Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 8 of 16
Found at i:1185123 original size:20 final size:19
Alignment explanation
Indices: 1185096--1185133 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1185086 AACACAGTTT
1185096 TTTTAAAAATTTAATTAAA
1 TTTTAAAAATTTAATTAAA
*
1185115 TTTTAAAAATTTTATTAAA
1 TTTTAAAAATTTAATTAAA
1185134 AATATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAAAAATTTAATTAAA
Found at i:1186356 original size:6 final size:6
Alignment explanation
Indices: 1186345--1186377 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1186335 GTTAGCCAAA
1186345 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCT
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCT
1186378 TCCTCTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTCCC
Found at i:1186385 original size:6 final size:6
Alignment explanation
Indices: 1186376--1186418 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1186366 CCCCCTCCCC
* * * *
1186376 CTTCCT CTTCCT CTTCCC CTCCCT CTTCCC CTTCCT CTCCCT C
1 CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT C
1186419 CATATTCCTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CTTCCT
Found at i:1186391 original size:12 final size:12
Alignment explanation
Indices: 1186376--1186413 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1186366 CCCCCTCCCC
*
1186376 CTTCCTCTTCCT
1 CTTCCCCTTCCT
*
1186388 CTTCCCCTCCCT
1 CTTCCCCTTCCT
1186400 CTTCCCCTTCCT
1 CTTCCCCTTCCT
1186412 CT
1 CT
1186414 CCCTCCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
CTTCCCCTTCCT
Found at i:1186394 original size:18 final size:18
Alignment explanation
Indices: 1186349--1186418 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
1186339 GCCAAACCTC
* * *
1186349 CCCCTCCCCCTCCCCCTC
1 CCCCTTCCCCTCCCTCTT
* *
1186367 CCCCTCCCCCTTCCTCTT
1 CCCCTTCCCCTCCCTCTT
*
1186385 CCTCTTCCCCTCCCTCTT
1 CCCCTTCCCCTCCCTCTT
*
1186403 CCCCTTCCTCTCCCTC
1 CCCCTTCCCCTCCCTC
1186419 CATATTCCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (18 bp):
CCCCTTCCCCTCCCTCTT
Found at i:1186394 original size:24 final size:24
Alignment explanation
Indices: 1186345--1186413 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
1186335 GTTAGCCAAA
* * * *
1186345 CCTCCCCCTCCCCCTCCCCCTCCC
1 CCTCCCCCTTCCCCTTCCTCTTCC
*
1186369 CCTCCCCCTTCCTCTTCCTCTTCC
1 CCTCCCCCTTCCCCTTCCTCTTCC
*
1186393 CCTCCCTCTTCCCCTTCCTCT
1 CCTCCCCCTTCCCCTTCCTCT
1186414 CCCTCCATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (24 bp):
CCTCCCCCTTCCCCTTCCTCTTCC
Found at i:1190901 original size:25 final size:24
Alignment explanation
Indices: 1190825--1190902 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 24
1190815 ATTAAATCGA
*
1190825 ATTTAAATAAATTTTTTTA-TAATTCA
1 ATTT-AAT-AATTTTTTTATTAATT-T
1190851 ATTTAATTAATTTTATATTATT-ATTT
1 ATTTAA-TAATTTT-T-TTATTAATTT
1190877 ATTTAATAATTTTTTTATTAAATTT
1 ATTTAATAATTTTTTTATT-AATTT
1190902 A
1 A
1190903 GTTATAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
23 5 0.11
24 1 0.02
25 20 0.44
26 12 0.27
27 6 0.13
28 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTAATAATTTTTTTATTAATTT
Found at i:1193102 original size:2 final size:2
Alignment explanation
Indices: 1193095--1193167 Score: 64
Period size: 2 Copynumber: 38.5 Consensus size: 2
1193085 TAACATTATC
*
1193095 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A- AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** * *
1193135 -T AT TT GC AG GT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1193168 CTTAATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
1 4 0.07
2 53 0.93
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1193119 original size:13 final size:13
Alignment explanation
Indices: 1193095--1193130 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1193085 TAACATTATC
1193095 ATATAT-ATATAT
1 ATATATAATATAT
1193107 ATATATAATATAT
1 ATATATAATATAT
1193120 ATATATAATAT
1 ATATATAATAT
1193131 GTATTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:1199650 original size:22 final size:18
Alignment explanation
Indices: 1199610--1199654 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 18
1199600 ATTTAGCTAT
1199610 TATTTTTTTATAAATATC
1 TATTTTTTTATAAATATC
1199628 TATTTATTTTGATAGAATGATC
1 TATTT-TTTT-ATA-AAT-ATC
1199650 TATTT
1 TATTT
1199655 CAATACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 3 0.13
21 3 0.13
22 8 0.35
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (18 bp):
TATTTTTTTATAAATATC
Found at i:1199854 original size:26 final size:26
Alignment explanation
Indices: 1199825--1199875 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1199815 ATTTATTATC
1199825 AAATATATTTATTA-ATATAAATATAA
1 AAATAT-TTTATTATATATAAATATAA
* *
1199851 AAATATTTTTTTATATTTAAATATA
1 AAATATTTTATTATATATAAATATA
1199876 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATATTTTATTATATATAAATATAA
Found at i:1200454 original size:2 final size:2
Alignment explanation
Indices: 1200412--1200438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1200402 TATAATAACA
1200412 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
1200439 AACAATGAAT
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:1200833 original size:3 final size:3
Alignment explanation
Indices: 1200825--1200878 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1200815 ATTGAACTAT
1200825 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1200873 ATA ATA
1 ATA ATA
1200879 GTAAGTCATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1201428 original size:15 final size:16
Alignment explanation
Indices: 1201398--1201429 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1201388 TTTAATATTA
1201398 ATTTAAAATATTTAAT
1 ATTTAAAATATTTAAT
1201414 ATTTAAAAT-TTTAAT
1 ATTTAAAATATTTAAT
1201429 A
1 A
1201430 ATATATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAAATATTTAAT
Found at i:1201945 original size:15 final size:14
Alignment explanation
Indices: 1201914--1201949 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1201904 ATTAACGATT
*
1201914 ATATATTTAATATA
1 ATATATTTAAGATA
1201928 ATATATTTATAGATA
1 ATATATTTA-AGATA
1201943 ATATATT
1 ATATATT
1201950 AATTATCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
ATATATTTAAGATA
Found at i:1202561 original size:2 final size:2
Alignment explanation
Indices: 1202554--1202590 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1202544 CATTCAACTG
1202554 TC TC TC TC 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 TC TC TC TC T
1202591 GTCTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1216628 original size:18 final size:18
Alignment explanation
Indices: 1216607--1216679 Score: 51
Period size: 18 Copynumber: 3.8 Consensus size: 18
1216597 AATTGGATAA
1216607 ATATATAGAAATATTTAT
1 ATATATAGAAATATTTAT
1216625 ATATATATTGATAAATATGATT-T
1 ATATATA--G--AAATAT--TTAT
*
1216648 ATATA-AGAAATATTAAAT
1 ATATATAGAAATATT-TAT
*
1216666 ATATAAAGAAATAT
1 ATATATAGAAATAT
1216680 ATAGAAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
16 1 0.02
18 19 0.42
19 8 0.18
20 2 0.04
22 7 0.16
23 6 0.13
24 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (18 bp):
ATATATAGAAATATTTAT
Found at i:1216931 original size:17 final size:17
Alignment explanation
Indices: 1216828--1216937 Score: 62
Period size: 19 Copynumber: 6.1 Consensus size: 17
