Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold58
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: 1582273
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 125418 characters in sequence are not A, C, G, or T
File 7 of 10
Found at i:1021517 original size:30 final size:29
Alignment explanation
Indices: 1021451--1021561 Score: 101
Period size: 27 Copynumber: 4.0 Consensus size: 29
1021441 ATTTATTCAG
*
1021451 TAAAAT-TAATATTTTAATAATAAAAA-ATA
1 TAAAATATAATA-TATAAT-ATAAAAATATA
* *
1021480 TATAATATAATTATATAATATAAAAATAAA
1 TAAAATATAA-TATATAATATAAAAATATA
*
1021510 TAAAATAT-A-ATATAATA-AAAAATTTA
1 TAAAATATAATATATAATATAAAAATATA
*
1021536 T-AAATATAATATA-AATATATAAATAT
1 TAAAATATAATATATAATATAAAAATAT
1021562 TTTATTTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
25 6 0.09
26 13 0.19
27 17 0.25
29 13 0.19
30 17 0.25
31 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAAATATAATATATAATATAAAAATATA
Found at i:1021540 original size:25 final size:25
Alignment explanation
Indices: 1021467--1021549 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 25
1021457 TAATATTTTA
*
1021467 ATAATAAAAAATATATAATATAATTAT
1 ATAATAAAAAATATATAA-AT-ATAAT
*
1021494 ATAATATAAAAATAAATAAAATATAAT
1 ATAATA-AAAAATATAT-AAATATAAT
*
1021521 ATAATAAAAAATTTATAAATATAAT
1 ATAATAAAAAATATATAAATATAAT
1021546 ATAA
1 ATAA
1021550 ATATATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.26
26 8 0.16
27 16 0.32
28 11 0.22
29 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
ATAATAAAAAATATATAAATATAAT
Found at i:1021566 original size:30 final size:30
Alignment explanation
Indices: 1021479--1021566 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
1021469 AATAAAAAAT
* ***
1021479 ATATAATATAATTATAT-AATATAAAAATAA
1 ATATAATATAAATATATAAATAT-TTTATAA
* * *
1021509 ATAAAATAT-AATATAATAAAAAATTTATAA
1 ATATAATATAAATAT-ATAAATATTTTATAA
1021539 ATATAATATAAATATATAAATATTTTAT
1 ATATAATATAAATATATAAATATTTTAT
1021567 TTTTAATATT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 4 0.09
30 33 0.73
31 8 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
ATATAATATAAATATATAAATATTTTATAA
Found at i:1026046 original size:87 final size:86
Alignment explanation
Indices: 1025885--1026059 Score: 298
Period size: 87 Copynumber: 2.0 Consensus size: 86
1025875 TTTTCGTGCT
* *
1025885 AATGGCAGTTCCACTTACACACCGCCTACTCATATATTGTGTATATCAATGCAAAGTAGTAGATA
1 AATGGCAGTTCCACTTACACACCACCTACTCATATAATGTGTATATCAATGCAAAGTAGTAGATA
*
1025950 TGTATAAAGTGGAAAGAAGGG
66 TGTATAAAGTGGAAAGAAAGG
1025971 AATGGCAGTTCCACTTACACACCACCTACTCATATAAATGTGTATATCAATGCAAA-TATGTAGA
1 AATGGCAGTTCCACTTACACACCACCTACTCATAT-AATGTGTATATCAATGCAAAGTA-GTAGA
1026035 TATGTATAAAGTGGAAAGAAAGG
64 TATGTATAAAGTGGAAAGAAAGG
1026058 AA
1 AA
1026060 ATGAGAATAA
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
86 36 0.43
87 48 0.57
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (86 bp):
AATGGCAGTTCCACTTACACACCACCTACTCATATAATGTGTATATCAATGCAAAGTAGTAGATA
TGTATAAAGTGGAAAGAAAGG
Found at i:1027577 original size:22 final size:21
Alignment explanation
Indices: 1027532--1027586 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 21
1027522 TATAAAAATT
1027532 ATAAATTATAAATTATATTAA
1 ATAAATTATAAATTATATTAA
*
1027553 ATAAATTATTAAATTTTTATTAATA
1 ATAAATTA-TAAA-TTATATT-A-A
1027578 ATAAATTAT
1 ATAAATTAT
1027587 GTTATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.28
22 4 0.14
23 6 0.21
24 2 0.07
25 9 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAATTATAAATTATATTAA
Found at i:1027793 original size:22 final size:22
Alignment explanation
Indices: 1027734--1027802 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
1027724 TATTAAAATT
*
1027734 ATTTAATAAAATTAAT-ATAAATA
1 ATTTAATAATA-TAATAATAAA-A
*
1027757 ATTTAACTTAT-TAATAATAAAA
1 ATTTAA-TAATATAATAATAAAA
1027779 ATTTAATAATATAATTAGATAAAA
1 ATTTAATAATATAA-TA-ATAAAA
1027803 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.08
22 14 0.37
23 13 0.34
24 8 0.21
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
ATTTAATAATATAATAATAAAA
Found at i:1028121 original size:2 final size:2
Alignment explanation
Indices: 1028114--1028143 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1028104 ATTGTAGTAA
1028114 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
1028144 TCTAAAATTT
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):
AT
Found at i:1029120 original size:1 final size:1
Alignment explanation
Indices: 1029116--1029140 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1029106 AACAGAAATG
1029116 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1029141 GAGAGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1031351 original size:27 final size:27
Alignment explanation
Indices: 1031311--1031430 Score: 86
Period size: 27 Copynumber: 4.2 Consensus size: 27
1031301 AAATTTGATA
1031311 ATTTATAAAT-TTTTATATTATAATTAT
1 ATTTA-AAATATTTTATATTATAATTAT
1031338 ATTTAAAATATTTTATATT-TATATTA-
1 ATTTAAAATATTTTATATTATA-ATTAT
*
1031364 ATTTTAAAAAATTATTA-ATTTATAATATAT
1 A-TTTAAAATATT-TTATA-TTATAAT-TAT
*
1031394 ATTTATATAAAATTATTTTATATTTTAATTAT
1 A--T-T-TAAAA-TATTTTATATTATAATTAT
*
1031426 TTTTA
1 ATTTA
1031431 TGTATCATAT
Statistics
Matches: 76, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
26 7 0.09
27 29 0.38
28 9 0.12
29 5 0.07
30 2 0.03
31 2 0.03
32 4 0.05
33 14 0.18
34 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTAAAATATTTTATATTATAATTAT
Found at i:1031355 original size:16 final size:16
Alignment explanation
Indices: 1031334--1031428 Score: 53
Period size: 16 Copynumber: 6.1 Consensus size: 16
1031324 TATATTATAA
1031334 TTATATTTAAAATATT
1 TTATATTTAAAATATT
1031350 TTATATTT---ATA-T
1 TTATATTTAAAATATT
* *
1031362 TAAT-TTTAAAAAATT
1 TTATATTTAAAATATT
1031377 ATTA-ATTTATAATATATAT
1 -TTATATTTA-AA-ATAT-T
1031396 TTATA--TAAAATTATT
1 TTATATTTAAAA-TATT
* *
1031411 TTATATTTTAATTATT
1 TTATATTTAAAATATT
1031427 TT
1 TT
1031429 TATGTATCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 26
0.65 0.07 0.28
Matches are distributed among these distances:
11 3 0.05
12 4 0.07
13 3 0.05
14 2 0.03
15 8 0.13
16 25 0.42
17 7 0.12
18 6 0.10
19 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:1032791 original size:34 final size:34
Alignment explanation
Indices: 1032722--1032792 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
1032712 GTTAGATCAA
* *
1032722 ATTAAATTATTATTTAACTAATAAAAAATATATT
1 ATTAAATTATTATTTAAATAATAAAAAATAAATT
* * *
1032756 ATTAAATT-TTATTATAAATATTAATATATAAATT
1 ATTAAATTATTATT-TAAATAATAAAAAATAAATT
1032790 ATT
1 ATT
1032793 TTTTAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 5 0.16
34 26 0.84
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (34 bp):
ATTAAATTATTATTTAAATAATAAAAAATAAATT
Found at i:1032798 original size:19 final size:20
Alignment explanation
Indices: 1032776--1032814 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1032766 ATTATAAATA
1032776 TTAATATATAA-ATTATTTT
1 TTAATATATAATATTATTTT
*
1032795 TTAATTTATAATATTATTTT
1 TTAATATATAATATTATTTT
1032815 GAATAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATATATAATATTATTTT
Found at i:1033505 original size:18 final size:19
Alignment explanation
Indices: 1033472--1033507 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1033462 TCGTAATAAA
1033472 ATATTAAATATAAATTTAC
1 ATATTAAATATAAATTTAC
1033491 ATATTAAAT-TAAATTTA
1 ATATTAAATATAAATTTA
