Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold425
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: 711097
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 5 of 5
Found at i:654107 original size:20 final size:21
Alignment explanation
Indices: 654078--654123 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
654068 ATTAATCAAT
*
654078 AAAATAATAATAATGATAGAA
1 AAAATAATAATAATAATAGAA
*
654099 AAAAT-ATAATAATAATAGTA
1 AAAATAATAATAATAATAGAA
654119 AAAAT
1 AAAAT
654124 TATTAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAATAATAATAATAATAGAA
Found at i:654130 original size:19 final size:19
Alignment explanation
Indices: 654088--654147 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
654078 AAAATAATAA
* * *
654088 TAATGATAGAAAAAATATAA
1 TAATAATAGTAAAAAT-TAT
654108 TAATAATAGTAAAAATTAT
1 TAATAATAGTAAAAATTAT
*
654127 TAATCAATA-TAATAATTAT
1 TAAT-AATAGTAAAAATTAT
654146 TA
1 TA
654148 TATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (19 bp):
TAATAATAGTAAAAATTAT
Found at i:654411 original size:2 final size:2
Alignment explanation
Indices: 654400--654436 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
654390 GTTGGCTAAG
654400 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
654437 TTGAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:654619 original size:21 final size:23
Alignment explanation
Indices: 654594--654642 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
654584 TATAATCATT
*
654594 TAAATATATAAAA-TT-TGTTTA
1 TAAATATATAAAACTTATATTTA
654615 TAAAT-TATAAAACTTATATTTA
1 TAAATATATAAAACTTATATTTA
654637 TAAATA
1 TAAATA
654643 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATATATAAAACTTATATTTA
Found at i:654636 original size:22 final size:21
Alignment explanation
Indices: 654594--654668 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
654584 TATAATCATT
*
654594 TAAATATATAAAATTTGTTTA
1 TAAATATATAAAATTTATTTA
654615 TAAAT-TATAAAACTTATATTTA
1 TAAATATATAAAA-TT-TATTTA
* *
654637 TAAATAATTATTAAATTTATAT-
1 TAAAT-A-TATAAAATTTATTTA
654659 TAAATA-ATAA
1 TAAATATATAA
654669 TAAATTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
19 3 0.07
20 7 0.16
21 8 0.18
22 15 0.33
23 4 0.09
24 2 0.04
25 6 0.13
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
TAAATATATAAAATTTATTTA
Found at i:654667 original size:25 final size:25
Alignment explanation
Indices: 654617--654669 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
654607 TTTGTTTATA
*
654617 AATTATAAAACTTATATTTATAAAT
1 AATTATAAAACTTATATTAATAAAT
* *
654642 AATTATTAAATTTATATTAA-ATAAT
1 AATTATAAAACTTATATTAATA-AAT
654667 AAT
1 AAT
654670 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTATAAAACTTATATTAATAAAT
Found at i:656148 original size:2 final size:2
Alignment explanation
Indices: 656143--656173 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
656133 ATATATATAT
*
656143 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
656174 TGAAATCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:657654 original size:4 final size:4
Alignment explanation
Indices: 657645--657670 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
657635 AAAAGTAGCT
657645 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
657671 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:659121 original size:3 final size:3
Alignment explanation
Indices: 659113--659138 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
659103 AATCATATTC
659113 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
659139 TTTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:659335 original size:146 final size:149
Alignment explanation
Indices: 659178--659470 Score: 477
Period size: 146 Copynumber: 2.0 Consensus size: 149
659168 TTTAAACGGT
* *
659178 GTTCATAAATATATATTAAAAATAATAAATATAAAAAGAATGAAAAAAAAT-TAATACTTCATTT
1 GTTCATAAATATATATTAAAAATAATAAATAAAAAAAGAATGAAAAAAAATCTAACACTTCATTT
*
659242 ATATGTATAG-AAAAATCATTTAACTTTTAAATAATTCAAT-AAAAAATTTTGATGG-AAAAAAT
