Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold101
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: 827217
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.34
Warning! 25308 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:585177 original size:2 final size:2
Alignment explanation
Indices: 585170--585195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
585160 ACCTGTTCAC
585170 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
585196 GCATTTGGGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:587664 original size:23 final size:24
Alignment explanation
Indices: 587638--587687 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
587628 TGGTATAAAT
587638 AATTTAACTTTT-TA-TATATTTAA
1 AATTTAA-TTTTATATTATATTTAA
*
587661 AATTTTATTTTATATTTATATTTAA
1 AATTTAATTTTATA-TTATATTTAA
587686 AA
1 AA
587688 ATATTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
25 11 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTAATTTTATATTATATTTAA
Found at i:587949 original size:16 final size:17
Alignment explanation
Indices: 587923--587960 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
587913 CATTAATTAC
587923 AATAAATATTAATAAAA-
1 AATAAATATT-ATAAAAT
587940 AATAAA-ATTATAAAAT
1 AATAAATATTATAAAAT
587956 AATAA
1 AATAA
587961 TCATAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
17 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAATATTATAAAAT
Found at i:588265 original size:9 final size:9
Alignment explanation
Indices: 588253--588301 Score: 62
Period size: 10 Copynumber: 5.1 Consensus size: 9
588243 GATGAAAAGG
588253 AAGAAAAAA
1 AAGAAAAAA
588262 AAGATAAAAA
1 AAGA-AAAAA
*
588272 AGGAAAAAA
1 AAGAAAAAA
588281 AAGAAAGAAA
1 AAGAAA-AAA
588291 AAGATAAAAA
1 AAGA-AAAAA
588301 A
1 A
588302 TTAACATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 14 0.40
10 19 0.54
11 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:588291 original size:19 final size:19
Alignment explanation
Indices: 588253--588301 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
588243 GATGAAAAGG
588253 AAGAAAAAAAAGATAAAAA
1 AAGAAAAAAAAGATAAAAA
*
588272 AGGAAAAAAAAGA-AAGAAA
1 AAGAAAAAAAAGATAA-AAA
588291 AAGATAAAAAA
1 AAGA-AAAAAA
588302 TTAACATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.69
20 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (19 bp):
AAGAAAAAAAAGATAAAAA
Found at i:588301 original size:10 final size:9
Alignment explanation
Indices: 588253--588301 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
588243 GATGAAAAGG
588253 AAGAAAAAA
1 AAGAAAAAA
588262 AAGATAAAAA
1 AAGA-AAAAA
*
588272 AGGAAAAAA
1 AAGAAAAAA
588281 AAGAAAGAAA
1 AAGAAA-AAA
*
588291 AAGATAAAA
1 AAGAAAAAA
588300 AA
1 AA
588302 TTAACATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 19 0.54
10 16 0.46
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:588420 original size:23 final size:24
Alignment explanation
Indices: 588382--588434 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
588372 TTTTTTAATG
* *
588382 TTTTTATATTCATGTTATATTTAT
1 TTTTTATATTCATGTTATAATTAA
* *
588406 TTTTTATATT-TTGTTTTAATTAA
1 TTTTTATATTCATGTTATAATTAA
588429 TTTTTA
1 TTTTTA
588435 ATGTGTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTATATTCATGTTATAATTAA
Found at i:588431 original size:24 final size:24
Alignment explanation
Indices: 588376--588433 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
588366 ATAAAATTTT
588376 TTAATGTTTTTATATTCATGTTATA
1 TTAAT-TTTTTATATTCATGTTATA
* * *
588401 TTTATTTTTTATATT-TTGTTTTAA
1 TTAATTTTTTATATTCATGTTAT-A
588425 TTAATTTTT
1 TTAATTTTT
588434 AATGTGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 5 0.18
24 19 0.68
25 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (24 bp):
TTAATTTTTTATATTCATGTTATA
Found at i:589363 original size:26 final size:28
Alignment explanation
Indices: 589330--589392 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
589320 TAAATAAATA
* *
589330 ATAATTATTTA-TTAATT-TATATTTAT
1 ATAATTATTAATTTAATTAAATATTTAT
589356 ATAATTATTAATTTAATTAAATATTTAT
1 ATAATTATTAATTTAATTAAATATTTAT
589384 A-AA-TATTAA
1 ATAATTATTAA
589393 AAATATCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 16 0.48
27 8 0.24
28 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATTATTAATTTAATTAAATATTTAT
Found at i:589379 original size:22 final size:22
Alignment explanation
Indices: 589338--589383 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
589328 TAATAATTAT
*
589338 TTATTAATTTATATTTATATAA
1 TTATTAATTTATATTAATATAA
*
589360 TTATTAATTTA-ATTAA-ATAT
1 TTATTAATTTATATTAATATAA
589380 TTAT
1 TTAT
589384 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTAATTTATATTAATATAA
Found at i:590119 original size:2 final size:2
Alignment explanation
Indices: 590101--590141 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
590091 ACGAATGATA
* *
590101 AT AT AT CT AT AT CT AT AT A- AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
590141 A
1 A
590142 ATTTTTTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:590128 original size:17 final size:18
Alignment explanation
Indices: 590098--590141 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
590088 ACGACGAATG
*
590098 ATAATATATCTATATCTAT
1 ATAATATA-CTATATATAT
590117 ATAATATA-TATATATAT
1 ATAATATACTATATATAT
590134 ATAATATA
1 ATAATATA
590142 ATTTTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.67
19 8 0.33
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATATACTATATATAT
Found at i:590496 original size:274 final size:278
Alignment explanation
Indices: 590118--590681 Score: 994
Period size: 274 Copynumber: 2.0 Consensus size: 278
590108 TATATCTATA
* *
590118 TAATAT-ATATATATATATAATATAATTTTTTTACATAAATGTTAATATTTATTATGAGTTTTTT
1 TAATATAATATATATATATAATATAAGTTTTTTACATAAATGTTAATATTTATTATGAATTTTTT
*
590182 CAAAAAGAATTTATATATTATAATAATTTATTAAATTCAATATATAATATTAATTTAACTAATTA
66 CAAAAAGAATTCATATATTATAATAATTTATTAAATTCAATATATAATATTAATTTAACTAATTA
* * *
590247 ATTTTATCTCATTTATTTTCATTCATTGTATATAATATAATATATTAATTTTATCTTAGTTTCAT
131 ATTTTATCTCATTCATTTTCATTCATTATATATAATATAATATATTAATTTTATCTTAGCTTCAT
590312 TAATTGAATTTAATATAATATATTAATTTCATTAAATATTTTTTAAATTACATTTTAATTC-TTT
196 TAATTGAATTTAATATAATATATTAATTTCATTAAATATTTTTTAAATTACATTTTAATTCTTTT
590376 TAATAGAATCATTGAATT
261 TAATAGAATCATTGAATT
*
590394 TAATATAATATATATATATAATAT-AGTTTTTTATATAAATGTTAATATTTATTATGAATTTTTT
1 TAATATAATATATATATATAATATAAGTTTTTTACATAAATGTTAATATTTATTATGAATTTTTT
* * *
590458 TAAAAA-AA-TCATATATTATAATAATTTATTAAATTCAATGTATAATATTAATTTGACTAATTA
66 CAAAAAGAATTCATATATTATAATAATTTATTAAATTCAATATATAATATTAATTTAACTAATTA
590521 ATTTTATCTCATTCATTTTCATTCATTATATATAATATAATATATTAATTTTATCTTAGCTTCAT
131 ATTTTATCTCATTCATTTTCATTCATTATATATAATATAATATATTAATTTTATCTTAGCTTCAT
*
590586 TCATTGAATTTAATATAATATATTAATTTCATTAAATATTTTTTAAATTACATTTTAATTCTTTT
196 TAATTGAATTTAATATAATATATTAATTTCATTAAATATTTTTTAAATTACATTTTAATTCTTTT
590651 TAATAGAATCATTGAATT
261 TAATAGAATCATTGAATT
590669 TAATATAATATAT
1 TAATATAATATAT
590682 TAATTTCATT
Statistics
Matches: 275, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
274 174 0.63
275 36 0.13
276 48 0.17
277 17 0.06
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.51
Consensus pattern (278 bp):
TAATATAATATATATATATAATATAAGTTTTTTACATAAATGTTAATATTTATTATGAATTTTTT
CAAAAAGAATTCATATATTATAATAATTTATTAAATTCAATATATAATATTAATTTAACTAATTA
ATTTTATCTCATTCATTTTCATTCATTATATATAATATAATATATTAATTTTATCTTAGCTTCAT
