGTAAA
*
10280 TGTATCGATAC
1 TATATCGATAC
10291 TAGACTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (20 bp):
TATATCGATACATAAGTAAA
Found at i:10442 original size:52 final size:50
Alignment explanation
Indices: 10328--10464 Score: 170
Period size: 52 Copynumber: 2.7 Consensus size: 50
10318 TTTGAAAAGA
* * *
10328 AAATGTATCGATACATT-TTTATTATATCGATACATTCTGGGTTTGATCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTGACCC
* * * *
10377 AAATGTATTGATACATTCTTCATTGTATCTATACATTTTGGGTTTTTTACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGG--TTTGACCC
10429 AAATGTATCGATACATTCTTTCA-TGTATCGATACAT
1 AAATGTATCGATACATTC-TTCATTGTATCGATACAT
10465 CCAGTTAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 16 0.21
50 20 0.27
52 35 0.47
53 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (50 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTGACCC
Found at i:12958 original size:27 final size:26
Alignment explanation
Indices: 12920--12971 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
12910 ATCGTCATCA
*
12920 GAGATACTCTAACCCCATTCTTTCAAG
1 GAGACACTCTAACCCCATT-TTTCAAG
* *
12947 GAGACACTCTAATCCCGTTTTTCAA
1 GAGACACTCTAACCCCATTTTTCAA
12972 CCAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (26 bp):
GAGACACTCTAACCCCATTTTTCAAG
Found at i:18430 original size:36 final size:36
Alignment explanation
Indices: 18373--18445 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
18363 ATAACTTGTT
* * *
18373 TTTTCTTTTTATGTTTATTATTATAAGTTAAATAAAA
1 TTTTCTTTTAATGTTTATTATTACAAATT-AATAAAA
*
18410 TTTTC-TTTAATGTTTGTTATTACAAATTAATAAAA
1 TTTTCTTTTAATGTTTATTATTACAAATTAATAAAA
18445 T
1 T
18446 CTAAATTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 8 0.25
36 19 0.59
37 5 0.16
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (36 bp):
TTTTCTTTTAATGTTTATTATTACAAATTAATAAAA
Found at i:19799 original size:7 final size:7
Alignment explanation
Indices: 19789--19822 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
19779 TAAACAATAG
19789 AAGAAAA
1 AAGAAAA
19796 AAG-AAA
1 AAGAAAA
19802 AAGAAAA
1 AAGAAAA
19809 AAGAAAA
1 AAGAAAA
19816 AAGAAAA
1 AAGAAAA
19823 GAAAAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:19807 original size:13 final size:13
Alignment explanation
Indices: 19789--19828 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
19779 TAAACAATAG
19789 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
19802 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
*
19815 AA-AGAAAAGAAA
1 AAGAAAAAAGAAA
19827 AA
1 AA
19829 TAAGCTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:19814 original size:20 final size:19
Alignment explanation
Indices: 19789--19828 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19779 TAAACAATAG
19789 AAGAAAAAAGAAAAAGAAAA
1 AAGAAAAAAG-AAAAGAAAA
19809 AAGAAAAAAGAAAAGAAAA
1 AAGAAAAAAGAAAAGAAAA
19828 A
1 A
19829 TAAGCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAGAAAAGAAAA
Found at i:21460 original size:28 final size:28
Alignment explanation
Indices: 21398--21474 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
21388 TGGAGATAAT
* *
21398 ACGAGGTTGGAGTGTTCCTCG--GAAGTA
1 ACGAGGTTGGAGT-ATCCTCGATGAAATA
* *
21425 ACGGGGTTGGAGTATCCCCGATGAAATA
1 ACGAGGTTGGAGTATCCTCGATGAAATA
21453 ACGAGGTTGGAGTATCCTCGAT
1 ACGAGGTTGGAGTATCCTCGAT
21475 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.12
27 12 0.29
28 25 0.60
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.25
Consensus pattern (28 bp):
ACGAGGTTGGAGTATCCTCGATGAAATA
Found at i:21520 original size:52 final size:52
Alignment explanation
Indices: 21457--21629 Score: 181
Period size: 52 Copynumber: 3.3 Consensus size: 52
21447 GAAATAACGA
* *
21457 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
** * * *
21509 AATTGGAGTATCCCCGATTAAAG-GAGAAAATTGGT-GTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGA-AAAATTGGTATTTTTGAAAATAAAATCGG
* * * *
21563 GGTTGGAGTATCCCCGATTATGAAAAAATCG-ATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT-TTTTGAAAATAAAATCGG
21615 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
21630 TCAGAAATAA
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
51 6 0.06
52 48 0.49
54 34 0.35
55 10 0.10
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
Found at i:21688 original size:25 final size:25
Alignment explanation
Indices: 21612--21688 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 25
21602 AAAATAAAGT
* *
21612 CGGGGTTGGAGTATCCCCTCAGAAATAA
1 CGGGGTTGGAGTAT-CCCAC-G-ATTAA
*
21640 CGGGGTTGGAGTATCCCGATGATTAA
1 CGGGGTTGGAGTATCCC-ACGATTAA
*
21666 CGGGTGTTGGAGTGTCCC-CGATT
1 CGGG-GTTGGAGTATCCCACGATT
21689 GTGAAGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.10
26 8 0.19
27 16 0.38
28 14 0.33
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (25 bp):
CGGGGTTGGAGTATCCCACGATTAA
Found at i:24184 original size:34 final size:34
Alignment explanation
Indices: 24141--24205 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
24131 ATTTCCAAAT
***
24141 GTATCGATACAAAGATCCATGTATCGATACAATG
1 GTATCGATACAAAGAAAAATGTATCGATACAATG
*
24175 GTATCGATACACAGAAAAATGTATCGATACA
1 GTATCGATACAAAGAAAAATGTATCGATACA
24206 TTTCCTTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (34 bp):
GTATCGATACAAAGAAAAATGTATCGATACAATG
Found at i:24253 original size:19 final size:19