1216818 AAAAATTGGG
*
1216828 TAAATTTATAGAAATATT
1 TAAATATATAGAAATA-T
* *
1216846 TATATATATTGGTAAATAT
1 TAAATATA-TAG-AAATAT
* *
1216865 TATTTATATATAGAAAAAT
1 TA--AATATATAGAAATAT
*
1216884 TAAATGTATATAGAAAACAT
1 TAAA--TATATAG-AAATAT
*
1216904 T--GTATACTAGAAATAT
1 TAAATATA-TAGAAATAT
1216920 TAAATATATAGAAATAT
1 TAAATATATAGAAATAT
1216937 T
1 T
1216938 TATCCAATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
16 10 0.14
17 14 0.19
18 10 0.14
19 19 0.26
20 13 0.18
21 6 0.08
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (17 bp):
TAAATATATAGAAATAT
Found at i:1217080 original size:2 final size:2
Alignment explanation
Indices: 1217073--1217102 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1217063 CTTAGCTCTC
1217073 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
1217103 GTATGTATGT
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:1217107 original size:4 final size:4
Alignment explanation
Indices: 1217100--1217131 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1217090 TATATATATA
1217100 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
1217132 GTAGATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1217716 original size:2 final size:2
Alignment explanation
Indices: 1217709--1217790 Score: 55
Period size: 2 Copynumber: 43.0 Consensus size: 2
1217699 TTGTCCATAA
** *
1217709 AT AT AT AT AT AT AT AT AT AT -T AT -T AT CC AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * ** *
1217749 AT AA AA AT -T AT -T GT CC AT AC 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 AT AT AT
1217789 AT
1 AT
1217791 CCACGACAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
1 4 0.06
2 58 0.94
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1217731 original size:32 final size:32
Alignment explanation
Indices: 1217695--1217788 Score: 142
Period size: 32 Copynumber: 3.1 Consensus size: 32
1217685 CATAGCAAAA
1217695 ATTATTGTCCATAAATATATATATATATATAT
1 ATTATTGTCCATAAATATATATATATATATAT
*
1217727 ATTATTATCCATAAATATATATATA-A-A-A-
1 ATTATTGTCCATAAATATATATATATATATAT
*
1217755 ATTATTGTCCATACATATATATATATATATAT
1 ATTATTGTCCATAAATATATATATATATATAT
1217787 AT
1 AT
1217789 ATCCACGACA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 23 0.42
29 2 0.04
30 2 0.04
31 2 0.04
32 26 0.47
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (32 bp):
ATTATTGTCCATAAATATATATATATATATAT
Found at i:1217744 original size:28 final size:28
Alignment explanation
Indices: 1217713--1217793 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
1217703 CCATAAATAT
1217713 ATATATATATATATATTATTATCCATAA
1 ATATATATATATATATTATTATCCATAA
* * * *
1217741 ATATATATATAAAAATTATTGTCCATAC
1 ATATATATATATATATTATTATCCATAA
1217769 ATATATATATATATA-TATATATCCA
1 ATATATATATATATATTAT-TATCCA
1217794 CGACAAGACT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 42 0.93
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (28 bp):
ATATATATATATATATTATTATCCATAA
Found at i:1217954 original size:19 final size:18
Alignment explanation
Indices: 1217919--1217958 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1217909 TGTTCGAAAG
*
1217919 TATTGAAAATTTTTAAAA
1 TATTAAAAATTTTTAAAA
1217937 TATTAAAAATTATTTAAAA
1 TATTAAAAATT-TTTAAAA
1217956 TAT
1 TAT
1217959 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TATTAAAAATTTTTAAAA
Found at i:1218602 original size:32 final size:34
Alignment explanation
Indices: 1218553--1218627 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
1218543 TATGAGTGTG
*
1218553 ATATGAAAA-TATAAATATTTTAAAATTTATAT-A
1 ATAT-AAAATTATAAATATATTAAAATTTATATAA
* *
1218586 ATA-AAAATTATTAATATATTAAATTTTATATAA
1 ATATAAAATTATAAATATATTAAAATTTATATAA
1218619 ATATAAAAT
1 ATATAAAAT
1218628 ATTTTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 4 0.11
32 20 0.56
33 7 0.19
34 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
ATATAAAATTATAAATATATTAAAATTTATATAA
Found at i:1218614 original size:18 final size:18
Alignment explanation
Indices: 1218573--1218627 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1218563 ATAAATATTT
1218573 TAAAA-TTTATAT-AATA
1 TAAAATTTTATATAAATA
1218589 -AAAA--TTAT-TAATATA
1 TAAAATTTTATATAA-ATA
*
1218604 TTAAATTTTATATAAATA
1 TAAAATTTTATATAAATA
1218622 TAAAAT
1 TAAAAT
1218628 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 7 0.23
16 3 0.10
18 12 0.39
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTTATATAAATA
Found at i:1221101 original size:3 final size:3
Alignment explanation
Indices: 1221095--1221135 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1221085 AATAATAGTA
*
1221095 ATT ATT ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1221136 AAAATCCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1221619 original size:16 final size:17
Alignment explanation
Indices: 1221600--1221632 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1221590 AAATAATTAA
*
1221600 AACATGATAT-AATATG
1 AACATAATATAAATATG
1221616 AACATAATATAAATATG
1 AACATAATATAAATATG
1221633 TGAACGCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (17 bp):
AACATAATATAAATATG
Found at i:1221872 original size:26 final size:27
Alignment explanation
Indices: 1221843--1221893 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1221833 AAATTACTAT
*
1221843 AAAACATTATATAAA-ATATAAAAATC
1 AAAACATGATATAAACATATAAAAATC
1221869 AAAACATGATATAAACATATAAAAA
1 AAAACATGATATAAACATATAAAAA
1221894 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (27 bp):
AAAACATGATATAAACATATAAAAATC
Found at i:1221902 original size:11 final size:10
Alignment explanation
Indices: 1221887--1221953 Score: 71
Period size: 11 Copynumber: 6.3 Consensus size: 10
1221877 ATATAAACAT
1221887 ATAAAAAATA
1 ATAAAAAATA
*
1221897 ATTAAAATATA
1 A-TAAAAAATA
1221908 ATATAAAAATA
1 ATA-AAAAATA
*
1221919 ATAATAATATA
1 ATAA-AAAATA
1221930 ATATAAAAATA
1 ATA-AAAAATA
*
1221941 ATAAAATATA
1 ATAAAAAATA
1221951 ATA
1 ATA
1221954 TAAATATATG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 13 0.27
11 34 0.71
12 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:1221921 original size:16 final size:16
Alignment explanation
Indices: 1221894--1221951 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
1221884 CATATAAAAA
1221894 ATAAT-TAAAATATAAT
1 ATAATATAAAA-ATAAT
* *
1221910 ATAAAAATAATAATAAT
1 AT-AATATAAAAATAAT
1221927 ATAATATAAAAATAAT
1 ATAATATAAAAATAAT
*
1221943 AAAATATAA
1 ATAATATAA
1221952 TATAAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 22 0.63
17 9 0.26
18 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATATAAAAATAAT
Found at i:1221940 original size:19 final size:19
Alignment explanation
Indices: 1221857--1221957 Score: 72
Period size: 19 Copynumber: 5.4 Consensus size: 19
1221847 CATTATATAA
*
1221857 AATATAAAAATCAA-AACAT
1 AATATAAAAAT-AATAATAT
* *
1221876 GATATAAACATATAA-AAAAT
1 AATATAAA-A-ATAATAATAT
1221896 AAT-T-AAAAT-ATAATAT
1 AATATAAAAATAATAATAT
*
1221912 AA-A-AATAATAATAATAT
1 AATATAAAAATAATAATAT
1221929 AATATAAAAATAATAAAATAT
1 AATATAAAAATAAT--AATAT
1221950 AATATAAA
1 AATATAAA
1221958 TATATGAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
15 1 0.02
16 12 0.18
17 10 0.15
18 3 0.05
19 16 0.24
20 9 0.14
21 15 0.23
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (19 bp):
AATATAAAAATAATAATAT
Found at i:1221958 original size:11 final size:11