TAATTGAATTTAATATAATATATTAATTTCATTAAATATTTTTTAAATTACATTTTAATTCTTTT
TAATAGAATCATTGAATT
Found at i:590671 original size:73 final size:73
Alignment explanation
Indices: 590586--590728 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 73
590576 TTAGCTTCAT
*
590586 TCATTGAATTTAATATAATATATTAATTTCATTAAATATTTTTTAAATTACATTTTAATTCTTTT
1 TCATTGAATTTAATATAATATATTAATTTCATTAAATACTTTTTAAATTACATTTTAATTCTTTT
590651 TAATAGAA
66 TAATAGAA
* **
590659 TCATTGAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTATGTTTTAATTCTTTT
1 TCATTGAATTTAATATAATATATTAATTTCATTAAATACTTTTTAAATTACATTTTAATTCTTTT
590724 TAATA
66 TAATA
590729 ATTCTTATCC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (73 bp):
TCATTGAATTTAATATAATATATTAATTTCATTAAATACTTTTTAAATTACATTTTAATTCTTTT
TAATAGAA
Found at i:591942 original size:8 final size:8
Alignment explanation
Indices: 591929--592049 Score: 54
Period size: 8 Copynumber: 14.0 Consensus size: 8
591919 ATACGATATG
591929 ATATAAAT
1 ATATAAAT
591937 ATAT-AAT
1 ATATAAAT
591944 -T-TAAAT
1 ATATAAAT
591950 ATAATACGAAT
1 AT-ATA--AAT
*
591961 -TATTAAT
1 ATATAAAT
591968 ATATAAATTT
1 ATATAAA--T
591978 ATATAAAT
1 ATATAAAT
591986 ATA-AAAT
1 ATATAAAT
*
591993 AATTTAAAT
1 -ATATAAAT
592002 ATTATTATAAT
1 A-TA-TA-AAT
592013 ATGATAAAAT
1 AT-AT-AAAT
592023 ATATAACTAT
1 ATATAA--AT
*
592033 AATACAAAT
1 -ATATAAAT
592042 ATATAAAT
1 ATATAAAT
592050 TATCACTACA
Statistics
Matches: 88, Mismatches: 6, Indels: 38
0.67 0.05 0.29
Matches are distributed among these distances:
5 1 0.01
6 4 0.05
7 11 0.12
8 25 0.28
9 13 0.15
10 20 0.23
11 14 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:592059 original size:21 final size:19
Alignment explanation
Indices: 592007--592047 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
591997 TAAATATTAT
*
592007 TATAA-TATGATA-AAATA
1 TATAACTATAATACAAATA
592024 TATAACTATAATACAAATA
1 TATAACTATAATACAAATA
592043 TATAA
1 TATAA
592048 ATTATCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
TATAACTATAATACAAATA
Found at i:594534 original size:14 final size:14
Alignment explanation
Indices: 594507--594540 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
594497 ATATTTAATA
594507 AATTTTAAATTTAT
1 AATTTTAAATTTAT
594521 -ATTTTAATATTTAT
1 AATTTTAA-ATTTAT
594535 AATTTT
1 AATTTT
594541 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTAAATTTAT
Found at i:594721 original size:12 final size:12
Alignment explanation
Indices: 594706--594769 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 12
594696 TAATTTAAAA
594706 ATAATATAAATT
1 ATAATATAAATT
*
594718 ATAATATAAAAT
1 ATAATATAAATT
594730 ATAATAT--ATT
1 ATAATATAAATT
594740 A-AA-A-AAATT
1 ATAATATAAATT
*
594749 ATAAAATAAATT
1 ATAATATAAATT
594761 ATTAATATA
1 A-TAATATA
594770 TTATAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
8 1 0.02
9 6 0.14
10 5 0.12
11 1 0.02
12 24 0.56
13 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATATAAATT
Found at i:594751 original size:31 final size:32
Alignment explanation
Indices: 594713--594820 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 32
594703 AAAATAATAT
*
594713 AAATTATAATATAAAATA-TAATATATTAAAA
1 AAATTATAAAATAAAATATTAATATATTAAAA
* *
594744 AAATTATAAAATAAATTATTAATATATT--AT
1 AAATTATAAAATAAAATATTAATATATTAAAA
* * * *
594774 AATTTATATAAATATTTAATATTTATATATTATAA
1 AAATTATA-AAATA--AAATATTAATATATTAAAA
594809 AAATATATAAAA
1 AAAT-TATAAAA
594821 ATATATAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
30 8 0.13
31 21 0.34
32 9 0.15
33 12 0.20
35 7 0.11
36 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATTATAAAATAAAATATTAATATATTAAAA
Found at i:594799 original size:26 final size:28
Alignment explanation
Indices: 594754--594816 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
594744 AAATTATAAA
594754 ATAAAT-TATTAATATATTATA-ATTTAT
1 ATAAATATATTAATATATTATATA-TTAT
594781 ATAAATAT-TTAATAT-TTATATATTAT
1 ATAAATATATTAATATATTATATATTAT
*
594807 AAAAATATAT
1 ATAAATATAT
594817 AAAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 16 0.50
27 15 0.47
28 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
ATAAATATATTAATATATTATATATTAT
Found at i:594819 original size:10 final size:10
Alignment explanation
Indices: 594804--594829 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
594794 ATTTATATAT
594804 TATAAAAATA
1 TATAAAAATA
594814 TATAAAAATA
1 TATAAAAATA
594824 TATAAA
1 TATAAA
594830 TACAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TATAAAAATA
Found at i:594875 original size:2 final size:2
Alignment explanation
Indices: 594868--594892 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
594858 AGGGGACCAT
594868 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
594893 TTTTAATCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:596960 original size:25 final size:25
Alignment explanation
Indices: 596903--596961 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
596893 AATTATTTAT
* *
596903 ATTTAAATATATATTTAAATTAAAA
1 ATTTAATTATATATTAAAATTAAAA
**
596928 ATAAAATTATATATTAAAA-TATAAA
1 ATTTAATTATATATTAAAATTA-AAA
596953 ATTTAATTA
1 ATTTAATTA
596962 AAATATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATTATATATTAAAATTAAAA
Found at i:596961 original size:18 final size:19
Alignment explanation
Indices: 596897--596967 Score: 85
Period size: 18 Copynumber: 3.8 Consensus size: 19
596887 AAATTTAATT
* *
596897 ATTTATATTTAAATAT-AT
1 ATTTATATTAAAATATAAA
*
596915 ATTTAAATTAAAA-ATAAA
1 ATTTATATTAAAATATAAA
596933 ATTATATATTAAAATATAAA
1 ATT-TATATTAAAATATAAA
596953 ATTTA-ATTAAAATAT
1 ATTTATATTAAAATAT
596968 TTAAATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.04
18 25 0.54
19 11 0.24
20 8 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTATATTAAAATATAAA
Found at i:597259 original size:2 final size:2
Alignment explanation
Indices: 597252--597280 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
597242 GTTCTTCACT
597252 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
597281 AAACAGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:604767 original size:17 final size:17
Alignment explanation
Indices: 604712--604801 Score: 65
Period size: 17 Copynumber: 5.0 Consensus size: 17
604702 TTAAATATAT
*
604712 AATAAATAATTTAATATTA
1 AATAAAT-ATTTAATA-AA
* * *
604731 AGTAAATATTAAAT-AT
1 AATAAATATTTAATAAA
604747 AATAAATATTTAATAAA
1 AATAAATATTTAATAAA
*
604764 AATATATATTTAATTAAA
1 AATAAATATTTAA-TAAA
*
604782 TAATATAATTTTTATATAAA
1 -AATA-AATATTTA-ATAAA
604802 TCGAAAGAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
16 12 0.21
17 13 0.23
18 10 0.18
19 10 0.18
20 10 0.18
21 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (17 bp):
AATAAATATTTAATAAA
Found at i:606678 original size:22 final size:22
Alignment explanation
Indices: 606653--606727 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
606643 TTTACTTAAT
606653 TTAATAATAAAATATATAAATA
1 TTAATAATAAAATATATAAATA
* ***
606675 TTAAT-ATAAAAATAATCTTTTTA
1 TTAATAAT-AAAAT-ATATAAATA
*
606698 TTAATTAT-AAATA-ATAAATA
1 TTAATAATAAAATATATAAATA
606718 -TAATAATAAA
1 TTAATAATAAA
606728 CAAACCAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
19 6 0.15
20 5 0.12
21 3 0.08
22 14 0.35
23 10 0.25
24 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATAATAAAATATATAAATA
Found at i:606979 original size:2 final size:2
Alignment explanation
Indices: 606941--606965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
