Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold321
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: 1060354
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 6 of 6
Found at i:1013716 original size:13 final size:13
Alignment explanation
Indices: 1013677--1013719 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1013667 GGTAGGAGAC
1013677 AGAAAAATATGAAA
1 AGAAAAATA-GAAA
*
1013691 AGGAAAAAAAGAAA
1 A-GAAAAATAGAAA
*
1013705 AGAAAGATAGAAA
1 AGAAAAATAGAAA
1013718 AG
1 AG
1013720 GAGAGAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.48
14 6 0.24
15 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (13 bp):
AGAAAAATAGAAA
Found at i:1013868 original size:23 final size:22
Alignment explanation
Indices: 1013837--1013896 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
1013827 TTTGTATCAT
*
1013837 ATTTATTTTTATATTATGTTTTA
1 ATTT-TTTTTATATTATATTTTA
* * *
1013860 ATTATTTTTTACATCATATTTTT
1 ATT-TTTTTTATATTATATTTTA
*
1013883 ATTTTTTGTATATT
1 ATTTTTTTTATATT
1013897 TAAAGTAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
22 8 0.28
23 20 0.69
24 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (22 bp):
ATTTTTTTTATATTATATTTTA
Found at i:1014767 original size:24 final size:25
Alignment explanation
Indices: 1014727--1014784 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1014717 TATATTTAAA
* *
1014727 ATATTATATTTTCATTTT-TTTTAT
1 ATATTATAATTTCATTTTATTTCAT
1014751 ATATTAATAATTT-ATTTTATTTCAT
1 ATATT-ATAATTTCATTTTATTTCAT
1014776 ATATATATA
1 ATAT-TATA
1014785 TTTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 10 0.34
25 18 0.62
26 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATTATAATTTCATTTTATTTCAT
Found at i:1014767 original size:30 final size:30
Alignment explanation
Indices: 1014712--1014772 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
1014702 GTTCGTGTTA
1014712 TTTTTTATATTTAAAATATTATATTTTCATT
1 TTTTTTATATTTAAAATATTATATTTT-ATT
*
1014743 TTTTTTATATATTAATA-ATT-TATTTTATT
1 TTTTTTATAT-TTAAAATATTATATTTTATT
1014772 T
1 T
1014773 CATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 6 0.21
31 13 0.46
32 5 0.18
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTTTATATTTAAAATATTATATTTTATT
Found at i:1015349 original size:23 final size:23
Alignment explanation
Indices: 1015320--1015378 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1015310 ATATTTTAGT
1015320 TATATTTATATATTAATAATAAA
1 TATATTTATATATTAATAATAAA
* *
1015343 TATATTTTTATATTATTAATAAA
1 TATATTTATATATTAATAATAAA
*
1015366 T-TATATA-ATATTA
1 TATATTTATATATTA
1015379 TTTTATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 6 0.19
22 4 0.12
23 22 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATTTATATATTAATAATAAA
Found at i:1015371 original size:26 final size:25
Alignment explanation
Indices: 1015320--1015392 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 25
1015310 ATATTTTAGT
* *
1015320 TATATTTATATATTAATAAT-AA-A
1 TATATTTTTATATTATTAATAAATA
1015343 TATATTTTTATATTATTAATAAATTA
1 TATATTTTTATATTATTAATAAA-TA
* * *
1015369 TATAATATTATTTTATTAA-AAATA
1 TATATTTTTATATTATTAATAAATA
1015393 AAAATAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.43
24 4 0.10
25 3 0.07
26 17 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTTTATATTATTAATAAATA
Found at i:1015399 original size:26 final size:26
