Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2308
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: 385994
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
File 3 of 3
Found at i:348642 original size:25 final size:23
Alignment explanation
Indices: 348582--348676 Score: 59
Period size: 23 Copynumber: 3.9 Consensus size: 23
348572 ATATATGCAT
* *
348582 TATATTTAATTATGTTTA-ATTATA
1 TATATTT-ATTAT-TTTATTTTTTA
348606 TAATATTATATTTATTTTAGTTTTTTA
1 T-ATATT-TA-TTATTTTA-TTTTTTA
**
348633 TATATTTATTACATTATTTTTTA
1 TATATTTATTATTTTATTTTTTA
* *
348656 TAT-TGTATTATATTTAATTTT
1 TATATTTATTAT-TTTATTTTT
348677 ATTTAAACAT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
22 6 0.11
23 17 0.30
24 7 0.12
25 12 0.21
26 10 0.18
27 5 0.09
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (23 bp):
TATATTTATTATTTTATTTTTTA
Found at i:348643 original size:30 final size:32
Alignment explanation
Indices: 348570--348652 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 32
348560 ATCATAAATG
** *
348570 TTATATATGCATTATATTTA-ATTATGTTTAA
1 TTATATATATATTATATTTATTTTATGTTTAA
*
348601 TTATATA-ATATTATATTTATTTTA-GTTT-T
1 TTATATATATATTATATTTATTTTATGTTTAA
* *
348630 TTATATATTTATTACA-TTATTTT
1 TTATATATATATTATATTTATTTT
348653 TTATATTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 14 0.32
30 20 0.45
31 10 0.23
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (32 bp):
TTATATATATATTATATTTATTTTATGTTTAA
Found at i:349558 original size:102 final size:99
Alignment explanation
Indices: 349384--349583 Score: 258
Period size: 102 Copynumber: 2.0 Consensus size: 99
349374 TGGCTGGCTG
* * * * * *
349384 GGTCATTGTCATTAATGACCAGAACAAATATGGGGAATATTTTAGATTGGCCTTCGCCTTTTGTC
1 GGTCATTGTCATTAATGACCAAAAAAAATATAGGGAATATTTTAGATTGGCCTACGCCCTTTGGC
*
349449 ATGTTTCCCCACATCT-ATACCAAGAAGCCAAACC
66 ATCTTTCCCCACATCTCA-ACCAAGAAGCCAAACC
* * *
349483 GGTCATTGTTATTGATGACCAAAAAAAATTCTAGGGAATAATTTTTAGATTGGCCTACGCCCTTT
1 GGTCATTGTCATTAATGACCAAAAAAAA-TATAGGGAAT-A-TTTTAGATTGGCCTACGCCCTTT
*
349548 GGCATCTTTCCCCACATCTCAGCCAAGAAGCCAAAC
63 GGCATCTTTCCCCACATCTCAACCAAGAAGCCAAAC
349584 TAGAAAATCT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
99 24 0.28
100 8 0.09
101 1 0.01
102 52 0.60
103 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (99 bp):
GGTCATTGTCATTAATGACCAAAAAAAATATAGGGAATATTTTAGATTGGCCTACGCCCTTTGGC
ATCTTTCCCCACATCTCAACCAAGAAGCCAAACC
Found at i:349608 original size:102 final size:100
Alignment explanation
Indices: 349416--349608 Score: 217
Period size: 102 Copynumber: 1.9 Consensus size: 100
349406 AACAAATATG
* * * *
349416 GGGAATATTTTAGATTGGCCTTCGCCTTTTGTCATGTTTCCCCACATCTATACCAAGAAGCCAAA
1 GGGAATATTTTAGATTGGCCTACGCCCTTTGGCATCTTTCCCCACATCTATACCAAGAAGCCAAA
* ** * * * ** *
349481 CCGGTCATTGTTATTGATGACCAAAAAAAATTCTA
66 CCAGAAAATCTTAATGAACAACAAAAAAAATTCTA
*
349516 GGGAATAATTTTTAGATTGGCCTACGCCCTTTGGCATCTTTCCCCACATCTCA-GCCAAGAAGCC
1 GGGAAT-A-TTTTAGATTGGCCTACGCCCTTTGGCATCTTTCCCCACATCT-ATACCAAGAAGCC
*
349580 AAACTAGAAAATCTTAATGAACAACAAAA
63 AAACCAGAAAATCTTAATGAACAACAAAA
349609 TTATAGATTA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
100 6 0.08
101 1 0.01
102 67 0.89
103 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (100 bp):
GGGAATATTTTAGATTGGCCTACGCCCTTTGGCATCTTTCCCCACATCTATACCAAGAAGCCAAA
CCAGAAAATCTTAATGAACAACAAAAAAAATTCTA
Found at i:350550 original size:35 final size:35
Alignment explanation
Indices: 350504--350573 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
350494 GTTTAGCTCA
