Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold174
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: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 4 of 15
Found at i:411284 original size:26 final size:26
Alignment explanation
Indices: 411255--411308 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
411245 TTTTATATTC
* * * *
411255 ATGTTTAATATTTATATTTGATGTAT
1 ATGTTCAATACTTATATCTAATGTAT
*
411281 ATGTTCGATACTTATATCTAATGTAT
1 ATGTTCAATACTTATATCTAATGTAT
411307 AT
1 AT
411309 TATCTTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (26 bp):
ATGTTCAATACTTATATCTAATGTAT
Found at i:412258 original size:13 final size:13
Alignment explanation
Indices: 412240--412264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
412230 ATGATTGCAA
412240 AAAATAATTTTTG
1 AAAATAATTTTTG
412253 AAAATAATTTTT
1 AAAATAATTTTT
412265 ATAATTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AAAATAATTTTTG
Found at i:412516 original size:21 final size:21
Alignment explanation
Indices: 412490--412556 Score: 57
Period size: 25 Copynumber: 3.0 Consensus size: 21
412480 TTAATAAATA
412490 TTATAATATTAAATAATTATT
1 TTATAATATTAAATAATTATT
412511 TTATAATTAAATTTAAATATATTA-T
1 TTATAA-T--A-TTAAATA-ATTATT
* *
412536 TTATTA-ATTAAATAATAATT
1 TTATAATATTAAATAATTATT
412556 T
1 T
412557 AAATTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 7 0.18
22 1 0.03
24 1 0.03
25 13 0.34
26 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAATATTAAATAATTATT
Found at i:412537 original size:26 final size:26
Alignment explanation
Indices: 412489--412549 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
412479 TTTAATAAAT
412489 ATTATAATATTAAATAATTATTT-TATA
1 ATTA-AATATTAAATAATTATTTAT-TA
412516 ATTAAAT-TTAAATATATTATTTATTA
1 ATTAAATATTAAATA-ATTATTTATTA
412542 ATTAAATA
1 ATTAAATA
412550 ATAATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 7 0.23
26 19 0.61
27 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTAAATATTAAATAATTATTTATTA
Found at i:412571 original size:19 final size:17
Alignment explanation
Indices: 412513--412579 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 17
412503 TAATTATTTT
412513 ATAA-TTAAATTTAAATA
1 ATAATTTAAA-TTAAATA
*
412530 TATTATTTATTAATTAAATA
1 -ATAATTTA--AATTAAATA
412550 ATAATTTAAATTAAATAAA
1 ATAATTTAAATTAAAT--A
412569 ATAATTTAAAT
1 ATAATTTAAAT
412580 CATAAAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 8 0.19
18 3 0.07
19 22 0.52
20 7 0.17
21 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATTTAAATTAAATA
Found at i:412688 original size:20 final size:21
Alignment explanation
Indices: 412663--412703 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
412653 AACAAGTGTG
*
412663 ATAAAA-TTAATTTCTTAAAA
1 ATAAAAGTTAATCTCTTAAAA
412683 ATAAAATGTTAATCTCTTAAA
1 ATAAAA-GTTAATCTCTTAAA
412704 TTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAAAAGTTAATCTCTTAAAA
Found at i:412710 original size:21 final size:22
Alignment explanation
Indices: 412668--412715 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
412658 GTGTGATAAA
*
412668 ATTAATTTCTTAAAAATAAAAT
1 ATTAATCTCTTAAAAATAAAAT
* *
412690 GTTAATCTCTT-AAATTAAAAT
1 ATTAATCTCTTAAAAATAAAAT
412711 ATTAA
1 ATTAA
412716 AAATTCTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTAATCTCTTAAAAATAAAAT
Found at i:413506 original size:13 final size:13
Alignment explanation
Indices: 413488--413518 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
413478 TTTATTACTG
413488 AAATATAATTTTA
1 AAATATAATTTTA
*
413501 AAATATATTTTTA
1 AAATATAATTTTA
413514 AAATA
1 AAATA
413519 AATATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATATAATTTTA
Found at i:413924 original size:19 final size:21
Alignment explanation
Indices: 413900--413952 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
413890 TTATTTAAAA
413900 ATATTAAAATTT-TAT-TTTT
1 ATATTAAAATTTATATATTTT
*
413919 ATATTAATATTTATATATTTT
1 ATATTAAAATTTATATATTTT
413940 ATAATT-AAATTTA
1 AT-ATTAAAATTTA
413953 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 12 0.41
22 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAAAATTTATATATTTT
Found at i:420337 original size:6 final size:6
Alignment explanation
Indices: 420328--420364 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
420318 CTCAAACAAG
420328 TTTTAA TTTTAA TTTT-A -TTT-A TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
420365 TATAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 4 0.14
6 21 0.72
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTAA
Found at i:420582 original size:24 final size:24
Alignment explanation
Indices: 420555--420631 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
420545 TGTAATCATA
420555 TATTTTTTATATTATAATTTTATT
1 TATTTTTTATATTATAATTTTATT
* *
420579 TATTTTATATA-TATATTTTTTATT
1 TATTTTTTATATTATA-ATTTTATT
*
420603 ATATTTTATATCATATT-TAATTATATT
1 -TATTTT-T-T-ATATTATAATTTTATT
420630 TA
1 TA
420632 CAATTATCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
23 4 0.10
24 17 0.40
25 6 0.14
26 2 0.05
27 7 0.17
28 5 0.12
29 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTTTATATTATAATTTTATT
Found at i:420584 original size:22 final size:23
Alignment explanation
Indices: 420559--420630 Score: 85
Period size: 22 Copynumber: 3.1 Consensus size: 23
420549 ATCATATATT
420559 TTTTATATTATAATTTTATT-TA
1 TTTTATATTATAATTTTATTATA
*
420581 TTTTATATATATATTTTTTATTATA
1 TTTTATAT-TATA-ATTTTATTATA
* *
420606 TTTTATATCAT-ATTTAATTATA
1 TTTTATATTATAATTTTATTATA
420628 TTT
1 TTT
420631 ACAATTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
22 20 0.47
23 4 0.09
24 9 0.21
25 10 0.23
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATATTATAATTTTATTATA
Found at i:420620 original size:37 final size:35
Alignment explanation
Indices: 420547--420630 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 35
420537 GCAATATGTG
420547 TAATCATATATTTTTTATATTATAATTTTATTTATT
1 TAAT-ATATATTTTTTATATTATAATTTTATTTATT
*
420583 TTATATATATATTTTT-TATTAT-ATTTTATATCATATT
1 TAATATATAT-TTTTTATATTATAATTTTAT-T--TATT
420620 TAAT-TATATTT
1 TAATATATATTT
420631 ACAATTATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
34 7 0.17
35 15 0.36
36 13 0.31
37 7 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (35 bp):
TAATATATATTTTTTATATTATAATTTTATTTATT
Found at i:420626 original size:25 final size:24
Alignment explanation
Indices: 420559--420626 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
420549 ATCATATATT
420559 TTTTATAT-TATAATT--TTATTTA
1 TTTTATATATAT-ATTAATTATTTA
**
420581 TTTTATATATATATTTTTTATTATA
1 TTTTATATATATATTAATTATT-TA
420606 TTTTATATCATAT-TTAATTAT
1 TTTTATAT-ATATATTAATTAT
420627 ATTTACAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 11 0.28
23 3 0.08
24 5 0.13
25 16 0.41
26 4 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTATATATATATTAATTATTTA
Found at i:420649 original size:2 final size:2
Alignment explanation
Indices: 420642--420673 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
420632 CAATTATCAC
*