66 ATATGTATAGAAAAAATCATTTAA-TTTTAAATAATCCAATAAAAAAATTTTGATGGAAAAAAAT
659304 TTAATTTATTTAATTTTTTG
130 TTAATTTATTTAATTTTTTG
* * *
659324 GTTCATAAATATATATTAAAAGTAATAAATAAAAAAATAATGAAAGAAAATCTAACACTTCATTT
1 GTTCATAAATATATATTAAAAATAATAAATAAAAAAAGAATGAAAAAAAATCTAACACTTCATTT
*
659389 ATATGTATAGAAAAAATCATTTAATTTTAAGTAATCCAATAAAAAAATTTTGATGGAAAAAAATT
66 ATATGTATAGAAAAAATCATTTAATTTTAAATAATCCAATAAAAAAATTTTGATGGAAAAAAATT
*
659454 TAATTTGTTTAATTTTT
131 TAATTTATTTAATTTTT
659471 CATTTGTCAA
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
146 47 0.35
147 36 0.27
148 28 0.21
149 24 0.18
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.38
Consensus pattern (149 bp):
GTTCATAAATATATATTAAAAATAATAAATAAAAAAAGAATGAAAAAAAATCTAACACTTCATTT
ATATGTATAGAAAAAATCATTTAATTTTAAATAATCCAATAAAAAAATTTTGATGGAAAAAAATT
TAATTTATTTAATTTTTTG
Found at i:659890 original size:21 final size:21
Alignment explanation
Indices: 659851--659909 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
659841 AAGTAATTAA
* *
659851 ATTTAAAAAAAATTATTT-TT
1 ATTTAAAAAATATTTTTTATT
659871 ATTTAAAAAATTATTTTTTTATT
1 ATTTAAAAAA-TA-TTTTTTATT
*
659894 ATTTAAAATATATTTT
1 ATTTAAAAAATATTTT
659910 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 10 0.30
21 5 0.15
22 7 0.21
23 11 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAAAAAATATTTTTTATT
Found at i:659893 original size:20 final size:20
Alignment explanation
Indices: 659851--659888 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
659841 AAGTAATTAA
659851 ATTTAAAAAAAATTATTTTT
1 ATTTAAAAAAAATTATTTTT
659871 ATTT--AAAAAATTATTTTT
1 ATTTAAAAAAAATTATTTTT
659889 TTATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
20 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAAAAAAATTATTTTT
Found at i:659909 original size:20 final size:19
Alignment explanation
Indices: 659851--659909 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
659841 AAGTAATTAA
*
659851 ATTTAAAAAAAATTATTTTT
1 ATTTAAAAAATA-TATTTTT
*
659871 ATTTAAAAAATTATTTTTTT
1 ATTTAAAAAA-TATATTTTT
**
659891 ATTATTTAAAATATATTTT
1 ATT-TAAAAAATATATTTT
659910 AATGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAAAAATATATTTTT
Found at i:659947 original size:22 final size:22
Alignment explanation
Indices: 659846--659970 Score: 55
Period size: 22 Copynumber: 5.6 Consensus size: 22
659836 AAATTAAGTA
* *
659846 ATTAA-ATTTAAAAAAAATTAT
1 ATTAATATTTAAAAATATTTAT
*
659867 -TT-TTATTTAAAAAATTATTT-T
1 ATTAATATTT-AAAAA-TATTTAT
* *
659888 TTTATTATTTAAAATATATTTTAAT
1 ATTAATATTTAAAA-ATA-TTT-AT
*
659913 GTTTAAT-TATTAAAAATATTTAT
1 -ATTAATAT-TTAAAAATATTTAT
* * *
659936 ATTAATATTTAAATATTTTTAAA
1 ATTAATATTTAAAAATATTT-AT
659959 ATTAA-ATTTAAA
1 ATTAATATTTAAA
659971 TAAATATATT
Statistics
Matches: 83, Mismatches: 8, Indels: 25
0.72 0.07 0.22
Matches are distributed among these distances:
20 6 0.07
21 6 0.07
22 33 0.40
23 19 0.23
24 3 0.04
25 5 0.06
26 11 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTAATATTTAAAAATATTTAT
Found at i:661160 original size:21 final size:22
Alignment explanation
Indices: 661135--661185 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
661125 ATCTTTTAAA
* *
661135 ATTTTTAAGATAATTTTTCATC
1 ATTTTTAAAATAATTATTCATC
* *
661157 -TTTTGAAAATAATTATTGATC
1 ATTTTTAAAATAATTATTCATC
661178 ATTTTTAA
1 ATTTTTAA
661186 CTCTTTTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (22 bp):
ATTTTTAAAATAATTATTCATC
Found at i:661411 original size:13 final size:13
Alignment explanation
Indices: 661393--661418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
661383 AAAAATAAAA
661393 AATTAATTAATTT
1 AATTAATTAATTT
661406 AATTAATTAATTT
1 AATTAATTAATTT
661419 TAAATCCATC
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):
AATTAATTAATTT
Found at i:663138 original size:29 final size:31
Alignment explanation
Indices: 663072--663177 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 31
663062 TTTTTTAAAA
* * * *
663072 ATATAT-ATTATTTATATTTAAATAAATATTT
