Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold385
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: 1395621
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 6 of 10
Found at i:587534 original size:26 final size:28
Alignment explanation
Indices: 587470--587534 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
587460 ACAAATTTTT
*
587470 ATAAATATAATTTTAAAAAATAATTATTA
1 ATAAATAT-TTTTTAAAAAATAATTATTA
*
587499 A-AAATAATTTTTTAATAAA-AA-TATTA
1 ATAAAT-ATTTTTTAAAAAATAATTATTA
587525 ATAAATATTT
1 ATAAATATTT
587535 AATCAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
26 10 0.31
27 6 0.19
28 13 0.41
29 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAAATATTTTTTAAAAAATAATTATTA
Found at i:588242 original size:30 final size:30
Alignment explanation
Indices: 588198--588273 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
588188 CTTAACATAA
588198 ACATATTAAT-TATTATATTATAAAAAATTT
1 ACAT-TTAATATATTATATTATAAAAAATTT
* *
588228 ACATTTAATATATTATTTTTTTAAAAAATTT
1 ACATTTAATATATTA-TATTATAAAAAATTT
588259 A-ATTT--TATATTATAT
1 ACATTTAATATATTATAT
588274 ATCGAATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 2 0.05
28 7 0.17
29 5 0.12
30 13 0.32
31 14 0.34
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
ACATTTAATATATTATATTATAAAAAATTT
Found at i:588719 original size:2 final size:2
Alignment explanation
Indices: 588673--588702 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
588663 CTTTAACTCG
*
588673 AT AT AT AT AT TT 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
588703 TAGAGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:588968 original size:22 final size:23
Alignment explanation
Indices: 588925--588977 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
588915 GGTGGTCCCT
588925 TTTTTTAAGTAAAAAAGTGGGTAA
1 TTTTTTAAGTAAAAAAG-GGGTAA
* * *
588949 TTTTTTAGGTGAAAAA-GGGTTA
1 TTTTTTAAGTAAAAAAGGGGTAA
588971 TTTTTTA
1 TTTTTTA
588978 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 12 0.46
24 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (23 bp):
TTTTTTAAGTAAAAAAGGGGTAA
Found at i:591950 original size:20 final size:22
Alignment explanation
Indices: 591927--591981 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 22
591917 AAATAAATAA
591927 TTAAATAAAATATGA-ATAT-T
1 TTAAATAAAATATGATATATAT
*
591947 TT-AATCAAATATGATATATAT
1 TTAAATAAAATATGATATATAT
591968 TTAAGATAAAATAT
1 TTAA-ATAAAATAT
591982 CATAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 3 0.10
22 1 0.03
23 8 0.28
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
TTAAATAAAATATGATATATAT
Found at i:592169 original size:28 final size:27
Alignment explanation
Indices: 592111--592170 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
592101 TATTATATAT
*
592111 TTTATAATTAAATTTAAATAAAAATTT
1 TTTATAATTAAATTTAAATAAAAATTA
* *
592138 TTTATTATTAAATATTAAAT-CAAATTGA
1 TTTATAATTAAAT-TTAAATAAAAATT-A
592166 TTTAT
1 TTTAT
592171 CTCACAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTATAATTAAATTTAAATAAAAATTA
Found at i:592782 original size:17 final size:17
Alignment explanation
Indices: 592730--592784 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
592720 GAGTCCTAAC
*
592730 TTAAAAATTTTAATTTTTT
1 TTAAAAA-TTT-ATTTTAT
* *
592749 TTTAAAATTCATATTTAT
1 TTAAAAATTTAT-TTTAT
592767 TTAAAAATTTATTTTAT
1 TTAAAAATTTATTTTAT
592784 T
1 T
592785 ATTTATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.27
18 16 0.53
19 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAAAATTTATTTTAT
Found at i:592831 original size:22 final size:21
Alignment explanation
Indices: 592782--592842 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
592772 AATTTATTTT
*
592782 ATTATTTATTATATTATTAAAA
1 ATTATTT-TTATATTAATAAAA
**
592804 ATTATTTTTATATTAATATTA
1 ATTATTTTTATATTAATAAAA
592825 ATATATTTTTATAATTAA
1 AT-TATTTTTAT-ATTAA
592843 ATTTAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.38
22 16 0.47
23 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTTTTATATTAATAAAA
Found at i:593650 original size:41 final size:45
Alignment explanation
Indices: 593596--593680 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 45
593586 ATTAAAAATT
*
593596 TTAAAATTATTTTTA-TA-TT-AATATTTAT-AATTAAATTAAAA
1 TTAAAATTATTTTTATTACTTAAATATTAATAAATTAAATTAAAA
593637 TTAAAA-TATTTTTTATTACTTAAATATTAATCAAATTAAATTAA