420642 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
420674 TTATGCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:420866 original size:34 final size:33
Alignment explanation
Indices: 420821--420888 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
420811 TAATAGTTAA
**
420821 TAATTAAAAATA-AAAAATATTTTTATTTAAATT
1 TAATTAAAAATATAAAAATAAATTT-TTTAAATT
*
420854 TAATTATAAAATATAAATATAAATTTTTTAAATT
1 TAATTA-AAAATATAAAAATAAATTTTTTAAATT
420888 T
1 T
420889 TTATTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 6 0.20
34 15 0.50
35 9 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAATTAAAAATATAAAAATAAATTTTTTAAATT
Found at i:421340 original size:16 final size:15
Alignment explanation
Indices: 421321--421366 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
421311 TATTAAAAAG
421321 TAAATTTTAATAATTT
1 TAAATTTT-ATAATTT
421337 TAAATTTTA-AATTT
1 TAAATTTTATAATTT
421351 T-AATATTTATAATTT
1 TAAAT-TTTATAATTT
421366 T
1 T
421367 TTAGATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.11
14 10 0.36
15 7 0.25
16 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTTATAATTT
Found at i:421342 original size:7 final size:7
Alignment explanation
Indices: 421321--421381 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
421311 TATTAAAAAG
421321 TAAATTT
1 TAAATTT
421328 TAATAATTT
1 T-A-AATTT
421337 TAAATTT
1 TAAATTT
421344 TAAATTT
1 TAAATTT
421351 TAATATTT
1 TAA-ATTT
*
421359 ATAATTTTT
1 -TAA-ATTT
*
421368 TAGATTTT
1 TA-AATTT
421376 TAAATT
1 TAAATT
421382 ATGATTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
7 19 0.40
8 14 0.30
9 14 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:421650 original size:13 final size:13
Alignment explanation
Indices: 421632--421656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
421622 TTTTAAATTA
421632 TAAATTAAATTTT
1 TAAATTAAATTTT
421645 TAAATTAAATTT
1 TAAATTAAATTT
421657 AATATAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTAAATTTT
Found at i:422189 original size:20 final size:20
Alignment explanation
Indices: 422144--422190 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
422134 ATGTAAAAAT
*
422144 AAAATATTATAAATACGATT
1 AAAATATTATAAATACGATA
* *
422164 ATAATATTATAAAATA-TATA
1 AAAATATTAT-AAATACGATA
422184 AAAATAT
1 AAAATAT
422191 GAAATTGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATATTATAAATACGATA
Found at i:424025 original size:40 final size:40
Alignment explanation
Indices: 423949--424025 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
423939 TCAAATTCAA
**
423949 ATTATTAAAATTAAATAATATTTTAAATTATTTTAAATTT
1 ATTATTAAAATTAAATAATATTTTAAATTAAATTAAATTT
*
423989 ATTATTTAAATATAAAT-A-ATTTTAAATTTAAATTAAA
1 ATTATTAAAAT-TAAATAATATTTTAAA-TTAAATTAAA
424026 CGAATAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 8 0.25
40 19 0.59
41 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
ATTATTAAAATTAAATAATATTTTAAATTAAATTAAATTT
Found at i:424359 original size:16 final size:17
Alignment explanation
Indices: 424328--424361 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
424318 TAAATATATC
424328 ATATTATATTAAAATTT
1 ATATTATATTAAAATTT
*
424345 ATATTA-ATTATAATTT
1 ATATTATATTAAAATTT
424361 A
1 A
424362 AAAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATTAAAATTT
Found at i:425156 original size:16 final size:16
Alignment explanation
Indices: 425132--425168 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
425122 GATCCCAAGA
* *
425132 TAAAATAATTTTTTTT
1 TAAATTAATTTTCTTT
425148 TAAATTAATTTTCTTT
1 TAAATTAATTTTCTTT
425164 TAAAT
1 TAAAT
425169 ATATTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTAATTTTCTTT
Found at i:430185 original size:105 final size:105
Alignment explanation
Indices: 430003--430212 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
429993 AGCTTCTCTG
430003 CATCATTCTACATGCAACATGTAATTGTCAAAACTCTTTAAAAAATAGCAAAACAGAAAGGGAGA
1 CATCATTCTACATGCAACATGTAATTGTCAAAACTCTTTAAAAAATAGCAAAACAGAAAGGGAGA
* *
430068 AAAAGGATAAATTTGGTGTCAAAAGTCGTAGTTTCAATCT
66 AAAAGGATAAATTTGGTGTCAAAAGTCGCAATTTCAATCT
430108 CATCATTCTACATGCAACATGTAATTGTCAAAACTCTTTAAAAAATAGCAAAACAGAAAGGGAGA
1 CATCATTCTACATGCAACATGTAATTGTCAAAACTCTTTAAAAAATAGCAAAACAGAAAGGGAGA
430173 AAAAGGATAAATTTGGTGTCAAAAGTCGCAATTTCAATCT
66 AAAAGGATAAATTTGGTGTCAAAAGTCGCAATTTCAATCT
430213 TACATCTATG
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (105 bp):
CATCATTCTACATGCAACATGTAATTGTCAAAACTCTTTAAAAAATAGCAAAACAGAAAGGGAGA
AAAAGGATAAATTTGGTGTCAAAAGTCGCAATTTCAATCT
Found at i:434060 original size:14 final size:16
Alignment explanation
Indices: 434026--434115 Score: 67
Period size: 17 Copynumber: 5.5 Consensus size: 16
434016 TATTTTTAAA
434026 TAATTTTATATTATAT
1 TAATTTTATATTATAT
*
434042 AAATTTTA-A-TATAT
1 TAATTTTATATTATAT
*
434056 TAATTATTTTTATTATAT
1 TAA-T-TTTATATTATAT
* * * *
434074 AAATTTTAAAATATTT
1 TAATTTTATATTATAT
*
434090 TAAATTTTATTTTATAT
1 T-AATTTTATATTATAT
434107 TATATTTTA
1 TA-ATTTTA
434116 ATGTTTATAA
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
14 7 0.13
15 2 0.04
16 19 0.35
17 20 0.36
18 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTTATATTATAT
Found at i:434060 original size:44 final size:46
Alignment explanation
Indices: 433977--434067 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 46
433967 AAGAGTAGTC
* * *
433977 AATAATTTTATATATTTATATATTTTATCGTATAATAATTATTTTTA
1 AATAATTTTATATATATATAAATTTTA-CATATAATAATTATTTTTA
*
434024 AATAATTTTATAT-TATATAAATTTTA-ATATATTAATTATTTTTA
1 AATAATTTTATATATATATAAATTTTACATATAATAATTATTTTTA
434068 TTATATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 16 0.40
46 11 0.28
47 13 0.32
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (46 bp):
AATAATTTTATATATATATAAATTTTACATATAATAATTATTTTTA
Found at i:434072 original size:18 final size:18
Alignment explanation
Indices: 434031--434078 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
434021 TTAAATAATT
*
434031 TTATATTATATAAATTTTA
1 TTATATTA-ATTAATTTTA
* *
434050 ATATATTAATTATTTTTA
1 TTATATTAATTAATTTTA
*
434068 TTATATAAATT
1 TTATATTAATT
434079 TTAAAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTAATTAATTTTA
Found at i:434097 original size:32 final size:33
Alignment explanation
Indices: 434027--434116 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 33
434017 ATTTTTAAAT
434027 AATTTTATATTATATAAATTTT--AATATATTA
1 AATTTTATATTATATAAATTTTAAAATATATTA
*
434058 ATTATTTT-TATTATATAAATTTTAAAATATTTTA
1 A--ATTTTATATTATATAAATTTTAAAATATATTA
* *
434092 AATTTTATTTTATATTATATTTTAA
1 AATTTTATATTATA-TAAATTTTAA
434117 TGTTTATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 20 0.40
33 11 0.22
34 18 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
AATTTTATATTATATAAATTTTAAAATATATTA
Found at i:434102 original size:12 final size:12
Alignment explanation
Indices: 434076--434116 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
434066 TATTATATAA
434076 ATTTTAAA--AT
1 ATTTTAAATTAT
*
434086 ATTTTAAATTTT
1 ATTTTAAATTAT
*
434098 ATTTTATATTAT
1 ATTTTAAATTAT
434110 ATTTTAA
1 ATTTTAA