1 ATATATAAATATTTATATTT-ATTATATAATT
* *
663103 ACTATATAAATATTTTTATTT-TTTTA-AATT
1 A-TATATAAATATTTATATTTATTATATAATT
**
663133 ATATATTTATATTTATATTTAATTATATAATT
1 ATATATAAATATTTATATTT-ATTATATAATT
663165 ATATATTAAATAT
1 ATATA-TAAATAT
663178 AAATAATTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
29 16 0.28
30 4 0.07
31 7 0.12
32 14 0.25
33 16 0.28
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
ATATATAAATATTTATATTTATTATATAATT
Found at i:663161 original size:24 final size:23
Alignment explanation
Indices: 663112--663168 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
663102 TACTATATAA
*
663112 ATATTTTTATTTTTTTAAATTAT
1 ATATTTATATTTTTTTAAATTAT
663135 ATATTTATATTTATATTT-AATTAT
1 ATATTTATATTT-T-TTTAAATTAT
*
663159 ATAATTATAT
1 ATATTTATAT
663169 ATTAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 11 0.37
24 16 0.53
25 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTTATATTTTTTTAAATTAT
Found at i:663175 original size:62 final size:60
Alignment explanation
Indices: 663061--663177 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 60
663051 GTGATAGAAT
*
663061 TTTTTTTAAAAATATATATTATTTATATTTAAATAAATATTTACTATATAAATATTTTTA
1 TTTTTTTAAAAATATATATTATTTATATTTAAATAAATAATTACTATATAAATATTTTTA
* * * *
663121 TTTTTTTAAATTATATATTTATATTTATATTTAATTATATAATTA-TATATTAAATAT
1 TTTTTTTAAA-AATATATAT-TATTTATATTTAAATAAATAATTACTATA-TAAATAT
663178 AAATAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 10 0.20
61 11 0.22
62 28 0.57
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (60 bp):
TTTTTTTAAAAATATATATTATTTATATTTAAATAAATAATTACTATATAAATATTTTTA
Found at i:663742 original size:2 final size:2
Alignment explanation
Indices: 663735--663765 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
663725 TTTCAAGTTT
663735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
663766 TTCAAATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:663931 original size:18 final size:18
Alignment explanation
Indices: 663910--663990 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
663900 TTATTAAAAA
663910 ATTATAATTTAAAATAAT
1 ATTATAATTTAAAATAAT
*
663928 ATTAAAATTT-AAATATAT
1 ATTATAATTTAAAATA-AT
*
663946 ATTA-AATTATTAAAT-AT
1 ATTATAATT-TAAAATAAT
663963 AATT-T--TTTAAAATAAT
1 -ATTATAATTTAAAATAAT
* *
663979 AATATAAATTAA
1 ATTATAATTTAA
663991 TTAGATAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
15 7 0.14
16 5 0.10
17 11 0.22
18 23 0.46
19 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATAATTTAAAATAAT
Found at i:663960 original size:19 final size:18
Alignment explanation
Indices: 663910--663963 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
663900 TTATTAAAAA
*
663910 ATTATAATTTAAA-ATAAT
1 ATTAAAATTTAAATAT-AT
663928 ATTAAAATTTAAATATAT
1 ATTAAAATTTAAATATAT
*
663946 ATTAAATTATTAAATATA
1 ATTAAAAT-TTAAATATA
663964 ATTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 21 0.66
19 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAAATTTAAATATAT
Found at i:664178 original size:17 final size:18
Alignment explanation
Indices: 664155--664203 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
664145 AAAAAAAAAA
664155 AAAATAAATAATAATAAT
1 AAAATAAATAATAATAAT
664173 -AAATAAATAAATAA-AAT
1 AAAATAAAT-AATAATAAT
664190 AAAATAAA-AATAAT
1 AAAATAAATAATAAT
664204 TAGCCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.18
17 11 0.39
18 12 0.43
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATAAATAATAATAAT
Found at i:666852 original size:3 final size:3
Alignment explanation
Indices: 666846--666883 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
666836 GAGTGATGAT
*
666846 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
666884 GAAGAGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:667113 original size:2 final size:2
Alignment explanation
Indices: 667106--667135 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
667096 TCGAATTTCA
*
667106 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