1 TTAAAATTA-TTTTTATTACTTAAATATTAAT-AAATTAAATTAA
593681 TTTAAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
40 2 0.05
41 12 0.32
42 2 0.05
43 2 0.05
44 8 0.22
46 11 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (45 bp):
TTAAAATTATTTTTATTACTTAAATATTAATAAATTAAATTAAAA
Found at i:596089 original size:20 final size:19
Alignment explanation
Indices: 596054--596091 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
596044 ATAAATACTT
596054 AAATTATTATTTTATTAAA
1 AAATTATTATTTTATTAAA
*
596073 AAATTATTTTATTTATTAA
1 AAATTATTAT-TTTATTAA
596092 TTTTATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTATTATTTTATTAAA
Found at i:596114 original size:29 final size:28
Alignment explanation
Indices: 596057--596122 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 28
596047 AATACTTAAA
**
596057 TTATTATTTTATTAAAAAATTATTTTAT
1 TTATTATTTTATTAAAAAATTATGATAT
*
596085 TTATTAATTTTATTGAAAAA-TATCGATA-
1 TTATT-ATTTTATTAAAAAATTAT-GATAT
*
596113 TTAATATTTT
1 TTATTATTTT
596123 TAATAAGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.16
28 12 0.38
29 15 0.47
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (28 bp):
TTATTATTTTATTAAAAAATTATGATAT
Found at i:597656 original size:19 final size:19
Alignment explanation
Indices: 597620--597658 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
597610 TCTTATACAA
* **
597620 ATATATTTTAAATTTTTTT
1 ATATATTTAAAAGATTTTT
597639 ATATATTTAAAAGATTTTT
1 ATATATTTAAAAGATTTTT
597658 A
1 A
597659 AAAGATTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATATTTAAAAGATTTTT
Found at i:599985 original size:14 final size:14
Alignment explanation
Indices: 599966--599993 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
599956 TCTGACAGAC
599966 AATGATAACAGTTA
1 AATGATAACAGTTA
599980 AATGATAACAGTTA
1 AATGATAACAGTTA
599994 TTTGTTCTAG
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:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
AATGATAACAGTTA
Found at i:600897 original size:6 final size:6
Alignment explanation
Indices: 600886--600916 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
600876 AGATGGGGAC
600886 GCATTG GCATTG GCATTG GCATTG GCATTG G
1 GCATTG GCATTG GCATTG GCATTG GCATTG G
600917 AATCCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32
Consensus pattern (6 bp):
GCATTG
Found at i:601905 original size:15 final size:17
Alignment explanation
Indices: 601885--601917 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
601875 ATTAATATTA
601885 ATAAAATA-A-AAAATT
1 ATAAAATATATAAAATT
601900 ATAAAATATATAAAATT
1 ATAAAATATATAAAATT
601917 A
1 A
601918 ATTTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATATATAAAATT
Found at i:601935 original size:22 final size:22
Alignment explanation
Indices: 601885--601954 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 22
601875 ATTAATATTA
* *
601885 ATAAA-ATAAA-AAATTATAAA
1 ATAAATATAAATAAATTTTAAT
* *
601905 ATATATA-AAATTAATTTT-AT
1 ATAAATATAAATAAATTTTAAT
*
601925 ATTAATATAAATAAATTTTAAT
1 ATAAATATAAATAAATTTTAAT
601947 ATAAATAT
1 ATAAATAT
601955 GATATAATAC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 13 0.34
21 16 0.42
22 9 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATATAAATAAATTTTAAT
Found at i:606885 original size:2 final size:2
Alignment explanation
Indices: 606878--606909 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
606868 CAGAGGTAGA
606878 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
606910 GATACGACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:607252 original size:19 final size:18
Alignment explanation
Indices: 607201--607253 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
607191 AAAATAATTT
607201 TAATAATA-AATATTTAA
1 TAATAATATAATATTTAA
*
607218 TAAAAATAT-ATATTTAA
1 TAATAATATAATATTTAA
607235 TTGAATAATATAAT-TTTAA
1 -T-AATAATATAATATTTAA
607254 ATTTAACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 15 0.50
18 1 0.03
19 12 0.40
20 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATAATATAATATTTAA
Found at i:608661 original size:33 final size:29
Alignment explanation
Indices: 608618--608680 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 29
608608 ATTGAAAAAA
608618 ATTATAATTTTTAAATATATTTATATTGTATTAT
1 ATTATAATTTTT---TAT-TTTATA-TGTATTAT
608652 ATTA-AATTTTTTATTTTATATGTATTAT