Alignment explanation
Indices: 1221901--1221961 Score: 81
Period size: 11 Copynumber: 5.6 Consensus size: 11
1221891 AAAATAATTA
1221901 AAATATAATAT
1 AAATATAATAT
*
1221912 AAAAATAATA-
1 AAATATAATAT
1221922 ATAATATAATAT
1 A-AATATAATAT
*
1221934 AAAAATAATA-
1 AAATATAATAT
1221944 AAATATAATAT
1 AAATATAATAT
1221955 AAATATA
1 AAATATA
1221962 TGAAAAACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
10 10 0.23
11 32 0.74
12 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1221967 original size:21 final size:21
Alignment explanation
Indices: 1221885--1221957 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 21
1221875 TGATATAAAC
1221885 ATATAAAAAATAATTAAAATATA
1 ATAT-AAAAATAA-TAAAATATA
1221908 ATATAAAAATAATAATAATATA
1 ATATAAAAATAATAA-AATATA
1221930 ATATAAAAATAATAAAATATA
1 ATATAAAAATAATAAAATATA
1221951 ATATAAA
1 ATATAAA
1221958 TATATGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.33
22 29 0.59
23 4 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAAAAATAATAAAATATA
Found at i:1222215 original size:16 final size:15
Alignment explanation
Indices: 1222188--1222218 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1222178 ATGCGGGGAA
1222188 GAGAAAGAAGAAAAG
1 GAGAAAGAAGAAAAG
1222203 GAGAAAGGAAGAAAAG
1 GAGAAA-GAAGAAAAG
1222219 AAAAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAGAAAGAAGAAAAG
Found at i:1222275 original size:22 final size:20
Alignment explanation
Indices: 1222238--1222290 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 20
1222228 AGAAAGTGAA
1222238 GAAAAGAAAAGAAAGGAAAGG
1 GAAAA-AAAAGAAAGGAAAGG
1222259 GAAAAAAAAGAAGAAGGAAAGTG
1 GAAAAAAAAG-A-AAGGAAAG-G
1222282 AGAAAAAAA
1 -GAAAAAAA
1222291 TTTTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 8 0.29
23 1 0.04
24 8 0.29
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (20 bp):
GAAAAAAAAGAAAGGAAAGG
Found at i:1222288 original size:25 final size:25
Alignment explanation
Indices: 1222212--1222290 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
1222202 GGAGAAAGGA
* * *
1222212 AGAAAAGAAAA-ATGAAAGAAAGTG
1 AGAAAAAAAAAGAAGAAGGAAAGTG
*
1222236 AAGAAAAGAAAAG-A-AAGGAAAG-G
1 -AGAAAAAAAAAGAAGAAGGAAAGTG
1222259 -G-AAAAAAAAGAAGAAGGAAAGTG
1 AGAAAAAAAAAGAAGAAGGAAAGTG
1222282 AGAAAAAAA
1 AGAAAAAAA
1222291 TTTTATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
20 8 0.18
21 2 0.04
22 8 0.18
23 2 0.04
24 8 0.18
25 17 0.38
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.04
Consensus pattern (25 bp):
AGAAAAAAAAAGAAGAAGGAAAGTG
Found at i:1223159 original size:20 final size:21
Alignment explanation
Indices: 1223121--1223159 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1223111 ATATAATTTA
*
1223121 ATTTAAATTACATAATTATTG
1 ATTTAAATTAAATAATTATTG
*
1223142 ATTT-AATTAAATATTTAT
1 ATTTAAATTAAATAATTAT
1223160 AAATACACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
ATTTAAATTAAATAATTATTG
Found at i:1223889 original size:17 final size:17
Alignment explanation
Indices: 1223867--1223900 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1223857 ATAAATATAA
1223867 AAATAATCTTG-ACAATT
1 AAATAAT-TTGAACAATT
1223884 AAATAATTTGAACAATT
1 AAATAATTTGAACAATT
1223901 TCAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (17 bp):
AAATAATTTGAACAATT
Found at i:1225058 original size:2 final size:2
Alignment explanation
Indices: 1225053--1225081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1225043 GTGTGAACAA
1225053 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 A
1225082 GTTGGTGATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1225755 original size:29 final size:30
Alignment explanation
Indices: 1225723--1225781 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1225713 AATATAATTT
*
1225723 TAAAAATTATGAA-AAAAATAAAATATTAA
1 TAAAAATTATAAATAAAAATAAAATATTAA
*
1225752 TAAAAATTATAAATAAAAATGAAATATTAA
1 TAAAAATTATAAATAAAAATAAAATATTAA
1225782 CAGAATTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (30 bp):
TAAAAATTATAAATAAAAATAAAATATTAA
Found at i:1234068 original size:22 final size:22
Alignment explanation
Indices: 1233992--1234065 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
1233982 ATATAAAAAT
1233992 ATATATATT-TAAAAT-TTTATATA
1 ATATA-ATTATAAAATATTT-TA-A
* *
1234015 ATATAAATTAT-TAATATTTTAT
1 ATAT-AATTATAAAATATTTTAA
1234037 ATATAATTATAAAATATTTTAA
1 ATATAATTATAAAATATTTTAA
1234059 ATA-AATT
1 ATATAATT
1234066 TATGATATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 10 0.23
22 16 0.37
23 12 0.28
24 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAATTATAAAATATTTTAA
Found at i:1234413 original size:3 final size:3
Alignment explanation
Indices: 1234405--1234431 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1234395 AATTACTTAC
1234405 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1234432 CCCACTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1244187 original size:3 final size:3
Alignment explanation
Indices: 1244179--1244362 Score: 188
Period size: 3 Copynumber: 61.3 Consensus size: 3
1244169 CCTTCTCTTC
* *
1244179 GCT GCT GCT GCT GCT GCT GCT GCT GTT GCT GCT GCT GTT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * *
1244227 GCT GTT GCT GCT GCT GCT GTT GCT GCT GCT GCT GCT GTT GTT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * * * * * *
1244275 GCA GCT GTT GTT GCT GCT GCA GCT GTT GTT GCT GCT GCT GCT GTT GTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * * * *
1244323 GTT GCT GCT GCT GTT GTT GTT GCT GCA GCT GTT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1244363 AGCATGCCTC
Statistics
Matches: 155, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 155 1.00
ACGTcount: A:0.02, C:0.24, G:0.34, T:0.41
Consensus pattern (3 bp):
GCT
Found at i:1244202 original size:18 final size:18
Alignment explanation
Indices: 1244181--1244362 Score: 244
Period size: 18 Copynumber: 10.3 Consensus size: 18
1244171 TTCTCTTCGC
* *
1244181 TGCTGCTGCTGCTGCTGC
1 TGCTGCTGCTGCTGTTGT
* *
1244199 TGCTGTTGCTGCTGCTGT
1 TGCTGCTGCTGCTGTTGT
1244217 TGCTGCTGCTGC---TGT
1 TGCTGCTGCTGCTGTTGT
*
1244232 TGCTGCTGCTGCTGTTGC
1 TGCTGCTGCTGCTGTTGT
1244250 TGCTGCTGCTGCTGTTGT
1 TGCTGCTGCTGCTGTTGT
*
1244268 TGCTGCTGCAGCTGTTGT
1 TGCTGCTGCTGCTGTTGT
*
1244286 TGCTGCTGCAGCTGTTGT
1 TGCTGCTGCTGCTGTTGT
1244304 TGCTGCTGCTGCTGTTGT
1 TGCTGCTGCTGCTGTTGT
*
1244322 TGTTGCTGCTGCTGTTGT
1 TGCTGCTGCTGCTGTTGT
* * *
1244340 TGTTGCTGCAGCTGTTGC
1 TGCTGCTGCTGCTGTTGT
1244358 TGCTG
1 TGCTG
1244363 AGCATGCCTC
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
15 15 0.10
18 135 0.90
ACGTcount: A:0.02, C:0.24, G:0.34, T:0.41
Consensus pattern (18 bp):
TGCTGCTGCTGCTGTTGT
Found at i:1247091 original size:25 final size:23
Alignment explanation
Indices: 1247063--1247112 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
1247053 ATATAGTACT
1247063 TTAAA-TATAATTAAAATATAAATTA
1 TTAAATTA-AATTAAAAT-T-AATTA
*
1247088 TTAAGTTAAATTAAAATTAATTA
1 TTAAATTAAATTAAAATTAATTA
1247111 TT
1 TT
1247113 TCATAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 7 0.30
24 1 0.04
25 13 0.57
26 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAAATTAAATTAAAATTAATTA
Found at i:1247651 original size:17 final size:17
Alignment explanation
Indices: 1247631--1247682 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