434117 TGTTTATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 8 0.32
12 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTTAAATTAT
Found at i:434114 original size:34 final size:33
Alignment explanation
Indices: 434026--434116 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 33
434016 TATTTTTAAA
*
434026 TAATTTTATATTATA-TAAATTTT--AATATAT
1 TAATTTTATTTTATATTAAATTTTAAAATATAT
* *
434056 TAATTAT-TTTTATTATATAAATTTTAAAATATTT
1 TAATTTTATTTTA-TAT-TAAATTTTAAAATATAT
*
434090 TAAATTTTATTTTATATTATATTTTAA
1 T-AATTTTATTTTATATTAAATTTTAA
434117 TGTTTATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
29 4 0.08
30 8 0.16
32 8 0.16
34 16 0.33
35 8 0.16
36 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TAATTTTATTTTATATTAAATTTTAAAATATAT
Found at i:434201 original size:25 final size:23
Alignment explanation
Indices: 434173--434233 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
434163 TTTAAAAATG
*
434173 ATATTTCTTATATTAATTTTATTAA
1 ATATTTATTATATT-ATTTTA-TAA
*
434198 ATATTTATTATATTTTTTTATAA
1 ATATTTATTATATTATTTTATAA
*
434221 ATA-TTATTTTATT
1 ATATTTATTATATT
434234 TAGAACCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.27
23 6 0.18
24 5 0.15
25 13 0.39
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTTATTATATTATTTTATAA
Found at i:434214 original size:22 final size:22
Alignment explanation
Indices: 434189--434234 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
434179 CTTATATTAA
434189 TTTTAT-TAAATATTTATTATAT
1 TTTTATATAAATA-TTATTATAT
* *
434211 TTTTTTATAAATATTATTTTAT
1 TTTTATATAAATATTATTATAT
434233 TT
1 TT
434235 AGAACCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATATAAATATTATTATAT
Found at i:435629 original size:174 final size:177
Alignment explanation
Indices: 435310--435660 Score: 568
Period size: 174 Copynumber: 2.0 Consensus size: 177
435300 ATTAATCTTA
* * * *
435310 AAATGTAAATGAATTTATTTGATTAATAAATAAAAGAATTAATATTTTTATTGATCTTTTAAATT
1 AAATGTAAATGAATTTACTTGAATAACAAATAAAAGAATTAATATTTTTATTAATCTTTTAAATT
*
435375 TTTATAAATTTAATTTTATATTAACACAAAATAATAAATTTATAAATTTAAATTATTAACACACT
66 TTTATAAATTTAATTTTATATTAACACAAAATAATAAATTTATAAATTTAAATTATTAACAAACT
*
435440 TTACATGTTAATAATATATTTATTGATTTTAAAAAATAATAAATATT
131 TTACATGTTAATAATATATTTATTAATTTTAAAAAATAATAAATATT
* *
435487 AAATGTGAATGAATTTACTT-AATAACAAATAAAA-AAGTTAATA-TTTTATTAATCTTTT-TAT
1 AAATGTAAATGAATTTACTTGAATAACAAATAAAAGAA-TTAATATTTTTATTAATCTTTTAAAT
*
435548 TTTTATAAATTTAATTTTATATTAATACAAAATAATAAATTTATAAATTTAAA-TATTTAACAAA
65 TTTTATAAATTTAATTTTATATTAACACAAAATAATAAATTTATAAATTTAAATTA-TTAACAAA
435612 CTTTACATGTTAATAATATATTTATTAATTTTAAAAAATAATAAATATT
129 CTTTACATGTTAATAATATATTTATTAATTTTAAAAAATAATAAATATT
435661 TATCTATAAC
Statistics
Matches: 163, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
173 2 0.01
174 109 0.67
175 16 0.10
176 18 0.11
177 18 0.11
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (177 bp):
AAATGTAAATGAATTTACTTGAATAACAAATAAAAGAATTAATATTTTTATTAATCTTTTAAATT
TTTATAAATTTAATTTTATATTAACACAAAATAATAAATTTATAAATTTAAATTATTAACAAACT
TTACATGTTAATAATATATTTATTAATTTTAAAAAATAATAAATATT
Found at i:435917 original size:29 final size:27
Alignment explanation
Indices: 435880--435933 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
435870 AAATAAAATT
*
435880 AATACATTTAAAGAGAAATATATTTATCA
1 AATACATTT-AAGAGAAA-ATACTTATCA
*
435909 AATATATTTAAGAGAAAATACTTAT
1 AATACATTTAAGAGAAAATACTTAT
435934 AAACAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 8 0.35
29 8 0.35
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (27 bp):
AATACATTTAAGAGAAAATACTTATCA
Found at i:442737 original size:29 final size:27
Alignment explanation
Indices: 442693--442769 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
442683 AGGGTCTTTT
*
442693 AAATAATTTGTATATTTATATTTTATTT-
1 AAAT-ATTT-TATATTTATATTATATTTA
*
442721 ATATATTTTATTATATTATAATTATATTTA
1 AAATATTTTA-TAT-TTAT-ATTATATTTA
442751 AAATATTTTATATTTATAT
1 AAATATTTTATATTTATAT
442770 AAATTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
26 2 0.05
27 9 0.21
28 11 0.26
29 11 0.26
30 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
AAATATTTTATATTTATATTATATTTA
Found at i:442838 original size:11 final size:11
Alignment explanation
Indices: 442815--442871 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
442805 TTTTAAAATA
442815 TTTA-TATATTT
1 TTTATTATA-TT
442826 TTTATTATATT
1 TTTATTATATT
*
442837 TTAATTTATATT
1 TTTA-TTATATT
* *
442849 TTAATTATTTT
1 TTTATTATATT
442860 TTTATTATATT
1 TTTATTATATT
442871 T
1 T
442872 AATATGTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
11 25 0.62
12 15 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTATATT
Found at i:443004 original size:16 final size:16
Alignment explanation
Indices: 442963--443006 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
442953 ATTATTATTT
442963 AATAATT-ATTATTAA
1 AATAATTAATTATTAA
* **
442978 ATTAAAAAATTATTAA
1 AATAATTAATTATTAA
442994 AATAATTAATTAT
1 AATAATTAATTAT
443007 ATAATTAAGT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATTAATTATTAA
Found at i:443334 original size:28 final size:27
Alignment explanation
Indices: 443279--443364 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
443269 AGTTATTTTA
*
443279 AATTTTA-AT-ATAAATTATTTAAAAATT
1 AATTTTATATAATAAATTATTT--ATATT
443306 AATTTTATATAATAAATTAATTTATATT
1 AATTTTATATAATAAATT-ATTTATATT
* *
443334 AATTTTGATGTAAATAAA-TATTGATATT
1 AATTTT-ATAT-AATAAATTATTTATATT
443362 AAT
1 AAT
443365 ATGTAAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.14
28 23 0.45
29 11 0.22
30 10 0.20
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
AATTTTATATAATAAATTATTTATATT
Found at i:443336 original size:18 final size:18
Alignment explanation
Indices: 443293--443336 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
443283 TTAATATAAA
443293 TTAT-TTAA-AAATTAAT
1 TTATATTAATAAATTAAT
443309 TT-TATATAATAAATTAAT
1 TTATAT-TAATAAATTAAT
443327 TTATATTAAT
1 TTATATTAAT
443337 TTTGATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 3 0.12
18 14 0.58
19 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATATTAATAAATTAAT
Found at i:447521 original size:24 final size:26
Alignment explanation
Indices: 447487--447538 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
447477 AAACACGAAA
*
447487 ATAATATAATA-AGATATATTTAA-AT
1 ATAATATAATATA-AAATATTTAATAT
447512 ATAAT-TAATATAAAATATTTAATAT
1 ATAATATAATATAAAATATTTAATAT
447537 AT
1 AT
447539 TTATTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
ATAATATAATATAAAATATTTAATAT
Found at i:447546 original size:23 final size:24
Alignment explanation
Indices: 447502--447546 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
447492 ATAATAAGAT
447502 ATATTTAAATATAATTAATATAAA
1 ATATTTAAATATAATTAATATAAA
* *
447526 ATATTT-AATATATTTATTATA
1 ATATTTAAATATAATTAATATA
447547 TTCATGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTTAAATATAATTAATATAAA
Found at i:450630 original size:2 final size:2
Alignment explanation
Indices: 450623--450648 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