Alignment explanation
Indices: 24229--24294 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
24219 TAGCTAATTA
24229 TGTATCGATACAATACTTT
1 TGTATCGATACAATACTTT
24248 TGTATCGATAC---A---T
1 TGTATCGATACAATACTTT
* *
24261 TGTATCGATACAAAACTTA
1 TGTATCGATACAATACTTT
24280 TGTATCGATACAATA
1 TGTATCGATACAATA
24295 TGTTAATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 12 0.31
16 2 0.05
19 25 0.64
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAATACTTT
Found at i:24265 original size:13 final size:13
Alignment explanation
Indices: 24247--24272 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24237 TACAATACTT
24247 TTGTATCGATACA
1 TTGTATCGATACA
24260 TTGTATCGATACA
1 TTGTATCGATACA
24273 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:24270 original size:32 final size:32
Alignment explanation
Indices: 24229--24291 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
24219 TAGCTAATTA
* *
24229 TGTATCGATACAATACTTTTGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
24261 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
24292 ATATGTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:24390 original size:21 final size:21
Alignment explanation
Indices: 24348--24403 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
24338 ACATTGTAGG
*
24348 ATGTATCGATACA-TCCACAA
1 ATGTATCGATACATTCAACAA
24368 ATGTATCGATACATTCAACAA
1 ATGTATCGATACATTCAACAA
24389 ATGTATCGATACATT
1 ATGTATCGATACATT
24404 TTAAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATTCAACAA
Found at i:24428 original size:19 final size:18
Alignment explanation
Indices: 24402--24437 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
24392 TATCGATACA
24402 TTTTAAATTTTTTTTTTT
1 TTTTAAATTTTTTTTTTT
24420 TTTTCAAATTTTTTTTTT
1 TTTT-AAATTTTTTTTTT
24438 CAAACACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTAAATTTTTTTTTTT
Found at i:24431 original size:15 final size:14
Alignment explanation
Indices: 24414--24441 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24404 TTAAATTTTT
24414 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
24428 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
24442 CACTTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:25113 original size:55 final size:55
Alignment explanation
Indices: 25018--25862 Score: 916
Period size: 55 Copynumber: 15.3 Consensus size: 55
25008 ATAAAGTGAA
* * * * * * * * * *
25018 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCACCTCGTGTGGGCTTTGATAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
25073 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* ** * *
25128 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
**
25183 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
25238 TCCTGCTC-TCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * * * **
25292 TCCTGCTCTTTGAGGACTAAAAGGCGGCCACCAACTTGTGTGGGGCTTTAAAATAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGG-TGCCACCAACTTGTGT-GGGC-TT----TAAGAGGTG
* ** * * *
25354 TCCTGCTCCTTGAGGACTGAAAAATG-CACCAACCTGTGTGGGCTTTAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
** * *
25408 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGA-GGTG
*
25464 TCCTGCTCTTTGAGGACCTGGAAA--T-ACACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGA-CT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * **
25518 TTCCTGCTCTTCGGGGACTGAAAGGTGCCACCAAC-TGTGTGGGGCTTTGCGAGGTG
1 -TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT-GGGCTTTAAGAGGTG
* * *
25574 T-CTGCTC-TTAAGGACTGGAAAGGTGCCACCAACTTGTGGGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
25628 TCCTGCTC-TTGAGGACTGGAAGGCGCCACCAAC-TGTGTGGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT-GGGCTTTAAGAGGTG
* * * *
25682 TCCTGCTCTTTGAGGGACTGGAAA-ATGCCACCCACTTTTGTGGG-ATT--GCAGGT-
1 TCCTGCTCTTTGA-GGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAG-AGGTG
*
25735 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
25790 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGACGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
25845 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
25863 AAAAAGCGGA
Statistics
Matches: 685, Mismatches: 70, Indels: 70
0.83 0.08 0.08
Matches are distributed among these distances:
52 28 0.04
53 31 0.05
54 169 0.25
55 321 0.47
56 74 0.11
57 13 0.02
58 8 0.01
59 4 0.01
60 12 0.02
61 1 0.00
62 24 0.04
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:26848 original size:16 final size:16
Alignment explanation
Indices: 26827--26880 Score: 83
Period size: 15 Copynumber: 3.4 Consensus size: 16
26817 CTTAAGTAGG
*
26827 TTTTTTCTTTTCTCTT
1 TTTTTTTTTTTCTCTT
26843 TTTTTTTTTTTC-CTT
1 TTTTTTTTTTTCTCTT
26858 TTTTTTTTTTTGCTCTT
1 TTTTTTTTTTT-CTCTT
26875 TTTTTT
1 TTTTTT
26881 GAAGAGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 14 0.40
16 12 0.34
17 9 0.26
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTTCTCTT
Found at i:26866 original size:14 final size:14
Alignment explanation
Indices: 26827--26867 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
26817 CTTAAGTAGG
* *
26827 TTTTTTCTTTTCTCT
1 TTTTTT-TTTTTTCC
26842 TTTTTTTTTTTTCC
1 TTTTTTTTTTTTCC
26856 TTTTTTTTTTTT
1 TTTTTTTTTTTT
26868 TGCTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTCC
Done.