1247621 TTAATTTGAT
1247631 TTTATTTAAAATTATTA
1 TTTATTTAAAATTATTA
*
1247648 TTTATATAATAAAA-TATTT
1 TTTAT-T--TAAAATTATTA
*
1247667 TTTATTTAAATTTATT
1 TTTATTTAAAATTATT
1247683 TATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
18 2 0.07
19 9 0.31
20 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTTAAAATTATTA
Found at i:1250516 original size:107 final size:108
Alignment explanation
Indices: 1250330--1250533 Score: 338
Period size: 107 Copynumber: 1.9 Consensus size: 108
1250320 GTGGATTTGT
* *
1250330 CAAACAAACATCTACATAAACAAACTCTAGCTAGTTCTATGCCAATCTTGCTCCCTCTACCTCGG
1 CAAACAAACATCTACATAAACAAACTCTAGCCAGTTCTATGCCAATCTTGCTCCCTCTACCTCGA
* *
1250395 AAACATTATTGAATG-ATAGTCCCACAGACAAATGTGTTTTTC
66 AAACATTAGTGAATGAACAGTCCCACAGACAAATGTGTTTTTC
* * *
1250437 CAAACAAACATCTACATTAACAAACTCTAGCCAGTTCTGTGCCAATCTTGCTTCCTCTACCTCGA
1 CAAACAAACATCTACATAAACAAACTCTAGCCAGTTCTATGCCAATCTTGCTCCCTCTACCTCGA
1250502 AAACATTAGTGAATGAACAGTCCCACAGACAA
66 AAACATTAGTGAATGAACAGTCCCACAGACAA
1250534 TGTCAAATAT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
107 74 0.83
108 15 0.17
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.26
Consensus pattern (108 bp):
CAAACAAACATCTACATAAACAAACTCTAGCCAGTTCTATGCCAATCTTGCTCCCTCTACCTCGA
AAACATTAGTGAATGAACAGTCCCACAGACAAATGTGTTTTTC
Found at i:1253758 original size:67 final size:67
Alignment explanation
Indices: 1253621--1253748 Score: 193
Period size: 67 Copynumber: 1.9 Consensus size: 67
1253611 TTATAATATC
* * * * *
1253621 TTTAAAATATAATAAAATTATAAATTTTTGAGTAGAATAGTGAAAATAATAGAATAAAAATATCC
1 TTTAAAATATAATAAAATCATAAATTTTTGAATAAAATAATGAAAATAACAGAATAAAAATATCC
1253686 TT
66 TT
* *
1253688 TTTAAGATATAATAAAATCATAAATTTTTGAATAAAATAATGAAAATGACAGAATAAAAAT
1 TTTAAAATATAATAAAATCATAAATTTTTGAATAAAATAATGAAAATAACAGAATAAAAAT
1253749 GTTTTTTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.34
Consensus pattern (67 bp):
TTTAAAATATAATAAAATCATAAATTTTTGAATAAAATAATGAAAATAACAGAATAAAAATATCC
TT
Found at i:1258405 original size:14 final size:12
Alignment explanation
Indices: 1258370--1258395 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1258360 AAGCTTGGAC
1258370 ATATAAAATATG
1 ATATAAAATATG
1258382 ATATAAAATATG
1 ATATAAAATATG
1258394 AT
1 AT
1258396 GGCTAAAATA
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:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
ATATAAAATATG
Found at i:1258504 original size:34 final size:33
Alignment explanation
Indices: 1258428--1258504 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
1258418 ATTTTATATA
*
1258428 TTATATAAATAAGTTTTTATAATTTTATTACAT
1 TTATATAAATAAATTTTTATAATTTTATTACAT
* **
1258461 TTATTTAAATAAATTTTTA-AATTTTAATTTGTAT
1 TTATATAAATAAATTTTTATAATTTT-A-TTACAT
1258495 TTATATAAAT
1 TTATATAAAT
1258505 CTTAAGATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 6 0.16
33 18 0.49
34 13 0.35
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (33 bp):
TTATATAAATAAATTTTTATAATTTTATTACAT
Found at i:1259021 original size:2 final size:2
Alignment explanation
Indices: 1259014--1259041 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1259004 CATATCATTG
1259014 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
1259042 TAAGATAATA
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:1259691 original size:20 final size:22
Alignment explanation
Indices: 1259655--1259704 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1259645 GAATAAGGTT
*
1259655 TTTTTTTAATATAAATT-TATA
1 TTTTTATAATATAAATTCTATA
1259676 TTTTTATAATAT-AATTCTATA
1 TTTTTATAATATAAATTCTATA
1259697 -TTTTATAA
1 TTTTTATAA
1259705 AAATAGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTATAATATAAATTCTATA
Found at i:1259842 original size:22 final size:23
Alignment explanation
Indices: 1259817--1259862 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1259807 AATACTTAAT
* *
1259817 TATTAAAAATTAAA-TTAAAATA
1 TATTAAAAATAAAACATAAAATA
1259839 TATTAAAAATAAAACATAAAATA
1 TATTAAAAATAAAACATAAAATA
1259862 T
1 T
1259863 GAACGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TATTAAAAATAAAACATAAAATA
Found at i:1259945 original size:11 final size:11
Alignment explanation
Indices: 1259929--1259953 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1259919 AAATGCTTAT
1259929 AATTTAAATTA
1 AATTTAAATTA
1259940 AATTTAAATTA
1 AATTTAAATTA
1259951 AAT
1 AAT
1259954 AAATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:1260264 original size:20 final size:19
Alignment explanation
Indices: 1260239--1260280 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1260229 TATTGTATAA
*
1260239 AATTTTTATAATTAATAAAT
1 AATTTTTAT-ATAAATAAAT
*
1260259 AATTTTTATGTAAATAAAT
1 AATTTTTATATAAATAAAT
1260278 AAT
1 AAT
1260281 AATAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTTTTATATAAATAAAT
Found at i:1263396 original size:15 final size:15
Alignment explanation
Indices: 1263376--1263424 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1263366 AAGTTAATTG
1263376 ATATAATTAAATAAA
1 ATATAATTAAATAAA
*
1263391 ATATAA-TATATAAA
1 ATATAATTAAATAAA
*
1263405 A-ATAATATAATTAAA
1 ATATAAT-TAAATAAA
1263420 ATATA
1 ATATA
1263425 TTTGTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 13 0.46
16 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAATTAAATAAA
Found at i:1263463 original size:42 final size:42
Alignment explanation
Indices: 1263417--1263496 Score: 94
Period size: 43 Copynumber: 1.9 Consensus size: 42
1263407 TAATATAATT
1263417 AAAA-TATATTTGT-AAATT-TAATAAAAATAATTTATTAAATAA
1 AAAATTATATTT-TAAAATTATAA-AAAAATAATTT-TTAAATAA
* *
1263459 AAAATTTTATTTTAAAATTATAAATAAATAATTTTTAA
1 AAAATTATATTTTAAAATTATAAAAAAATAATTTTTAA
1263497 TTGATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
42 9 0.27
43 21 0.64
44 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (42 bp):
AAAATTATATTTTAAAATTATAAAAAAATAATTTTTAAATAA
Found at i:1263723 original size:2 final size:2
Alignment explanation
Indices: 1263718--1263759 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1263708 CCCCCCCCCT
1263718 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1263760 ATTTCTCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1266210 original size:25 final size:25
Alignment explanation
Indices: 1266156--1266218 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1266146 ATGTTTGATG
* * *
1266156 AATATTTTTTTTATATAGGTATGAT
1 AATATATTTTTTATATAAGTAAGAT
*
1266181 GATATATTTTTTATATAAGTACAG-T
1 AATATATTTTTTATATAAGTA-AGAT
1266206 AATATGATTTTTT
1 AATAT-ATTTTTT
1266219 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 23 0.74
26 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (25 bp):
AATATATTTTTTATATAAGTAAGAT
Found at i:1268845 original size:14 final size:15
Alignment explanation
Indices: 1268794--1268845 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1268784 TATATTATAT
1268794 TTATATAAATTTTAA
1 TTATATAAATTTTAA
1268809 TATATTAATAAATTTT-A
1 T-TA-T-ATAAATTTTAA
*
1268826 TTTTATAAAATTTTAA
1 TTATAT-AAATTTTAA
1268842 TTAT
1 TTAT
1268846 TTATTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 9 0.30
16 7 0.23
17 3 0.10
18 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATAAATTTTAA
Found at i:1268872 original size:16 final size:17
Alignment explanation
Indices: 1268836--1268882 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1268826 TTTTATAAAA