450613 AGTGAAGCTT
450623 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
450649 CGCATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:450657 original size:2 final size:2
Alignment explanation
Indices: 450652--450687 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
450642 GTGTGTGCGC
450652 AT 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 AT
450688 GTTAATAGGT
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):
AT
Found at i:451010 original size:38 final size:39
Alignment explanation
Indices: 450929--451012 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 39
450919 TTATTTCATT
* * *
450929 ATTTAAAATAAAAAATAATTTTTATATTATTAATAATTAA
1 ATTT-AAATAAAAAAAAATTTTTATATTATAAATAAGTAA
450969 ATTTAAATAAAAATAAAATTTTTAGTATT-TAAAT-AGT-A
1 ATTTAAATAAAAA-AAAATTTTTA-TATTATAAATAAGTAA
451007 ATTTAA
1 ATTTAA
451013 GTTGATCTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
38 7 0.18
39 11 0.28
40 17 0.44
41 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (39 bp):
ATTTAAATAAAAAAAAATTTTTATATTATAAATAAGTAA
Found at i:451392 original size:20 final size:21
Alignment explanation
Indices: 451355--451398 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
451345 ATAATTTATT
451355 TATTATATATATATTTTA-AA
1 TATTATATATATATTTTATAA
*
451375 TATTATCTATACTA-TTTATAA
1 TATTATATATA-TATTTTATAA
451396 TAT
1 TAT
451399 CTTTAACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATATATATATTTTATAA
Found at i:452133 original size:2 final size:2
Alignment explanation
Indices: 452126--452153 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
452116 AAATGGTAAC
452126 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
452154 CTCATTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453207 original size:2 final size:2
Alignment explanation
Indices: 453200--453232 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
453190 CTCAATCTTC
453200 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 A
453233 ACATGTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:457114 original size:22 final size:23
Alignment explanation
Indices: 457086--457141 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
457076 TGGACATGTT
457086 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
457108 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
457131 AAAAATGCATG
1 AAAAATGCATG
457142 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:458099 original size:20 final size:20
Alignment explanation
Indices: 458052--458126 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
458042 AAAAAGACAT
*
458052 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
458071 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
458092 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
458112 AATGTATTGATACAT
1 AATGTATCGATACAT
458127 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:458124 original size:40 final size:39
Alignment explanation
Indices: 458049--458126 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
458039 GGTAAAAAGA
* *
458049 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
458088 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
458127 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:459678 original size:3 final size:3
Alignment explanation
Indices: 459670--459700 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
459660 TAAAATTAAA
459670 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
459701 CTGTGATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:460269 original size:34 final size:34
Alignment explanation
Indices: 460195--460276 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
460185 AGTTTGTCAT
* *
460195 TGATTTGGTGGTTTGTCATTGTTGATTAAATAAA
1 TGATTTGGTAGTTTATCATTGTTGATTAAATAAA
** ***
460229 AAATTTGGTAGTTTATCATTGTTGATTAAATGGG
1 TGATTTGGTAGTTTATCATTGTTGATTAAATAAA
460263 TGATTTGGTAGTTT
1 TGATTTGGTAGTTT
460277 TTACCTAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (34 bp):
TGATTTGGTAGTTTATCATTGTTGATTAAATAAA
Found at i:460612 original size:19 final size:19
Alignment explanation
Indices: 460578--460631 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
460568 TGGTTGTCGA
*
460578 GGCACTATTTACGTATCTA-
1 GGCACTATTCACGTAT-TAG
* *
460597 GGTACTATTCATGTATTAG
1 GGCACTATTCACGTATTAG
460616 GGCACTATTCACGTAT
1 GGCACTATTCACGTAT
460632 ACGGTACTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 2 0.07
19 27 0.93
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (19 bp):
GGCACTATTCACGTATTAG
Found at i:465283 original size:6 final size:6
Alignment explanation
Indices: 465272--465312 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
465262 TAAATTAATG
465272 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATGA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAA
465313 ATTGCTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:466168 original size:3 final size:3
Alignment explanation
Indices: 466160--466199 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
466150 AAATCAAAAG
466160 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
466200 ATGAGACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:467373 original size:2 final size:2
Alignment explanation
Indices: 467360--467405 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
467350 CCATCTATTT
* *
467360 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
467402 TA TA
1 TA TA
467406 CACAAAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:474466 original size:8 final size:9
Alignment explanation
Indices: 474455--474500 Score: 51
Period size: 8 Copynumber: 5.0 Consensus size: 9
474445 GAAATATTAT
474455 ATATAAA-A
1 ATATAAATA
474463 ATATAATATA
1 ATATAA-ATA
474473 ATATTAACATA
1 ATA-TAA-ATA
474484 ATATAAAT-
1 ATATAAATA
474492 ATATAAATA
1 ATATAAATA
474501 TTTTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
8 14 0.42
9 3 0.09
10 7 0.21
11 9 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
ATATAAATA
Found at i:474497 original size:29 final size:28
Alignment explanation
Indices: 474455--474588 Score: 76
Period size: 29 Copynumber: 4.6 Consensus size: 28
474445 GAAATATTAT
* *
474455 ATATAAAAATATAATATAATATTAACATA
1 ATATAAATATATAA-ATAATATTAAAATA
* * *
474484 ATATAAATATATAAATATTTTTAAAATT
1 ATATAAATATATAAATAATATTAAAATA
* *
474512 ATATAATATATTTTATTAAT-ATATTAAAATTT
1 ATATAA-ATA---TATAAATAATATTAAAA-TA
*
474544 ATATAAATA-A-AATAAAATATATAAATATA
1 ATATAAATATATAA-ATAATAT-TAAA-ATA
* *
474573 ATAAAAATATAAAAAT
1 ATATAAATATATAAAT
474589 TATCGTCTCC
Statistics
Matches: 81, Mismatches: 13, Indels: 21
0.70 0.11 0.18
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 20 0.25
29 29 0.36
30 3 0.04
31 12 0.15
32 14 0.17
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAAATATATAAATAATATTAAAATA
Found at i:474544 original size:18 final size:18
Alignment explanation
Indices: 474512--474578 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
474502 TTTTAAAATT
* *
474512 ATATAATATATTTTATTA
1 ATATAATAAAATTTATTA
*