350504 TCAGCCTTGAGTTCTCCTTATCCAGTCTAGAATAT
1 TCAGCCTTGAGTTCTCCTTATCCAGTCTAGAATAT
350539 TCAGCCTTGAGTTCTCCTTATCCAGTCTAGAATAT
1 TCAGCCTTGAGTTCTCCTTATCCAGTCTAGAATAT
350574 CAGAACAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (35 bp):
TCAGCCTTGAGTTCTCCTTATCCAGTCTAGAATAT
Found at i:351610 original size:32 final size:32
Alignment explanation
Indices: 351568--351629 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
351558 AGGTGGGTGG
* * *
351568 TTGATATATGAAAGGATGAAACTAGTTAGTGT
1 TTGATATATGAAAAGATAAAACTAATTAGTGT
*
351600 TTGATGTATGAAAAGATAAAACTAATTAGT
1 TTGATATATGAAAAGATAAAACTAATTAGT
351630 TTTACCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (32 bp):
TTGATATATGAAAAGATAAAACTAATTAGTGT
Found at i:355673 original size:16 final size:17
Alignment explanation
Indices: 355649--355696 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 17
355639 AAAAATTGCA
*
355649 TATACTAATTAAT-TTT
1 TATATTAATTAATATTT
355665 TATATTAATTATATATTT
1 TATATTAATTA-ATATTT
355683 TATAATTAAATTAA
1 TAT-ATT-AATTAA
355697 ATAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.37
17 2 0.07
18 6 0.22
19 4 0.15
20 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTAATTAATATTT
Found at i:360411 original size:18 final size:18
Alignment explanation
Indices: 360388--360422 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
360378 AGGCAGCCAA
360388 CATAATTTCTTTATGTGT
1 CATAATTTCTTTATGTGT
360406 CATAATTTCTTTATGTG
1 CATAATTTCTTTATGTG
360423 CTTAAAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (18 bp):
CATAATTTCTTTATGTGT
Found at i:361441 original size:2 final size:2
Alignment explanation
Indices: 361436--361460 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
361426 GCGTGTGTCC
361436 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
361461 AGAGAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:361465 original size:2 final size:2
Alignment explanation
Indices: 361460--361517 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
361450 GTGTGTGTGT
361460 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
361502 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
361518 CCTTGTATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:365920 original size:17 final size:16
Alignment explanation
Indices: 365891--365929 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
365881 TTTTAACAAA
* *
365891 TAAAAAATTAAAATTT
1 TAAAAAATAAAAATCT
365907 TAAATAAATAAAAATCT
1 TAAA-AAATAAAAATCT
365924 TAAAAA
1 TAAAAA
365930 TATTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAAATAAAAATCT
Found at i:372792 original size:22 final size:21
Alignment explanation
Indices: 372767--372809 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
372757 AATAAACTTG
* *
372767 AAAATATTACACATGATTTAAA
1 AAAATAATACAAAT-ATTTAAA
372789 AAAATAATACAAATATTTAAA
1 AAAATAATACAAATATTTAAA
372810 TATCATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAATACAAATATTTAAA
Found at i:373253 original size:20 final size:20
Alignment explanation
Indices: 373228--373269 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
373218 AAAAAAATAT
373228 ATTAAAGATTATATT-ATTAA
1 ATTAAA-ATTATATTGATTAA
*
373248 ATTAAAATTATTTTGATTAA
1 ATTAAAATTATATTGATTAA
373268 AT
1 AT
373270 ATTCAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTAAAATTATATTGATTAA
Found at i:375774 original size:127 final size:130
Alignment explanation
Indices: 375483--375820 Score: 381
Period size: 119 Copynumber: 2.7 Consensus size: 130
375473 TTTTTAATAC
* * * *