1033508 TATAATCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAATATAAATTTAC
Found at i:1034075 original size:16 final size:17
Alignment explanation
Indices: 1034056--1034088 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1034046 ACTTTTTCAT
*
1034056 TTTTTGAATT-TTTTTA
1 TTTTTAAATTCTTTTTA
1034072 TTTTTAAATTCTTTTTA
1 TTTTTAAATTCTTTTTA
1034089 AAAAATAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTTAAATTCTTTTTA
Found at i:1040399 original size:39 final size:39
Alignment explanation
Indices: 1040345--1040472 Score: 220
Period size: 39 Copynumber: 3.3 Consensus size: 39
1040335 ATATATATAT
* *
1040345 ATAAACAAAACTGACAAAACCAAAGTCAAATGAACTGCA
1 ATAAAAAAAACTGACAAAACCAAAGTCAAATGAATTGCA
1040384 ATAAAAAAAACTGACAAAACCAAAGTCAAATGAATTGCA
1 ATAAAAAAAACTGACAAAACCAAAGTCAAATGAATTGCA
*
1040423 ATAAAAAAAAACTGACAAAACCAAAATCAAATGAATTGCA
1 AT-AAAAAAAACTGACAAAACCAAAGTCAAATGAATTGCA
1040463 ATAAAAAAAA
1 ATAAAAAAAA
1040473 TTGATGGACA
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
39 47 0.55
40 38 0.45
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.14
Consensus pattern (39 bp):
ATAAAAAAAACTGACAAAACCAAAGTCAAATGAATTGCA
Found at i:1040441 original size:40 final size:40
Alignment explanation
Indices: 1040351--1040472 Score: 219
Period size: 40 Copynumber: 3.1 Consensus size: 40
1040341 ATATATAAAC
*
1040351 AAAACTGACAAAACCAAAGTCAAATGAACTGCAAT-AAAA
1 AAAACTGACAAAACCAAAGTCAAATGAATTGCAATAAAAA
1040390 AAAACTGACAAAACCAAAGTCAAATGAATTGCAATAAAAA
1 AAAACTGACAAAACCAAAGTCAAATGAATTGCAATAAAAA
*
1040430 AAAACTGACAAAACCAAAATCAAATGAATTGCAATAAAAA
1 AAAACTGACAAAACCAAAGTCAAATGAATTGCAATAAAAA
1040470 AAA
1 AAA
1040473 TTGATGGACA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
39 34 0.43
40 46 0.57
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14
Consensus pattern (40 bp):
AAAACTGACAAAACCAAAGTCAAATGAATTGCAATAAAAA
Found at i:1041975 original size:2 final size:2
Alignment explanation
Indices: 1041968--1042004 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1041958 GTCTTTGCAA
1041968 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
1042005 GTGATACTAA
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:1047554 original size:6 final size:6
Alignment explanation
Indices: 1047545--1047579 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1047535 TTTAAAAAAT
*
1047545 TTTAAA TTTAAA TTTAAA TTTAAA TTTGAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
1047580 TTTGATTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:1047673 original size:21 final size:21
Alignment explanation
Indices: 1047647--1047686 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1047637 TAAAAAAAAT
1047647 TATTTTAT-ATTAAAATTTATA
1 TATTTTATAATT-AAATTTATA
1047668 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1047687 AAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1047695 original size:25 final size:23
Alignment explanation
Indices: 1047678--1047740 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 23
1047668 TATTTTATAA
1047678 TTAAATTTAAAAATATATATTAT
1 TTAAATTTAAAAATATATATTAT
* *
1047701 TTTAATTTAAAAATATATCATTGT
1 TTAAATTTAAAAATATAT-ATTAT
1047725 TTAAAAATTTAAAAAT
1 TT--AAATTTAAAAAT
1047741 CAAAATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.50
24 6 0.18
26 11 0.32
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAAATTTAAAAATATATATTAT
Found at i:1047711 original size:51 final size:49
Alignment explanation
Indices: 1047629--1047740 Score: 119
Period size: 51 Copynumber: 2.3 Consensus size: 49
1047619 ATCTCATTAA
*
1047629 AAAAATTTTAAAAA-A-A-ATTATTTTATATTAAAATTTATAT-ATT-TTAT
1 AAAAA-TTTAAAAATATATATTATTTTATATTAAAA-ATATATCATTGTT-T
1047676 AATTAAATTTAAAAATATATATTATTTTA-ATTTAAAAATATATCATTGTTT
1 AA--AAATTTAAAAATATATATTATTTTATA-TTAAAAATATATCATTGTTT
1047727 AAAAATTTAAAAAT
1 AAAAATTTAAAAAT
1047741 CAAAATTTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
47 2 0.04
48 8 0.14
49 16 0.29
50 7 0.12
51 21 0.38
52 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (49 bp):
AAAAATTTAAAAATATATATTATTTTATATTAAAAATATATCATTGTTT
Found at i:1057073 original size:3 final size:3
Alignment explanation
Indices: 1057065--1057089 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1057055 GAAAAACTTG
1057065 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1057090 TTCTTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1057719 original size:28 final size:26
Alignment explanation
Indices: 1057686--1057752 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 26
1057676 CAATTCGATT
*
1057686 TTTTAATTTTTTTA-AAATTAAAAATATA
1 TTTTAATTTATTTATAAATT--AAATA-A
1057714 TTTTAATAGTTATTTATAAATTAAATAA
1 TTTTAAT--TTATTTATAAATTAAATAA
1057742 TTTTAATTTAT
1 TTTTAATTTAT
1057753 AAATAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 4 0.11
28 15 0.43
29 5 0.14
30 6 0.17
31 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTTAATTTATTTATAAATTAAATAA
Found at i:1057742 original size:22 final size:21
Alignment explanation
Indices: 1057717--1057774 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1057707 AAATATATTT
*
1057717 TAATAGTTATTTATAAATTAAA
1 TAATA-TTATTTATAAATAAAA
*
1057739 TAATTTTAATTTATAAATAAAA
1 TAATATT-ATTTATAAATAAAA
1057761 T-ATATT-TTTATAAA
1 TAATATTATTTATAAA
1057775 ATTTAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.25
21 6 0.19
22 18 0.56
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATATTATTTATAAATAAAA
Found at i:1057921 original size:15 final size:16
Alignment explanation
Indices: 1057881--1057921 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1057871 AAAAATTATT
*
1057881 TTTTTTAAA-TTTAGA
1 TTTTTAAAATTTTAGA
1057896 TTTTTATAAATTTTA-A
1 TTTTTA-AAATTTTAGA
1057912 TTTTTAAAAT
1 TTTTTAAAAT
1057922 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 10 0.43
17 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTTAAAATTTTAGA
Found at i:1059227 original size:20 final size:20
Alignment explanation
Indices: 1059199--1059237 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1059189 TTAAATAAAA
*
1059199 TATATTTATTAATAATTTAT
1 TATAATTATTAATAATTTAT
*
1059219 TATAATTATTAATTATTTA
1 TATAATTATTAATAATTTA
1059238 ATATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATAATTATTAATAATTTAT
Found at i:1059327 original size:19 final size:19
Alignment explanation
Indices: 1059303--1059367 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
1059293 CTGCTTAGTG
1059303 AGAATCCGTTGTCTTGACC
1 AGAATCCGTTGTCTTGACC
* **
1059322 AGAATCCCGTAGTCTT-AGTG
1 AGAAT-CCGTTGTCTTGA-CC
1059342 AGAATCCGTTGTCTTGACC
1 AGAATCCGTTGTCTTGACC
1059361 AGAATCC
1 AGAATCC
1059368 CGTAGTCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (19 bp):
AGAATCCGTTGTCTTGACC
Found at i:1059339 original size:39 final size:39
Alignment explanation
Indices: 1059296--1059387 Score: 184
Period size: 39 Copynumber: 2.4 Consensus size: 39
1059286 TATTTAACTG
1059296 CTTAGTGAGAATCCGTTGTCTTGACCAGAATCCCGTAGT
1 CTTAGTGAGAATCCGTTGTCTTGACCAGAATCCCGTAGT
1059335 CTTAGTGAGAATCCGTTGTCTTGACCAGAATCCCGTAGT
1 CTTAGTGAGAATCCGTTGTCTTGACCAGAATCCCGTAGT
1059374 CTTAGTGAGAATCC
1 CTTAGTGAGAATCC
1059388 TTTATTTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (39 bp):
CTTAGTGAGAATCCGTTGTCTTGACCAGAATCCCGTAGT
Found at i:1059384 original size:20 final size:20
Alignment explanation
Indices: 1059296--1059387 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