474530 ATATATTAAAATTTATATAA
1 ATATAATAAAATTTAT-T-A
* * *
474550 ATAAAATAAAATATATAA
1 ATATAATAAAATTTATTA
474568 ATATAATAAAA
1 ATATAATAAAA
474579 ATATAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 24 0.62
19 1 0.03
20 14 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATAAAATTTATTA
Found at i:474552 original size:20 final size:20
Alignment explanation
Indices: 474484--474578 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
474474 TATTAACATA
474484 ATATAAATAT-ATAAATATTT
1 ATATAAATATAATAAA-ATTT
*
474504 TTA-AAAT-TATATAATATATTT
1 ATATAAATATA-ATAA-A-ATTT
* *
474525 -TATTAATATATTAAAATTT
1 ATATAAATATAATAAAATTT
*
474544 ATATAAATAAAATAAAA--T
1 ATATAAATATAATAAAATTT
474562 ATATAAATATAATAAAA
1 ATATAAATATAATAAAA
474579 ATATAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
18 18 0.29
19 8 0.13
20 22 0.35
21 12 0.19
22 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAAATATAATAAAATTT
Found at i:480720 original size:15 final size:15
Alignment explanation
Indices: 480702--480737 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
480692 AAAATAATAT
480702 AAATATTAAAATTTA
1 AAATATTAAAATTTA
* *
480717 AAATATTATATTTTA
1 AAATATTAAAATTTA
480732 AAATAT
1 AAATAT
480738 AATTACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTAAAATTTA
Found at i:481036 original size:29 final size:30
Alignment explanation
Indices: 480973--481042 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
480963 ATTTATTTAA
* *
480973 AATATAATTAAAATACTTTAAATACGATCAT
1 AATATAA-TAAAATACTATAAATACAATCAT
*
481004 AATATAATAAAATA-TATAAATATAAT-AT
1 AATATAATAAAATACTATAAATACAATCAT
481032 GAATAT-ATAAA
1 -AATATAATAAA
481043 TTATCAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.20
29 14 0.40
30 7 0.20
31 7 0.20
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (30 bp):
AATATAATAAAATACTATAAATACAATCAT
Found at i:481038 original size:19 final size:18
Alignment explanation
Indices: 481004--481043 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
480994 ATACGATCAT
481004 AATATAATAAAATATATA
1 AATATAATAAAATATATA
*
481022 AATATAATATGAATATATA
1 AATATAATA-AAATATATA
481041 AAT
1 AAT
481044 TATCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:481803 original size:20 final size:20
Alignment explanation
Indices: 481755--481808 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
481745 ATAAAATTAA
481755 ATTGAATTTAAAATAAGATAT
1 ATTGAATTT-AAATAAGATAT
* *
481776 ATTTAATTTAAAT-AGATTT
1 ATTGAATTTAAATAAGATAT
481795 GATTGAATTTAAAT
1 -ATTGAATTTAAAT
481809 TTTTATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 16 0.55
21 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.44
Consensus pattern (20 bp):
ATTGAATTTAAATAAGATAT
Found at i:482803 original size:24 final size:24
Alignment explanation
Indices: 482776--482822 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
482766 TAATATTGAT
482776 AAATAAAATTATATTAT-TTTATTA
1 AAATAAAATTAT-TTATATTTATTA
482800 AAATAAAATTATTTATATTTATT
1 AAATAAAATTATTTATATTTATT
482823 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATAAAATTATTTATATTTATTA
Found at i:484034 original size:17 final size:16
Alignment explanation
Indices: 483989--484035 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
483979 TATATTTTAT
483989 TAAA-AAATTTAAAAA
1 TAAATAAATTTAAAAA
* *
484004 TAAATATATCTAAAGAA
1 TAAATAAATTTAAA-AA
*
484021 TCAATAAATTTAAAA
1 TAAATAAATTTAAAA
484036 TGATATGTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 13 0.52
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAATAAATTTAAAAA
Found at i:484070 original size:2 final size:2
Alignment explanation
Indices: 484063--484109 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
484053 TCTATACACT
484063 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
484105 TA TA T
1 TA TA T
484110 TAACATCGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:485073 original size:2 final size:2
Alignment explanation
Indices: 485066--485104 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
485056 TCTGAATTGG
485066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
485105 AAAAAACCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:487527 original size:13 final size:13
Alignment explanation
Indices: 487511--487548 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
487501 AAAATCATAT
487511 ATATATATATTAG
1 ATATATATATTAG
487524 ATAT-TAATATTAG
1 ATATAT-ATATTAG
*
487537 ATATAAATATTA
1 ATATATATATTA
487549 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
ATATATATATTAG
Found at i:488263 original size:3 final size:3
Alignment explanation
Indices: 488255--488280 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
488245 ACATTTATTT
488255 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
488281 TGAAATAAAT
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):
TAA
Found at i:488591 original size:27 final size:28
Alignment explanation
Indices: 488561--488648 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 28
488551 TTAAATTTAA
488561 TAAAAATAATAATATTTTAAAAAAA-AT
1 TAAAAATAATAATATTTTAAAAAAATAT
488588 TAAAAAT-ATCAATAATTATCTAAAAAAATTAT
1 TAAAAATAAT-AAT-ATT-T-TAAAAAAA-TAT
* *
488620 TCAAAATAA-ATATATTTTAATATAAATAT
1 TAAAAATAATA-ATATTTTAA-AAAAATAT
488649 ATTTATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
26 2 0.04
27 10 0.20
28 3 0.06
29 7 0.14
30 13 0.26
31 4 0.08
32 10 0.20
33 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAAATAATAATATTTTAAAAAAATAT
Found at i:488595 original size:21 final size:20
Alignment explanation
Indices: 488556--488596 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
488546 TATTTTTAAA
* *
488556 TTTAATAAAAATAATAATAT
1 TTTAAAAAAAATAAAAATAT
488576 TTTAAAAAAAATTAAAAATAT
1 TTTAAAAAAAA-TAAAAATAT
488597 CAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAAAAAAATAAAAATAT
Found at i:488989 original size:16 final size:16
Alignment explanation
Indices: 488949--488989 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
488939 ATACAGACTC
* *
488949 AAAATAATCTAAATTT
1 AAAATAATTTAAACTT
488965 AAAATAATTTAAACTT
1 AAAATAATTTAAACTT
*
488981 AAATTAATT
1 AAAATAATT
488990 CAAATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATAATTTAAACTT
Found at i:489053 original size:14 final size:13
Alignment explanation
Indices: 489022--489073 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
489012 TCAAACTTAA
489022 AATTATTAAATTT
1 AATTATTAAATTT
489035 -A-TA--AAATTT
1 AATTATTAAATTT
489044 AATTATTAAATTT
1 AATTATTAAATTT
489057 AATTAACTTAAATTT
1 AATT-A-TTAAATTT
489072 AA
1 AA
489074 AATAACTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.18
10 1 0.03
11 4 0.12
12 1 0.03
13 10 0.30
14 1 0.03
15 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTATTAAATTT
Found at i:489081 original size:16 final size:16
Alignment explanation
Indices: 489049--489126 Score: 86
Period size: 16 Copynumber: 4.8 Consensus size: 16
489039 AATTTAATTA
*
489049 TTAAATTT-AATTAAC
1 TTAAATTTAAAATAAC
489064 TTAAATTTAAAATAAC
1 TTAAATTTAAAATAAC
* *
489080 TTAAATCTAAAATAAT