375483 AAAAATAATATTTAATTAA-CTTAAAAAATTTTACATTAATAAATTAAAATATT-A--ACTAT-T
1 AAAAATAATATTTAATTAAGTTTAAAAAA-ATTACATTAACAAATTAAAATATTAATTATTATAT
* * *
375543 TTTTAAAAATAAAAA-ATTAAAT------TAAAAAAGGTTTATTATTATTATTTTTTAATAAAAT
65 TTTTTAAAATAAAAATATTAAATAAAAAATAAAAAAGGTTTATTATTATTATATTGTAATAAAAT
375601 T
130 T
*
375602 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTA-TATGTT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTATATT
*
375666 TTTATAAAAATAAAAAGTATTAAATAAAAAATAAAAAA-GTTTTTTATTA-TA-ATTGTAATAAA
66 TTT-T-AAAATAAAAA-TATTAAATAAAAAATAAAAAAGGTTTATTATTATTATATTGTAATAAA
375728 A-T
128 ATT
* *
375730 -AAAATAAATATTTAATTAAGTTT-AAAAATTTATATTAACAAATTAAAATATTAATTATTATAT
1 AAAAAT-AATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTATAT
* *
375793 TTTTTAAAATAAAAATTTTAAATTAAAA
65 TTTTTAAAATAAAAATATTAAATAAAAA
375821 TTTTATTAAT
Statistics
Matches: 190, Mismatches: 12, Indels: 28
0.83 0.05 0.12
Matches are distributed among these distances:
119 41 0.22
120 9 0.05
121 3 0.02
122 6 0.03
124 10 0.05
125 11 0.06
126 17 0.09
127 38 0.20
128 26 0.14
129 10 0.05
130 2 0.01
131 10 0.05
132 7 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (130 bp):
AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTATATT
TTTTAAAATAAAAATATTAAATAAAAAATAAAAAAGGTTTATTATTATTATATTGTAATAAAATT
Found at i:379608 original size:23 final size:23
Alignment explanation
Indices: 379571--379623 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
379561 ATAAATTTCA
*
379571 TAAAAATAAATTAAATTA-ATTT
1 TAAAAATAAAATAAATTAGATTT
379593 TAAAAATAAAAATAAATTAGATTT
1 TAAAAAT-AAAATAAATTAGATTT
379617 TAAAAAT
1 TAAAAAT
379624 TTTTTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 7 0.25
23 10 0.36
24 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAAATAAAATAAATTAGATTT
Found at i:379953 original size:32 final size:34
Alignment explanation
Indices: 379906--379972 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 34
379896 AAATCATACC
* * *
379906 TTAATTTTTTTAAAAT-TTAATT-AAATATTATT
1 TTAATTTTATAAAAATAATAATTGAAATATTATT
*
379938 TTAATTTTATAAAAATAATAATTGATATATTATT
1 TTAATTTTATAAAAATAATAATTGAAATATTATT
379972 T
1 T
379973 ATTAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 14 0.48
33 5 0.17
34 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
TTAATTTTATAAAAATAATAATTGAAATATTATT
Found at i:380162 original size:18 final size:18
Alignment explanation
Indices: 380135--380171 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
380125 ATATATTATT
* *
380135 ATTTATTTAATTTTTAAA
1 ATTTAATTAATTTATAAA
380153 ATTTAATTAATTTATAAA
1 ATTTAATTAATTTATAAA
380171 A
1 A
380172 AAATTACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATTAATTTATAAA
Found at i:384737 original size:2 final size:2
Alignment explanation
Indices: 384732--384761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
384722 AAAAACCTTT
384732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
384762 AGATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:384797 original size:19 final size:19
Alignment explanation
Indices: 384775--384835 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
384765 TTTTTTTTAA
384775 AAGAAAGTGATAATTTTTT
1 AAGAAAGTGATAATTTTTT
* * *
384794 AAGAGAA-TGGTAAATTTTA
1 AAGA-AAGTGATAATTTTTT
* * *
384813 AAGGAAGTGATAGTTTCTT
1 AAGAAAGTGATAATTTTTT
384832 AAGA
1 AAGA
384836 GAACCATAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 2 0.07
19 26 0.87
20 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (19 bp):
AAGAAAGTGATAATTTTTT
Done.