1059286 TATTTAACTG
*
1059296 CTTAGTGAGAAT-CCGTTGT
1 CTTAGTGAGAATCCCGTAGT
**
1059315 CTT-GACCAGAATCCCGTAGT
1 CTTAG-TGAGAATCCCGTAGT
*
1059335 CTTAGTGAGAAT-CCGTTGT
1 CTTAGTGAGAATCCCGTAGT
**
1059354 CTT-GACCAGAATCCCGTAGT
1 CTTAG-TGAGAATCCCGTAGT
1059374 CTTAGTGAGAATCC
1 CTTAGTGAGAATCC
1059388 TTTATTTTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.04
19 22 0.39
20 30 0.54
21 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
CTTAGTGAGAATCCCGTAGT
Found at i:1060650 original size:29 final size:30
Alignment explanation
Indices: 1060597--1060665 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
1060587 TAAATTAACT
*
1060597 TTTAAGTTTTAACTTATACTTAAATAAATC
1 TTTAACTTTTAACTTATACTTAAATAAATC
* *
1060627 TTTAACTTTT-ACTTTTACTTAAATAAATT
1 TTTAACTTTTAACTTATACTTAAATAAATC
1060656 TTTAATCTTT
1 TTTAA-CTTT
1060666 AATTTAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTAACTTTTAACTTATACTTAAATAAATC
Found at i:1060666 original size:29 final size:29
Alignment explanation
Indices: 1060586--1060666 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
1060576 TTTATTACAT
* *
1060586 TTAAATTAACTTTTAAGT-TTTAACTTATAC
1 TTAAATAAATTTTTAA-TCTTT-ACTTATAC
* *
1060616 TTAAATAAATCTTTAA-CTTTTACTTTTAC
1 TTAAATAAATTTTTAATC-TTTACTTATAC
1060645 TTAAATAAATTTTTAATCTTTA
1 TTAAATAAATTTTTAATCTTTA
1060667 ATTTAAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 26 0.60
30 17 0.40
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (29 bp):
TTAAATAAATTTTTAATCTTTACTTATAC
Found at i:1060721 original size:27 final size:29
Alignment explanation
Indices: 1060699--1060763 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
1060689 AATATTTATT
1060699 TAAAATAAAAATA-AA-AAATTATTTAAA
1 TAAAATAAAAATATAATAAATTATTTAAA
* *
1060726 TATAATAAAAATATAATAACTTATTTACAA
1 TAAAATAAAAATATAATAAATTATTTA-AA
*
1060756 AAAAATAA
1 TAAAATAA
1060764 CACATGACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 12 0.39
28 2 0.06
29 9 0.29
30 8 0.26
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (29 bp):
TAAAATAAAAATATAATAAATTATTTAAA
Found at i:1064343 original size:24 final size:24
Alignment explanation
Indices: 1064298--1064343 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1064288 TTTAAAATAT
**
1064298 ATTTAAAGAATTATTTTTTAATTA
1 ATTTAAAGAATTATTTAATAATTA
**
1064322 ATTTAAATTATTATTTAATAAT
1 ATTTAAAGAATTATTTAATAAT
1064344 AAAAATATTT
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:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTAAAGAATTATTTAATAATTA
Found at i:1065832 original size:7 final size:6
Alignment explanation
Indices: 1065814--1065873 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 6
1065804 AATAATAAAA
*
1065814 AAAGAG AAAGAG TAAAGAG -AAG-C AAAGA- AAAGA- AAAGA- AAAGA-
1 AAAGAG AAAGAG -AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG
*
1065857 AAAAAG AAAGAG AAAGA
1 AAAGAG AAAGAG AAAGA
1065874 TTTGTTCATG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 25 0.53
6 16 0.34
7 6 0.13
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.02
Consensus pattern (6 bp):
AAAGAG
Found at i:1080096 original size:20 final size:20
Alignment explanation
Indices: 1080044--1080099 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1080034 TTTGGATCAC
* **
1080044 AATGTGTCAATACATGGTCA
1 AATGTATCAATACATTCTCA
*
1080064 AATGTATTAATACATTCTCA
1 AATGTATCAATACATTCTCA
*
1080084 AATGTATCCATACATT
1 AATGTATCAATACATT
1080100 TGACCATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (20 bp):
AATGTATCAATACATTCTCA
Found at i:1085106 original size:3 final size:3
Alignment explanation
Indices: 1085098--1085139 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1085088 GAACTTGTTA
* * *
1085098 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1085140 CTAACAACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1089025 original size:27 final size:27
Alignment explanation
Indices: 1088987--1089041 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1088977 ATAGATCTTA
* *
1088987 ATTTATAGATAAATAAATTATTTATTT
1 ATTTATAGATAAATAAATGATATATTT
* *
1089014 ATTTATCGATAATTAAATGATATATTT
1 ATTTATAGATAAATAAATGATATATTT
1089041 A
1 A
1089042 AAATAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
ATTTATAGATAAATAAATGATATATTT
Found at i:1089673 original size:22 final size:23
Alignment explanation
Indices: 1089631--1089674 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1089621 AAATTTAAAA
* *
1089631 ATATTTTTATAGTTAATATTTAT
1 ATATTTTTATAGATAAAATTTAT
1089654 ATATTTTTATA-ATAAAATTTA
1 ATATTTTTATAGATAAAATTTA
1089675 AATAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATATTTTTATAGATAAAATTTAT
Found at i:1090105 original size:32 final size:32
Alignment explanation
Indices: 1090060--1090123 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
1090050 AAAAAATTAA
* *
1090060 ATATAAGTCTTAAT-CAAATATTATTGTAAAAT
1 ATATAAATATTAATACAAATA-TATTGTAAAAT
* *
1090092 ATATAAATATTAATATAAATATATTGTTAAAT
1 ATATAAATATTAATACAAATATATTGTAAAAT
1090124 TTTTATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (32 bp):
ATATAAATATTAATACAAATATATTGTAAAAT
Found at i:1090643 original size:22 final size:22
Alignment explanation
Indices: 1090618--1090665 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1090608 TTGATTTAAA
1090618 TAAA-TTTAAAAAATTAAAAATT
1 TAAATTTTAAAAAATT-AAAATT
*
1090640 TAAATTTTAAAAAATTTAAATT
1 TAAATTTTAAAAAATTAAAATT
1090662 TAAA
1 TAAA
1090666 AAGATCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTTAAAAAATTAAAATT
Found at i:1090652 original size:16 final size:16
Alignment explanation
Indices: 1090633--1090688 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
1090623 TTAAAAAATT
1090633 AAAAATTTAAATTTTA
1 AAAAATTTAAATTTTA
1090649 AAAAATTTAAA-TTTA
1 AAAAATTTAAATTTTA
* *
1090664 AAAAGATCTAAATTTAA
1 AAAA-ATTTAAATTTTA
1090681 AACAAATT
1 AA-AAATT
1090689 CAAAAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 17 0.50
17 7 0.21
18 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAAATTTAAATTTTA
Found at i:1090802 original size:20 final size:19
Alignment explanation
Indices: 1090777--1090814 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1090767 CAAAACCTAT
*
1090777 AAAAATTTGAATTTATAATA
1 AAAAATTT-AAATTATAATA
1090797 AAAAATTTAAATTATAAT
1 AAAAATTTAAATTATAAT
1090815 TATATGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATTTAAATTATAATA
Found at i:1094195 original size:25 final size:25
Alignment explanation
Indices: 1094167--1094240 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
1094157 TAATTACATG
*
1094167 AATATTAATGTAATTATAAAAATAT
1 AATATTAATATAATTATAAAAATAT
* *
1094192 AATATTTATATAATTATAAAATTAT
1 AATATTAATATAATTATAAAAATAT
* * * *
1094217 AAAATT-ATAAAAATATAAATATAT
1 AATATTAATATAATTATAAAAATAT
1094241 TTTTAAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 14 0.34
25 27 0.66
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
AATATTAATATAATTATAAAAATAT
Found at i:1094208 original size:8 final size:8
Alignment explanation
Indices: 1094178--1094235 Score: 71
Period size: 8 Copynumber: 7.1 Consensus size: 8
1094168 ATATTAATGT
1094178 AATTATAA
1 AATTATAA
*
1094186 AAATATAA
1 AATTATAA
* *
1094194 TATTTATAT
1 -AATTATAA
1094203 AATTATAA
1 AATTATAA
1094211 AATTATAA
1 AATTATAA
1094219 AATTATAA
1 AATTATAA
*
1094227 AAATATAA
1 AATTATAA
1094235 A
1 A
1094236 TATATTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