606931 TTATTTTTGA
606941 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 A
606966 AAAGAAAGAT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:607233 original size:10 final size:10
Alignment explanation
Indices: 607210--607312 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 10
607200 ATTAACTCGT
607210 TAAAA-TATA
1 TAAAATTATA
*
607219 AAAAATTATA
1 TAAAATTATA
607229 TAAAATTAT-
1 TAAAATTATA
*
607238 GAAAA-TATA
1 TAAAATTATA
607247 TAAAATTA-A
1 TAAAATTATA
*
607256 TTAATATTAATTTA
1 -TAAAATT-A--TA
*
607270 TTAAA--ATA
1 TAAAATTATA
607278 TAAAA-TATA
1 TAAAATTATA
*
607287 TAAAATAATA
1 TAAAATTATA
607297 -AAAATT-TA
1 TAAAATTATA
607305 TAAAATTA
1 TAAAATTA
607313 AACTAGTTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 23
0.69 0.10 0.22
Matches are distributed among these distances:
8 11 0.15
9 32 0.44
10 24 0.33
11 1 0.01
13 3 0.04
14 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (10 bp):
TAAAATTATA
Found at i:607248 original size:18 final size:18
Alignment explanation
Indices: 607210--607312 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 18
607200 ATTAACTCGT
607210 TAAAA-TATAAAAAATTATA
1 TAAAATTAT-AAAAA-TATA
*
607229 TAAAATTATGAAAATATA
1 TAAAATTATAAAAATATA
*
607247 TAAAATTAATTAATATTAATTTA
1 TAAAATT-A-TAA-A--AATATA
607270 TTAAAA-TAT-AAAATATA
1 -TAAAATTATAAAAATATA
* *
607287 TAAAATAATAAAAATTTA
1 TAAAATTATAAAAATATA
607305 TAAAATTA
1 TAAAATTA
607313 AACTAGTTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 19
0.72 0.07 0.20
Matches are distributed among these distances:
16 5 0.07
17 7 0.10
18 25 0.37
19 11 0.16
20 6 0.09
21 2 0.03
22 1 0.01
23 6 0.09
24 5 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (18 bp):
TAAAATTATAAAAATATA
Found at i:607346 original size:2 final size:2
Alignment explanation
Indices: 607339--607366 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
607329 ATATTGCAAG
607339 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
607367 GGTGAATCTA
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:607599 original size:20 final size:18
Alignment explanation
Indices: 607562--607614 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
607552 ATAATACATA
607562 AAATTATTATAATTATAT
1 AAATTATTATAATTATAT
607580 AAATATATTATAAGTTATAT
1 AAAT-TATTATAA-TTATAT
607600 AAATCT-TTATAATTA
1 AAAT-TATTATAATTA
607615 AAAAAGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 7 0.22
19 14 0.44
20 11 0.34
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATTATTATAATTATAT
Found at i:611013 original size:3 final size:3
Alignment explanation
Indices: 611007--611038 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
610997 TTATTATCAA
611007 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A
611039 GCTCGATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:611192 original size:20 final size:21
Alignment explanation
Indices: 611167--611208 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
611157 TTTTTAAAAG
611167 TTTTTATGA-ATAATT-TTTAT
1 TTTTTA-GATATAATTATTTAT
611187 TTTTTAGATATAATTATTTAT
1 TTTTTAGATATAATTATTTAT
611208 T
1 T
611209 GTTTCTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTAGATATAATTATTTAT
Found at i:611382 original size:13 final size:13
Alignment explanation
Indices: 611364--611388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
611354 TAATTAATTT
611364 TAAAATTTTTTAA
1 TAAAATTTTTTAA
611377 TAAAATTTTTTA
1 TAAAATTTTTTA
611389 TATTTATTTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAAATTTTTTAA
Found at i:612099 original size:2 final size:2
Alignment explanation
Indices: 612092--612140 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
612082 ATAAATTGAT
*
612092 TA TA TA TA CA 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
612134 TA TA TA T
1 TA TA TA T
612141 TAAATTAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:613978 original size:29 final size:28
Alignment explanation
Indices: 613946--614037 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 28
613936 TATTACATCC
* *
613946 AAATAAATCTTAATTTTTAATTTATACTT
1 AAATAAATCTT-ATCTTTAATTTATACCT
* *
613975 AAATAGATCCTATCCTTTAATTTATATCCT
1 AAATAAATCTTAT-CTTTAATTTATA-CCT
*
614005 -AATAAAACATTGATCTTTAATTTATACCT
1 AAATAAATC-TT-ATCTTTAATTTATACCT
614034 AAAT
1 AAAT
614038 TAATATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
28 2 0.04
29 29 0.57
30 18 0.35
31 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATAAATCTTATCTTTAATTTATACCT
Found at i:621104 original size:43 final size:45
Alignment explanation
Indices: 621043--621134 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 45
621033 GGATTCAAAC
* *
621043 ATCAAACTTATCAGATGTC-GGCTCTTAGGGC-TTATATGAACTA
1 ATCAAACTTATCAGATGTCAGCCTCTTAAGGCATTATATGAACTA
* *
621086 ATCAAACTTGTCTGATGTCAGCCTCTTAAGGCTAGTTATATGAACTA
1 ATCAAACTTATCAGATGTCAGCCTCTTAAGGC-A-TTATATGAACTA
621133 AT
1 AT
621135 TGAACTAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 17 0.41
44 10 0.24
47 14 0.34
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (45 bp):
ATCAAACTTATCAGATGTCAGCCTCTTAAGGCATTATATGAACTA
Found at i:624949 original size:16 final size:16
Alignment explanation
Indices: 624930--624963 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
624920 TAAATAATTA
624930 ATTTAAATTTATTCAT
1 ATTTAAATTTATTCAT
* *
624946 ATTTTAATTTATTTAT
1 ATTTAAATTTATTCAT
624962 AT
1 AT
624964 AAAAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTAAATTTATTCAT
Found at i:625239 original size:19 final size:18
Alignment explanation
Indices: 625190--625244 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
625180 AAATTCAATT
* *
625190 ATTTTTTAAGTAAATCTA
1 ATTTTTTAATTAAATTTA
*
625208 ATTTTTTATTTAAATTTA
1 ATTTTTTAATTAAATTTA
*
625226 TTTTTTTAACTTAATATTT
1 ATTTTTTAA-TTAA-ATTT
625245 TTACTTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.73
19 4 0.13
20 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTTAATTAAATTTA
Found at i:626693 original size:27 final size:27
Alignment explanation
Indices: 626640--626697 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
626630 TGACAATCTC
** *
626640 ATATTATATTATGTAATATTATTTTTT
1 ATATTATATTATGTAATAAGATATTTT
626667 ATATTATATTATTGT-ATAAGATATTTT
1 ATATTATATTA-TGTAATAAGATATTTT
626694 ATAT
1 ATAT
626698 ATAATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (27 bp):
ATATTATATTATGTAATAAGATATTTT
Found at i:626713 original size:29 final size:29
Alignment explanation
Indices: 626659--626758 Score: 73
Period size: 29 Copynumber: 3.3 Consensus size: 29
626649 TATGTAATAT
* * *
626659 TATTTTTTATATTATATTATTGTATAAGA
1 TATTTTATATATAATATTATTATATAAGA
626688 TATTTTATATATAATA-TATTTATATAA-A
1 TATTTTATATATAATATTA-TTATATAAGA
*
626716 -ATTTAATATAGTATTAATTTGTATTATATAA-A
1 TATTT--TATA-TA-TAATAT-TATTATATAAGA
626748 TATATTTATAT
1 TAT-TTTATAT
626759 CGTGTCTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
27 4 0.07
28 3 0.05
29 25 0.43
30 2 0.03
31 5 0.09
32 13 0.22
33 4 0.07
34 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (29 bp):
TATTTTATATATAATATTATTATATAAGA
Found at i:626974 original size:30 final size:31
Alignment explanation
Indices: 626906--626975 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
626896 TACTCTTTAT
* * * *
626906 TAATTTTTTTAATAATTTAAATTATTAAATT
1 TAATATTTTTAATAATTAAAATTATAAAATA
*
626937 TTA-ATTTTTAATAATTAAAATTA-AAAATA
1 TAATATTTTTAATAATTAAAATTATAAAATA
626966 TAATATTTTT
