Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1426
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: 170309
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
File 2 of 2
Found at i:151228 original size:2 final size:2
Alignment explanation
Indices: 151221--151290 Score: 50
Period size: 2 Copynumber: 34.0 Consensus size: 2
151211 TTGTTTACAG
* * * * * *
151221 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TCG TT TG TT TA CA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA -TA
* *
151265 TA TA TA AA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
151291 GTTTACAGTA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:151268 original size:42 final size:42
Alignment explanation
Indices: 151209--151290 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
151199 ATGTATAGCT
*
151209 GTTTGTTTACAGTATATATAAATATATATATATATATATATC
1 GTTTGTTTACAGTATATATAAATATATATACATATATATATC
151251 GTTTGTTTACAGTATATATAAATATATATACATATATATA
1 GTTTGTTTACAGTATATATAAATATATATACATATATATA
151291 GTTTACAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (42 bp):
GTTTGTTTACAGTATATATAAATATATATACATATATATATC
Found at i:152167 original size:25 final size:24
Alignment explanation
Indices: 152108--152171 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
152098 TTTTTAATAT
152108 AAAATAATATATAAATAAAAATTTA
1 AAAATAA-ATATAAATAAAAATTTA
* * *
152133 AATATCAAATATGAATAATAATTATA
1 AAAAT-AAATATAAATAAAAATT-TA
152159 AAAATAAAT-TAAA
1 AAAATAAATATAAA
152172 ACTTTAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.09
25 21 0.66
26 8 0.25
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAATAAATATAAATAAAAATTTA
Found at i:154496 original size:15 final size:16
Alignment explanation
Indices: 154478--154514 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
154468 TTGATATTTA
154478 AAAATTTTA-AATATT
1 AAAATTTTATAATATT
*
154493 AAAATTTTATAATTTT
1 AAAATTTTATAATATT
154509 AAAATT
1 AAAATT
154515 AATTTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATTTTATAATATT
Found at i:154513 original size:16 final size:15
Alignment explanation
Indices: 154473--154514 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
154463 TTTATTTGAT
*
154473 ATTTAAAAATTTTAA
1 ATTTTAAAATTTTAA
*
154488 ATATTAAAATTTTATA
1 ATTTTAAAATTTTA-A
154504 ATTTTAAAATT
1 ATTTTAAAATT
154515 AATTTTTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAAAATTTTAA
Found at i:154514 original size:8 final size:8
Alignment explanation
Indices: 154473--154514 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
154463 TTTATTTGAT
*
154473 ATTTAAAA
1 ATTTTAAA
154481 ATTTT-AA
1 ATTTTAAA
*
154488 ATATTAAA
1 ATTTTAAA
*
154496 ATTTTATA
1 ATTTTAAA
154504 ATTTTAAA
1 ATTTTAAA
154512 ATT
1 ATT
154515 AATTTTTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:154615 original size:21 final size:21
Alignment explanation
Indices: 154548--154625 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
154538 ATACATAATA
*
154548 AAAATATAT-AATATATTTTATT
1 AAAATATATAAAAATA-TTT-TT
***
154570 AAAA-ATATAAAAATA-AACT
1 AAAATATATAAAAATATTTTT
154589 ATAAATATATAAAAATATTTTT
1 A-AAATATATAAAAATATTTTT
154611 AAAATAT-TAATAAAT
1 AAAATATATAA-AAAT
154626 CTAAAATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.05
20 6 0.14
21 25 0.57
22 11 0.25
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATATAAAAATATTTTT
Found at i:155111 original size:16 final size:16
Alignment explanation
Indices: 155090--155124 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
155080 AATAATAATT
*
155090 TAAAATTTAAATTTTA
1 TAAAATTTAAATTATA
155106 TAAAATTTAAATTATA
1 TAAAATTTAAATTATA
155122 TAA
1 TAA
155125 TTTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAATTTAAATTATA
Found at i:157033 original size:12 final size:12
Alignment explanation
Indices: 157017--157049 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
157007 ATGTAATTAA
157017 AAATTATA-TTT
1 AAATTATATTTT
157028 ATAATTATATTTT
1 A-AATTATATTTT
157041 AAATTATAT
1 AAATTATAT
157050 ATAAGTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 15 0.75
13 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAATTATATTTT
Found at i:157598 original size:29 final size:27
Alignment explanation
Indices: 157560--157617 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 27
157550 AAATAAATAA
157560 TTAATAATTTTTAAAAATATATATTTAAT
1 TTAATAATTTTTAAAAAT-TA-ATTTAAT
*
157589 TTAATAATTTTTAATAATTAATTTAAT
1 TTAATAATTTTTAAAAATTAATTTAAT
157616 TT
1 TT
157618 TGAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 9 0.32
28 2 0.07
29 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAATAATTTTTAAAAATTAATTTAAT
Found at i:159792 original size:2 final size:2
Alignment explanation