8 37 0.88
9 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATTATAA
Found at i:1094311 original size:27 final size:28
Alignment explanation
Indices: 1094251--1094311 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
1094241 TTTTAAATTT
1094251 ATATAATATAAATTATTAATATATTAAA
1 ATATAATATAAATTATTAATATATTAAA
*
1094279 AT-TAATATAAA-TA-TAATATATTTTAA
1 ATATAATATAAATTATTAATATA-TTAAA
1094305 ATATAAT
1 ATATAAT
1094312 TATGATGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 8 0.27
27 13 0.43
28 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATAATATAAATTATTAATATATTAAA
Found at i:1094800 original size:29 final size:30
Alignment explanation
Indices: 1094745--1094802 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1094735 ATGCTAAAAT
* *
1094745 CATATATATATATATATATAAATATTATAG
1 CATATATACATATATATATAAAAATTATAG
1094775 CATATTATACATATA-ATA-AAAAATTATA
1 CATA-TATACATATATATATAAAAATTATA
1094803 TATACTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 7 0.28
31 9 0.36
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
CATATATACATATATATATAAAAATTATAG
Found at i:1095176 original size:15 final size:14
Alignment explanation
Indices: 1095131--1095181 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
1095121 AAAATATCTT
1095131 ATAATTTATATAAA
1 ATAATTTATATAAA
* *
1095145 ATAAATTATACATAA
1 ATAATTTATATA-AA
1095160 ATATATTTATATAAA
1 ATA-ATTTATATAAA
1095175 ATTAATT
1 A-TAATT
1095182 ATTAACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.33
15 11 0.37
16 9 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATTTATATAAA
Found at i:1095183 original size:14 final size:14
Alignment explanation
Indices: 1095136--1095183 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1095126 ATCTTATAAT
*
1095136 TTATATAAAATAAA
1 TTATATAAAATTAA
* *
1095150 TTATACATAAATATAT
1 TTATATA-AAAT-TAA
1095166 TTATATAAAATTAA
1 TTATATAAAATTAA
1095180 TTAT
1 TTAT
1095184 TAACATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.44
15 8 0.30
16 7 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATATAAAATTAA
Found at i:1095191 original size:26 final size:28
Alignment explanation
Indices: 1095134--1095192 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
1095124 ATATCTTATA
*
1095134 ATTTATATAAAATAAATTATACATAAATAT
1 ATTTATATAAAATAAATTAT--ATAAACAT
*
1095164 ATTTATATAAAATTAATTAT-T-AACAT
1 ATTTATATAAAATAAATTATATAAACAT
1095190 ATT
1 ATT
1095193 AAAATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.26
27 1 0.04
30 19 0.70
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTATATAAAATAAATTATATAAACAT
Found at i:1097705 original size:21 final size:21
Alignment explanation
Indices: 1097658--1097704 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1097648 TTCTGATGAA
* *
1097658 AATTCTGTCAAAAAGAAGTTT
1 AATTTTGTCAAAAAGAAGTTG
*
1097679 AATTTTGTCAAAAATAA-TTG
1 AATTTTGTCAAAAAGAAGTTG
1097699 AATTTT
1 AATTTT
1097705 TCAGATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (21 bp):
AATTTTGTCAAAAAGAAGTTG
Found at i:1098125 original size:31 final size:31
Alignment explanation
Indices: 1098090--1098153 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1098080 CACCTAAAGC
*
1098090 AACCATTTCTACAGGATACATTTAAGTATAT
1 AACCATTTCTACAGAATACATTTAAGTATAT
* *
1098121 AACCATTTCTACAGAATATATTTCAGTATAT
1 AACCATTTCTACAGAATACATTTAAGTATAT
1098152 AA
1 AA
1098154 TCAATACCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.36
Consensus pattern (31 bp):
AACCATTTCTACAGAATACATTTAAGTATAT
Found at i:1098947 original size:4 final size:4
Alignment explanation
Indices: 1098931--1098965 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1098921 CCTATAAATA
*
1098931 TATC TACC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TAT
1098966 TTATATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
TATC
Found at i:1101096 original size:21 final size:20
Alignment explanation
Indices: 1101072--1101111 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1101062 ATAAAAAATT
*
1101072 TTATTTAAAATTAATTATAAG
1 TTATATAAAATTAA-TATAAG
*
1101093 TTATATAAATTTAATATAA
1 TTATATAAAATTAATATAA
1101112 AAATATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATATAAAATTAATATAAG
Found at i:1101458 original size:30 final size:30
Alignment explanation
Indices: 1101424--1101505 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
1101414 TAATTTGTTA
* *
1101424 AATTTAATTAACTCAAAATTTAACATAC-AT
1 AATTTAATTAA-TCAAAATATAAAATACAAT
*
1101454 AATTTATATAAAT-AAAATATAAAATACAAT
1 AATTTA-ATTAATCAAAATATAAAATACAAT
*
1101484 AAATTAATTAATC-AAATATAAA
1 AATTTAATTAATCAAAATATAAA
1101506 TCATATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 26 0.59
30 14 0.32
31 4 0.09
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (30 bp):
AATTTAATTAATCAAAATATAAAATACAAT
Found at i:1101480 original size:29 final size:29
Alignment explanation
Indices: 1101438--1101524 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
1101428 TAATTAACTC
* *
1101438 AAAATTTAACATACATAATTTATATAAAT
1 AAAATATAAAATACATAATTTATATAAAT
* *
1101467 AAAATATAAAATACAATAAATTA-ATTAAT
1 AAAATATAAAATAC-ATAATTTATATAAAT
*
1101496 CAAATAT-AAAT-CAT-ATTTATATAAA-
1 AAAATATAAAATACATAATTTATATAAAT
1101521 AAAA
1 AAAA
1101525 GACTATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
25 7 0.15
26 6 0.12
27 1 0.02
28 4 0.08
29 23 0.48
30 7 0.15
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATATAAAATACATAATTTATATAAAT
Found at i:1109608 original size:104 final size:104
Alignment explanation
Indices: 1109428--1109635 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 104
1109418 TAAACATCAG
* *
1109428 AAAAATAATCAGTCAAAACCGATCAAATTGCAATGACTAAATCACTAACGTTCGGGAAAAAATAG
1 AAAAATAATCAGTCAAAACCGATCAAATTGCAATGACTAAATCACTAACATTCGGGAAAAAATAA
*
1109493 AAATCTGAACTTGACAGAATCAGAATCACAATAATCAAC
66 AAATCTGAACTTGACAGAATCAGAATCACAATAACCAAC
* * *
1109532 AAAAATAA-CAAGTCAAAACCTATCAAATTGCAATGACTATATCCCTAACATTCGGGAAAAAATA
1 AAAAATAATC-AGTCAAAACCGATCAAATTGCAATGACTAAATCACTAACATTCGGGAAAAAATA
*
1109596 AAAATCTGAACTTGACAGAATCATAATCACAATAACCAAC
65 AAAATCTGAACTTGACAGAATCAGAATCACAATAACCAAC
1109636 TATAACTATG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 1 0.01
104 95 0.99
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.21
Consensus pattern (104 bp):
AAAAATAATCAGTCAAAACCGATCAAATTGCAATGACTAAATCACTAACATTCGGGAAAAAATAA
AAATCTGAACTTGACAGAATCAGAATCACAATAACCAAC
Found at i:1114572 original size:15 final size:16
Alignment explanation
Indices: 1114536--1114575 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1114526 TGTAATATTT
*
1114536 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1114553 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1114568 ATAAAATT
1 ATAAAATT
1114576 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1114578 original size:16 final size:17
Alignment explanation
Indices: 1114536--1114578 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1114526 TGTAATATTT
*
1114536 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1114553 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1114568 ATAAAATTTAT
1 ATAAAATTTAT
1114579 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1114678 original size:24 final size:24
Alignment explanation
Indices: 1114645--1114698 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1114635 AAAATATAGG
*
1114645 ATAA-ATTAAAACACAA-TATAAAT
1 ATAATATTAAAAAACAATTA-AAAT