1268836 TTTTA-ATTAT-TTATT
1 TTTTATATTATATTATT
1268851 TATTTATATTATATT-TT
1 T-TTTATATTATATTATT
*
1268868 TTTTATGTTATATTA
1 TTTTATATTATATTA
1268883 GCTAAAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.04
16 16 0.59
17 8 0.30
18 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTATATTATATTATT
Found at i:1271255 original size:3 final size:3
Alignment explanation
Indices: 1271247--1271291 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1271237 ACAGTGTCAA
1271247 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1271292 GTCCATTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1274737 original size:16 final size:16
Alignment explanation
Indices: 1274716--1274766 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1274706 AGGAGGTTTG
1274716 AGTTATTTTAAATTTA
1 AGTTATTTTAAATTTA
*
1274732 AGTTATTTTGAATTT-
1 AGTTATTTTAAATTTA
* *
1274747 AGATCATTTTAGATTTA
1 AG-TTATTTTAAATTTA
1274764 AGT
1 AGT
1274767 CAATCGAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (16 bp):
AGTTATTTTAAATTTA
Found at i:1275597 original size:16 final size:16
Alignment explanation
Indices: 1275576--1275629 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1275566 ATTATCCGAG
*
1275576 TCATTTCGGATTCGGA
1 TCATTTCGGATTCGAA
*
1275592 TCATTTTAGG-TTCGAA
1 TCA-TTTCGGATTCGAA
1275608 TCATTTCGGATTCGAA
1 TCATTTCGGATTCGAA
1275624 TCATTT
1 TCATTT
1275630 TAAGTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 5 0.15
16 23 0.70
17 5 0.15
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (16 bp):
TCATTTCGGATTCGAA
Found at i:1275612 original size:32 final size:32
Alignment explanation
Indices: 1275576--1275636 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1275566 ATTATCCGAG
* *
1275576 TCATTTCGGATTCGGATCATTTTAGGTTCGAA
1 TCATTTCGGATTCGAATCATTTTAAGTTCGAA
1275608 TCATTTCGGATTCGAATCATTTTAAGTTC
1 TCATTTCGGATTCGAATCATTTTAAGTTC
1275637 AGATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (32 bp):
TCATTTCGGATTCGAATCATTTTAAGTTCGAA
Found at i:1275645 original size:16 final size:16
Alignment explanation
Indices: 1275618--1275674 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1275608 TCATTTCGGA
*
1275618 TTCGAATCATTTTAAG
1 TTCGAATTATTTTAAG
*
1275634 TTC-AGATTATTTTAGG
1 TTCGA-ATTATTTTAAG
*
1275650 TTCGAATTATTTTAAAT
1 TTCGAATTATTTT-AAG
1275667 TTCGAATT
1 TTCGAATT
1275675 GATCGGTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.03
16 23 0.68
17 10 0.29
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (16 bp):
TTCGAATTATTTTAAG
Found at i:1275954 original size:2 final size:2
Alignment explanation
Indices: 1275947--1275990 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1275937 CAAGCTTTGA
1275947 AT AT AT 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 AT AT AT
1275989 AT
1 AT
1275991 CCTTACCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276202 original size:7 final size:7
Alignment explanation
Indices: 1276190--1276250 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
1276180 GATATATCTC
1276190 ATTAATT
1 ATTAATT
1276197 ATTAATT
1 ATTAATT
*
1276204 ATTAATA
1 ATTAATT
*
1276211 ATTTATT
1 ATTAATT
**
1276218 ATTTTTAT
1 ATTAAT-T
1276226 ATATAATT
1 AT-TAATT
*
1276234 ATTAATA
1 ATTAATT
*
1276241 ATTTATT
1 ATTAATT
1276248 ATT
1 ATT
1276251 TATATTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
7 35 0.81
8 6 0.14
9 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTAATT
Found at i:1276949 original size:2 final size:2
Alignment explanation
Indices: 1276936--1276967 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1276926 TTAAATCAGC
*
1276936 AT AT AC 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
1276968 TAAAAAGCAT
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1277272 original size:17 final size:17
Alignment explanation
Indices: 1277250--1277285 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1277240 TGTCTAAAAT
1277250 AACTAATTACTCAATGA
1 AACTAATTACTCAATGA
1277267 AACTAATTACTCAATGA
1 AACTAATTACTCAATGA
1277284 AA
1 AA
1277286 TAAAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (17 bp):
AACTAATTACTCAATGA
Found at i:1277976 original size:2 final size:2
Alignment explanation
Indices: 1277969--1278002 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1277959 CAAAGCTCAC
1277969 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
1278003 ATGTTGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1279027 original size:34 final size:34
Alignment explanation
Indices: 1278970--1279188 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
1278960 ATATATAATA
*
1278970 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1279003 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1279037 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1279071 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1279105 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1279139 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1279173 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1279189 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1279145 original size:102 final size:101
Alignment explanation
Indices: 1278970--1279188 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
1278960 ATATATAATA
** * * *
1278970 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1279035 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1279071 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1279136 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1279173 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1279189 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1279550 original size:19 final size:19
Alignment explanation
Indices: 1279494--1279556 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1279484 TGGTTGTCGA
**
1279494 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1279513 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1279532 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1279551 GTTACT
1 GGTACT
1279557 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1283679 original size:34 final size:34
Alignment explanation
Indices: 1283622--1283840 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
1283612 AAGTGGGAGA
*
1283622 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1283655 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1283689 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1283723 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
1283757 ATTATTGATTAAATGGGTGATTTGGT-GACTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAG-CTTACC
* * *
1283791 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1283825 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1283841 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
33 17 0.11
34 141 0.88
35 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1283762 original size:102 final size:101
Alignment explanation
Indices: 1283622--1283840 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
1283612 AAGTGGGAGA
** * ** *
1283622 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGACTTA
1283687 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1283723 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGACTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGACTT
* * *
1283788 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1283825 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1283841 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGACTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1284300 original size:2 final size:2
Alignment explanation
Indices: 1284290--1284339 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1284280 AAAAAAAGAT
*
1284290 TA TA CA 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
1284332 TA TA TA TA
1 TA TA TA TA
1284340 GCTTGGATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1284556 original size:21 final size:21
Alignment explanation
Indices: 1284530--1284569 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1284520 TACTAAATGA
1284530 ATTTCTTCTTTTTTTTCTTTG
1 ATTTCTTCTTTTTTTTCTTTG
1284551 ATTTCTTCTTTTTTTTCTT
1 ATTTCTTCTTTTTTTTCTT
1284570 CTCAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (21 bp):
ATTTCTTCTTTTTTTTCTTTG
Found at i:1284647 original size:23 final size:22
Alignment explanation
Indices: 1284617--1284672 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
1284607 AGATAAACAT
1284617 AAATATAATATAAAAAATAATTA
1 AAATATAATATAAAAAATAA-TA
*
1284640 AAATATAATATAAAATATAATA
1 AAATATAATATAAAAAATAATA
*
1284662 AAATAAAATAT
1 AAATATAATAT
1284673 TAATACATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATATAATATAAAAAATAATA
Found at i:1284682 original size:15 final size:13
Alignment explanation
Indices: 1284617--1284683 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 13
1284607 AGATAAACAT
1284617 AAATATAAT-ATA
1 AAATATAATAATA
*
1284629 AAAAATAAT--TA
1 AAATATAATAATA
1284640 AAATATAAT-ATA
1 AAATATAATAATA
1284652 AAATATAATAAAATA
1 AAATATAAT--AATA
1284667 AAATATTAATACATA
1 AAATA-TAATA-ATA
1284682 AA
1 AA
1284684 TATTTTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.21
12 19 0.40
14 1 0.02
15 13 0.28
16 4 0.09
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATATAATAATA
Found at i:1284705 original size:7 final size:8
Alignment explanation
Indices: 1284638--1284734 Score: 50
Period size: 7 Copynumber: 12.8 Consensus size: 8
1284628 AAAAAATAAT
1284638 TAAA-ATA
1 TAAATATA
1284645 T-AATATA
1 TAAATATA
1284652 -AAATATAA
1 TAAATAT-A
1284660 TAAA-ATA
1 TAAATATA
1284667 -AAATAT-
1 TAAATATA
*
1284673 T-AATACA
1 TAAATATA
*
1284680 TAAATATTT
1 TAAATA-TA
* *
1284689 TTAATTTA
1 TAAATATA
1284697 TAAAATATA
1 T-AAATATA
1284706 TAAAT-TA
1 TAAATATA
*
1284713 TTAATATAA
1 TAAATAT-A
1284722 TAAATAT-
1 TAAATATA
1284729 TAAATA
1 TAAATA
1284735 AATATAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 24
0.67 0.10 0.24
Matches are distributed among these distances:
6 9 0.13
7 25 0.37
8 14 0.21
9 20 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAATATA
Found at i:1284724 original size:16 final size:15
Alignment explanation
Indices: 1284600--1284735 Score: 61
Period size: 14 Copynumber: 8.9 Consensus size: 15
1284590 TGAGAACTCA
*
1284600 AAATATTAGATAAACAT
1 AAATATTA-ATATA-AT
*
1284617 AAATA-TAATATAAA
1 AAATATTAATATAAT
1284631 AAATAATTAAAATATAAT
1 AAAT-ATT--AATATAAT
* *
1284649 ATAAAATATAATAAAAT
1 A-AATAT-TAATATAAT
*
1284666 AAAATATTAATA-CAT
1 -AAATATTAATATAAT
*
1284681 AAATATT--TTTAAT
1 AAATATTAATATAAT
** *
1284694 TTATA-AAATAT-AT
1 AAATATTAATATAAT
1284707 AAATTATTAATATAAT
1 AAA-TATTAATATAAT
1284723 AAATATTAA-ATAA
1 AAATATTAATATAA
1284736 ATATAAAATA
Statistics
Matches: 90, Mismatches: 16, Indels: 29
0.67 0.12 0.21
Matches are distributed among these distances:
12 1 0.01
13 8 0.09
14 20 0.22
15 18 0.20
16 13 0.14
17 16 0.18
18 11 0.12
19 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (15 bp):
AAATATTAATATAAT
Found at i:1284738 original size:20 final size:22
Alignment explanation
Indices: 1284715--1284764 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1284705 ATAAATTATT
1284715 AATATAATAA-ATATTAAATA-
1 AATATAATAATATATTAAATAC
*
1284735 AATATAA-AATATTTTAAATAC
1 AATATAATAATATATTAAATAC
1284756 AATTATAAT
1 AA-TATAAT
1284765 TTACAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 2 0.08
22 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATAATAATATATTAAATAC
Found at i:1285239 original size:27 final size:27
Alignment explanation
Indices: 1285186--1285239 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1285176 AGGAGAGTCG
* *
1285186 CCTTTTTCTTTTAGTTGCTTTGCTTTT
1 CCTTTTCCTTTTAGTTGCTTTACTTTT
* *
1285213 CCTTTTCCTTTTCGTTGCTTTATTTTT
1 CCTTTTCCTTTTAGTTGCTTTACTTTT
1285240 ATTATTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.04, C:0.20, G:0.09, T:0.67
Consensus pattern (27 bp):
CCTTTTCCTTTTAGTTGCTTTACTTTT
Found at i:1285389 original size:3 final size:3
Alignment explanation
Indices: 1285375--1285406 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1285365 CATCTCCAGC
1285375 CAT CAT CA- CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1285407 TAACCAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:1286424 original size:2 final size:2
Alignment explanation
Indices: 1286415--1286470 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1286405 TCTGAATATA
1286415 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1286456 TC TC TC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC
1286471 CCTATATGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1292119 original size:20 final size:21
Alignment explanation
Indices: 1292078--1292137 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
1292068 AAATGTACTT
1292078 TTAAATATTATTTATTGAATTA
1 TTAAATATTATTTATT-AATTA
1292100 TTAAATTATTATTT-TT-ATTA
1 TTAAA-TATTATTTATTAATTA
*
1292120 TTCAAAAATTAATTTATT
1 TT-AAATATT-ATTTATT
1292138 TAAAAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 9 0.27
21 7 0.21
22 9 0.27
23 8 0.24
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAAATATTATTTATTAATTA
Found at i:1292151 original size:17 final size:16
Alignment explanation
Indices: 1292117--1292147 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1292107 ATTATTTTTA
1292117 TTATTCAAAAATTAAT
1 TTATTCAAAAATTAAT
*
1292133 TTATTTAAAAATTAA
1 TTATTCAAAAATTAA
1292148 ATTTTAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTCAAAAATTAAT
Found at i:1292390 original size:18 final size:19
Alignment explanation
Indices: 1292335--1292392 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
1292325 TAAAAAATCA
*
1292335 ATAACATAGAATTTAAAATAT
1 ATAACAAAG-ATTTAAAA-AT
* *
1292356 TTAACAAAGATTAAAAAAT
1 ATAACAAAGATTTAAAAAT
*
1292375 AT-ACAAATATTTAAAAAT
1 ATAACAAAGATTTAAAAAT
1292393 TATTTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 14 0.45
19 3 0.10
20 7 0.23
21 7 0.23
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAACAAAGATTTAAAAAT
Found at i:1293944 original size:52 final size:52
Alignment explanation
Indices: 1293860--1293964 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
1293850 ATTAATATTT
* *
1293860 ATATTTTATATTAAATATAATTTAAATTAAATTAAATTAACAAAAATATAAA
1 ATATTATATATTAAATATAATTTAAATTAAATTAAATTAACAAAAATAAAAA
* * *
1293912 ATATTATATTTTAAATTTAATTT-AATTCAAATTAAATTTACAAAAATAAAAA
1 ATATTATATATTAAATATAATTTAAATT-AAATTAAATTAACAAAAATAAAAA
1293964 A
1 A
1293965 AACTAGTGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.09
52 43 0.91
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (52 bp):