1 TAATATTTTT
626976 TATCTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 6 0.19
30 24 0.75
31 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TAATATTTTTAATAATTAAAATTATAAAATA
Found at i:627404 original size:15 final size:14
Alignment explanation
Indices: 627384--627429 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
627374 GGACGAATTG
627384 TAATTTTTATATTAT
1 TAATTTTTATATT-T
*
627399 TAATTTTAATATTT
1 TAATTTTTATATTT
*
627413 AAATTTTTATATTT
1 TAATTTTTATATTT
627427 TAA
1 TAA
627430 AAATTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATTTTTATATTT
Found at i:627430 original size:15 final size:15
Alignment explanation
Indices: 627385--627430 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
627375 GACGAATTGT
627385 AATTTTTATATTATT-
1 AATTTTTATATT-TTA
*
627400 AATTTTAATA-TTTA
1 AATTTTTATATTTTA
627414 AATTTTTATATTTTA
1 AATTTTTATATTTTA
627429 AA
1 AA
627431 AATTATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTTTTATATTTTA
Found at i:627480 original size:18 final size:19
Alignment explanation
Indices: 627444--627500 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
627434 TATAATAAAT
*
627444 AAAAATATTAAATAGTATTA
1 AAAAATATTTAATA-TATTA
627464 AAAAATATTTAAT-TATTA
1 AAAAATATTTAATATATTA
627482 ATAAAATA-TTAATATATTA
1 A-AAAATATTTAATATATTA
627501 TTTAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.32
19 11 0.32
20 12 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAAATATTTAATATATTA
Found at i:627499 original size:19 final size:18
Alignment explanation
Indices: 627444--627500 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
627434 TATAATAAAT
627444 AAAAATATTAAATAGTATTA
1 AAAAATATT-AATA-TATTA
627464 AAAAATATTTAAT-TATTA
1 AAAAATA-TTAATATATTA
627482 ATAAAATATTAATATATTA
1 A-AAAATATTAATATATTA
627501 TTTAATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 11 0.32
19 11 0.32
20 10 0.29
21 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAATATTAATATATTA
Found at i:627534 original size:24 final size:26
Alignment explanation
Indices: 627484--627535 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
627474 AATTATTAAT
* * *
627484 AAAATATTAATATATTATTTAATATA
1 AAAATATTAAAATATTATATAAAATA
627510 AAAAT-TTAAAAT-TTATATAAAATA
1 AAAATATTAAAATATTATATAAAATA
627534 AA
1 AA
627536 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 6 0.26
26 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATATTAAAATATTATATAAAATA
Found at i:627864 original size:18 final size:17
Alignment explanation
Indices: 627843--627886 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
627833 TTATAAAATT
627843 TAATATATTAATAATTTA
1 TAATATATTAA-AATTTA
*
627861 TAATATA-TAAATTTTA
1 TAATATATTAAAATTTA
*
627877 TATTATATTA
1 TAATATATTA
627887 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATATATTAAAATTTA
Found at i:627923 original size:24 final size:25
Alignment explanation
Indices: 627882--627937 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
627872 TTTTATATTA
*
627882 TATTATATTTTTTATTATTTTT-AAT
1 TATT-TATTTTGTATTATTTTTGAAT
*
627907 TATTTATTTTGTGTTATTTTTGAAT
1 TATTTATTTTGTATTATTTTTGAAT
*
627932 TTTTTA
1 TATTTA
627938 ATATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.71
Consensus pattern (25 bp):
TATTTATTTTGTATTATTTTTGAAT
Found at i:627927 original size:25 final size:24
Alignment explanation
Indices: 627882--627937 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
627872 TTTTATATTA
* *
627882 TATTATATTTTTTATTATTTTTAAT
1 TATT-TATTTTGTATTATTTTGAAT
*
627907 TATTTATTTTGTGTTATTTTTGAAT
1 TATTTATTTTGTATTA-TTTTGAAT
*
627932 TTTTTA
1 TATTTA
627938 ATATTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.71
Consensus pattern (24 bp):
TATTTATTTTGTATTATTTTGAAT
Found at i:640306 original size:31 final size:31
Alignment explanation
Indices: 640262--640332 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
640252 AAGCAAGGCC
640262 ACTCATCCA-TTCCAAGATGCTCTACATGTAT
1 ACTCAT-CATTTCCAAGATGCTCTACATGTAT
* * *
640293 ACTCATCATTTCCAGGATTCTCTGCATGTAT
1 ACTCATCATTTCCAAGATGCTCTACATGTAT
*
640324 ACTTATCAT
1 ACTCATCAT
640333 AATCTTCCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (31 bp):
ACTCATCATTTCCAAGATGCTCTACATGTAT
Found at i:640743 original size:2 final size:2
Alignment explanation
Indices: 640738--640770 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
640728 CGTGTGTGTG
640738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
640771 CAGTTAGAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:642734 original size:12 final size:12
Alignment explanation
Indices: 642701--642760 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
642691 TATAAAAGTA
642701 ATATAATTATA-
1 ATATAATTATAT
*
642712 ATATAAATATAT
1 ATATAATTATAT
*
642724 ATATATTTATAT
1 ATATAATTATAT
*
642736 -TAAAATTTATAT
1 ATATAA-TTATAT
*
642748 AAATAATTA-AT
1 ATATAATTATAT
642759 AT
1 AT
642761 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 16 0.42
12 19 0.50
13 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATAATTATAT
Found at i:643363 original size:2 final size:2
Alignment explanation
Indices: 643356--643391 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
643346 AGGCTCTGTT
643356 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
643392 ATTTATTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:644642 original size:2 final size:2
Alignment explanation
Indices: 644637--644661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
644627 TATATATATA
644637 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
644662 AAAAGCTACA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:645495 original size:6 final size:6
Alignment explanation
Indices: 645484--645513 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
645474 GAATAATACA
645484 ATGTAC ATGTAC ATGTAC ATGTAC ATGTAC
1 ATGTAC ATGTAC ATGTAC ATGTAC ATGTAC
645514 TCTTACTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (6 bp):
ATGTAC
Found at i:646022 original size:12 final size:12
Alignment explanation
Indices: 645993--646035 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
645983 AAACTATTTT
645993 TATGTATATATG
1 TATGTATATATG
646005 TA--TATATATG
1 TATGTATATATG
*
646015 TATGTATATGTG
1 TATGTATATATG
*
646027 TGTGTATAT
1 TATGTATAT
646036 TATAGCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.37
12 17 0.63
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (12 bp):
TATGTATATATG
Found at i:648203 original size:18 final size:17
Alignment explanation
Indices: 648156--648205 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
648146 TATTATAGTA
648156 TAAA-TATTAAAAATTT
1 TAAATTATTAAAAATTT
* *
648172 AAAATTTAATAAAAATTT
1 TAAA-TTATTAAAAATTT
*
648190 TAAATTATTCAAAATT
1 TAAATTATTAAAAATT
648206 ATATAATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.11
17 10 0.37
18 14 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTATTAAAAATTT
Found at i:651535 original size:13 final size:13
Alignment explanation
Indices: 651517--651541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
651507 TTTTTTTTTT
651517 GGGGGGTGGGGGG
1 GGGGGGTGGGGGG
651530 GGGGGGTGGGGG
1 GGGGGGTGGGGG
651542 CTAAACCCTC
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:0.00, C:0.00, G:0.92, T:0.08
Consensus pattern (13 bp):
GGGGGGTGGGGGG
Found at i:654213 original size:46 final size:46
Alignment explanation
Indices: 654146--654236 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