*
1114668 ATAATATTAAAAAATAATTAAAAT
1 ATAATATTAAAAAACAATTAAAAT
1114692 ATAATAT
1 ATAATAT
1114699 GACACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 21 0.78
25 2 0.07
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
ATAATATTAAAAAACAATTAAAAT
Found at i:1115006 original size:15 final size:14
Alignment explanation
Indices: 1114979--1115036 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
1114969 AATACATAAT
*
1114979 TTTTTTCTCTTTTT
1 TTTTTTCTCTTTTC
*
1114993 TTTCTTTCTTTTTTCC
1 TTT-TTTCTCTTTT-C
*
1115009 CTTTTTCTCTTTTC
1 TTTTTTCTCTTTTC
1115023 TTTCTTTCT-TTTTC
1 TTT-TTTCTCTTTTC
1115037 CAACCTTGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 11 0.31
15 23 0.64
16 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTCTTTTC
Found at i:1115007 original size:22 final size:23
Alignment explanation
Indices: 1114979--1115035 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
1114969 AATACATAAT
*
1114979 TTTTTTCTCTTTTTTTTC-TTTC
1 TTTTTTCTCTTTTTTCTCTTTTC
*
1115001 TTTTTTC-CCTTTTTCTCTTTTC
1 TTTTTTCTCTTTTTTCTCTTTTC
*
1115023 TTTCTT-TCTTTTT
1 TTTTTTCTCTTTTT
1115036 CCAACCTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTCTCTTTTTTCTCTTTTC
Found at i:1115030 original size:8 final size:7
Alignment explanation
Indices: 1114979--1115035 Score: 53
Period size: 8 Copynumber: 7.7 Consensus size: 7
1114969 AATACATAAT
1114979 TTTTTTC
1 TTTTTTC
1114986 TCTTTTT-
1 T-TTTTTC
1114993 TTTCTTTC
1 TTT-TTTC
1115001 TTTTTTCC
1 TTTTTT-C
*
1115009 CTTTTTC
1 TTTTTTC
*
1115016 TCTTTTC
1 TTTTTTC
1115023 TTTCTTTC
1 TTT-TTTC
1115031 TTTTT
1 TTTTT
1115036 CCAACCTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 2 0.05
7 18 0.44
8 21 0.51
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:1115292 original size:31 final size:32
Alignment explanation
Indices: 1115215--1115293 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
1115205 TGTGAAAAAT
*
1115215 AATATAAATACGATATGAATACATGAATATGTCAA
1 AATATAAATA--A-ATGAATACATGAATATGTAAA
* *
1115250 AATATAAATAAATGAATA-ATTAATCTGTAAA
1 AATATAAATAAATGAATACATGAATATGTAAA
* *
1115281 AATTTATATAAAT
1 AATATAAATAAAT
1115294 TTGTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 21 0.54
32 7 0.18
33 1 0.03
35 10 0.26
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (32 bp):
AATATAAATAAATGAATACATGAATATGTAAA
Found at i:1115417 original size:15 final size:16
Alignment explanation
Indices: 1115378--1115419 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1115368 ATATGTAAAT
1115378 AATAAGAATATACATAC
1 AATAA-AATATACATAC
*
1115395 ATATAAAATATACAT-G
1 A-ATAAAATATACATAC
1115411 AATAAAATA
1 AATAAAATA
1115420 AATTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 10 0.43
18 4 0.17
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (16 bp):
AATAAAATATACATAC
Found at i:1115539 original size:16 final size:15
Alignment explanation
Indices: 1115506--1115548 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
1115496 TTTTCTTTTT
1115506 TTTCTTTTTTTCTTA
1 TTTCTTTTTTTCTTA
1115521 TTTCTTTATTTAT-TTA
1 TTTCTTT-TTT-TCTTA
1115537 TTTCTTTCTTTT
1 TTTCTTT-TTTT
1115549 TTGACAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 8 0.32
16 16 0.64
17 1 0.04
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTTCTTA
Found at i:1116223 original size:22 final size:24
Alignment explanation
Indices: 1116198--1116242 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1116188 ACAAACTTAG
1116198 CATAT-ATATAAAAA-AAT-TAAAA
1 CATATCATA-AAAAATAATATAAAA
1116220 CATATCATAAAAAATAATATAAA
1 CATATCATAAAAAATAATATAAA
1116243 TACGATACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (24 bp):
CATATCATAAAAAATAATATAAAA
Found at i:1116500 original size:22 final size:24
Alignment explanation
Indices: 1116452--1116502 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1116442 TTCAAATTTT
* *
1116452 AAAAAATATAATATTTGACATATA
1 AAAAAATATAATATATGACATAAA
1116476 AAAAAATATAA-ATATGA-ATAAA
1 AAAAAATATAATATATGACATAAA
1116498 AAAAA
1 AAAAA
1116503 TTTCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAAAATATAATATATGACATAAA
Found at i:1116518 original size:4 final size:4
Alignment explanation
Indices: 1116511--1116571 Score: 72
Period size: 4 Copynumber: 15.5 Consensus size: 4
1116501 AATTTCTCTT
* * *
1116511 TTTC TTTC TTTC CTT- TTTC TTTT TTTC TCT- TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1116557 TTTTC TTTC TTTC TT
1 -TTTC TTTC TTTC TT
1116572 CCTTCTATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 4 0.08
4 40 0.83
5 4 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:1116560 original size:17 final size:17
Alignment explanation
Indices: 1116511--1116571 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
1116501 AATTTCTCTT
1116511 TTTCTTTCTTTCCTTTTTC
1 TTTCTTTCTTT-C-TTTTC
*
1116530 TTT-TTT-TCTCTTTTC
1 TTTCTTTCTTTCTTTTC
1116545 TTTCTTTCTTTCTTTTC
1 TTTCTTTCTTTCTTTTC
1116562 TTTCTTTCTT
1 TTTCTTTCTT
1116572 CCTTCTATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.21
16 4 0.11
17 20 0.53
18 3 0.08
19 3 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTTC
Found at i:1117390 original size:16 final size:17
Alignment explanation
Indices: 1117371--1117413 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1117361 AAATAATTAA
*
1117371 AATATGATAT-AAATAT
1 AATATGATATAAAAAAT
1117387 AATATGATATAAAAAAT
1 AATATGATATAAAAAAT
*
1117404 AATATAATAT
1 AATATGATAT
1117414 GAATGTGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
AATATGATATAAAAAAT
Found at i:1117563 original size:26 final size:26
Alignment explanation
Indices: 1117487--1117557 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
1117477 TAATATCTTA
1117487 AATACAATTATAATATGTAAAAATAT
1 AATACAATTATAATATGTAAAAATAT
1117513 AATACAATTATAATATGTAAAAATAT
1 AATACAATTATAATATGTAAAAATAT
1117539 -ATA-AA-TATAATATGATAAA
1 AATACAATTATAATATG-TAAA
1117558 CAAATAGCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
23 9 0.20
24 6 0.14
25 3 0.07
26 26 0.59
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (26 bp):
AATACAATTATAATATGTAAAAATAT
Found at i:1119199 original size:15 final size:14
Alignment explanation
Indices: 1119157--1119200 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1119147 TTTATAAACA
1119157 TATAAAAC-ATTTT
1 TATAAAACTATTTT
* *
1119170 TATAAAATTAATTT
1 TATAAAACTATTTT
1119184 TATAAAAACTATTTT
1 TAT-AAAACTATTTT
1119199 TA
1 TA
1119201 ATTTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 7 0.28
14 7 0.28
15 11 0.44
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAAAACTATTTT
Found at i:1119288 original size:18 final size:17
Alignment explanation
Indices: 1119267--1119308 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1119257 ATAATTTATA
1119267 TTATAAT-TTAAATTAATT
1 TTATAATATTAAA-TAA-T
1119285 TTATAAATATTAAATAAT
1 TTAT-AATATTAAATAAT
1119303 TTATAA
1 TTATAA
1119309 AATATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 6 0.27
20 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATAATATTAAATAAT
Found at i:1119309 original size:18 final size:19
Alignment explanation
Indices: 1119256--1119324 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 19
1119246 AAATATAAAT
1119256 AATAATTTATATTATAAT-TTA
1 AATAATTTATA--A-AATATTA
1119277 AATTAATTT-TATAAATATTA
1 AA-TAATTTATA-AAATATTA
*
1119297 AATAATTTATAAAATATAA
1 AATAATTTATAAAATATTA
1119316 AAT-ATTTAT
1 AATAATTTAT