Indices: 159785--159821 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
159775 TCTTTATTTC
159785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
159822 AGAGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:160438 original size:24 final size:24
Alignment explanation
Indices: 160393--160438 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
160383 TTTTAACTAA
* * *
160393 TTTTTAATATTTTTTGTCTTTGTT
1 TTTTTAATATTTTATATATTTGTT
*
160417 TTTTTCATATTTTATATATTTG
1 TTTTTAATATTTTATATATTTG
160439 ATATCAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTTAATATTTTATATATTTGTT
Found at i:161476 original size:171 final size:171
Alignment explanation
Indices: 161175--161518 Score: 472
Period size: 171 Copynumber: 2.0 Consensus size: 171
161165 ACAGCTAGTT
* * * * * *
161175 GAAAGCTAACAAGCAAAAAAATAGATGGTTTTAAGGTTAGAGATCTACTAAGAGGGTAGTGGTGA
1 GAAAGCTAACAAGCAAAAAAACAGATGGTTTCAAGGTCAAAGATATACTAAAAGGGTAGTGGTGA
* * *
161240 TAGATGAAAGGCATCACACATTGGGAAAATTGGCTTCCATATTGTCTAAGGAATTGTTGAAAGGG
66 TAGATGAAAGGCATCACACATTGGGAAAATTAGCTTCCATATTGGCTAAGGAATTGTTAAAAGGG
* *
161305 CAAAAAGTAGTGGTGGTGTGATGTAAAGAGATTTGCATGTC
131 CAAAAAGTAGTGGTGGTGAGATGTAAAAAGATTTGCATGTC
* * * *
161346 GAAAGCTAACAAGCAAAGAAACAGATGGTTTCAAGGTCAAAGATATGCTAAAAGGGTGGTGGTGG
1 GAAAGCTAACAAGCAAAAAAACAGATGGTTTCAAGGTCAAAGATATACTAAAAGGGTAGTGGTGA
* * ** * ***
161411 TGGATGAAAGGCATTACATGTTGGGAAGATTAGCTTCCATATTGGCTAAGTTGTTGTTAAAAGGG
66 TAGATGAAAGGCATCACACATTGGGAAAATTAGCTTCCATATTGGCTAAGGAATTGTTAAAAGGG
*
161476 CAAAAGGTAGTGGTGGTGAGATGTAAAAAGATTTGCATGTC
131 CAAAAAGTAGTGGTGGTGAGATGTAAAAAGATTTGCATGTC
161517 GA
1 GA
161519 TTGGTTTGGT
Statistics
Matches: 149, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
171 149 1.00
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.26
Consensus pattern (171 bp):
GAAAGCTAACAAGCAAAAAAACAGATGGTTTCAAGGTCAAAGATATACTAAAAGGGTAGTGGTGA
TAGATGAAAGGCATCACACATTGGGAAAATTAGCTTCCATATTGGCTAAGGAATTGTTAAAAGGG
CAAAAAGTAGTGGTGGTGAGATGTAAAAAGATTTGCATGTC
Found at i:163696 original size:27 final size:27
Alignment explanation
Indices: 163660--163722 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
163650 CAACTTGGTT
163660 AGTTTATTGAAAAAGTATGCATGATATA
1 AGTTT-TTGAAAAAGTATGCATGATATA
**
163688 AGTTTTTG--AATTTATGCATGATATA
1 AGTTTTTGAAAAAGTATGCATGATATA
*
163713 AGCTTTTGAA
1 AGTTTTTGAA
163723 TTTTCCTCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 22 0.73
27 3 0.10
28 5 0.17
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (27 bp):
AGTTTTTGAAAAAGTATGCATGATATA
Found at i:163704 original size:25 final size:25
Alignment explanation
Indices: 163675--163725 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
163665 ATTGAAAAAG
*
163675 TATGCATGATATAAGTTTTTGAATT
1 TATGCATGATATAAGCTTTTGAATT
163700 TATGCATGATATAAGCTTTTGAATT
1 TATGCATGATATAAGCTTTTGAATT
163725 T
1 T
163726 TCCTCGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (25 bp):
TATGCATGATATAAGCTTTTGAATT
Found at i:164633 original size:14 final size:14
Alignment explanation
Indices: 164614--164651 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
164604 AAATTAATAT
164614 ATATAATATAGTAA
1 ATATAATATAGTAA
164628 ATATAATATAGTAA
1 ATATAATATAGTAA
164642 ATATAATATA
1 ATATAATATA
164652 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
ATATAATATAGTAA
Found at i:164634 original size:23 final size:22
Alignment explanation
Indices: 164604--164646 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
164594 TATTACATCA
164604 AAATTAATATA-TATAATATAGT
1 AAATTAATATAGTA-AATATAGT
164626 AAATATAATATAGTAAATATA
1 AAAT-TAATATAGTAAATATA
164647 ATATAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
AAATTAATATAGTAAATATAGT
Found at i:164635 original size:5 final size:5
Alignment explanation
Indices: 164608--164654 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
164598 ACATCAAAAT
* *
164608 TAATA T-ATA TAATA TAGTA -AATA TAATA TAGTA -AATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
164655 AGTAAATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 10 0.29
5 25 0.71
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:169508 original size:2 final size:2
Alignment explanation
Indices: 169501--169527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
169491 ACCAGTTTGA
169501 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
169528 ATTTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:169669 original size:20 final size:21
Alignment explanation
Indices: 169646--169684 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
169636 TAAATTTAAT
169646 ATTTATTTAA-CA-TTAAAATC
1 ATTT-TTTAAGCATTTAAAATC
169666 ATTTTTTAAGCATTTAAAA
1 ATTTTTTAAGCATTTAAAA
169685 CTGTGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTTTTTAAGCATTTAAAATC
Done.