Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1415
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: 31641
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1372 original size:11 final size:11
Alignment explanation
Indices: 1356--1381 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1346 TTTAATAATT
1356 TTATTATTTTA
1 TTATTATTTTA
1367 TTATTATTTTA
1 TTATTATTTTA
1378 TTAT
1 TTAT
1382 ATATATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:3564 original size:46 final size:46
Alignment explanation
Indices: 3450--3762 Score: 507
Period size: 46 Copynumber: 7.0 Consensus size: 46
3440 AGTGTGCTCT
3450 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3496 C-----TGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3537 CTGATATGAAATGTGTAAGACCATGGTTGAAAG--ACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3581 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3627 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3673 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
3719 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3763 TCATGTCAAA
Statistics
Matches: 253, Mismatches: 6, Indels: 16
0.92 0.02 0.06
Matches are distributed among these distances:
41 41 0.16
44 44 0.17
45 1 0.00
46 167 0.66
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3689 original size:136 final size:132
Alignment explanation
Indices: 3450--3762 Score: 495
Period size: 136 Copynumber: 2.3 Consensus size: 132
3440 AGTGTGCTCT
3450 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAAATGTGTAAGACCAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAAATGTGTAAGACCAT
3515 GGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG-ACCATGGCA
66 GGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGAACCATGGCA
3579 AC
131 AC
3581 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TGAAATGTGTAAG
3646 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
61 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA-ACC
3711 ATGGCAAC
125 ATGGCAAC
* * * * * *
3719 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3763 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
131 47 0.28
136 73 0.43
137 1 0.01
138 47 0.28
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (132 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAAATGTGTAAGACCAT
GGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGAACCATGGCA
AC
Found at i:12496 original size:26 final size:26
Alignment explanation
Indices: 12467--12573 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
12457 TGGTACAAAT
12467 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
12493 TGATAGTGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12519 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12545 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12570 TGAT
1 TGAT
12574 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
25 22 0.29
26 53 0.71
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:15434 original size:50 final size:50
Alignment explanation
Indices: 15359--15461 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
15349 TCATCAATAA
*
15359 TATCTAGGGCCTAATTGCCACTTAAGTCCTTTCTCATTTAGTAATTAAGC
1 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAAGC
15409 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAAGC
1 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAAGC
15459 TAT
1 TAT
15462 TTGATCACCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (50 bp):
TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAAGC
Found at i:15945 original size:297 final size:296
Alignment explanation
Indices: 15409--15948 Score: 956
Period size: 297 Copynumber: 1.8 Consensus size: 296
15399 GTAATTAAGC
*
15409 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAAGCTATTTGATCACCTAA
1 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAACCTATTTGATCACCTAA
* *
15474 ATGAAATAGTTACCATGTTTTGCACCTTTTTCAATTTAGTCCTTCTTTCTTTAATTAGTTATCTA
66 ATGAAATAATTACCATGTTTTGCACCTTTCTCAATTTAGTCCTTCTTTCTTTAATTAGTTATCTA
* * * *
15539 AACGATAAAATTTCTTAACCAAAAATTACTAGGACTCTAATGACTCGAAAAATATTCTATAAATC
131 AACGATAAAATTTCTTAACCAAAAATTAATACGACTCTAATGACTCAAAAAATATTCTATAAATA
* *
15604 AAATCTTTGAGTCGACACAATGGAAATTTGTGGTTCAGAAACCACTGTTCCATCACATATATTAT
196 AAATCTGTGAGTCAACACAATGGAAATTTGTGGTTCAGAAACCACTGTTCCATCACATATATTAT
15669 TTTATCATTTTCAATCAAATTATCACTCATCAATAA
261 TTTATCATTTTCAATCAAATTATCACTCATCAATAA
15705 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAACCTATTTGATCACCTAA
1 TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAACCTATTTGATCACCTAA
* *
15770 ATGCAATAATTACCATGTTTTGCACCTTTCTCAATTTTAGTCCTTCTTTCTTTAATTATTTATCT
66 ATGAAATAATTACCATGTTTTGCACCTTTCTCAA-TTTAGTCCTTCTTTCTTTAATTAGTTATCT
15835 AAACGATAAAATTTCTTAACCAAAAATTAATACGACTCTAATGACTCAAAAAATATTCTATAAAT
130 AAACGATAAAATTTCTTAACCAAAAATTAATACGACTCTAATGACTCAAAAAATATTCTATAAAT
15900 AAAATCTGTGAGTCAACACAATGGAAATTTGTGGTTC-GTAAACCACTGT