667136 TTGCAGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:674746 original size:2 final size:2
Alignment explanation
Indices: 674739--674776 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
674729 AATAATTTCT
* *
674739 TA TA TA TA TA TA TA T- TA TC TA TA TC TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
674777 GTATTGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:674761 original size:15 final size:15
Alignment explanation
Indices: 674738--674776 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
674728 TAATAATTTC
674738 TTATATATATATATA
1 TTATATATATATATA
* *
674753 TTATCTATATCTATA
1 TTATATATATATATA
674768 -TATATATAT
1 TTATATATAT
674777 GTATTGAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:675036 original size:2 final size:2
Alignment explanation
Indices: 675029--675065 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
675019 AAGGTAGATT
*
675029 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
675066 CTCCAAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:675645 original size:3 final size:3
Alignment explanation
Indices: 675637--675686 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
675627 GCCAGCTCAA
675637 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
675684 ATT
1 ATT
675687 CATTTTCCAG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:677333 original size:1 final size:1
Alignment explanation
Indices: 677295--677326 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
677285 ACAAGCTTCG
677295 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
677327 CATTTTTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:677943 original size:8 final size:8
Alignment explanation
Indices: 677930--677960 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
677920 GGAGTTAATG
*
677930 ATATATAT
1 ATATATTT
677938 ATATATTT
1 ATATATTT
677946 ATATATTT
1 ATATATTT
677954 ATATATT
1 ATATATT
677961 ATACTTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATATTT
Found at i:678495 original size:20 final size:21
Alignment explanation
Indices: 678457--678496 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
678447 TGAAACAAGA
* *
678457 ATTTATTTTGTATAGAATAAG
1 ATTTATTTTGAATACAATAAG
678478 ATTTA-TTTGAATACAATAA
1 ATTTATTTTGAATACAATAA
678497 AAATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (21 bp):
ATTTATTTTGAATACAATAAG
Found at i:680322 original size:2 final size:2
Alignment explanation
Indices: 680315--680379 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
680305 AAAATTTGAT
680315 TA TA TA TA TA TA 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 TA TA TA TA TA TA
680357 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
680380 CCGTTCTCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:681972 original size:16 final size:17
Alignment explanation
Indices: 681951--681993 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
681941 TTGTACGCGA
681951 TATTATAAAAATTTT-T
1 TATTATAAAAATTTTGT
* *
681967 TATTATGTAATATTTTGT
1 TATTAT-AAAAATTTTGT
681985 TATTATAAA
1 TATTATAAA
681994 TGTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATTATAAAAATTTTGT
Found at i:685011 original size:3 final size:3
Alignment explanation
Indices: 685003--685034 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
684993 CCAATTTTTG
685003 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
685035 ATGCTTGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:685881 original size:2 final size:2
Alignment explanation
Indices: 685874--685906 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
685864 TCCTTTTATT
*
685874 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
685907 GTAAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:687675 original size:20 final size:20
Alignment explanation
Indices: 687652--687737 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 20
687642 ATATTTATAT
687652 TATTTTAAATATTATAATTA
1 TATTTTAAATATTATAATTA
**
687672 TATTAAAAATATTATATAATTATA
1 TATTTTAAATA-T-TATAA-T-TA
