Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3570
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: 18081
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:10342 original size:28 final size:28
Alignment explanation
Indices: 10304--10381 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
10294 AATGCGTATG
*
10304 AATGTGTTTGGGCCTAATGGGCCACATA
1 AATGTGATTGGGCCTAATGGGCCACATA
* *
10332 AATGTGATTGGGCCTAATGGGCC-TATG
1 AATGTGATTGGGCCTAATGGGCCACATA
* *
10359 AA-GAGATTGGGCCTAGTGGGCCA
1 AATGTGATTGGGCCTAATGGGCCA
10382 TTATAGGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 18 0.41
27 4 0.09
28 22 0.50
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATGGGCCACATA
Found at i:10373 original size:26 final size:28
Alignment explanation
Indices: 10311--10381 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 28
10301 ATGAATGTGT
*
10311 TTGGGCCTAATGGGCCACATAAATGTGA
1 TTGGGCCTAATGGGCCACATAAATGAGA
* *
10339 TTGGGCCTAATGGGCC-TATGAA-GAGA
1 TTGGGCCTAATGGGCCACATAAATGAGA
*
10365 TTGGGCCTAGTGGGCCA
1 TTGGGCCTAATGGGCCA
10382 TTATAGGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 18 0.47
27 4 0.11
28 16 0.42
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCACATAAATGAGA
Found at i:10914 original size:13 final size:13
Alignment explanation
Indices: 10896--10921 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10886 CACAAACGAT
10896 TAAAATTTTCACA
1 TAAAATTTTCACA
10909 TAAAATTTTCACA
1 TAAAATTTTCACA
10922 ATGTCATATT
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:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATTTTCACA
Found at i:13329 original size:46 final size:45
Alignment explanation
Indices: 13279--13398 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 45
13269 GACGAGTGCT
13279 GTGTAAGACATGTCTGGGACATGCATCGGCCT-TGA-AACGTAAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGG-CTATGAGAACGT--GCCA
* * **
13325 GTGTAAGACATGTCTAGGACATGCTTCGGCTATGAGAGGGTGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCTATGAGAACGTGCCA
* *
13370 GTGTAAGACCATGTCTGGAACATGGATCG
1 GTGTAAGA-CATGTCTGGGACATGCATCG
13399 ACACAAATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 14 0.22
46 46 0.73
47 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (45 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCTATGAGAACGTGCCA
Found at i:13345 original size:92 final size:93
Alignment explanation
Indices: 13226--13398 Score: 205
Period size: 92 Copynumber: 1.9 Consensus size: 93
13216 CCACATTATA
* *
13226 AAGCCAGGTGTAAAACCAGTCTGGGACATGGCATT-GGC-ATTGAGACGAGTG-CTGTGTAAGA-
1 AAGCCAGGTGTAAAACCAGTCTAGGACAT-GC-TTCGGCTA-TGAGA-GAGTGCCAGTGTAAGAC
*
13287 CATGTCTGGGACATGCATCGGCCTTGAAACGT
62 CATGTCTGGAACATGCATCGGCCTTGAAACGT
* *
13319 AAGCCA-GTGTAAGA-CATGTCTAGGACATGCTTCGGCTATGAGAGGGTGCCAGTGTAAGACCAT
1 AAGCCAGGTGTAAAACCA-GTCTAGGACATGCTTCGGCTATGAGAGAGTGCCAGTGTAAGACCAT
*
13382 GTCTGGAACATGGATCG
65 GTCTGGAACATGCATCG
13399 ACACAAATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
90 6 0.09
91 21 0.30
92 36 0.52
93 6 0.09
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (93 bp):
AAGCCAGGTGTAAAACCAGTCTAGGACATGCTTCGGCTATGAGAGAGTGCCAGTGTAAGACCATG
TCTGGAACATGCATCGGCCTTGAAACGT
Found at i:14941 original size:29 final size:28
Alignment explanation
Indices: 14895--14949 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
14885 CCTATTCAGT
* * *
14895 AACAGTACAGTTTGGGCCTTAGCCCTTA
1 AACAGTACAGTATAGGCCTAAGCCCTTA
14923 AACAGTAGCAGTATAGGCCTAAGCCCT
1 AACAGTA-CAGTATAGGCCTAAGCCCT