Alignment explanation
Indices: 1015325--1015408 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
1015315 TTAGTTATAT
* * *
1015325 TTATA-TATTAATAATAAATATATTT
1 TTATATTATTAAAAATAAATATAATA
*
1015350 TTATATTATTAATAAAT-TATATAATA
1 TTATATTATTAA-AAATAAATATAATA
* *
1015376 TTATTTTATTAAAAATAAAAATAAATA
1 TTATATTATTAAAAATAAATAT-AATA
1015403 TTATAT
1 TTATAT
1015409 AATGTAACAC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 9 0.19
26 26 0.55
27 12 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATATTATTAAAAATAAATATAATA
Found at i:1022942 original size:13 final size:13
Alignment explanation
Indices: 1022924--1022948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1022914 GTCATTTTTT
1022924 GCATCGTTTGTTC
1 GCATCGTTTGTTC
1022937 GCATCGTTTGTT
1 GCATCGTTTGTT
1022949 GTTTTCAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (13 bp):
GCATCGTTTGTTC
Found at i:1030238 original size:2 final size:2
Alignment explanation
Indices: 1030231--1030274 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1030221 TTGAAGAGCT
*
1030231 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1030273 TC
1 TC
1030275 CATATGAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1034915 original size:2 final size:2
Alignment explanation
Indices: 1034908--1034939 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1034898 AAAAGCTCAA
1034908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1034940 TAGTGGGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1035826 original size:22 final size:23
Alignment explanation
Indices: 1035801--1035852 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
1035791 AGTAAAAAAT
1035801 TATAAATTTTAAAATT-ATTAAA
1 TATAAATTTTAAAATTAATTAAA
* *
1035823 TAT-AATTTTTAAATTAATTATA
1 TATAAATTTTAAAATTAATTAAA
1035845 T-TAAATTT
1 TATAAATTT
1035853 ACATTAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAAATTTTAAAATTAATTAAA
Found at i:1036597 original size:65 final size:63
Alignment explanation
Indices: 1036502--1036636 Score: 143
Period size: 65 Copynumber: 2.1 Consensus size: 63
1036492 CTTATCATAT
*
1036502 AAAAATTTTATAAAAAATTTAATATATTTATAT-A-TTATTAATGAAGTAAATACATTATATTAA
1 AAAAATTTTATAAAAAATATAATATATTTATATAATTTATTAAT-AA-TAAATA-A-TATATTAA
1036565 TA
62 TA
* * * *
1036567 AAAAATTTTA-AAATAATATAAGTA-ATTTTATTTAATTTATTAATAATATATAATATATTATTA
1 AAAAATTTTATAAAAAATATAA-TATA-TTTATATAATTTATTAATAATAAATAATATATTAATA
1036630 AAAAATT
1 AAAAATT
1036637 AAATAAAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
63 16 0.26
64 11 0.18
65 23 0.38
66 3 0.05
67 8 0.13
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (63 bp):
AAAAATTTTATAAAAAATATAATATATTTATATAATTTATTAATAATAAATAATATATTAATA
Found at i:1037140 original size:13 final size:13
Alignment explanation
Indices: 1037122--1037146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1037112 AAGCATGGTT
1037122 TTTTTATTTTTTA
1 TTTTTATTTTTTA
1037135 TTTTTATTTTTT
1 TTTTTATTTTTT
1037147 TAACAACGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1040463 original size:23 final size:22
Alignment explanation
Indices: 1040425--1040494 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
1040415 TACTATTAAA
1040425 AAAT-ATATTTTATAATTAAATGT
1 AAATAATATTTTATAATT-AAT-T
*
1040448 AAATAATATTTT-TAATTTATT
1 AAATAATATTTTATAATTAATT
* *
1040469 AAATAATAATTTAAAATTAATT