654136 AATGAATTGA
654146 AGAGATATAAATATATATTTATATTTGATATTTATAATTGAGTTGG
1 AGAGATATAAATATATATTTATATTTGATATTTATAATTGAGTTGG
654192 AGAGATATAAATATATATTTATATTTGATATTTATAATTGAGTTG
1 AGAGATATAAATATATATTTATATTTGATATTTATAATTGAGTTG
654237 AGATGACATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (46 bp):
AGAGATATAAATATATATTTATATTTGATATTTATAATTGAGTTGG
Found at i:654995 original size:18 final size:19
Alignment explanation
Indices: 654974--655009 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
654964 ATTTCTGACT
*
654974 TTTATTT-TTTTTAAAATA
1 TTTATTTGTATTTAAAATA
654992 TTTATTTGTATTTAAAAT
1 TTTATTTGTATTTAAAAT
655010 TAATATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATTTGTATTTAAAATA
Found at i:655928 original size:33 final size:36
Alignment explanation
Indices: 655880--655951 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
655870 CTTTAAAAAA
*
655880 TTATTAAATTAAATA-T-ATATT-TTTATTAATTAT
1 TTATTAAATTAAATATTAAAATTATTTATTAATTAT
* * *
655913 TTATTATATTTAATATTAAAATTATTTTTTAATTAT
1 TTATTAAATTAAATATTAAAATTATTTATTAATTAT
655949 TTA
1 TTA
655952 AATTCTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 13 0.41
34 1 0.03
35 4 0.12
36 14 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
TTATTAAATTAAATATTAAAATTATTTATTAATTAT
Found at i:656245 original size:31 final size:32
Alignment explanation
Indices: 656210--656278 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
656200 TAAATTATAT
656210 TATAATATAAATAA-TAATTATTTAATA-TAAA
1 TATAATATAAATAATTAATT-TTTAATATTAAA
* * *
656241 TATAATTTTAATAATTTATTTTTAATATTAAA
1 TATAATATAAATAATTAATTTTTAATATTAAA
656273 TATAAT
1 TATAAT
656279 TGACTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TATAATATAAATAATTAATTTTTAATATTAAA
Found at i:656255 original size:20 final size:21
Alignment explanation
Indices: 656207--656255 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
656197 TATTAAATTA
656207 TATTATAATATAAATAATAAT
1 TATTATAATATAAATAATAAT
656228 TATT-TAATATAAAT-ATAAT
1 TATTATAATATAAATAATAAT
656247 T-TTAATAAT
1 TATT-ATAAT
656256 TTATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.23
20 14 0.54
21 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTATAATATAAATAATAAT
Found at i:658592 original size:31 final size:32
Alignment explanation
Indices: 658523--658592 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
658513 TGATTTAATT
* * *
658523 TTAATTAATTTACTAATAATTTTAAAATTAAA
1 TTAATTTATTTACTAATAATATAAAAATTAAA
** *
658555 AAAATTTATTTA-TATTAATATAAAAATTAAA
1 TTAATTTATTTACTAATAATATAAAAATTAAA
658586 TTAATTT
1 TTAATTT
658593 TAAATATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
TTAATTTATTTACTAATAATATAAAAATTAAA
Found at i:659647 original size:11 final size:11
Alignment explanation
Indices: 659622--659681 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
659612 AAATTTTAAA
*
659622 ATATTA-ATAT
1 ATATTATATTT
*
659632 ATATTTTATTT
1 ATATTATATTT
659643 ATATTATATTT
1 ATATTATATTT
*
659654 -TAATTATTTTT
1 AT-ATTATATTT
*
659665 ATATTATATTC
1 ATATTATATTT
659676 ATATTA
1 ATATTA
659682 AGATAAGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
10 6 0.15
11 34 0.83
12 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTATATTT
Found at i:659651 original size:20 final size:20
Alignment explanation
Indices: 659603--659673 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
659593 ATAATACTTC
* **
659603 ATATTATATAAATTTTA-AA
1 ATATTATATATATTTTATTT
659622 ATATTAATATATATTTTATTT
1 ATATT-ATATATATTTTATTT
*
659643 ATATTATATTTTAATTATT-TTT
1 ATATTATA-TAT-ATT-TTATTT
659665 ATATTATAT
1 ATATTATAT
659674 TCATATTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.12
20 14 0.33
21 8 0.19
22 14 0.33
23 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTATATATATTTTATTT
Found at i:662033 original size:20 final size:21
Alignment explanation
Indices: 662008--662058 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
661998 ATATTTAATA
662008 TTTATAATTAAAAAATTAT-T
1 TTTATAATTAAAAAATTATAT
* *
662028 TTTAT-ATT-AATATTTATAT
1 TTTATAATTAAAAAATTATAT
662047 TTTATAATTAAA
1 TTTATAATTAAA
662059 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 9 0.35
20 8 0.31
21 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATAATTAAAAAATTATAT
Found at i:662957 original size:2 final size:2
Alignment explanation
Indices: 662950--662976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
662940 GCACCAGCGA
662950 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 A
662977 ATAGTTTAGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:687535 original size:2 final size:2
Alignment explanation
Indices: 687528--687557 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
687518 TATGAGATTA
687528 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
687558 GTATGCAAGC
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:688264 original size:7 final size:7
Alignment explanation
Indices: 688252--688280 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
688242 ACAACCCCCG
688252 ACTTGGT
1 ACTTGGT
688259 ACTTGGT
1 ACTTGGT
688266 ACTTGGT
1 ACTTGGT
688273 ACTTGGT
1 ACTTGGT
688280 A
1 A
688281 ACAGTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (7 bp):
ACTTGGT
Found at i:688609 original size:18 final size:18
Alignment explanation
Indices: 688583--688643 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 18
688573 ACCCATACAA
688583 TTATAAATTAGTATAAAT
1 TTATAAATTAGTATAAAT
* * * *
688601 TTATGAATT-TTTTTAAT
1 TTATAAATTAGTATAAAT
688618 TT-TAAATTAGTATAAAT
1 TTATAAATTAGTATAAAT
*
688635 TTATGAATT
1 TTATAAATT
688644 TTGATCTATC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
16 5 0.16
17 14 0.44
18 13 0.41
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TTATAAATTAGTATAAAT
Found at i:688629 original size:34 final size:34
Alignment explanation
Indices: 688581--688645 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
688571 GGACCCATAC
688581 AATTATAAATTAGTATAAATTTATGAATTTTTTT
1 AATTATAAATTAGTATAAATTTATGAATTTTTTT
*
688615 AATTTTAAATTAGTATAAATTTATGAATTTT
1 AATTATAAATTAGTATAAATTTATGAATTTT
688646 GATCTATCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (34 bp):
AATTATAAATTAGTATAAATTTATGAATTTTTTT
Found at i:688850 original size:15 final size:15
Alignment explanation
Indices: 688830--688881 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
688820 AAATTGAGTA
688830 TTAAATTTGATTAAC
1 TTAAATTTGATTAAC
* *
688845 TTAAATTTAAAATAAC
1 TTAAATTT-GATTAAC
*
688861 TTAAAATTGATTAAC
1 TTAAATTTGATTAAC
*
688876 TCAAAT
1 TTAAAT
688882 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (15 bp):
TTAAATTTGATTAAC
Found at i:689630 original size:20 final size:19
Alignment explanation
Indices: 689605--689647 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
689595 TAAATTATCC
689605 TATAAATAAAATAA-ATAATA
1 TATAAATAAAA-AATATAA-A
689625 TATAAATAAAAAATATAAA
1 TATAAATAAAAAATATAAA
689644 TATA
1 TATA
689648 TTATAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TATAAATAAAAAATATAAA
Found at i:689642 original size:24 final size:23
Alignment explanation
Indices: 689606--689659 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
689596 AAATTATCCT
689606 ATAAATAAAATAAATA-ATATATAA
1 ATAAA-AAAATAAATATAT-TATAA
689630 ATAAAAAATATAAATATATTATAA
1 ATAAAAAA-ATAAATATATTATAA
689654 ATAAAA
1 ATAAAA
689660 TTATAATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.11
24 23 0.82