1119325 TTGCAATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 6 0.14
19 19 0.43
20 9 0.20
21 4 0.09
22 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTTATAAAATATTA
Found at i:1119471 original size:16 final size:17
Alignment explanation
Indices: 1119437--1119477 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1119427 TTAAATTATT
1119437 TTTATAAAAATTAATAA
1 TTTATAAAAATTAATAA
1119454 TTTATCAAAAA-T-ATAA
1 TTTAT-AAAAATTAATAA
1119470 TTTATAAA
1 TTTATAAA
1119478 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 9 0.39
17 6 0.26
18 5 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATAAAAATTAATAA
Found at i:1119625 original size:16 final size:18
Alignment explanation
Indices: 1119582--1119627 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1119572 ATTGATTTAA
*
1119582 ATAAATATTTATATGTTT
1 ATAAATAATTATATGTTT
1119600 ATAAATTAATTATAT-TTT
1 ATAAA-TAATTATATGTTT
1119618 A-AAATAATTA
1 ATAAATAATTA
1119628 GTTCAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.23
17 3 0.12
18 9 0.35
19 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAAATAATTATATGTTT
Found at i:1120560 original size:21 final size:21
Alignment explanation
Indices: 1120534--1120575 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1120524 TTTTAGAATT
1120534 TTTAATTT-AAATTAAATAATA
1 TTTAATTTAAAATTAAA-AATA
1120555 TTTAATTTAAAATTAAAAATA
1 TTTAATTTAAAATTAAAAATA
1120576 AAATCGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAATTTAAAATTAAAAATA
Found at i:1124537 original size:16 final size:14
Alignment explanation
Indices: 1124510--1124548 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1124500 TTACTGGATG
1124510 TAAAAAAATTATTT
1 TAAAAAAATTATTT
*
1124524 TAAAAAATATT-TAT
1 TAAAAAA-ATTATTT
1124538 TAAAAAAATTA
1 TAAAAAAATTA
1124549 ATTATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAAAATTATTT
Found at i:1124552 original size:13 final size:13
Alignment explanation
Indices: 1124510--1124562 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1124500 TTACTGGATG
*
1124510 TAAAAAAATTATTT
1 TAAAAAAATTA-AT
*
1124524 TAAAAAATATTTAT
1 TAAAAAA-ATTAAT
1124538 TAAAAAAATTAAT
1 TAAAAAAATTAAT
**
1124551 TATGAAAATTAA
1 TAAAAAAATTAA
1124563 AAATATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 15 0.45
14 15 0.45
15 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
TAAAAAAATTAAT
Found at i:1124553 original size:16 final size:16
Alignment explanation
Indices: 1124510--1124558 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1124500 TTACTGGATG
1124510 TAAAAAAATT-ATT-T
1 TAAAAAAATTAATTAT
*
1124524 T-AAAAAA-TATTTAT
1 TAAAAAAATTAATTAT
1124538 TAAAAAAATTAATTAT
1 TAAAAAAATTAATTAT
*
1124554 GAAAA
1 TAAAA
1124559 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 1 0.04
13 8 0.29
14 3 0.11
15 6 0.21
16 10 0.36
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAAAATTAATTAT
Found at i:1124661 original size:76 final size:76
Alignment explanation
Indices: 1124510--1124659 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 76
1124500 TTACTGGATG
* * * * * *
1124510 TAAAAAAATTATTTTAAAAAATATTTATTAAAAAAATTAATTATGAAAATTAAAAATATTATTAT
1 TAAAAAAATGATTTCAAAAAATAGTTATCAAAAAAATTAATTATCAAAAATAAAAATATTATTAT
1124575 TTTAATAAAAA
66 TTTAATAAAAA
*
1124586 TAAAAAAATGATTTCAAAAAAT-GTTAGTCAAAAAACTTAATTA-CAAAAATAAAAATATTATTA
1 TAAAAAAATGATTTCAAAAAATAGTTA-TCAAAAAAATTAATTATCAAAAATAAAAATATTATTA
1124649 -TTTAATAAAAA
65 TTTTAATAAAAA
1124660 AACCTCAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
74 11 0.17
75 21 0.32
76 34 0.52
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (76 bp):
TAAAAAAATGATTTCAAAAAATAGTTATCAAAAAAATTAATTATCAAAAATAAAAATATTATTAT
TTTAATAAAAA
Found at i:1131714 original size:27 final size:26
Alignment explanation
Indices: 1131657--1131736 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 26
1131647 TTCGGTGCTC
* * *
1131657 ATTTTACTAGTTATTTTTCGA-ATGTTC
1 ATTTT-CTAATTATTTTTAGATAT-TTT
1131684 ATTTTGCTAATTATTTTTAGATATTTT
1 ATTTT-CTAATTATTTTTAGATATTTT
1131711 A--TT-T-ATTATTTTTTAGATATTTT
1 ATTTTCTAATTA-TTTTTAGATATTTT
1131734 ATT
1 ATT
1131737 ATTTATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 4 0.09
23 16 0.36
25 2 0.04
27 21 0.47
28 2 0.04
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (26 bp):
ATTTTCTAATTATTTTTAGATATTTT
Found at i:1131727 original size:23 final size:22
Alignment explanation
Indices: 1131693--1131747 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
1131683 CATTTTGCTA
1131693 ATTA-TTTTTAGATATTTTATTT
1 ATTATTTTTTAGATATTTTA-TT
1131715 ATTATTTTTTAGATATTTTATT
1 ATTATTTTTTAGATATTTTATT
1131737 ATTTATTTTTT
1 A-TTATTTTTT
1131748 GAATGTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTATTTTTTAGATATTTTATT
Found at i:1132082 original size:16 final size:17
Alignment explanation
Indices: 1132050--1132099 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
1132040 TATATATATA
1132050 TATAAATTATAAAAATT
1 TATAAATTATAAAAATT
*
1132067 TATAAA-TATTAAAATT
1 TATAAATTATAAAAATT
* *
1132083 TA-AATTTTTAAAAATT
1 TATAAATTATAAAAATT
1132099 T
1 T
1132100 TACGATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 2 0.07
16 20 0.71
17 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAAATTATAAAAATT
Found at i:1132924 original size:30 final size:31
Alignment explanation
Indices: 1132873--1132971 Score: 107
Period size: 30 Copynumber: 3.3 Consensus size: 31
1132863 TTAAAAATTT
* *
1132873 AATAAAAATAATGTATTAATTATTATTTTTT
1 AATAAAAATAATATATTAATTATTATTTTTA
1132904 AATAAAAATAATAT-TTAATTA--ATTTTTAAA
1 AATAAAAATAATATATTAATTATTATTTTT--A
* * *
1132934 AATTAAAATAAAATATTAATTATT-TTTTAA
1 AATAAAAATAATATATTAATTATTATTTTTA
1132964 AATAAAAA
1 AATAAAAA
1132972 ATTAAATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 6 0.11
30 27 0.47
31 20 0.35
32 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
AATAAAAATAATATATTAATTATTATTTTTA
Found at i:1132973 original size:31 final size:31
Alignment explanation
Indices: 1132876--1132978 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
1132866 AAAATTTAAT
** **
1132876 AAAAATAATGTATTAATTATTATTTTTTAAT-
1 AAAAATAAAATATTAATTATT-TTTTAAAATA
* *
1132907 AAAAATAATAT-TTAATTAATTTTTAAAA-A
1 AAAAATAAAATATTAATTATTTTTTAAAATA
*
1132936 TTAAAATAAAATATTAATTATTTTTTAAAATA
1 -AAAAATAAAATATTAATTATTTTTTAAAATA
*
1132968 AAAAATTAAAT
1 AAAAATAAAAT
1132979 TAAAAAGGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
29 6 0.10
30 17 0.29
31 35 0.59
32 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
AAAAATAAAATATTAATTATTTTTTAAAATA
Found at i:1133082 original size:30 final size:30
Alignment explanation
Indices: 1133037--1133099 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1133027 AAAATTTTAA
* **
1133037 TAAATAATATATTAATTATTTTTTATAAAAT
1 TAAAAAATATATTAATTAAATTTTA-AAAAT
1133068 TAAAAAATAT-TTAATTAAATTTTAAAAAT
1 TAAAAAATATATTAATTAAATTTTAAAAAT
1133097 TAA
1 TAA
1133100 GGTATGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.28
30 12 0.41
31 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAAAATATATTAATTAAATTTTAAAAAT
Found at i:1133378 original size:11 final size:11
Alignment explanation
Indices: 1133362--1133395 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1133352 ATTATTACTT
1133362 TTATTTATAAA
1 TTATTTATAAA
* *
1133373 TTATTTTTAAT
1 TTATTTATAAA
1133384 TTATTTATAAA
1 TTATTTATAAA
1133395 T
1 T
1133396 ATACAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1133543 original size:46 final size:46