1 AAATAATATTTTATAATTAATT
1040491 AAAT
1 AAAT
1040495 TATAATATCG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.29
22 13 0.32
23 9 0.22
24 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
AAATAATATTTTATAATTAATT
Found at i:1040486 original size:22 final size:22
Alignment explanation
Indices: 1040419--1040500 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
1040409 TTATTTTACT
* *
1040419 ATTAAAAAATATATTTTATAATTAA
1 ATTAAATAATA-A-TTTAAAATT-A
** *
1040444 ATGTAAATAAT-ATTTTTAATTT
1 AT-TAAATAATAATTTAAAATTA
1040466 ATTAAATAATAATTTAAAATTA
1 ATTAAATAATAATTTAAAATTA
*
1040488 ATTAAATTATAAT
1 ATTAAATAATAAT
1040501 ATCGTGTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 8 0.17
22 22 0.46
23 8 0.17
24 1 0.02
25 2 0.04
26 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (22 bp):
ATTAAATAATAATTTAAAATTA
Found at i:1044410 original size:112 final size:112
Alignment explanation
Indices: 1044213--1044440 Score: 438
Period size: 112 Copynumber: 2.0 Consensus size: 112
1044203 ATGTTGTTGG
1044213 GACAAATAAATGTGCCTGCATTTCAAACCTTTTTTTATATTTAAACATTTCTTTGTTGTGTCTTT
1 GACAAATAAATGTGCCTGCATTTCAAACCTTTTTTTATATTTAAACATTTCTTTGTTGTGTCTTT
1044278 TCAACAGTGAACTGCCAGAGTTTTTGGGTGGTAGCTGTAATTGTGCA
66 TCAACAGTGAACTGCCAGAGTTTTTGGGTGGTAGCTGTAATTGTGCA
* *
1044325 GACAAATAAATGTGCCTGCATTTGAAACCTTTTTTTATATTTAAACATTTCTTTGTTGTGTTTTT
1 GACAAATAAATGTGCCTGCATTTCAAACCTTTTTTTATATTTAAACATTTCTTTGTTGTGTCTTT
1044390 TCAACAGTGAACTGCCAGAGTTTTTGGGTGGTAGCTGTAATTGTGCA
66 TCAACAGTGAACTGCCAGAGTTTTTGGGTGGTAGCTGTAATTGTGCA
1044437 GACA
1 GACA
1044441 GAGGTGGTTG
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (112 bp):
GACAAATAAATGTGCCTGCATTTCAAACCTTTTTTTATATTTAAACATTTCTTTGTTGTGTCTTT
TCAACAGTGAACTGCCAGAGTTTTTGGGTGGTAGCTGTAATTGTGCA
Found at i:1051904 original size:2 final size:2
Alignment explanation
Indices: 1051897--1051925 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1051887 GCGAAGCATC
1051897 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1051926 GGAAAGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1052789 original size:16 final size:16
Alignment explanation
Indices: 1052749--1052816 Score: 82
Period size: 16 Copynumber: 4.1 Consensus size: 16
1052739 AAATTTTCAA
*
1052749 AAATATAAATTATTAT
1 AAATATAAAATATTAT
*
1052765 AACATATAAAATAATAT
1 AA-ATATAAAATATTAT
*
1052782 AAATATAAAATATTTT
1 AAATATAAAATATTAT
*
1052798 AAATATAATTATATTAT
1 AAATATAA-AATATTAT
1052815 AA
1 AA
1052817 TAAAATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 22 0.50
17 22 0.50
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAAAATATTAT
Found at i:1052830 original size:17 final size:17
Alignment explanation
Indices: 1052748--1052831 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
1052738 TAAATTTTCA
*
1052748 AAAATATAAATTATTAT
1 AAAATATAAATTATAAT
*
1052765 AACATATAAA--ATAAT
1 AAAATATAAATTATAAT
* **
1052780 ATAAATATAAAATATTTT
1 A-AAATATAAATTATAAT
*
1052798 AAATATAATTATATTATAAT
1 AAA-AT-A-TAAATTATAAT
1052818 AAAATATAAATTAT
1 AAAATATAAATTAT
1052832 TTAATATAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 5 0.10
16 8 0.16
17 18 0.35
18 7 0.14
19 3 0.06
20 10 0.20
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATAAATTATAAT
Found at i:1052857 original size:35 final size:34
Alignment explanation
Indices: 1052729--1052859 Score: 104