25 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAAAAAATAAATATATTATAA
Found at i:689668 original size:15 final size:14
Alignment explanation
Indices: 689606--689645 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
689596 AAATTATCCT
689606 ATAAATA-AAATAA
1 ATAAATATAAATAA
689619 ATAATATATAAATAA
1 ATAA-ATATAAATAA
689634 A-AAATATAAATA
1 ATAAATATAAATA
689646 TATTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 5 0.20
15 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATATAAATAA
Found at i:690384 original size:28 final size:28
Alignment explanation
Indices: 690353--690410 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
690343 ATATTCTTTG
*
690353 ATTT-TATATTTACTGATTATATTAATAT
1 ATTTATATAATTA-TGATTATATTAATAT
* *
690381 ATTTATATAATTATTATTTTATTAATAT
1 ATTTATATAATTATGATTATATTAATAT
690409 AT
1 AT
690411 AAAATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
ATTTATATAATTATGATTATATTAATAT
Found at i:690409 original size:22 final size:24
Alignment explanation
Indices: 690384--690439 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
690374 TTAATATATT
690384 TATAT-AATTATTAT-TTTATTAA
1 TATATAAATTATTATATTTATTAA
*
690406 TATATAAAATTTTTATATTTATTAAA
1 TATAT-AAATTATTATATTTATT-AA
*
690432 TAAATAAA
1 TATATAAA
690440 AAATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.18
24 8 0.29
25 9 0.32
26 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATAAATTATTATATTTATTAA
Found at i:690416 original size:24 final size:26
Alignment explanation
Indices: 690384--690440 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
690374 TTAATATATT
*
690384 TATATAATTATTAT-TTTATT-AATA
1 TATAAAATTATTATATTTATTAAATA
*
690408 TATAAAATTTTTATATTTATTAAATA
1 TATAAAATTATTATATTTATTAAATA
*
690434 AATAAAA
1 TATAAAA
690441 AATATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 12 0.43
25 6 0.21
26 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATAAAATTATTATATTTATTAAATA
Found at i:693313 original size:22 final size:23
Alignment explanation
Indices: 693288--693337 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
693278 ATATGTGAAT
693288 TTAAATTAAAT-AAATATTAAAA
1 TTAAATTAAATAAAATATTAAAA
* *
693310 TT-AATTGAATAAAATATTAAAT
1 TTAAATTAAATAAAATATTAAAA
693332 TTAAAT
1 TTAAAT
693338 ATTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATTAAATAAAATATTAAAA
Found at i:693937 original size:5 final size:5
Alignment explanation
Indices: 693922--693952 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
693912 CATGAGTTTC
*
693922 CCTTT CATTT CCTTT CCTTT CCTTT CCTTT C
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT C
693953 ATTGTTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (5 bp):
CCTTT
Found at i:696924 original size:72 final size:72
Alignment explanation
Indices: 696843--696976 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
696833 AATTTATATG
* * *
696843 AAATTAATTATTAACATATAAAATATATTATCTAATTATGATTAT-GACATAAAAAAGTAATATG
1 AAATCAATTATTAACATATAAAATATAATACCTAATTATGATTATAG-CATAAAAAAGTAATATG
696907 AACACATA
65 AACACATA
* * *
696915 AAATCAATTATTAACGTGTCAAATATAATACCTAATTATGATTATAGCATAAAAAAGTAATA
1 AAATCAATTATTAACATATAAAATATAATACCTAATTATGATTATAGCATAAAAAAGTAATA
696977 AGAATATAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 54 0.98
73 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (72 bp):
AAATCAATTATTAACATATAAAATATAATACCTAATTATGATTATAGCATAAAAAAGTAATATGA
ACACATA
Found at i:697873 original size:20 final size:20
Alignment explanation
Indices: 697848--697902 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
697838 AAAAGATATG
697848 AATATTTTTAATTTTATAAT
1 AATATTTTTAATTTTATAAT
* *
697868 AATATTATTAAGTTTTTTTAAT
1 AATATTTTTAA--TTTTATAAT
697890 AA-ATTTTTAATTT
1 AATATTTTTAATTT
697903 GATTCGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 7 0.23
22 10 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATATTTTTAATTTTATAAT
Found at i:697889 original size:22 final size:21
Alignment explanation
Indices: 697859--697899 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
697849 ATATTTTTAA
697859 TTTTATAATAATATTATTAAGT
1 TTTTATAATAA-ATTATTAAGT
* *
697881 TTTTTTAATAAATTTTTAA
1 TTTTATAATAAATTATTAA
697900 TTTGATTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATAATAAATTATTAAGT
Found at i:700375 original size:15 final size:15
Alignment explanation
Indices: 700355--700389 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
700345 AACATTCGAG
700355 TATAATTTACAAAAA
1 TATAATTTACAAAAA
**
700370 TATAATTTATTAAAA
1 TATAATTTACAAAAA
700385 TATAA
1 TATAA
700390 ATTTTAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAATTTACAAAAA
Found at i:701790 original size:15 final size:14
Alignment explanation
Indices: 701770--701820 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
701760 AAATTTGAAT
701770 TTTAAAGTTTTTAAA
1 TTTAAA-TTTTTAAA
*
701785 TTTAAATTAATTTCAA
1 TTTAAATT--TTTAAA
701801 TTTAAATTTTTTAAA
1 TTTAAA-TTTTTAAA
701816 TTTAA
1 TTTAA
701821 CTTAAATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 2 0.06
15 16 0.52
16 11 0.35
17 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTAAATTTTTAAA
Found at i:701812 original size:31 final size:32
Alignment explanation
Indices: 701751--701825 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
701741 TGAAAAAATT
* *
701751 ATTTATATTAAATTTGAATTTTAAAGTTTTTAA
1 ATTTAAATT-AATTTCAATTTTAAAGTTTTTAA
*
701784 ATTTAAATTAATTTCAA-TTTAAATTTTTTAA
1 ATTTAAATTAATTTCAATTTTAAAGTTTTTAA
*
701815 ATTTAACTTAA
1 ATTTAAATTAA
701826 ATATGACTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 23 0.61
32 7 0.18
33 8 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (32 bp):
ATTTAAATTAATTTCAATTTTAAAGTTTTTAA
Found at i:701837 original size:31 final size:31
Alignment explanation
Indices: 701771--701838 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
701761 AATTTGAATT
* * *
701771 TTAAAGTTTTTAAATTTAAATTAATTTCAAT
1 TTAAATTTTTTAAATTTAAATTAATATCAAC
* *
701802 TTAAATTTTTTAAATTTAACTTAAATAT-GAC
1 TTAAATTTTTTAAATTTAAATT-AATATCAAC
701833 TTAAAT
1 TTAAAT
701839 CATTAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (31 bp):
TTAAATTTTTTAAATTTAAATTAATATCAAC
Found at i:703243 original size:25 final size:25
Alignment explanation
Indices: 703216--703264 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
703206 TATATAACAT
703216 AAAATTTAAAATTATTATATAATTTA
1 AAAATTTAAAA-TATTATATAATTTA
* *
703242 AAAATTTTAAATATAATATAATT
1 AAAATTTAAAATATTATATAATT
703265 ATATGAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAAATTTAAAATATTATATAATTTA
Found at i:703250 original size:27 final size:24
Alignment explanation
Indices: 703216--703330 Score: 73
Period size: 24 Copynumber: 4.8 Consensus size: 24
703206 TATATAACAT
*
703216 AAAATTTAAAATTATTATATAATTTA
1 AAAATTT-AAA-TATAATATAATTTA
703242 AAAATTTTAAATATAATATAATTATA
1 AAAA-TTTAAATATAATATAATT-TA
*
703268 TGAAA--TAAATATAATAT-A---A
1 -AAAATTTAAATATAATATAATTTA
* * *
703287 AAAATTAAAAAATTATATAATATTA
1 AAAATTTAAATATAATATAAT-TTA
*
703312 AAAA-ATAAATATAATATAA
1 AAAATTTAAATATAATATAA
703331 ATATATAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 9 0.13
21 1 0.01
23 1 0.01
24 23 0.33
25 16 0.23
26 9 0.13
27 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (24 bp):
AAAATTTAAATATAATATAATTTA
Found at i:703281 original size:44 final size:44
Alignment explanation
Indices: 703232--703331 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