14950 AATTCAGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (28 bp):
AACAGTACAGTATAGGCCTAAGCCCTTA
Found at i:15268 original size:25 final size:25
Alignment explanation
Indices: 15239--15303 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
15229 TTAATAATTA
15239 GGGCAAAGCCCTTTTCGGTAAACTG
1 GGGCAAAGCCCTTTTCGGTAAACTG
15264 GGGCAAAGCCCTTTTCGGTAAACTG
1 GGGCAAAGCCCTTTTCGGTAAACTG
*
15289 GGGCATAGCCCTTTT
1 GGGCAAAGCCCTTTT
15304 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.26
Consensus pattern (25 bp):
GGGCAAAGCCCTTTTCGGTAAACTG
Found at i:16141 original size:27 final size:27
Alignment explanation
Indices: 16111--16175 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
16101 GGGCATATTC
16111 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
16138 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
* *
16165 GACTTTTTACC
1 GTCATTTTACC
16176 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:16334 original size:56 final size:54
Alignment explanation
Indices: 16226--16362 Score: 143
Period size: 56 Copynumber: 2.5 Consensus size: 54
16216 TTGGTAAATC
* * *
16226 TACAAACCAAGGGTATTTTAGTAATTTTGTAAACTAATGGTATTACTATAATTTT
1 TACAAATCAAGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTACTATAA-TTT
* * * * *
16281 TAGATAGTCAAGGGTATTTCGGTAATTTTGTAAA-TCAAGGGTATT-TTGGTAATTT
1 TACA-AATCAAGGGTATTTTGGTAATTTTGTAAACT-AAGGGTATTACT-ATAATTT
*
16336 TACAAATTAAGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTTGGTAATTT
16363 CACAAACCAG
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
54 20 0.30
55 11 0.16
56 36 0.54
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTACTATAATTT
Found at i:16367 original size:27 final size:27
Alignment explanation
Indices: 16207--16442 Score: 183
Period size: 27 Copynumber: 8.7 Consensus size: 27
16197 TTCATCCTAC
* * * *
16207 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
* **
16234 AAGGGTATTTTAGTAATTTTGTAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
* * * * * *
16261 AATGGTATTACT-ATAATTTTTAGATAGT
1 AAGGGTATT-TTGGTAA-TTTTACAAACT
* **
16289 CAAGGGTATTTCGGTAATTTTGTAAA-T
1 -AAGGGTATTTTGGTAATTTTACAAACT
*
16316 CAAGGGTATTTTGGTAATTTTACAAATT
1 -AAGGGTATTTTGGTAATTTTACAAACT
*
16344 AAGGGTATTTTGGTAATTTCACAAAC-
1 AAGGGTATTTTGGTAATTTTACAAACT
* * *
16370 CAGTGGTACTTTGGCAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTTTACAAACT
*
16398 AGGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
16425 -AGAGGTATTTGGGTAATT
1 AAG-GGTATTTTGGTAATT
16443 CTATCCTACA
Statistics
Matches: 165, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
26 3 0.02
27 135 0.82
28 16 0.10
29 11 0.07
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAACT
Found at i:16456 original size:54 final size:54
Alignment explanation
Indices: 16320--16475 Score: 154
Period size: 54 Copynumber: 2.9 Consensus size: 54
16310 GTAAATCAAG
* * * * * *
16320 GGTATTTTGGTAATTTTACAAATTAAGGGTATTTTGGTAATTTCACAAACCAGT
1 GGTACTTTGGCAATTCTACAAACTAGGGGTATTTTGGTAATTTCACAAACCAGA
* * *
16374 GGTACTTTGGCAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGA
1 GGTACTTTGGCAATTCTACAAACTAGGGGTATTTTGGTAATTTCACAAACCAGA
* ** **
16428 GGTA-TTTGGGTAATTCTATCCTAC-AGGGGTATTTCAGTAATTTCACAA
1 GGTACTTT-GGCAATTCTA-CAAACTAGGGGTATTTTGGTAATTTCACAA
16476 TCGAGGGTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 3 0.03
54 80 0.93
55 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (54 bp):
GGTACTTTGGCAATTCTACAAACTAGGGGTATTTTGGTAATTTCACAAACCAGA