Period size: 36 Copynumber: 3.7 Consensus size: 34
1052719 ATAATATAAA
* * *
1052729 AATATATTTTAAATTTTCAAAAATATAAATTATTAT
1 AATATAATTAAAATATT-AAAAATATAAATTATT-T
* * * *
1052765 AACAT-A-TAAAATAATATAAATATAAAATATTTT
1 AATATAATTAAAATATTAAAAATATAAATTA-TTT
* * *
1052798 AAATATAATTATATTATAATAAAATATAAATTATTT
1 -AATATAATTAAAATATTA-AAAATATAAATTATTT
1052834 AATATAATTAAAAATATTAAAAATAT
1 AATATAATT-AAAATATTAAAAATAT
1052860 CTATTATCTA
Statistics
Matches: 72, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
33 13 0.18
34 12 0.17
35 17 0.24
36 19 0.26
37 11 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (34 bp):
AATATAATTAAAATATTAAAAATATAAATTATTT
Found at i:1053334 original size:18 final size:16
Alignment explanation
Indices: 1053312--1053350 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1053302 ATTTATTATG
1053312 TATATAAAATTTTGAAT
1 TATATAAAATTTT-AAT
*
1053329 TGATATAACATTTTAAT
1 T-ATATAAAATTTTAAT
1053346 TATAT
1 TATAT
1053351 CACTCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 5 0.25
18 11 0.55
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (16 bp):
TATATAAAATTTTAAT
Found at i:1053485 original size:24 final size:25
Alignment explanation
Indices: 1053458--1053510 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1053448 AGTATGTGAT
*
1053458 TTATGTAAA-TAAATAAA-ATTAAAA
1 TTAT-TAAATTAAATAAATATAAAAA
1053482 TTATTAAATTAAATAAATATAAAAA
1 TTATTAAATTAAATAAATATAAAAA
1053507 TTAT
1 TTAT
1053511 ACAAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 12 0.46
25 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TTATTAAATTAAATAAATATAAAAA
Found at i:1054107 original size:19 final size:18
Alignment explanation
Indices: 1054059--1054109 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
1054049 ATTTTATATT
1054059 TATATTTATT-TTAAATA
1 TATATTTATTATTAAATA
1054076 -AGT-TTTAATTATTAAGATA
1 TA-TATTT-ATTATTAA-ATA
1054095 TATATTTATTATTAA
1 TATATTTATTATTAA
1054110 TTTATGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 4 0.14
19 12 0.43
20 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TATATTTATTATTAAATA
Found at i:1054145 original size:19 final size:19
Alignment explanation
Indices: 1054086--1054145 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1054076 AGTTTTAATT
* *
1054086 ATTAAGATAT-ATATTTATT
1 ATTAATATATGATATTT-TA
*
1054105 ATTAATTTATG-T-TTTTA
1 ATTAATATATGATATTTTA
1054122 A-TAATATATGATATTTTA
1 ATTAATATATGATATTTTA
1054140 ATTAAT
1 ATTAAT
1054146 TTTGTGTCGG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 8 0.24
17 3 0.09
18 9 0.27
19 13 0.39
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATATATGATATTTTA
Found at i:1058302 original size:22 final size:21
Alignment explanation
Indices: 1058279--1058376 Score: 75
Period size: 22 Copynumber: 4.8 Consensus size: 21
1058269 TATTTAAGTA
*
1058279 ATTATATAATTAATAAATTTT
1 ATTATATAATTAATTAATTTT
1058300 A--ATA-AATTAA-TAATTTTT
1 ATTATATAATTAATTAA-TTTT
1058318 ATTATATAAATT--TTAATTTT
1 ATTATAT-AATTAATTAATTTT
*
1058338 ATTATATATTTATATTAATTTT
1 ATTATATAATTA-ATTAATTTT
*
1058360 -TATATATTATATAATTA
1 AT-TATATAAT-TAATTA
1058377 CCTTTGCCTG
Statistics
Matches: 62, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
17 2 0.03
18 11 0.18
19 6 0.10
20 14 0.23
21 5 0.08
22 22 0.35
23 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATATAATTAATTAATTTT
Done.