1 TTAAATTTAAAATAAC
*
489096 TTAAATTTAAAAATAATT
1 TTAAATTT-AAAATAA-C
489114 TTAAATTTTAAAA
1 TTAAA-TTTAAAA
489127 ATTTAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
15 8 0.15
16 27 0.49
17 7 0.13
18 10 0.18
19 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATAAC
Found at i:489149 original size:26 final size:28
Alignment explanation
Indices: 489090--489150 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
489080 TTAAATCTAA
489090 AATAATTT--AAATTTAAAAATAATTTT
1 AATAATTTAAAAATTTAAAAATAATTTT
*
489116 AA-ATTTTAAAAATTT-AAAATAA-TTT
1 AATAATTTAAAAATTTAAAAATAATTTT
489141 AATAATTTAA
1 AATAATTTAA
489151 CTTAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 9 0.30
26 15 0.50
27 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAATTTAAAAATTTAAAAATAATTTT
Found at i:489758 original size:19 final size:19
Alignment explanation
Indices: 489723--489762 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
489713 ATATATTAAA
489723 AATCAAACATTTAATTAATG
1 AATCAAACATTTAATT-ATG
*
489743 AATCAAAC-TTTGATTATG
1 AATCAAACATTTAATTATG
489761 AA
1 AA
489763 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (19 bp):
AATCAAACATTTAATTATG
Found at i:489846 original size:18 final size:19
Alignment explanation
Indices: 489823--489859 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
489813 AGTAATTTTA
489823 ATTTTAAAAATTT-TTCAT
1 ATTTTAAAAATTTATTCAT
*
489841 ATTTTAAAATTTTATTCAT
1 ATTTTAAAAATTTATTCAT
489860 CCAAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAAAAATTTATTCAT
Found at i:490230 original size:3 final size:3
Alignment explanation
Indices: 490222--490246 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
490212 CTAAATTTTA
490222 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
490247 TGTAGCCTTA
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:497261 original size:27 final size:29
Alignment explanation
Indices: 497221--497284 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 29
497211 ATCGATTTTA
**
497221 AATATTTTCATAA-TCTTTTAT-ATAATT
1 AATATTTTCATAATTCGATTATCATAATT
** *
497248 AATATTTTTTTAATTCGATTATCATATTT
1 AATATTTTCATAATTCGATTATCATAATT
497277 AATATTTT
1 AATATTTT
497285 ATTGATATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 11 0.37
28 6 0.20
29 13 0.43
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (29 bp):
AATATTTTCATAATTCGATTATCATAATT
Found at i:497420 original size:19 final size:18
Alignment explanation
Indices: 497396--497433 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
497386 ATATTTTTTA
497396 TTAATATAATCATATATAT
1 TTAATATAATCATAT-TAT
*
497415 TTAATATAATTATATTAT
1 TTAATATAATCATATTAT
497433 T
1 T
497434 AAATTTAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATATAATCATATTAT
Found at i:497945 original size:21 final size:22
Alignment explanation
Indices: 497921--497971 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
497911 ATCCAAATCG
* * *
497921 TAAATTCATTATATTAATT-TT
1 TAAATTAATTATATAAATTAAT
*
497942 TAAAATAATTATATAAATTAAT
1 TAAATTAATTATATAAATTAAT
497964 TAAATTAA
1 TAAATTAA
497972 ATAAATTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATTAATTATATAAATTAAT
Found at i:498861 original size:2 final size:2
Alignment explanation
Indices: 498854--498884 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
498844 GAGCTCGTTT
498854 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
498885 TATGAAATGA
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:499024 original size:24 final size:24
Alignment explanation
Indices: 498961--499024 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
498951 TTGATCATGG
* *
498961 ATGAAATATTACAATTATTCATTA
1 ATGAAATATTACATTTAATCATTA
* *
498985 A--AATATAATAATATTTAATCATTA
1 ATGAA-AT-ATTACATTTAATCATTA
499009 ATGAAATATTACATTT
1 ATGAAATATTACATTT
499025 TTCATCGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 22 0.73
25 2 0.07
26 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (24 bp):
ATGAAATATTACATTTAATCATTA
Found at i:501045 original size:12 final size:12
Alignment explanation
Indices: 501028--501052 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
501018 ATTCTCTTTC
501028 TCCTTTTATTTT
1 TCCTTTTATTTT
501040 TCCTTTTATTTT
1 TCCTTTTATTTT
501052 T
1 T
501053 TAGTGTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCCTTTTATTTT
Found at i:501323 original size:3 final size:3
Alignment explanation
Indices: 501315--501343 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
501305 TATGTTAATT
501315 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
501344 TTGTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:501574 original size:30 final size:28
Alignment explanation
Indices: 501498--501576 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 28
501488 ATATCTTATA
*
501498 TTTTTATTATACTT-AATAAGTCATTAAC
1 TTTTAATT-TACTTAAATAAGTCATTAAC
** *
501526 TTTTAATTTACATCTAAATAAGTTTTTAAT
1 TTTTAATTTAC-T-TAAATAAGTCATTAAC
501556 TTTTAATTTGTACTTAAATAA
1 TTTTAA-TT-TACTTAAATAA
501577 ACTGTTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.07
28 8 0.19
29 1 0.02
30 24 0.57
31 3 0.07
32 3 0.07
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (28 bp):
TTTTAATTTACTTAAATAAGTCATTAAC
Found at i:501844 original size:15 final size:15
Alignment explanation
Indices: 501824--501852 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
501814 TAAACCCCTT
501824 TATTATTTTTTAATG
1 TATTATTTTTTAATG
501839 TATTATTTTTTAAT
1 TATTATTTTTTAAT
501853 ATATGGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTTTTTAATG
Found at i:503173 original size:11 final size:11
Alignment explanation
Indices: 503145--503178 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
503135 TAAATATAAT
503145 ATAAAAA-TTA
1 ATAAAAATTTA
503155 ATAAAAATTTA
1 ATAAAAATTTA
*
503166 ATAAAAATATA
1 ATAAAAATTTA
503177 AT
1 AT
503179 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAAAATTTA
Found at i:503174 original size:34 final size:33
Alignment explanation
Indices: 503136--503217 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 33
503126 TCGTAATTTT
*
503136 AAATATAATATAAAAATTAATAAAAATTTAATAA
1 AAATATAATATAAAAATTAATAAAAATATAA-AA
* * *
503170 AAATATAATTTAAAAAATAATATAAATATAAAA
1 AAATATAATATAAAAATTAATAAAAATATAAAA
*
503203 TAA-AT-ATATAAAAAT
1 AAATATAATATAAAAAT
503218 AAATTATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 8 0.20
32 2 0.05
33 4 0.10
34 27 0.66
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (33 bp):
AAATATAATATAAAAATTAATAAAAATATAAAA
Found at i:503181 original size:16 final size:17
Alignment explanation
Indices: 503137--503194 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
503127 CGTAATTTTA
* *
503137 AATATAATATAAAAATT
1 AATATAATTTAAAAAAT
* *
503154 AATAAAAATTTAATAAA-
1 AAT-ATAATTTAAAAAAT
503171 AATATAATTTAAAAAAT
1 AATATAATTTAAAAAAT
503188 AATATAA
1 AATATAA
503195 ATATAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.33
17 13 0.39
18 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATAATTTAAAAAAT
Found at i:503184 original size:23 final size:22