1 ATTATAATTTTTTATTTTATATGTATTAT
608680 A
1 A
608681 ATTGTGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 9 0.31
29 6 0.21
30 3 0.10
33 7 0.24
34 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTATAATTTTTTATTTTATATGTATTAT
Found at i:609563 original size:32 final size:33
Alignment explanation
Indices: 609508--609569 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
609498 TAAAATCAAA
* *
609508 ATTCAAATATATTTCATTTATCTAAATGCATTT
1 ATTCAAATATAATTAATTTATCTAAATGCATTT
609541 ATTCAAATA-AATTAATTTATCTAAATGCA
1 ATTCAAATATAATTAATTTATCTAAATGCA
609570 CTTTTCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (33 bp):
ATTCAAATATAATTAATTTATCTAAATGCATTT
Found at i:613342 original size:27 final size:26
Alignment explanation
Indices: 613282--613336 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
613272 TATATTATAC
**
613282 AAAAATAAAATTAATTAAAATTTAAT
1 AAAAATAAAATTAATTAAAATCAAAT
*
613308 AAAAATAAAATTCAATTTAAATCAAAT
1 AAAAATAAAATT-AATTAAAATCAAAT
613335 AA
1 AA
613337 TTATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAATAAAATTAATTAAAATCAAAT
Found at i:613814 original size:18 final size:20
Alignment explanation
Indices: 613787--613824 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
613777 TTTTTTATTA
613787 AAAAATTATA-ATTTTAAAT
1 AAAAATTATATATTTTAAAT
*
613806 AAAAA-TATATTTTTTAAAT
1 AAAAATTATATATTTTAAAT
613825 TTATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATTATATATTTTAAAT
Found at i:614013 original size:16 final size:16
Alignment explanation
Indices: 613988--614026 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
613978 ATAATAGTAT
* *
613988 TTAAAATTAAATTAAA
1 TTAAATTTAAATAAAA
614004 TTAAATTTAAATAAAA
1 TTAAATTTAAATAAAA
*
614020 ATAAATT
1 TTAAATT
614027 CTATTACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATTTAAATAAAA
Found at i:619188 original size:44 final size:45
Alignment explanation
Indices: 619120--619210 Score: 175
Period size: 44 Copynumber: 2.0 Consensus size: 45
619110 GCAAAGAGTA
619120 ATATAATGCATTTTTCTATTCCCTTGTTTCTACAGATACGCAGGT
1 ATATAATGCATTTTTCTATTCCCTTGTTTCTACAGATACGCAGGT
619165 ATATAATGCA-TTTTCTATTCCCTTGTTTCTACAGATACGCAGGT
1 ATATAATGCATTTTTCTATTCCCTTGTTTCTACAGATACGCAGGT
619209 AT
1 AT
619211 CAATATAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 36 0.78
45 10 0.22
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (45 bp):
ATATAATGCATTTTTCTATTCCCTTGTTTCTACAGATACGCAGGT
Found at i:620276 original size:17 final size:17
Alignment explanation
Indices: 620254--620294 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
620244 CTAAGGATCC
620254 GTCCAAGCGTCATCATT
1 GTCCAAGCGTCATCATT
620271 GTCCAAGCGTCATCATT
1 GTCCAAGCGTCATCATT
*
620288 GTTCAAG
1 GTCCAAG
620295 AGACGCTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (17 bp):
GTCCAAGCGTCATCATT
Found at i:620992 original size:33 final size:32
Alignment explanation
Indices: 620921--620999 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
620911 CAGTAAAATA
* *
620921 TTTTATATTTATATAAATTTTGATATATCAATC
1 TTTTATA-TTATATAAATTTTAAAATATCAATC
* *
620954 ATTTATATTATATAAATTTTAAAATAATTATAT-
1 TTTTATATTATATAAATTTTAAAAT-ATCA-ATC
620987 TTTTATATTATAT
1 TTTTATATTATAT
621000 TTTATTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 16 0.41
33 21 0.54
34 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (32 bp):
TTTTATATTATATAAATTTTAAAATATCAATC
Found at i:621004 original size:20 final size:20
Alignment explanation
Indices: 620981--621024 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
620971 TTTAAAATAA
620981 TTATATTTTTATATTATAT-T
1 TTATATTTTT-TATTATATAT
621001 TTAT-TTTTTTATTATATAT
1 TTATATTTTTTATTATATAT
621020 TTATA
1 TTATA
621025 ATCGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.36
19 10 0.45
20 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATTTTTTATTATATAT
Found at i:621007 original size:18 final size:19
Alignment explanation
Indices: 620984--621023 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
620974 AAAATAATTA
620984 TATTTTTATATTATAT-TT
1 TATTTTTATATTATATATT
*
621002 TATTTTTTTATTATATATT
1 TATTTTTATATTATATATT
621021 TAT
1 TAT
621024 AATCGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTATATTATATATT
Found at i:621712 original size:30 final size:31
Alignment explanation