ATATTATATATTAAATATAATTTAAATTAAATTAAATTAACAAAAATAAAAA
Found at i:1294518 original size:6 final size:6
Alignment explanation
Indices: 1294507--1294531 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1294497 TCTTTTGCTT
1294507 GATTTG GATTTG GATTTG GATTTG G
1 GATTTG GATTTG GATTTG GATTTG G
1294532 GAGTCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GATTTG
Found at i:1294846 original size:2 final size:2
Alignment explanation
Indices: 1294839--1294867 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1294829 GTTGATGTAC
1294839 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 A
1294868 AAATTTGGTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1295004 original size:2 final size:2
Alignment explanation
Indices: 1294997--1295031 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1294987 TTTATCCATC
1294997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1295032 TCAATTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1295751 original size:32 final size:31
Alignment explanation
Indices: 1295715--1295818 Score: 129
Period size: 32 Copynumber: 3.3 Consensus size: 31
1295705 AATAATTATT
1295715 AAATTTATAAGTAATTATATATAATATTCATC
1 AAATTTATAAGTAATTATAT-TAATATTCATC
* *
1295747 AAATTTATAAGTAATTTTATTTAATATTTATC
1 AAATTTATAAGTAATTATA-TTAATATTCATC
** * *
1295779 AAATTTATAAAAAATTATATTTA-ATTCATT
1 AAATTTATAAGTAATTATATTAATATTCATC
1295809 AAATTTATAA
1 AAATTTATAA
1295819 TCAATATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 15 0.24
31 3 0.05
32 44 0.70
33 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (31 bp):
AAATTTATAAGTAATTATATTAATATTCATC
Found at i:1295783 original size:64 final size:63
Alignment explanation
Indices: 1295702--1295834 Score: 171
Period size: 64 Copynumber: 2.1 Consensus size: 63
1295692 ACTAAAACAT
* **
1295702 TTTAATAATTATTAAATTTATAAGTAATTATATATAATATTCATCAAATTTATAAGT-AAT-TTT
1 TTTAATAATTATCAAATTTATAAAAAATTATAT-TAA-ATTCATCAAATTTATAA-TCAATATTT
1295765 A
63 A
* * *
1295766 TTTAATATTTATCAAATTTATAAAAAATTATATTTAATTCATTAAATTTATAATCAATATTTA
1 TTTAATAATTATCAAATTTATAAAAAATTATATTAAATTCATCAAATTTATAATCAATATTTA
1295829 TTTAAT
1 TTTAAT
1295835 TTTTTTTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
61 1 0.02
62 19 0.31
63 12 0.20
64 29 0.48
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (63 bp):
TTTAATAATTATCAAATTTATAAAAAATTATATTAAATTCATCAAATTTATAATCAATATTTA
Found at i:1296566 original size:16 final size:16
Alignment explanation
Indices: 1296547--1296605 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
1296537 ATTAATTTTT
1296547 AATTATTTATTAATAA
1 AATTATTTATTAATAA
1296563 AATTATTGT-TTAATAA
1 AATTATT-TATTAATAA
* * *
1296579 AAATA-TAATT--TTA
1 AATTATTTATTAATAA
1296592 AATTATTTATTAAT
1 AATTATTTATTAAT
1296606 TTTATAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 3 0.09
16 19 0.58
17 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
AATTATTTATTAATAA
Found at i:1296623 original size:45 final size:47
Alignment explanation
Indices: 1296522--1296623 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 47
1296512 TAATTACATG
* * *
1296522 ATTAAATATAATAATATTAATTTTTAATTATTTATTAATAAAATTATT
1 ATTAAATA-AATAATATTAATTTTAAATTATTTATTAATAAAATAAAT
* * ***
1296570 GTTTAATAAA-AATA-TAATTTTAAATTATTTATTAATTTTATAAAT
1 ATTAAATAAATAATATTAATTTTAAATTATTTATTAATAAAATAAAT
1296615 ATTAAATAA
1 ATTAAATAA
1296624 TTAAAAATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
45 32 0.73
46 4 0.09
47 2 0.05
48 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (47 bp):
ATTAAATAAATAATATTAATTTTAAATTATTTATTAATAAAATAAAT
Found at i:1296624 original size:19 final size:18
Alignment explanation
Indices: 1296583--1296625 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1296573 TAATAAAAAT
* *
1296583 ATAATTTTAAATTATTTA
1 ATAATTTTAAAATATTAA
*
1296601 TTAATTTTATAAATATTAA
1 ATAATTTTA-AAATATTAA
1296620 ATAATT
1 ATAATT
1296626 AAAAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAATTTTAAAATATTAA
Found at i:1298293 original size:4 final size:4
Alignment explanation
Indices: 1298284--1298309 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1298274 CATGCTCCGA
1298284 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
1298310 CGTCATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:1300449 original size:24 final size:24
Alignment explanation
Indices: 1300414--1300463 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1300404 TTGATTATTA
1300414 TTAAAATATAATATTTAATAA-AT
1 TTAAAATATAATATTTAATAATAT
* * *
1300437 TTAAAATTTTAATTTTTGATAATAT
1 TTAAAA-TATAATATTTAATAATAT
1300462 TT
1 TT
1300464 TTTTATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAAAATATAATATTTAATAATAT
Found at i:1305549 original size:59 final size:59
Alignment explanation
Indices: 1305457--1305575 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1305447 TATATGGTAG
*
1305457 GTTCCTCCTTGCAACTGTACATTTGTTTTGACTAAATTTACTTATGATTAGCCAGATAA
1 GTTCCTCCTTGCAACTATACATTTGTTTTGACTAAATTTACTTATGATTAGCCAGATAA
1305516 GTTCCTCCTTGCAACTATACATTTGTTTTGACTAAATTTACTTATGATTAGCCAGATAA
1 GTTCCTCCTTGCAACTATACATTTGTTTTGACTAAATTTACTTATGATTAGCCAGATAA
1305575 G
1 G
1305576 AGTGTTTAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (59 bp):
GTTCCTCCTTGCAACTATACATTTGTTTTGACTAAATTTACTTATGATTAGCCAGATAA
Found at i:1312054 original size:17 final size:18
Alignment explanation
Indices: 1312029--1312073 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
1312019 TTTTATTTTT
1312029 ATATT-ATATTTA-AAAA
1 ATATTAATATTTATAAAA
1312045 ATATTAATA-TTATAAAA
1 ATATTAATATTTATAAAA
1312062 ATATTAATATTT
1 ATATTAATATTT
1312074 TAATAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.31
17 16 0.62
18 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTAATATTTATAAAA
Found at i:1312193 original size:32 final size:32
Alignment explanation
Indices: 1312157--1312225 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1312147 ACTATATAAA
* *
1312157 TATTTAAAATATTATAATAATTGTTAAAATAT
1 TATTTAAAATAATATAATAATTATTAAAATAT
* * *
1312189 TATTTATATTAATATAATTATTATTAAAATAT
1 TATTTAAAATAATATAATAATTATTAAAATAT
1312221 T-TTTA
1 TATTTA
1312226 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (32 bp):
TATTTAAAATAATATAATAATTATTAAAATAT
Found at i:1312380 original size:48 final size:49
Alignment explanation
Indices: 1312288--1312384 Score: 119
Period size: 48 Copynumber: 2.0 Consensus size: 49
1312278 ATCATTAAAC
* *
1312288 TATTAATTTTAAAATTAAAAAGTGAATAATATTTAATTCTAAAACATTA
1 TATTAATATTAAAACTAAAAAGTGAATAATATTTAATTCTAAAACATTA
* *
1312337 TATTAATATTAAATACTAAAAA-T-AATACTATTT-ATTATTAAAACATTA
1 TATTAATATTAAA-ACTAAAAAGTGAATAATATTTAATT-CTAAAACATTA
1312385 GTTATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 3 0.07
48 19 0.45
49 13 0.31
50 7 0.17
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (49 bp):
TATTAATATTAAAACTAAAAAGTGAATAATATTTAATTCTAAAACATTA
Found at i:1320353 original size:16 final size:16
Alignment explanation
Indices: 1320318--1320369 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1320308 TAAATATAAA
1320318 AATATAAAATGTAATA-
1 AATATAAAA-GTAATAT
*
1320334 AATATAAAAGTATTAT
1 AATATAAAAGTAATAT
1320350 AATA-AAAA-TAATAT
1 AATATAAAAGTAATAT
1320364 AATATA
1 AATATA
1320370 TTTAAATACG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.28
15 10 0.31
16 13 0.41