Alignment explanation
Indices: 503145--503218 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
503135 TAAATATAAT
**
503145 ATAAAAAT-TAATAAAAATTTA
1 ATAAAAATATAATAAAAAAATA
*
503166 ATAAAAATATAATTTAAAAAATA
1 ATAAAAATATAA-TAAAAAAATA
* *
503189 ATATAAATAT-A-AAATAAATA
1 ATAAAAATATAATAAAAAAATA
503209 TATAAAAATA
1 -ATAAAAATA
503219 AATTATTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 7 0.16
21 16 0.37
22 4 0.09
23 16 0.37
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAAATATAATAAAAAAATA
Found at i:503576 original size:16 final size:16
Alignment explanation
Indices: 503528--503588 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
503518 TTCAATTTTT
503528 AATATA-AAT-ATATA
1 AATATATAATAATATA
* *
503542 TAATATATAATATTTTA
1 -AATATATAATAATATA
*
503559 AATATATTATAATATA
1 AATATATAATAATATA
*
503575 AAAATATAAATAAT
1 AATATAT-AATAAT
503589 TTTACTTAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 6 0.17
16 22 0.61
17 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATAATAATATA
Found at i:503619 original size:2 final size:2
Alignment explanation
Indices: 503612--503637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
503602 GATGTAGTGT
503612 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
503638 GCTAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:503952 original size:16 final size:16
Alignment explanation
Indices: 503911--503952 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
503901 ATGTTTGAAT
503911 TTAAAT-TTAAATGTA
1 TTAAATCTTAAATGTA
* *
503926 TTAAATTTTAAATTTA
1 TTAAATCTTAAATGTA
*
503942 TTAGATCTTAA
1 TTAAATCTTAA
503953 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAAATCTTAAATGTA
Found at i:504264 original size:19 final size:19
Alignment explanation
Indices: 504240--504276 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
504230 TATCGAGTTA
*
504240 AAAAAATTATTATACTAAT
1 AAAAAATAATTATACTAAT
*
504259 AAAAAATAATTCTACTAA
1 AAAAAATAATTATACTAA
504277 CAAGTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATAATTATACTAAT
Found at i:505381 original size:20 final size:22
Alignment explanation
Indices: 505353--505393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
505343 TTTTAAAATT
*
505353 TTTTAAATATTTAA-AAAATAA
1 TTTTAAATATTGAATAAAATAA
505374 TTTT-AATATTGAATAAAATA
1 TTTTAAATATTGAATAAAATA
505394 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTTAAATATTGAATAAAATAA
Found at i:506623 original size:16 final size:16
Alignment explanation
Indices: 506602--506632 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
506592 GATCATGATG
506602 ATAATAATAATTAATA
1 ATAATAATAATTAATA
506618 ATAATAATAATTAAT
1 ATAATAATAATTAAT
506633 TTCATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATAATAATTAATA
Found at i:507468 original size:14 final size:14
Alignment explanation
Indices: 507440--507477 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
507430 GTTGAGAAAA
507440 TTATG-TAAATAAT
1 TTATGTTAAATAAT
*
507453 TTATGTTAAATGAT
1 TTATGTTAAATAAT
507467 TTAT-TTAAATA
1 TTATGTTAAATA
507478 TATATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
TTATGTTAAATAAT
Found at i:509797 original size:12 final size:12
Alignment explanation
Indices: 509776--509829 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
509766 TTTTAAATTT
*
509776 TTTATTATAATA
1 TTTATAATAATA
509788 TTTATAATAATA
1 TTTATAATAATA
*
509800 TTTATTATAATTA
1 TTTATAATAA-TA
* *
509813 ATTAAAATAATA
1 TTTATAATAATA
509825 TTTAT
1 TTTAT
509830 TATATTCAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 25 0.74
13 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTATAATAATA
Found at i:509827 original size:25 final size:24
Alignment explanation
Indices: 509776--509833 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 24
509766 TTTTAAATTT
* *
509776 TTTATTATAATATTTATAATAATA
1 TTTATTATAATAATTAAAATAATA
509800 TTTATTATAATTAATTAAAATAATA
1 TTTATTATAA-TAATTAAAATAATA
509825 TTTATTATA
1 TTTATTATA
509834 TTCAACCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTATTATAATAATTAAAATAATA
Found at i:520114 original size:18 final size:17
Alignment explanation
Indices: 520091--520138 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
520081 AATATAGTTT
*
520091 TTTATTATAAAATTTATG
1 TTTATTATAAAA-TTATA
*
520109 TTTATTAATATAATTATA
1 TTTATT-ATAAAATTATA
*
520127 TATATTATAAAA
1 TTTATTATAAAA
520139 ATAATCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTATTATAAAATTATA
Found at i:520245 original size:22 final size:21
Alignment explanation
Indices: 520213--520275 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 21
520203 CATGTATTTT
520213 TAAAATAATATTAATAAAAATAA
1 TAAAA-AATATTAATAAAAAT-A
*
520236 TAATAAATATT--TAAAAAT-
1 TAAAAAATATTAATAAAAATA
*
520254 TAAAAAATATATAATATAAATA
1 TAAAAAATAT-TAATAAAAATA
520276 GATCTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 9 0.27
19 1 0.03
20 7 0.21
21 6 0.18
22 6 0.18
23 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATATTAATAAAAATA
Found at i:520284 original size:41 final size:43
Alignment explanation
Indices: 520212--520293 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 43
520202 TCATGTATTT
520212 TTAAAATAATATTAATAAAAATAATAATAAA-TA-TTTAAAAA
1 TTAAAATAATATTAATAAAAATAATAATAAATTAGTTTAAAAA
* *
520253 TTAAAA-AATATATAATATAAATAGAT-CTAAATTAGTTTAAA
1 TTAAAATAATAT-TAATAAAAATA-ATAATAAATTAGTTTAAA
520294 CTATCAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 5 0.14
41 20 0.57
42 4 0.11
43 6 0.17
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (43 bp):
TTAAAATAATATTAATAAAAATAATAATAAATTAGTTTAAAAA
Found at i:520504 original size:18 final size:16
Alignment explanation
Indices: 520469--520511 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
520459 AGATAAAATG
520469 AAAAAAAAAAGAGAGA
1 AAAAAAAAAAGAGAGA
*
520485 AAAAAAAGAAATGAGTGA
1 AAAAAAA-AAA-GAGAGA
520503 AAGAAAAAA
1 AA-AAAAAA
520512 TTGTGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 3 0.13
18 8 0.35
19 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (16 bp):
AAAAAAAAAAGAGAGA
Found at i:528412 original size:18 final size:18
Alignment explanation
Indices: 528375--528413 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
528365 TAAATATAAA
* *
528375 TTTTAATATTATAATTTT
1 TTTTAAAATTATAATATT
*
528393 TTTTAAAATTATGATATT
1 TTTTAAAATTATAATATT
528411 TTT
1 TTT
528414 GGTAAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTAAAATTATAATATT
Found at i:530954 original size:17 final size:16
Alignment explanation
Indices: 530918--530956 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
530908 TAATTATATT
530918 TATAAAAATTTTGATA
1 TATAAAAATTTTGATA
* *
530934 TATAATAATTTATGTTA
1 TATAAAAATTT-TGATA
530951 TATAAA
1 TATAAA
530957 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
TATAAAAATTTTGATA
Found at i:531505 original size:22 final size:21
Alignment explanation
Indices: 531453--531507 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
531443 TATAATAAAA
*
531453 ATATTTTAAAAATTTAATTAT
1 ATATTTTATAAATTTAATTAT
* * *