703222 TAAAATTATT
* * * * **
703232 ATATAATTTAAAAATTTTAAATATAATATAAT-TATATGAAATAA
1 ATATAATATAAAAAATTAAAAAATAATATAATAT-TAAAAAATAA
*
703276 ATATAATATAAAAAATTAAAAAATTATATAATATTAAAAAATAA
1 ATATAATATAAAAAATTAAAAAATAATATAATATTAAAAAATAA
703320 ATATAATATAAA
1 ATATAATATAAA
703332 TATATAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 47 0.98
45 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (44 bp):
ATATAATATAAAAAATTAAAAAATAATATAATATTAAAAAATAA
Found at i:703295 original size:19 final size:17
Alignment explanation
Indices: 703280--703350 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 17
703270 AAATAAATAT
* *
703280 AATATAAAAAATTAAAA
1 AATATATAATATTAAAA
703297 AATTATATAATATTAAAA
1 AA-TATATAATATTAAAA
703315 AATAAATATAATA-T-AAA
1 AAT--ATATAATATTAAAA
* *
703332 TATATAAATATATTAAAA
1 AATATATA-ATATTAAAA
703350 A
1 A
703351 TTTATATAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 9 0.21
18 19 0.44
19 8 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATATAATATTAAAA
Found at i:703314 original size:25 final size:25
Alignment explanation
Indices: 703276--703359 Score: 82
Period size: 25 Copynumber: 3.2 Consensus size: 25
703266 TATGAAATAA
*
703276 ATATAATATAAAAAATTAAAAAATT
1 ATATAATATTAAAAATTAAAAAATT
*
703301 ATATAATATTAAAAAATAAATATAA-T
1 ATATAATATTAAAAATTAAA-A-AATT
*
703327 ATA-AATATATAAATATATTAAAAATTT
1 ATATAATAT-TAAA-A-ATTAAAAAATT
703354 ATATAA
1 ATATAA
703360 CAAAAGGAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
25 23 0.48
26 10 0.21
27 8 0.17
28 7 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAATATTAAAAATTAAAAAATT
Found at i:703351 original size:19 final size:18
Alignment explanation
Indices: 703280--703350 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 18
703270 AAATAAATAT
*
703280 AATATAAA-AAATTAAAA
1 AATATAAATATATTAAAA
*
703297 AAT-TATATAATATT-AAA
1 AATATAAAT-ATATTAAAA
*
703314 AA-ATAAATATAATATAAA
1 AATATAAATATATTA-AAA
*
703332 TATATAAATATATTAAAA
1 AATATAAATATATTAAAA
703350 A
1 A
703351 TTTATATAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
16 7 0.17
17 12 0.29
18 11 0.27
19 11 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATAAATATATTAAAA
Found at i:703356 original size:19 final size:19
Alignment explanation
Indices: 703290--703356 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
703280 AATATAAAAA
* *
703290 ATTAAAAAATTATATA-AT
1 ATTAAAAATTTATAAATAT
703308 ATTAAAAA---ATAAATAT
1 ATTAAAAATTTATAAATAT
* * *
703324 AATATAAATATATAAATAT
1 ATTAAAAATTTATAAATAT
703343 ATTAAAAATTTATA
1 ATTAAAAATTTATA
703357 TAACAAAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
15 4 0.10
16 8 0.21
18 8 0.21
19 19 0.49
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAAAAATTTATAAATAT
Found at i:703584 original size:27 final size:30
Alignment explanation
Indices: 703546--703600 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
703536 TTTTTATATA
703546 TTTATGTATATAA-A-TAAAA-AATTTACT
1 TTTATGTATATAACACTAAAATAATTTACT
703573 TTTAT-TATTATAACACTAAAATAATTTA
1 TTTATGTA-TATAACACTAAAATAATTTA
703601 ACATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.08
27 10 0.42
28 1 0.04
29 5 0.21
30 6 0.25
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTATGTATATAACACTAAAATAATTTACT
Found at i:703637 original size:15 final size:16
Alignment explanation
Indices: 703608--703651 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
703598 TTAACATATA
* *
703608 TAATTTTTATATAATT
1 TAATATTTATTTAATT
703624 T-ATATTTATTTAATT
1 TAATATTTATTTAATT
703639 TAATATTATATTT
1 TAATATT-TATTT
703652 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 6 0.25
17 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATATTTATTTAATT
Found at i:703880 original size:8 final size:8
Alignment explanation
Indices: 703843--703878 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
703833 ATTTGTTAGA
703843 ATATTTAT
1 ATATTTAT
703851 ATATTTAT
1 ATATTTAT
703859 ATATTTAT
1 ATATTTAT
*
703867 ATATATAT
1 ATATTTAT
703875 ATAT
1 ATAT
703879 ATGTTGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATTTAT
Found at i:704671 original size:3 final size:3
Alignment explanation
Indices: 704663--704705 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
704653 AATTTAAAAG
704663 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
704706 GATGATGGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:706786 original size:18 final size:18
Alignment explanation
Indices: 706763--706810 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
706753 TATATATATA
706763 TACACACACACACACACG
1 TACACACACACACACACG
* *
706781 TACACACACGCACGCACG
1 TACACACACACACACACG
* *
706799 CACGCACACACA
1 TACACACACACA
706811 TTGGCTTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.46, G:0.10, T:0.04
Consensus pattern (18 bp):
TACACACACACACACACG
Found at i:708137 original size:23 final size:23
Alignment explanation
Indices: 708107--708152 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
708097 AATCAATTAC
708107 TTTGCATGTATCCATCATAAACT
1 TTTGCATGTATCCATCATAAACT
708130 TTTGCATGTATCCATCATAAACT
1 TTTGCATGTATCCATCATAAACT
708153 ATATTTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTGCATGTATCCATCATAAACT
Found at i:714998 original size:12 final size:12
Alignment explanation
Indices: 714981--715006 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
714971 TTCTAGTTCT
714981 TTGTTATTATTA
1 TTGTTATTATTA
714993 TTGTTATTATTA
1 TTGTTATTATTA
715005 TT
1 TT
715007 ATTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTATTATTA
Found at i:716415 original size:24 final size:23
Alignment explanation
Indices: 716386--716443 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
716376 TTAACAATCA
716386 AAATAAAATAAAAATAATATTTTT
1 AAATAAAATAAAAATAA-ATTTTT
** ** *
716410 TTATAATTTAATAATAAATTTTT
1 AAATAAAATAAAAATAAATTTTT
716433 AAATAAAATAA
1 AAATAAAATAA
716444 TTATATTACA
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAAAATAAAAATAAATTTTT
Found at i:716483 original size:16 final size:16
Alignment explanation
Indices: 716459--716492 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
716449 TTACATTCAC
*
716459 ATTTTAATATATTATT
1 ATTTAAATATATTATT
*
716475 ATTTAAATATATTTTT
1 ATTTAAATATATTATT
716491 AT
1 AT
716493 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTAAATATATTATT
Found at i:717351 original size:23 final size:24
Alignment explanation
Indices: 717325--717386 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 24
717315 TTAATATAGA
717325 TATATTTAAATT-T-TTTATATATT
1 TATATTTAAATTATATTT-TATATT
717348 TATA---AAATTATATTTTATATT
1 TATATTTAAATTATATTTTATATT
*
717369 TATATTTTAATATATATT
1 TATATTTAAAT-TATATT
717387 GATATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 3 0.09
23 4 0.12
24 3 0.09
25 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATATTTAAATTATATTTTATATT
Found at i:717830 original size:34 final size:32
Alignment explanation
Indices: 717792--717855 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
717782 ATAAATCTAT
717792 ATTATATCAATTTAAAA-TTAAATTAATTTATATA
1 ATTAT-TCAATTTAAAATTTAAA--AATTTATATA
*
717826 ATTATTTAATTTAAAATTTAAAAATTTATA
1 ATTATTCAATTTAAAATTTAAAAATTTATA
717856 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 8 0.29
33 10 0.36
34 10 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTATTCAATTTAAAATTTAAAAATTTATATA
Found at i:722028 original size:144 final size:144
