Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1604
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: 38432
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:17 original size:1 final size:1
Alignment explanation
Indices: 12--89 Score: 129
Period size: 1 Copynumber: 78.0 Consensus size: 1
2 AGATACGGAG
* * *
12 AAAAAAAAAAAACAAAAAAAAAAAAAAAATAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
77 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
90 TATACGCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.96, C:0.03, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:696 original size:47 final size:46
Alignment explanation
Indices: 643--899 Score: 290
Period size: 47 Copynumber: 5.5 Consensus size: 46
633 ACTCGCCCTG
643 TCACATATATACACTTTCACATTCATGCACATCGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCAT-CACATCGCCATTAGGCCTTA
*
690 TCACATATAT-CACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTA
*
736 TC-CAAATAATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATAT-ATACACTTTCACATTCATCACATC-GCCATTAGGCCTTA
* * * *
783 TCACATAAATACACTTTCACATTCATCACATTGGCAATTCGGCCTTA
1 TCACATATATACACTTTCACATTCATCACA-TCGCCATTAGGCCTTA
* * * *
830 TGACATATATATACACTTTCACTATTCA--ACATTGGCCATT-CGCCTGA
1 T--CACATATATACACTTTCAC-ATTCATCACA-TCGCCATTAGGCCTTA
* *
877 TCACATATATACTCCTTCACATT
1 TCACATATATACACTTTCACATT
900 TATTCAAATA
Statistics
Matches: 186, Mismatches: 16, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
44 3 0.02
45 26 0.14
46 32 0.17
47 88 0.47
48 15 0.08
49 17 0.09
50 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (46 bp):
TCACATATATACACTTTCACATTCATCACATCGCCATTAGGCCTTA
Found at i:756 original size:93 final size:96
Alignment explanation
Indices: 647--899 Score: 331
Period size: 94 Copynumber: 2.7 Consensus size: 96
637 GCCCTGTCAC
*
647 ATATATACACTTTCACATTCATGCACATC-GCCATTAGGCCTTATCACATATAT-CACTTTCACA
1 ATATATACACTTTCACATTCAT-CACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACA
* *
710 TTCATCACATCGGCTATTAGGCCTTAT-CCAA
65 TTCATCACATCGGCAATTAGGCCTTATGACAA
741 ATA-ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACAT
* * *
805 TCATCACATTGGCAATTCGGCCTTATGACAT
66 TCATCACATCGGCAATTAGGCCTTATGACAA
* * * * * *
836 ATATATACACTTTCACTATTCA--ACATTGGCCATT-CGCCTGATCACATATATACTCCTTCACA
1 ATATATACACTTTCAC-ATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACA
898 TT
65 TT
900 TATTCAAATA
Statistics
Matches: 142, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
92 6 0.04
93 41 0.29
94 62 0.44
95 16 0.11
96 12 0.08
97 5 0.04
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (96 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACAT
TCATCACATCGGCAATTAGGCCTTATGACAA
Found at i:5305 original size:78 final size:78
Alignment explanation
Indices: 5164--5374 Score: 308
Period size: 78 Copynumber: 2.7 Consensus size: 78
5154 AACCCAAGTA
* * *
5164 CCTTCGGGATTTAG-CCGGATATA-CAACTCGCAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
5227 ACTCGCACAAATG
66 ACTCGCACAAATG
5240 CCTTCGGGACTTAGCCCGGATATAGTAACTCCACAAATGCCTTCGGGACTTA-CCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGTAACT-CACAAATGCCTTCGGGACTTAGCCCGGATATAGT
5304 AACTCGCACAAATG
65 AACTCGCACAAATG
*
5318 CCTTC-GGACTTA-CCCGGATATAGTCACTAGCACAAATGCCTTC-GGATCTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATATAGTAACT--CACAAATGCCTTCGGGA-CTTAGCCCGG
5375 TATCATCCGA
Statistics
Matches: 124, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
76 31 0.25
77 33 0.27
78 40 0.32
79 20 0.16
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTCGCACAAATG
Found at i:5363 original size:38 final size:40
Alignment explanation
Indices: 5164--5374 Score: 314
Period size: 38 Copynumber: 5.5 Consensus size: 40
5154 AACCCAAGTA
* *
5164 CCTTCGGGATTTAG-CCGGATATA-CAACTCG--CAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5200 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5240 CCTTCGGGACTTAGCCCGGATATAGTAACTC-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5279 CCTTCGGGACTTA-CCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
5318 CCTTC-GGACTTA-CCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5356 CCTTC-GGATCTTAGCCCGG
1 CCTTCGGGA-CTTAGCCCGG
5375 TATCATCCGA
Statistics
Matches: 164, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
36 13 0.08
37 9 0.05
38 62 0.38
39 38 0.23
40 42 0.26
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:5369 original size:116 final size:115
Alignment explanation
Indices: 5164--5374 Score: 320
Period size: 116 Copynumber: 1.8 Consensus size: 115
5154 AACCCAAGTA
* *
5164 CCTTCGGGATTTAGCCGGATATACAACTCGCAAATGCCTTCGGGACTTAGCCCGGATATAGTAAC
1 CCTTCGGGACTTACCCGGATATACAACTCGCAAATGCCTTCGGGACTTAGCCCGGATATAGTAAC
*
5229 TCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCCACAAATG
66 TAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCCACAAATG
*
5279 CCTTCGGGACTTACCCGGATATAGTAACTCGCACAAATGCCTTC-GGACTTA-CCCGGATATAGT
1 CCTTCGGGACTTACCCGGATATA-CAACTCG--CAAATGCCTTCGGGACTTAGCCCGGATATAGT
*
5342 CACTAGCACAAATGCCTTC-GGATCTTAGCCCGG
63 AACTAGCACAAATGCCTTCGGGA-CTTAGCCCGG
5375 TATCATCCGA