195 AAAATCTGTGAGTCAACACAATGGAAATTTGTGGTTCAG-AAACCACTGT
15949 CCTGTCACCA
Statistics
Matches: 231, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
296 96 0.42
297 135 0.58
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (296 bp):
TATCTAGGGCCTAATTGCCACTTAAGTCCTTCCTCATTTAGTAATTAACCTATTTGATCACCTAA
ATGAAATAATTACCATGTTTTGCACCTTTCTCAATTTAGTCCTTCTTTCTTTAATTAGTTATCTA
AACGATAAAATTTCTTAACCAAAAATTAATACGACTCTAATGACTCAAAAAATATTCTATAAATA
AAATCTGTGAGTCAACACAATGGAAATTTGTGGTTCAGAAACCACTGTTCCATCACATATATTAT
TTTATCATTTTCAATCAAATTATCACTCATCAATAA
Found at i:18528 original size:79 final size:79
Alignment explanation
Indices: 18426--18727 Score: 395
Period size: 79 Copynumber: 3.8 Consensus size: 79
18416 GCTCCTCGTT
* * *
18426 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGGACTTAGCCC
*
18489 GGATTTAGTAACTCGCA
63 GGATTTAGTATCTCGCA
18506 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
18570 ATTAGTATCTCGCA
66 TTTAGTATCTCGCA
*
18584 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
18648 ATTTAGTATCTCGCA
65 ATTTAGTATCTCGCA
* * *
18663 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCAC-AA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCACAAATGCCTTCGGGACTTAGCC
18724 CGGA
62 CGGA
18728 CATCATTCAA
Statistics
Matches: 202, Mismatches: 11, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
77 2 0.01
78 74 0.37
79 84 0.42
80 33 0.16
81 9 0.04
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TTTAGTATCTCGCA
Found at i:18543 original size:39 final size:39
Alignment explanation
Indices: 18426--18727 Score: 373
Period size: 39 Copynumber: 7.6 Consensus size: 39
18416 GCTCCTCGTT
* *
18426 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
18466 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
18506 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
18545 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
18584 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
18623 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
* * *
18663 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
18704 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
18728 CATCATTCAA
Statistics
Matches: 242, Mismatches: 13, Indels: 15
0.90 0.05 0.06
Matches are distributed among these distances:
39 132 0.55
40 100 0.41
41 10 0.04
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:25979 original size:93 final size:93
Alignment explanation
Indices: 25867--26038 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
25857 CGCCCATAAG
*
25867 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
25931 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
25960 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
26025 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
26039 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:26033 original size:46 final size:46
Alignment explanation
Indices: 25860--26035 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
25850 TGTAACCCGC
* *
25860 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
25906 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
25956 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
25999 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
26036 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28962 original size:27 final size:27
Alignment explanation
Indices: 28878--28976 Score: 105
Period size: 26 Copynumber: 3.7 Consensus size: 27
28868 TAAATGAACC
* * *
28878 GCCTTTATGGCATACTATG-ATATATG
1 GCCTTTGTGGCGTACTCTGTATATATG
* *
28904 GCCTTTGTGGCATA-TCTATAT-TATG
1 GCCTTTGTGGCGTACTCTGTATATATG
* *
28929 GCCTTTGTGCCGTACTCTGTATATATA
1 GCCTTTGTGGCGTACTCTGTATATATG
28956 GCCTTTGTGGCGTTACTCTGT
1 GCCTTTGTGGCG-TACTCTGT
28977 CGGTTCACCT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
25 18 0.30
26 21 0.34
27 14 0.23
28 8 0.13
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (27 bp):
GCCTTTGTGGCGTACTCTGTATATATG
Found at i:29800 original size:10 final size:10
Alignment explanation
Indices: 29785--29832 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
29775 AACATACATT
29785 TCATAAATTA
1 TCATAAATTA
*
29795 TCATAAACATA
1 TCATAAA-TTA
*
29806 TACATACATT-
1 T-CATAAATTA
29816 TCATAAATTA
1 TCATAAATTA
29826 TCATAAA
1 TCATAAA
29833 CATATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
9 7 0.23
10 15 0.48
11 4 0.13
12 5 0.16
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (10 bp):
TCATAAATTA
Found at i:29812 original size:31 final size:31
Alignment explanation
Indices: 29776--29838 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
29766 GTTAGAAATA
29776 ACATACATTTCATAAATTATCATAAACATAT
1 ACATACATTTCATAAATTATCATAAACATAT
29807 ACATACATTTCATAAATTATCATAAACATAT
1 ACATACATTTCATAAATTATCATAAACATAT
29838 A
1 A
29839 ATAAATAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (31 bp):
ACATACATTTCATAAATTATCATAAACATAT
Done.