Alignment explanation
Indices: 1133493--1133602 Score: 184
Period size: 46 Copynumber: 2.4 Consensus size: 46
1133483 ATATTTTACT
* * *
1133493 TTTTTCGATAATGACTTATTTCGGATTTACAGACGCACACATTTTA
1 TTTTTCGATAACGACTTATTTCGAATTTACAGACGCACACATTTCA
1133539 TTTTTCGATAACGACTTATTTCGAATTTACAGACGCACACATTTCA
1 TTTTTCGATAACGACTTATTTCGAATTTACAGACGCACACATTTCA
*
1133585 TTTTTCGGTAACGACTTA
1 TTTTTCGATAACGACTTA
1133603 AATACGAGCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (46 bp):
TTTTTCGATAACGACTTATTTCGAATTTACAGACGCACACATTTCA
Found at i:1133721 original size:11 final size:11
Alignment explanation
Indices: 1133705--1133741 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1133695 TTATTACTTT
1133705 TTATTTATAAA
1 TTATTTATAAA
* *
1133716 TTATTTTTAAT
1 TTATTTATAAA
1133727 TTATTTATAAA
1 TTATTTATAAA
1133738 TTAT
1 TTAT
1133742 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1134351 original size:23 final size:24
Alignment explanation
Indices: 1134325--1134370 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1134315 TTAATATTTT
*
1134325 AATTTATT-AATATAATTTTTTAA
1 AATTAATTAAATATAATTTTTTAA
*
1134348 AATTAATTAAATATTATTTTTTA
1 AATTAATTAAATATAATTTTTTA
1134371 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTAATTAAATATAATTTTTTAA
Found at i:1135911 original size:19 final size:19
Alignment explanation
Indices: 1135876--1135913 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1135866 TTGAACTTAA
1135876 TTAATAATATATTATATTT
1 TTAATAATATATTATATTT
*
1135895 TTAA-AATATTTTCATATTT
1 TTAATAATATATT-ATATTT
1135914 ATTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATAATATATTATATTT
Found at i:1136930 original size:22 final size:22
Alignment explanation
Indices: 1136902--1136951 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1136892 AATGATTTAT
* *
1136902 TAAAGAATGGAAGGAAAGAAAA
1 TAAAGAAAGAAAGGAAAGAAAA
1136924 TAAAGAAAGAAAGGAAAGAAAA
1 TAAAGAAAGAAAGGAAAGAAAA
*
1136946 AAAAGA
1 TAAAGA
1136952 GAAAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (22 bp):
TAAAGAAAGAAAGGAAAGAAAA
Found at i:1137505 original size:23 final size:21
Alignment explanation
Indices: 1137479--1137532 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
1137469 TGTTTGTATA
1137479 TTCATGTTGTGTTTATATTATTT
1 TTCATGTTGT-TTTA-ATTATTT
1137502 TTCATGATATGTTTTAATTATTT
1 TTCATG-T-TGTTTTAATTATTT
*
1137525 TTTATGTT
1 TTCATGTT
1137533 ACATTCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 18 0.64
24 5 0.18
25 3 0.11
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (21 bp):
TTCATGTTGTTTTAATTATTT
Found at i:1137754 original size:20 final size:21
Alignment explanation
Indices: 1137716--1137754 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1137706 TGTTCATGTA
*
1137716 TTTATATCGTATTCATATTAT
1 TTTATATCCTATTCATATTAT
*
1137737 TTTATATCCT-TTCGTATT
1 TTTATATCCTATTCATATT
1137755 TTAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTATATCCTATTCATATTAT
Found at i:1138013 original size:40 final size:41
Alignment explanation
Indices: 1137967--1138049 Score: 96
Period size: 45 Copynumber: 2.0 Consensus size: 41
1137957 TATTGGTTTT
*
1137967 CCAATTG-GGTGTAATTTGGTAATAAAAATAAAATTGAGGC
1 CCAATTGTAGTGTAATTTGGTAATAAAAATAAAATTGAGGC
* *
1138007 CCAATTGATTTTAGTGTAATTTTGTAATAAAAATCAAATTGAG
1 CCAATTG----TAGTGTAATTTGGTAATAAAAATAAAATTGAG
1138050 AAATGATGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 7 0.20
45 28 0.80
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (41 bp):
CCAATTGTAGTGTAATTTGGTAATAAAAATAAAATTGAGGC
Found at i:1138536 original size:18 final size:18
Alignment explanation
Indices: 1138513--1138547 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1138503 TGTATGTCAT
*
1138513 TATCATATTATTTTTTAG
1 TATCATATTATATTTTAG
*
1138531 TATCATGTTATATTTTA
1 TATCATATTATATTTTA
1138548 ATTATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (18 bp):
TATCATATTATATTTTAG
Found at i:1139178 original size:11 final size:11
Alignment explanation
Indices: 1139156--1139203 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1139146 ATTAGATTTA
*
1139156 TATATTTGTAT
1 TATATTTATAT
*
1139167 TTTATTTATAT
1 TATATTTATAT
1139178 TAT-TTTATAT
1 TATATTTATAT
1139188 CTATATTT-TAT
1 -TATATTTATAT
1139199 TATAT
1 TATAT
1139204 AAATTATCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 12 0.38
11 17 0.53
12 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1140702 original size:22 final size:22
Alignment explanation
Indices: 1140674--1140716 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1140664 TAAATCGATA
*
1140674 AAATAAATATAGAAAAATAAAT
1 AAATAAAGATAGAAAAATAAAT
* *
1140696 AAATAAAGGTATAAAAATAAA
1 AAATAAAGATAGAAAAATAAA
1140717 GGATTTTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (22 bp):
AAATAAAGATAGAAAAATAAAT
Found at i:1141164 original size:2 final size:2
Alignment explanation
Indices: 1141157--1141201 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1141147 ACCTATTTAC
* * * *
1141157 AT AT AT AT AT AT AT AT AT AT TT AT TT AT TT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1141199 AT A
1 AT A
1141202 AATTTAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1141194 original size:20 final size:20
Alignment explanation
Indices: 1141169--1141211 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1141159 ATATATATAT
* **
1141169 ATATATATTTATTTATTTAA
1 ATATATATATATAAATTTAA
1141189 ATATATATATATAAATTTAA
1 ATATATATATATAAATTTAA
1141209 ATA
1 ATA
1141212 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATATATATAAATTTAA
Found at i:1141213 original size:24 final size:24
Alignment explanation
Indices: 1141165--1141213 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1141155 ACATATATAT
** **
1141165 ATATATATATATTTATTTATTTAA
1 ATATATATATATAAATTTAAATAA
1141189 ATATATATATATAAATTTAAATAA
1 ATATATATATATAAATTTAAATAA
1141213 A
1 A
1141214 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATATATATATAAATTTAAATAA
Found at i:1149929 original size:2 final size:2
Alignment explanation
Indices: 1149922--1149946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1149912 TCAACCATAT
1149922 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1149947 GCTTGTTAAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1153020 original size:13 final size:13
Alignment explanation
Indices: 1152995--1153036 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1152985 GAATTTGAGA
1152995 AAAATATTAAATTT
1 AAAATA-TAAATTT
1153009 AAAATATAAATTT
1 AAAATATAAATTT
*
1153022 -AAATA-AATTTT
1 AAAATATAAATTT
1153033 AAAA
1 AAAA
1153037 CTCATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 5 0.19
12 8 0.31
13 7 0.27
14 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATATAAATTT
Found at i:1153927 original size:32 final size:32
Alignment explanation
Indices: 1153891--1153979 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 32
1153881 ACGAATGTAA
1153891 ATATAATAGAATACATAAATATATCAAAATTT
1 ATATAATAGAATACATAAATATATCAAAATTT
* * * *
1153923 ATATAATACGAAT-TATTAATTTATTAAAATTT
1 ATATAATA-GAATACATAAATATATCAAAATTT
*
1153955 ATATAAATATAATACATTAAATATA
1 ATAT-AATAGAATACA-TAAATATA
1153980 ATCATAACAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
32 30 0.67
33 9 0.20
34 6 0.13
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (32 bp):
ATATAATAGAATACATAAATATATCAAAATTT
Found at i:1156487 original size:22 final size:23