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
115 24 0.28
116 45 0.52
117 7 0.08
118 11 0.13
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (115 bp):
CCTTCGGGACTTACCCGGATATACAACTCGCAAATGCCTTCGGGACTTAGCCCGGATATAGTAAC
TAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCCACAAATG
Found at i:13127 original size:40 final size:40
Alignment explanation
Indices: 13058--13262 Score: 360
Period size: 40 Copynumber: 5.2 Consensus size: 40
13048 AACCCAAGTA
* *
13058 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13097 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13137 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13177 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
13217 CCTTCGGGACTTA-CCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13256 CCTTCGG
1 CCTTCGG
13263 ATCTTAGTCG
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
39 44 0.27
40 117 0.73
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:21143 original size:39 final size:40
Alignment explanation
Indices: 20993--21260 Score: 391
Period size: 40 Copynumber: 6.8 Consensus size: 40
20983 GAATATAGCT
*
20993 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
** * *
21033 GTTCACACAAATGCCTTCGGGATTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
21073 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
21113 ACTCGCACAAATGCC-TCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
21152 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
21192 ACTAGCACAAATGCCTTC-GGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
21231 ACTAGCACAAATGCCTTCGGGACTTAGCCC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC
21261 CGTTATCATC
Statistics
Matches: 214, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
39 76 0.36
40 136 0.64
41 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:21180 original size:79 final size:80
Alignment explanation
Indices: 21000--21260 Score: 404
Period size: 79 Copynumber: 3.3 Consensus size: 80
20990 GCTACTCGCT
** * *
21000 CAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAGTTCACACAAATGCCTTCGGGATTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
21064 G-ATATAGTAACTCGCA
65 GAAT-TAGTCACTAGCA
21080 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCC-TCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
21144 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
* *
21159 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTC-GGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
21223 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
21238 CAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
21261 CGTTATCATC
Statistics
Matches: 170, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
79 122 0.72
80 46 0.27
81 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTCACTAGCA
Found at i:27285 original size:49 final size:49
Alignment explanation
Indices: 27213--27438 Score: 281
Period size: 49 Copynumber: 4.6 Consensus size: 49
27203 CTAGTATGCA
* *
27213 TAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
* * * ** * *
27262 TAGTATCCTACACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACG
* * * * *
27312 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACG
* *
27363 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAGG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
27412 TAGTAGCCTGCACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
27439 ATGACCTCAC
Statistics
Matches: 150, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
49 66 0.44
50 46 0.31
51 38 0.25
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
Found at i:27386 original size:101 final size:98
Alignment explanation
Indices: 27213--27438 Score: 281
Period size: 100 Copynumber: 2.3 Consensus size: 98
27203 CTAGTATGCA
* * * *
27213 TAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTATCCTACACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
* *
27278 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACC-AACCATCCGATACACG
* * * * *
27312 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTACACT
* ** * *
27377 TAGTACTACACATGCGACCAATTATCCGGTACAGG
64 TAGTACTACACACGCGACCAACCATCCGATACACG
27412 TAGTAGCCTGCACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
27439 ATGACCTCAC
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
99 28 0.26
100 41 0.38
101 40 0.37
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCAACCATCCGATACACG
Found at i:32837 original size:20 final size:21
Alignment explanation
Indices: 32802--32842 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
32792 CTAACTCAAA
32802 GTATAAATATTTTTTCAATTT
1 GTATAAATATTTTTTCAATTT
32823 GTATAAATA-TTTTTCAATTT
1 GTATAAATATTTTTTCAATTT
32843 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
GTATAAATATTTTTTCAATTT
Found at i:36579 original size:13 final size:13
Alignment explanation
Indices: 36561--36586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36551 CAAAATCATA
36561 ATTATAATAATTT
1 ATTATAATAATTT
36574 ATTATAATAATTT
1 ATTATAATAATTT
36587 CGGTAAATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Done.