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AATATAAAAGTAATAT
Found at i:1320442 original size:18 final size:17
Alignment explanation
Indices: 1320396--1320446 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1320386 ATTAATATAT
*
1320396 ATTATATTTTTATTTAAA
1 ATTATA-TTATATTTAAA
* *
1320414 ATTTTAATATATTTAATA
1 ATTATATTATATTTAA-A
1320432 ATTATATTATATTTA
1 ATTATATTATATTTA
1320447 TATTTAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATATTATATTTAAA
Found at i:1320616 original size:2 final size:2
Alignment explanation
Indices: 1320609--1320657 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1320599 ATTAGTAACA
1320609 AT AT AT 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 AT AT AT
1320651 AT AT AT A
1 AT AT AT A
1320658 AAGAAGGACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1321063 original size:20 final size:21
Alignment explanation
Indices: 1321041--1321095 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1321031 AATAATATTT
1321041 AAAATATTATATATTTATATA
1 AAAATATTATATATTTATATA
* *
1321062 AAAAAATT-TATATTTAATGTA
1 AAAATATTATATATTT-ATATA
**
1321083 TTAATATTATATA
1 AAAATATTATATA
1321096 AATTTATACA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.26
21 16 0.59
22 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AAAATATTATATATTTATATA
Found at i:1328598 original size:24 final size:24
Alignment explanation
Indices: 1328556--1328604 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1328546 TTGATCTAAC
1328556 AAAATAAAAGAAAGGAAAATCAGAT
1 AAAATAAAAGAAAGGAAAA-CAGAT
**
1328581 AAAA-AAAAGAAATTAAAACAGAT
1 AAAATAAAAGAAAGGAAAACAGAT
1328604 A
1 A
1328605 GAATGGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.12
Consensus pattern (24 bp):
AAAATAAAAGAAAGGAAAACAGAT
Found at i:1335506 original size:18 final size:17
Alignment explanation
Indices: 1335479--1335512 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1335469 TATTTGCTTA
1335479 AATCTCAAAATAACATCT
1 AATCTCAAAAT-ACATCT
*
1335497 AATCTTAAAATACATC
1 AATCTCAAAATACATC
1335513 AATAACCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (17 bp):
AATCTCAAAATACATCT
Found at i:1335516 original size:26 final size:26
Alignment explanation
Indices: 1335487--1335570 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
1335477 TAAATCTCAA
1335487 AATAACATCTAATCTTAAAATACATC
1 AATAACATCTAATCTTAAAATACATC
* *
1335513 AATAACCT-TATTTGCTT-AAAT-C-TC
1 AATAACATCTA-AT-CTTAAAATACATC
*
1335537 AAAATAACATCTGATCTTAAAATACATC
1 --AATAACATCTAATCTTAAAATACATC
1335565 AATAAC
1 AATAAC
1335571 CTTAAAGCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 16
0.68 0.08 0.24
Matches are distributed among these distances:
24 2 0.04
25 6 0.13
26 30 0.67
27 5 0.11
28 2 0.04
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (26 bp):
AATAACATCTAATCTTAAAATACATC
Found at i:1335529 original size:52 final size:52
Alignment explanation
Indices: 1335467--1335574 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
1335457 TTTTCCCGAT
1335467 CTTATTTGCTTAAATCTCAAAATAACATCTAATCTTAAAATACATCAATAAC
1 CTTATTTGCTTAAATCTCAAAATAACATCTAATCTTAAAATACATCAATAAC
*
1335519 CTTATTTGCTTAAATCTCAAAATAACATCTGATCTTAAAATACATCAATAAC
1 CTTATTTGCTTAAATCTCAAAATAACATCTAATCTTAAAATACATCAATAAC
1335571 CTTA
1 CTTA
1335575 AAGCTAGTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (52 bp):
CTTATTTGCTTAAATCTCAAAATAACATCTAATCTTAAAATACATCAATAAC
Found at i:1337580 original size:17 final size:17
Alignment explanation
Indices: 1337515--1337580 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
1337505 AATTTTATAA
* *
1337515 ATAAATTTTTATTTTTT
1 ATAATTTTTTATATTTT
* *
1337532 A-AATGTCTTATATTTTT
1 ATAATTTTTTATA-TTTT
*
1337549 AAATATTTGTTTATATTTT
1 ATA-ATTT-TTTATATTTT
1337568 ATAATTTTTTATA
1 ATAATTTTTTATA
1337581 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 7 0.18
17 12 0.32
18 5 0.13
19 9 0.24
20 5 0.13
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (17 bp):
ATAATTTTTTATATTTT
Found at i:1337580 original size:37 final size:38
Alignment explanation
Indices: 1337487--1337607 Score: 91
Period size: 36 Copynumber: 3.4 Consensus size: 38
1337477 TTTATTTGAA
*
1337487 TATATTTT-TTATGTTTTTA-ATTTTATAAATAAATTTT
1 TATATTTTATAAT-TTTTTATATTTTATAAATAAATTTT
* * * *
1337524 TATTTTTTA-AATGTCTTATATTTT-TAAAT-ATTTGTT
1 TATATTTTATAATTTTTTATATTTTATAAATAAATT-TT
**
1337560 TATATTTTATAATTTTTTATA--AAATAAA-AAA-TTT
1 TATATTTTATAATTTTTTATATTTTATAAATAAATTTT
1337594 T-TATTTTATAATTT
1 TATATTTTATAATTT
1337608 ATTCATTTGA
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
33 13 0.19
34 3 0.04
35 4 0.06
36 24 0.36
37 23 0.34
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (38 bp):
TATATTTTATAATTTTTTATATTTTATAAATAAATTTT
Found at i:1343158 original size:38 final size:38
Alignment explanation
Indices: 1343077--1343175 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
1343067 AGATATTAGT
* *
1343077 ATTAAAATTTATAAAATTTTTTTAATTTTATGAGTGAT
1 ATTAAAATTTATAATATTTTTTTAATTTTATGAGTGAA
**
1343115 ATT-AAATTTATAATATATTTTTTAATTTTATTTGT-AA
1 ATTAAAATTTATAATAT-TTTTTTAATTTTATGAGTGAA
* *
1343152 AGTTAAAAATTACAATATTTTTTT
1 A-TTAAAATTTATAATATTTTTTT
1343176 TTAATGGATC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
37 14 0.27
38 27 0.52
39 11 0.21
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (38 bp):
ATTAAAATTTATAATATTTTTTTAATTTTATGAGTGAA
Found at i:1349710 original size:71 final size:71
Alignment explanation
Indices: 1349594--1349732 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
1349584 ATAGATAAGC
* * *
1349594 TTGGATAATTGAAATGCTGTTTTTGCTAGAGACCATAGGCTTTTGATTTACAATAAAATGTGTCA
1 TTGGATAATTGAAAGGCTGTTTTTGCAAGAGACCATAGGCTTTTGATTAACAATAAAATGTGTCA
1349659 TATTGT
66 TATTGT
1349665 TTGGATAATTGAAAGGCTGTTTTTGCAAGAGACCATAGGCTTTTGATTAACAATAAAATGTGTCA
1 TTGGATAATTGAAAGGCTGTTTTTGCAAGAGACCATAGGCTTTTGATTAACAATAAAATGTGTCA
1349730 TAT
66 TAT
1349733 CGACTTAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (71 bp):
TTGGATAATTGAAAGGCTGTTTTTGCAAGAGACCATAGGCTTTTGATTAACAATAAAATGTGTCA
TATTGT
Found at i:1350631 original size:36 final size:35
Alignment explanation
Indices: 1350568--1350638 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
1350558 TTTTAAGTTA
* * *
1350568 TTATTTTTTAAAAACTTTATTTCAACTTATGAATT
1 TTATTTTTTAAAAAATTGATTTCAACTTATAAATT
* *
1350603 TTATTTTTATAAAAAATTGGTTTTAACTTATAAATT
1 TTATTTTT-TAAAAAATTGATTTCAACTTATAAATT
1350639 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (35 bp):
TTATTTTTTAAAAAATTGATTTCAACTTATAAATT
Found at i:1353045 original size:22 final size:22
Alignment explanation
Indices: 1352990--1353047 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1352980 TACTTATACC
* *
1352990 TAAAAAAATTAATTATACCCAA
1 TAAACAAATTACTTATACCCAA
*
1353012 TAAACAAATTACTTATGCCCAA
1 TAAACAAATTACTTATACCCAA
*
1353034 TAAGCAAATTACTT
1 TAAACAAATTACTT
1353048 CGTAAGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.29
Consensus pattern (22 bp):
TAAACAAATTACTTATACCCAA
Found at i:1353521 original size:18 final size:19
Alignment explanation
Indices: 1353500--1353535 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1353490 TTAATAATGT
*
1353500 GATAATTTAT-AATATATC
1 GATAATATATAAATATATC
1353518 GATAATATATAAATATAT
1 GATAATATATAAATATAT
1353536 AAATTGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (19 bp):
GATAATATATAAATATATC
Done.