Found at i:16470 original size:81 final size:81
Alignment explanation
Indices: 16292--16484 Score: 191
Period size: 81 Copynumber: 2.4 Consensus size: 81
16282 AGATAGTCAA
** * *
16292 GGGTATTTCGGTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTTGG
1 GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTGGG
16357 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* * *
16373 TGGTACTTT-GGCAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACT-AGAGGTATTT
1 GGGTA-TTTCGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTACAAACTAAG-GGTATTT
**
16435 GGGTAA-TTCTATCCTA-CAG
63 GGGTAATTTC-A-CAAACCAG
* * *
16454 GGGTATTTCAGTAATTTCAC-AATCGAGGGTA
1 GGGTATTTCGGTAATTTTACAAATCAAGGGTA
16485 AAACGGTAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
80 16 0.18
81 69 0.77
82 5 0.06
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (81 bp):
GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTGGG
TAATTTCACAAACCAG
Found at i:16512 original size:27 final size:27
Alignment explanation
Indices: 16474--16727 Score: 312
Period size: 27 Copynumber: 9.4 Consensus size: 27
16464 GTAATTTCAC
* *
16474 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
** * **
16501 AACTC-AGGGTAAAATAGTAATTTTGGA
1 AA-TCGAGGGTAAAACGGTAATTCTATA
* * * *
16528 AATCGAGGATAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
16555 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
16582 AATCAAGGATAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
16609 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
16636 ATTCGAGGGCAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
16663 AATTGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
16690 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
16717 AATCGGGGGTA
1 AATCGAGGGTA
16728 CTCTGATAAT
Statistics
Matches: 198, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 2 0.01
27 194 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:16764 original size:81 final size:80
Alignment explanation
Indices: 16598--16835 Score: 196
Period size: 81 Copynumber: 3.0 Consensus size: 80
16588 GGATAAAATG
* * * ** * *
16598 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAATTCGAGGGCAAAAC-GGTAATTCTAT
1 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCG-GGG-GACTCTGGTAATTTTAC
* * *** *
16662 AAATTGAGGGTAAAACG
64 AAGTCGAGGGTATTTCA
*
16679 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGGGGGTACTCTGATAATTTTACA
1 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGGGGG-ACTCTGGTAATTTTACA
*
16744 AGTCAAGGGTATTTCA
65 AGTCGAGGGTATTTCA
* *** ** * * *
16760 GTAATT-T-TACAATCGACGGTATTTCATTAATTTTATAAA-CCGGGGACTTTGGTAATTTTACA
1 GTAATTCTATA-AATCGAGGGTAAAACGGTAATTCTATAAATCGGGGGACTCTGGTAATTTTACA
16822 AGTCGAGGGTATTT
65 AGTCGAGGGTATTT
16836 TTGTAATTGG
Statistics
Matches: 128, Mismatches: 26, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
78 28 0.22
79 7 0.05
80 28 0.22
81 65 0.51
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (80 bp):
GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGGGGGACTCTGGTAATTTTACAA
GTCGAGGGTATTTCA
Found at i:16790 original size:26 final size:27
Alignment explanation
Indices: 16734--16794 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
16724 GGTACTCTGA
*
16734 TAATTTTACAAGTCAAGGGTATTTCAG
1 TAATTTTACAAGTCAACGGTATTTCAG
* *
16761 TAATTTTACAA-TCGACGGTATTTCAT
1 TAATTTTACAAGTCAACGGTATTTCAG
16787 TAATTTTA
1 TAATTTTA
16795 TAAACCGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (27 bp):
TAATTTTACAAGTCAACGGTATTTCAG
Done.