Alignment explanation
Indices: 1156462--1156511 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1156452 TTAGTATTTA
1156462 TAAATTAAA-TTAAATTTTAATT
1 TAAATTAAATTTAAATTTTAATT
*
1156484 TAAA--AAATTTTAAATTTTTATT
1 TAAATTAAA-TTTAAATTTTAATT
1156506 TAAATT
1 TAAATT
1156512 TATTTTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.13
22 20 0.87
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTAAATTTAAATTTTAATT
Found at i:1156615 original size:42 final size:36
Alignment explanation
Indices: 1156546--1156622 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 36
1156536 TTAAATTATT
1156546 TATTTTATTATTTATAATTAATAAAAAATTATATTAA
1 TATTTTATTATTTATAATTAATAAAAAATTA-ATTAA
1156583 TATTTTATATATTTATAATTAAATTTAAAAAAATTAATTA
1 TATTTTAT-TATTTATAATT-AA--T-AAAAAATTAATTA
1156623 TTAAAGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
37 8 0.23
38 11 0.31
39 2 0.06
41 5 0.14
42 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
TATTTTATTATTTATAATTAATAAAAAATTAATTAA
Found at i:1157047 original size:14 final size:12
Alignment explanation
Indices: 1157008--1157047 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1156998 TCAAAAATAC
*
1157008 TATAAATTTCAA
1 TATAAATTTTAA
1157020 TATAAATTTTAA
1 TATAAATTTTAA
1157032 TATAATATTCTTAA
1 TATAA-ATT-TTAA
1157046 TA
1 TA
1157048 GTTATTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 16 0.64
13 3 0.12
14 6 0.24
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (12 bp):
TATAAATTTTAA
Found at i:1157264 original size:2 final size:2
Alignment explanation
Indices: 1157257--1157283 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1157247 TGTCAAAATT
1157257 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 T
1157284 GTAAAAGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1160615 original size:21 final size:21
Alignment explanation
Indices: 1160591--1160630 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1160581 AAATAAAAAT
*
1160591 TATTTTTAT-ATTAATATTTTA
1 TATTATTATAATTAA-ATTTTA
1160612 TATTATTATAATTAAATTT
1 TATTATTATAATTAAATTT
1160631 AAATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTATAATTAAATTTTA
Found at i:1164157 original size:25 final size:25
Alignment explanation
Indices: 1164110--1164157 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1164100 CCAAATGGCT
1164110 AGCTGCTGATAAGAGTAAAATATAA
1 AGCTGCTGATAAGAGTAAAATATAA
1164135 AGCTGCTGATAAGAGTAAAATAT
1 AGCTGCTGATAAGAGTAAAATAT
1164158 TTATAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (25 bp):
AGCTGCTGATAAGAGTAAAATATAA
Found at i:1164187 original size:125 final size:125
Alignment explanation
Indices: 1164029--1164260 Score: 464
Period size: 125 Copynumber: 1.9 Consensus size: 125
1164019 ACGTCAGTTT
1164029 ATATTTATAATTGGGGGATAATACACCATGAGAATTGAGAAGCACAAACTTTCTGGCGTTTATAG
1 ATATTTATAATTGGGGGATAATACACCATGAGAATTGAGAAGCACAAACTTTCTGGCGTTTATAG
1164094 TGTGGGCCAAATGGCTAGCTGCTGATAAGAGTAAAATATAAAGCTGCTGATAAGAGTAAA
66 TGTGGGCCAAATGGCTAGCTGCTGATAAGAGTAAAATATAAAGCTGCTGATAAGAGTAAA
1164154 ATATTTATAATTGGGGGATAATACACCATGAGAATTGAGAAGCACAAACTTTCTGGCGTTTATAG
1 ATATTTATAATTGGGGGATAATACACCATGAGAATTGAGAAGCACAAACTTTCTGGCGTTTATAG
1164219 TGTGGGCCAAATGGCTAGCTGCTGATAAGAGTAAAATATAAA
66 TGTGGGCCAAATGGCTAGCTGCTGATAAGAGTAAAATATAAA
1164261 TCTACTTTCT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 107 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (125 bp):
ATATTTATAATTGGGGGATAATACACCATGAGAATTGAGAAGCACAAACTTTCTGGCGTTTATAG
TGTGGGCCAAATGGCTAGCTGCTGATAAGAGTAAAATATAAAGCTGCTGATAAGAGTAAA
Found at i:1166764 original size:2 final size:2
Alignment explanation
Indices: 1166757--1166790 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1166747 TTAAAAATCC
1166757 AT 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 AT
1166791 GTATGGCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166923 original size:20 final size:20
Alignment explanation
Indices: 1166886--1166925 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1166876 GTTTCCTGAT
1166886 TTAATAATAATAAGATTTTA
1 TTAATAATAATAAGATTTTA
*
1166906 TTAATGAATATTAA-ATTTTA
1 TTAAT-AATAATAAGATTTTA
1166926 AGATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTAATAATAATAAGATTTTA
Found at i:1167963 original size:16 final size:16
Alignment explanation
Indices: 1167915--1167968 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1167905 TTTATACCAT
1167915 TTTTAATATATTAATA
1 TTTTAATATATTAATA
* *
1167931 ATTTAA-ATTATAAATA
1 TTTTAATA-TATTAATA
*
1167947 TTTTAATATATTTATA
1 TTTTAATATATTAATA
1167963 TATTTA
1 T-TTTA
1167969 TTTCATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 1 0.03
16 24 0.80
17 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAATATATTAATA
Found at i:1177335 original size:108 final size:109
Alignment explanation
Indices: 1177222--1177438 Score: 310
Period size: 109 Copynumber: 2.0 Consensus size: 109
1177212 TGTTCACTAT
* *
1177222 ATTTTTAAATTATAATTATAAA-TTTTTACTATTAATAAGGTTTTTCTAATTTATAAATTAAAAG
1 ATTTTTAAATTATAATTATAAATTTTTTACTATTAAAAAGATTTTTCTAATTTATAAATTAAAAG
* * *
1177286 TAAAAAGTTTAATTTTATTAAAATACTTTTGTTAAATAGATTAA
66 TAAAAAATTTAATTTCATTAAAACACTTTTGTTAAATAGATTAA
* * * * *
1177330 ATTTTTAAATTGTAATTATAAATTTTTTATTATTAAAAATATTTTTTTAATTTATAAATTATAAG
1 ATTTTTAAATTATAATTATAAATTTTTTACTATTAAAAAGATTTTTCTAATTTATAAATTAAAAG
* * *
1177395 TAAAAAATTTAATTTCATTACAACACTTTTTTTAAATGGATTAA
66 TAAAAAATTTAATTTCATTAAAACACTTTTGTTAAATAGATTAA
1177439 TTCAATAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
108 21 0.22
109 74 0.78
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (109 bp):
ATTTTTAAATTATAATTATAAATTTTTTACTATTAAAAAGATTTTTCTAATTTATAAATTAAAAG
TAAAAAATTTAATTTCATTAAAACACTTTTGTTAAATAGATTAA
Found at i:1177538 original size:26 final size:23
Alignment explanation
Indices: 1177509--1177568 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
1177499 ACTTTTTATA
1177509 ACATTAAAAATAAATCAATATATATC
1 ACATTAAAAATAAATCAA-A-AT-TC
* *
1177535 ACA-TAAATAAAAAATTAAAATTC
1 ACATTAAA-AATAAATCAAAATTC
1177558 ACATTAAAAAT
1 ACATTAAAAAT
1177569 TTTTAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
23 7 0.24
24 6 0.21
25 5 0.17
26 11 0.38
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (23 bp):
ACATTAAAAATAAATCAAAATTC
Found at i:1178363 original size:28 final size:30
Alignment explanation
Indices: 1178330--1178392 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
1178320 TAAATATAAG
* *
1178330 TAAGTCTTTGTATTTTTA-TTATAC-TAAA
1 TAAGTCTTTATATTTTGATTTATACTTAAA
*
1178358 TAAGTCTTTATCTTTTGATTTATACTTAAA
1 TAAGTCTTTATATTTTGATTTATACTTAAA
1178388 TAAGT
1 TAAGT
1178393 TCTTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 15 0.50
29 6 0.20
30 9 0.30
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (30 bp):
TAAGTCTTTATATTTTGATTTATACTTAAA
Found at i:1179743 original size:3 final size:3
Alignment explanation
Indices: 1179735--1179762 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1179725 TAACATTTCT
1179735 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1179763 GCTTCATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1179978 original size:5 final size:5
Alignment explanation
Indices: 1179968--1179992 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1179958 GATGTATGTC
1179968 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
1179993 TTTATCATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Done.