Alignment explanation
Indices: 721836--722120 Score: 461
Period size: 144 Copynumber: 2.0 Consensus size: 144
721826 TAGGGGTTAC
*
721836 TATTGCCAATAGATGGTTCATGGTTGCCAAGTGCCAACTGTTTTCATGAAGGCTTGGCTGTCAGC
1 TATTGCCAATAGATGGTTCATGGTTGCCAAGTGCCAACTGTTTTCATGAAGGCTTGGCTGCCAGC
* *
721901 CA-TTTCGCTATTCCCATGTATTAATGC-ATACATACATATGAATAATATATATATGTTTGTA-T
66 CATTTTCACTATTCCCATGTATTAAT-CTATACATACATAT--AT-ATATATATATGTATGTACT
*
721963 ATGTATGTATGTATGCTA
127 ATGTATCTATGTATGCTA
721981 TATT-CCAATAGATGGTTCATGGTTGCCAAGTGCCAACTGTTTTCATGAAGGCTTGGCTGCCAGC
1 TATTGCCAATAGATGGTTCATGGTTGCCAAGTGCCAACTGTTTTCATGAAGGCTTGGCTGCCAGC
722045 CATTTTCACTATTCCCATGTATTAATCTATACATACATATATATATATATATGTATGTACTTATG
66 CATTTTCACTATTCCCATGTATTAATCTATACATACATATATATATATATATGTATGTAC-TATG
722110 TATCTATGTAT
130 TATCTATGTAT
722121 AGGAAACTTA
Statistics
Matches: 132, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
142 16 0.12
143 2 0.02
144 76 0.58
145 38 0.29
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (144 bp):
TATTGCCAATAGATGGTTCATGGTTGCCAAGTGCCAACTGTTTTCATGAAGGCTTGGCTGCCAGC
CATTTTCACTATTCCCATGTATTAATCTATACATACATATATATATATATATGTATGTACTATGT
ATCTATGTATGCTA
Found at i:723810 original size:14 final size:14
Alignment explanation
Indices: 723791--723818 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
723781 AGTGACCACA
723791 GCCCCTTTTTCTCT
1 GCCCCTTTTTCTCT
723805 GCCCCTTTTTCTCT
1 GCCCCTTTTTCTCT
723819 CTTTGGCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (14 bp):
GCCCCTTTTTCTCT
Found at i:724374 original size:2 final size:2
Alignment explanation
Indices: 724367--724394 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
724357 GCATAGCTCG
724367 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
724395 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:724399 original size:2 final size:2
Alignment explanation
Indices: 724394--724418 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
724384 TCTCTCTCTC
724394 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 T
724419 TACATATTCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:725327 original size:17 final size:17
Alignment explanation
Indices: 725304--725342 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
725294 TCAAACATAA
*
725304 ATATTTAATATTAATAT
1 ATATTTAATATGAATAT
*
725321 GTATTTAATATGAATAT
1 ATATTTAATATGAATAT
725338 ATATT
1 ATATT
725343 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATATTTAATATGAATAT
Found at i:725359 original size:11 final size:11
Alignment explanation
Indices: 725343--725389 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
725333 AATATATATT
725343 AAATTTTTTAA
1 AAATTTTTTAA
725354 AAATTTTTTATA
1 AAATTTTTTA-A
*
725366 TAA---TTTAA
1 AAATTTTTTAA
725374 AAATTTTTTAA
1 AAATTTTTTAA
725385 AAATT
1 AAATT
725390 ATATTATCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
11 20 0.67
12 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AAATTTTTTAA
Found at i:731442 original size:88 final size:87
Alignment explanation
Indices: 731094--731429 Score: 291
Period size: 88 Copynumber: 3.8 Consensus size: 87
731084 TAAGAAATTT
* * * * * * * * **
731094 ATATTTTCTATCATGTCAGAAAAAAATCTAATACCTCATGCATCTGTCACATCTTTT-AGGTTCC
1 ATATTTTCTGTCATGTAAG-AAAGAATTTGATACC-CATGCATTTGTTACAT-TTTTCGGGTTTT
* *
731158 AAAAAATTTATTAGGCATTAATCGA
63 AAGAAATTTATTAGGCATTAGTCGA
* * * * * * ** * * *
731183 ATATTTTCTATTATATTAGAAAGAATCTGATACCATATGCATTTGCCACATCTTTCGAGTTTCAA
1 ATATTTTCTGTCATGTAAGAAAGAATTTGATACC-CATGCATTTGTTACATTTTTCGGGTTTTAA
*
731248 GAAATTTATTAGGCATTAGTTGA
65 GAAATTTATTAGGCATTAGTCGA
* ** * * *
731271 ATATTTTTTGTCATGTAAG-AAGGTTTTGATACCCCATGCATTTATTATATCTTTT-GGGTTCTA
1 ATATTTTCTGTCATGTAAGAAAGAATTTGATA-CCCATGCATTTGTTACAT-TTTTCGGGTTTTA
*
731334 AAAAATTTATTAGGCATTAGTCGA
64 AGAAATTTATTAGGCATTAGTCGA
* *
731358 ATATTTTCTGTCATGTCAGAAAGAATTTGATATCCCATGCATTTGTTGCATTTTTCGGGTTTTAA
1 ATATTTTCTGTCATGTAAGAAAGAATTTGATA-CCCATGCATTTGTTACATTTTTCGGGTTTTAA
731423 GAAATTT
65 GAAATTT
731430 GTTAAATATT
Statistics
Matches: 197, Mismatches: 45, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
87 71 0.36
88 110 0.56
89 16 0.08
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (87 bp):
ATATTTTCTGTCATGTAAGAAAGAATTTGATACCCATGCATTTGTTACATTTTTCGGGTTTTAAG
AAATTTATTAGGCATTAGTCGA
Found at i:731498 original size:175 final size:175
Alignment explanation
Indices: 731122--731519 Score: 397
Period size: 175 Copynumber: 2.3 Consensus size: 175
731112 GAAAAAAATC
* * * * * *
731122 TAATACCTCATGCATCTGTCACATCTTTTAGGTTCCAAAAAATTTATTAGGCATTAATCGAATAT
1 TAATACCCCATGCATTTATCATATCTTTTGGGTTCAAAAAAATTTATTAGGCATTAATCGAATAT
* * *
731187 TTTCTATTATATTAGAAAGAATCTGATACCATATGCATTTGCCACATCTTTCGAGTTTCAAGAAA
66 TTTCTATCATATCAGAAAGAATCTGATACCACATGCATTTGCCACATCTTTCGAGTTTCAAGAAA
** * * ***
731252 TTTATTAGGCATTAGTTGAATATTTTTTGTCATGTAAGAAGGTTT
131 TTTATTAAACATTAGTTAAATATTTTTAGTCATGTAAGAAGGAAA
* * * *
731297 TGATACCCCATGCATTTATTATATCTTTTGGGTTCTAAAAAATTTATTAGGCATTAGTCGAATAT
1 TAATACCCCATGCATTTATCATATCTTTTGGGTTCAAAAAAATTTATTAGGCATTAATCGAATAT
* * * *** * * *
731362 TTTCTGTCATGTCAGAAAGAATTTGATATCC-CATGCATTTGTTGCATTTTTCGGGTTTTAAGAA
66 TTTCTATCATATCAGAAAGAATCTGATA-CCACATGCATTTGCCACATCTTTCGAGTTTCAAGAA
* * ** *
731426 ATTTGTTAAATATTAGTTAAATATTTTCTAGTTGTGTCAGAA-GAAA
130 ATTTATTAAACATTAGTTAAATATTTT-TAGTCATGTAAGAAGGAAA
* ** * *
731472 TAATATCCCATTTATCTTA-CATATCTTTCGAGTTCAAAAAAATTTATT
1 TAATACCCCATGCAT-TTATCATATCTTTTGGGTTCAAAAAAATTTATT
731520 TTCTATTTTT
Statistics
Matches: 179, Mismatches: 41, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
175 164 0.92
176 15 0.08
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (175 bp):
TAATACCCCATGCATTTATCATATCTTTTGGGTTCAAAAAAATTTATTAGGCATTAATCGAATAT
TTTCTATCATATCAGAAAGAATCTGATACCACATGCATTTGCCACATCTTTCGAGTTTCAAGAAA
TTTATTAAACATTAGTTAAATATTTTTAGTCATGTAAGAAGGAAA
Found at i:731891 original size:15 final size:15
Alignment explanation
Indices: 731860--731907 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
731850 TCGTTGGTGT
* *
731860 TTCTTTCTGAATGGC
1 TTCTTCCTGAGTGGC
* *
731875 TTTTTCTTGAGTGGC
1 TTCTTCCTGAGTGGC
731890 TTCTTCCTGAGTGGC
1 TTCTTCCTGAGTGGC
731905 TTC
1 TTC
731908 ATCTGCAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.08, C:0.21, G:0.23, T:0.48
Consensus pattern (15 bp):
TTCTTCCTGAGTGGC
Found at i:734094 original size:20 final size:20
Alignment explanation
Indices: 734069--734106 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
734059 ATCATGATAA
734069 TAAATTATAAATTTAAAATT
1 TAAATTATAAATTTAAAATT
**
734089 TAAATTATTTATTTAAAA
1 TAAATTATAAATTTAAAA
734107 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTATAAATTTAAAATT
Found at i:736199 original size:13 final size:13
Alignment explanation
Indices: 736171--736208 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
736161 AGTGTCCATT
*
736171 TAAAAATAACAT-
1 TAAAAATAAAATA
736183 TAAAAATAAAATA
1 TAAAAATAAAATA
*
736196 TAAATATAAAATA
1 TAAAAATAAAATA
736209 CATCAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAATAAAATA
Found at i:737664 original size:21 final size:20
Alignment explanation
Indices: 737640--737682 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
737630 TAAGACATAA
*
737640 TTTATCTCATATTATTTTTAT
1 TTTATCTCATAATA-TTTTAT
* *
737661 TTTATTTTATAATATTTTAT
1 TTTATCTCATAATATTTTAT
737681 TT
1 TT
737683 AAAATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATCTCATAATATTTTAT
Done.