531474 TTATGATTATAACTTTAATTAT
1 ATAT-TTTATAAATTTAATTAT
531496 CATATTTTATAA
1 -ATATTTTATAA
531508 TAAATTATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 3 0.12
22 20 0.77
23 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATTTTATAAATTTAATTAT
Found at i:531860 original size:21 final size:21
Alignment explanation
Indices: 531843--531881 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
531833 AATTTATGTA
531843 CTTATA-TAT-TTATATTATT
1 CTTATATTATATTATATTATT
*
531862 TTTATATTATATTATATTAT
1 CTTATATTATATTATATTAT
531882 CTTTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
CTTATATTATATTATATTATT
Found at i:533554 original size:34 final size:33
Alignment explanation
Indices: 533492--533559 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 33
533482 ATTAATATTT
533492 TTAAAAATATATTTAATATATTATTTTTATTAAA
1 TTAAAAATATATTTAATATATTATTTTTA-TAAA
533526 TTAAAAATATATATTAAT-TA-TATTTTTTATAAA
1 TTAAAAATATAT-TTAATATATTA-TTTTTATAAA
533559 T
1 T
533560 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 7 0.22
34 20 0.62
35 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTAAAAATATATTTAATATATTATTTTTATAAA
Found at i:538119 original size:21 final size:20
Alignment explanation
Indices: 538077--538120 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
538067 AGAATCAGTA
*
538077 ATTCGTGTATTTGATATTTT
1 ATTCGTGTATTTGATATATT
**
538097 ATTCGTGTTATTTTTTATATT
1 ATTCGTG-TATTTGATATATT
538118 ATT
1 ATT
538121 ATCGTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.20, C:0.05, G:0.11, T:0.64
Consensus pattern (20 bp):
ATTCGTGTATTTGATATATT
Found at i:538226 original size:18 final size:18
Alignment explanation
Indices: 538205--538273 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 18
538195 TTTACAGTAT
538205 TTATATTATTTTTTTATA
1 TTATATTATTTTTTTATA
538223 TTATATTATATTTAATATTAATA
1 TTATATTAT-TTT--T-TT-ATA
*
538246 TTTTAATTA-TTTTTTATA
1 TTAT-ATTATTTTTTTATA
538264 TTCATATTAT
1 TT-ATATTAT
538274 ATAATTGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
18 18 0.44
19 6 0.15
20 1 0.02
21 1 0.02
22 5 0.12
23 6 0.15
24 4 0.10
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATTATTTTTTTATA
Found at i:543555 original size:218 final size:221
Alignment explanation
Indices: 543169--543614 Score: 790
Period size: 218 Copynumber: 2.0 Consensus size: 221
543159 CTACTTTTTT
*
543169 TATGCTACATTCTTAAAGAGTATATGCCAGTTGTTTTTCTATGATTTTTCTTTCGTCCAATTGTT
1 TATGCTACATTCTTAAAGAGTATATGCCAGTTGTTTTTCTATGATTTTTCTCTCGTCCAATTGTT
*
543234 TTTCTCAGGGGGTCAGGGGGTATTTGAGGCATGGAATGTGCCAATTGCATTTATTAGTGTTATCT
66 TTTCT-----GGTCAGGGGGTATTTCAGGCATGGAATGTGCCAATTGCATTTATTAGTGTTATCT
*
543299 TGCTCTCCATTATCGGGAATGCTACAGAGCATGCTACTGCTATTATGTTTGCCATGAAAGACAAG
126 CGCTCTCCATTATCGGGAATGCTACAGAGCATGCTACTGCTATTATGTTTGCCATGAAAGACAAG
543364 CTCATAAGTGATTCTCTTAACTTTCATTTCA
191 CTCATAAGTGATTCTCTTAACTTTCATTTCA
*
543395 TATGCTACATTCTTAAAGAGTATATGCCAGTTGTTTTTCTATGATTTTTCTCTCGTCCGATTG-T
1 TATGCTACATTCTTAAAGAGTATATGCCAGTTGTTTTTCTATGATTTTTCTCTCGTCCAATTGTT
543459 TTT-T-GTCAGGGGGTATTTCAGGCATGGAATGTGCCAATTGCATTTATTAGTGTTATCTCGCTC
66 TTTCTGGTCAGGGGGTATTTCAGGCATGGAATGTGCCAATTGCATTTATTAGTGTTATCTCGCTC
543522 TCCATTATCGGGAATGCTACAGAGCATGCTACTGCTATTATGTTTGCCATGAAAGACAAGCTCAT
131 TCCATTATCGGGAATGCTACAGAGCATGCTACTGCTATTATGTTTGCCATGAAAGACAAGCTCAT
543587 AAGTGATTCTCTTAACTTTCATTTCA
196 AAGTGATTCTCTTAACTTTCATTTCA
543613 TA
1 TA
543615 ATTTTTTTAT
Statistics
Matches: 216, Mismatches: 4, Indels: 8
0.95 0.02 0.04
Matches are distributed among these distances:
218 150 0.69
224 1 0.00
225 4 0.02
226 61 0.28
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (221 bp):
TATGCTACATTCTTAAAGAGTATATGCCAGTTGTTTTTCTATGATTTTTCTCTCGTCCAATTGTT
TTTCTGGTCAGGGGGTATTTCAGGCATGGAATGTGCCAATTGCATTTATTAGTGTTATCTCGCTC
TCCATTATCGGGAATGCTACAGAGCATGCTACTGCTATTATGTTTGCCATGAAAGACAAGCTCAT
AAGTGATTCTCTTAACTTTCATTTCA
Found at i:545592 original size:21 final size:20
Alignment explanation
Indices: 545568--545609 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
545558 ATTTTATTTG
* *
545568 ATAATTAATTTTTTATTTCAA
1 ATAAATAATTATTTA-TTCAA
545589 ATAAATAATTATTTATTCAA
1 ATAAATAATTATTTATTCAA
545609 A
1 A
545610 GTTTGATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATAATTATTTATTCAA
Found at i:546085 original size:3 final size:3
Alignment explanation
Indices: 546077--546102 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
546067 CCTAAAAATA
546077 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
546103 AAGATGATGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:546772 original size:2 final size:2
Alignment explanation
Indices: 546760--546797 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
546750 AAGAGATGAT
*
546760 TA TA AA 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
546798 GGATTTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:547067 original size:22 final size:23
Alignment explanation
Indices: 547040--547083 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
547030 ATAAAAATTT
*
547040 TAAATTTA-AATATTATATAAGA
1 TAAATTTATAATAATATATAAGA
547062 TAAATTTATTAATAATATATAA
1 TAAATTTA-TAATAATATATAA
547084 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTTATAATAATATATAAGA
Found at i:547107 original size:19 final size:20
Alignment explanation
Indices: 547056--547107 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
547046 TAAATATTAT
* *
547056 ATAAGATAAATTTATTAATA
1 ATAAAATAAATTTTTTAATA
*
547076 AT-ATATAAATTTTTTAA-A
1 ATAAAATAAATTTTTTAATA
547094 ATAAAATAAATTTT
1 ATAAAATAAATTTT
547108 AATTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 3 0.11
19 23 0.82
20 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAAATAAATTTTTTAATA
Found at i:547124 original size:22 final size:22
Alignment explanation
Indices: 547034--547124 Score: 53
Period size: 22 Copynumber: 4.1 Consensus size: 22
547024 TTTAATATAA
*
547034 AAATTTTAAATTTAAATATTAT
1 AAATTTTAATTTTAAATATTAT
** * *
547056 ATAAGATAAATTTATTAATAATATAT
1 A-AATTTTAATTT-TAAAT-AT-TAT
* **
547082 AAA-TTT--TTTAAAATAAAAT
1 AAATTTTAATTTTAAATATTAT
547101 AAATTTTAATTTTAAATATTAT
1 AAATTTTAATTTTAAATATTAT
547123 AA
1 AA
547125 TTCATGTTAT
Statistics
Matches: 48, Mismatches: 14, Indels: 14
0.63 0.18 0.18
Matches are distributed among these distances:
19 5 0.10
20 4 0.08
21 3 0.06
22 16 0.33
23 7 0.15
24 5 0.10
25 4 0.08
26 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (22 bp):
AAATTTTAATTTTAAATATTAT
Found at i:548713 original size:9 final size:11
Alignment explanation
Indices: 548647--548717 Score: 74
Period size: 11 Copynumber: 6.3 Consensus size: 11
548637 AAATGATTAT
*
548647 ATAATATAAAT
1 ATAATATAAAA
548658 ATAATATTATAAA
1 ATAATA-TA-AAA
*
548671 AT-ATGATACGAA
1 ATAAT-ATA-AAA
548683 ATAATATAAAA
1 ATAATATAAAA
548694 ATAATATAAAA
1 ATAATATAAAA
548705 ATAATA-AAAA
1 ATAATATAAAA
548715 ATA
1 ATA
548718 CGATTATGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.13
11 25 0.48
12 13 0.25
13 7 0.13
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Done.