687696 TAAATTTTAATATATTAATAATT-
1 T--ATTTTAA-ATATT-ATAATTA
687719 TATTTTTAAA-ATTATAATT
1 TA-TTTTAAATATTATAATT
687738 TTAAACATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
19 6 0.11
20 12 0.23
21 3 0.06
22 11 0.21
23 2 0.04
24 4 0.08
25 2 0.04
26 10 0.19
27 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTTAAATATTATAATTA
Found at i:687687 original size:45 final size:48
Alignment explanation
Indices: 687620--687722 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 48
687610 ATTTAAACGT
* * * * *
687620 ATAAGTTAATAAAATATTTTATATATTTATAT-TATTTTAA-ATATT-
1 ATAATTTATTAAAATATATTATATAATTATATAAATTTTAATATATTA
687665 ATAATTATATTAAAA-ATATTATATAATTATATAAATTTTAATATATTA
1 ATAATT-TATTAAAATATATTATATAATTATATAAATTTTAATATATTA
687713 ATAATTTATT
1 ATAATTTATT
687723 TTTAAAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 20 0.41
46 14 0.29
47 9 0.18
48 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (48 bp):
ATAATTTATTAAAATATATTATATAATTATATAAATTTTAATATATTA
Found at i:689378 original size:3 final size:3
Alignment explanation
Indices: 689370--689411 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
689360 GGCAAGCCTA
689370 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
689412 CATTCAGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:689766 original size:7 final size:7
Alignment explanation
Indices: 689719--689795 Score: 54
Period size: 7 Copynumber: 11.6 Consensus size: 7
689709 TTCTTTAAGA
*
689719 TTTAAAG
1 TTTAGAG
689726 TTTAGAG
1 TTTAGAG
*
689733 TATA-AG
1 TTTAGAG
*
689739 TTTAGAT
1 TTTAGAG
* *
689746 TTTATAC
1 TTTAGAG
689753 TTT-GAG
1 TTTAGAG
689759 TTTAGAG
1 TTTAGAG
*
689766 TTTAGAA
1 TTTAGAG
*
689773 TTAAG-G
1 TTTAGAG
*
689779 TTTAGAA
1 TTTAGAG
689786 TTTA-AG
1 TTTAGAG
689792 TTTA
1 TTTA
689796 CGTATAATGT
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
6 18 0.34
7 35 0.66
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (7 bp):
TTTAGAG
Found at i:689794 original size:13 final size:13
Alignment explanation
Indices: 689718--689795 Score: 61
Period size: 13 Copynumber: 5.8 Consensus size: 13
689708 ATTCTTTAAG
689718 ATTTAAAGTTTAGA
1 ATTT-AAGTTTAGA
* *
689732 GTATAAGTTTAGA
1 ATTTAAGTTTAGA
* *
689745 TTTTATACTTT-GA
1 ATTTA-AGTTTAGA
*
689758 GTTTAGAGTTTAGA
1 ATTTA-AGTTTAGA
689772 A-TTAAGGTTTAGA
1 ATTTAA-GTTTAGA
689785 ATTTAAGTTTA
1 ATTTAAGTTTA
689796 CGTATAATGT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
12 1 0.02
13 38 0.75
14 12 0.24
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (13 bp):
ATTTAAGTTTAGA
Found at i:691357 original size:2 final size:2
Alignment explanation
Indices: 691350--691385 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
691340 GAATTTGCTT
691350 TA TA TA 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 TA TA TA
691386 AGTTTAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:691561 original size:3 final size:3
Alignment explanation
Indices: 691553--691592 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
691543 TGTCAATATC
* *
691553 ATT ATT ATT ATT ATT ATT ATT GTT GTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
691593 ATTTCCGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:700650 original size:19 final size:21
Alignment explanation
Indices: 700609--700651 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
700599 GTCAAAATAT
**
700609 ATATAAATTCATAATATTTAA
1 ATATAAATTCATAATATAAAA
700630 ATAT-AATT-ATAATATAAAA
1 ATATAAATTCATAATATAAAA
700649 ATA
1 ATA
700652 ATATAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAAATTCATAATATAAAA
Found at i:700665 original size:11 final size:11
Alignment explanation
Indices: 700629--700674 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
700619 ATAATATTTA
*
700629 AATATAATTAT
1 AATATAAATAT
*
700640 AATATAAAAAT
1 AATATAAATAT
*
700651 AATATAAATAC
1 AATATAAATAT
*
700662 AATATTAATAT
1 AATATAAATAT
700673 AA
1 AA
700675 AAATTACTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAAATAT
Found at i:703328 original size:51 final size:51
Alignment explanation
Indices: 703250--703348 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
703240 AAAAGTCACA
* * * * *
703250 TTTTTATCCAGATGTATTGGTATATTTTTCAATGTATCGATATATTCTGTC
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATATATTCTGTC
703301 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATATATTCT
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATATATTCT
703349 TTAATGTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.48
Consensus pattern (51 bp):
TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATATATTCTGTC
Found at i:703336 original size:20 final size:20
Alignment explanation
Indices: 703311--703368 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
703301 TTTTTACCCA
703311 AATGTATCGATACATT-TTT
1 AATGTATCGATACATTCTTT
*
703330 CAATGTATCGATATATTCTTT
1 -AATGTATCGATACATTCTTT
703351 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
703369 GTCTTTTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 32 0.91
21 3 0.09
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (20 bp):
AATGTATCGATACATTCTTT
Found at i:703368 original size:71 final size:71
Alignment explanation
Indices: 703261--703416 Score: 233
Period size: 71 Copynumber: 2.2 Consensus size: 71
703251 TTTTATCCAG
* * *
703261 ATGTATTGGTATATTTTTCAATGTATCGATATATTCTGTCTTTTTACCCAAATGTATCGATACAT
1 ATGTATCGATATATTTTTCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATCGATACAT
*
703326 TTTTCA
66 TTTGCA
*
703332 ATGTATCGATATATTCTTT-AATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACA
1 ATGTATCGATATATT-TTTCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATCGATACA
703396 TTTTGCA
65 TTTTGCA
* *
703403 ATATATCAATATAT
1 ATGTATCGATATAT
703417 CTAGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
71 74 0.96
72 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.46
Consensus pattern (71 bp):
ATGTATCGATATATTTTTCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATCGATACAT
TTTGCA
Found at i:704540 original size:164 final size:164
Alignment explanation
Indices: 704269--704598 Score: 633
Period size: 164 Copynumber: 2.0 Consensus size: 164
704259 CAAACACTTC
704269 CTTCTTGTTACTACACAACTCCAATCCATCTTTACCCGTACTATAACCTAAACATCCACTTTTTC
1 CTTCTTGTTACTACACAACTCCAATCCATCTTTACCCGTACTATAACCTAAACATCCACTTTTTC
*
704334 AATATTTTTCAGTCTGTATGTAGCCTCATAAAGGTGTTAAATAAGCTGCATTACTTGTTCAGACC
66 AACATTTTTCAGTCTGTATGTAGCCTCATAAAGGTGTTAAATAAGCTGCATTACTTGTTCAGACC
704399 AACAAATCAGATTTCTATCTCATTGGTATATTTT
131 AACAAATCAGATTTCTATCTCATTGGTATATTTT
*
704433 CTTCTTGTTACTACACAACTCCAATCCATCTTTACCCGTACTATAACTTAAACATCCACTTTTTC
1 CTTCTTGTTACTACACAACTCCAATCCATCTTTACCCGTACTATAACCTAAACATCCACTTTTTC
*
704498 AACATTTTTCAGTCTGTATGTAGCCTCATAAAGGTGTTAAATAAGCTGCATTACTTGTTCAGACT
66 AACATTTTTCAGTCTGTATGTAGCCTCATAAAGGTGTTAAATAAGCTGCATTACTTGTTCAGACC
704563 AACAAATCAGATTTCTATCTCATTGGTATATTTT
131 AACAAATCAGATTTCTATCTCATTGGTATATTTT
704597 CT
1 CT
704599 AATCTTTTAA
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 163 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (164 bp):
CTTCTTGTTACTACACAACTCCAATCCATCTTTACCCGTACTATAACCTAAACATCCACTTTTTC
AACATTTTTCAGTCTGTATGTAGCCTCATAAAGGTGTTAAATAAGCTGCATTACTTGTTCAGACC
AACAAATCAGATTTCTATCTCATTGGTATATTTT
Found at i:706842 original size:2 final size:2
Alignment explanation
Indices: 706835--706873 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
706825 TGGCCCTTTT
706835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
706874 TTAATGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:711060 original size:23 final size:22
Alignment explanation
Indices: 711014--711063 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
711004 AGATTAAATA
*
711014 TTTTAATTTAAAATTGTTTGAT
1 TTTTAATTTAAAATTATTTGAT
* *
711036 TTTTAATTTTAAATTTATTTTAT
1 TTTTAA-TTTAAAATTATTTGAT
711059 TTTTA
1 TTTTA
711064 TATATGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTTAATTTAAAATTATTTGAT
Done.