Indices: 621662--621728 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
621652 AGGTATTTAA
*
621662 CTTTTATTTTATACTCAAATAAACTCTCAAT
1 CTTTAATTTTATACTCAAATAAACTCTCAAT
* * *
621693 CTTTAATTTT-TACTTAAATAAGCTCTTAAT
1 CTTTAATTTTATACTCAAATAAACTCTCAAT
621723 -TTTAAT
1 CTTTAAT
621729 ATATATCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.19
30 17 0.53
31 9 0.28
ACGTcount: A:0.34, C:0.15, G:0.01, T:0.49
Consensus pattern (31 bp):
CTTTAATTTTATACTCAAATAAACTCTCAAT
Found at i:622659 original size:24 final size:24
Alignment explanation
Indices: 622612--622681 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
622602 ACATGATCCG
*
622612 AATATAATATGAAAAATAATTAAA
1 AATATAATATGAAAAATAAATAAA
*
622636 AATATATTAT-AAAAATAACAT--A
1 AATATAATATGAAAAATAA-ATAAA
*
622658 AATATAATACGTAATAAATAAATA
1 AATATAATATG-AA-AAATAAATA
622682 TGTCAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
22 9 0.24
23 8 0.22
24 14 0.38
25 6 0.16
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (24 bp):
AATATAATATGAAAAATAAATAAA
Found at i:622660 original size:22 final size:24
Alignment explanation
Indices: 622612--622666 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
622602 ACATGATCCG
*
622612 AATATAATATGAAAAATAATTAAA
1 AATATAATATGAAAAATAATCAAA
* *
622636 AATATATTAT-AAAAATAA-CATA
1 AATATAATATGAAAAATAATCAAA
622658 AATATAATA
1 AATATAATA
622667 CGTAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 10 0.37
23 8 0.30
24 9 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AATATAATATGAAAAATAATCAAA
Found at i:622722 original size:17 final size:19
Alignment explanation
Indices: 622690--622724 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
622680 TATGTCAAAA
622690 TATATATTAAATATTTATT
1 TATATATTAAATATTTATT
622709 TATATA-TAAA-ATTTAT
1 TATATATTAAATATTTAT
622725 ATAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATTAAATATTTATT
Found at i:622752 original size:17 final size:19
Alignment explanation
Indices: 622710--622755 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
622700 ATATTTATTT
622710 ATATATAAAATTTATATAA
1 ATATATAAAATTTATATAA
* *
622729 ATTTATAATATTT-TA-AA
1 ATATATAAAATTTATATAA
622746 ATATATAAAA
1 ATATATAAAA
622756 AATAACTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATATAAAATTTATATAA
Found at i:626535 original size:18 final size:18
Alignment explanation
Indices: 626514--626563 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
626504 TTGTCAATCT
626514 TAAATTTTAAATATAATA
1 TAAATTTTAAATATAATA
* *
626532 TAAATTATTAATTATATTA
1 TAAATT-TTAAATATAATA
626551 -AAATTTTAAATAT
1 TAAATTTTAAATAT
626564 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.25
18 11 0.39
19 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTTTAAATATAATA
Found at i:627804 original size:18 final size:21
Alignment explanation
Indices: 627781--627819 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
627771 TATGAATATG
627781 TTTATTT-TTT-AAAA-TTTT
1 TTTATTTATTTGAAAACTTTT
627799 TTTATTTATTTGAAAACTTTT
1 TTTATTTATTTGAAAACTTTT
627820 AAAGAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 4 0.22
21 4 0.22
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTATTTATTTGAAAACTTTT
Found at i:628807 original size:2 final size:2
Alignment explanation
Indices: 628802--628829 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
628792 ACACACACAC
628802 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
628830 TGCTTATAGT
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:629898 original size:16 final size:16
Alignment explanation
Indices: 629870--629911 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
629860 AAAATGAATC
* *
629870 TTATTTTT-TATTTAT
1 TTATTTTTAAATTTAA
629885 TTATTTTTAAATTTAA
1 TTATTTTTAAATTTAA
*
629901 TAATTTTTAAA
1 TTATTTTTAAA
629912 CCATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTTAAATTTAA
Found at i:633061 original size:2 final size:2
Alignment explanation
Indices: 633054--633078 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
633044 ATTCCACTTG
633054 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
633079 GTTTACTTTA
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:635008 original size:21 final size:21
Alignment explanation
Indices: 634965--635008 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
634955 AATATAAAAA
*
634965 TATAAATTTTATATTAATTTT
1 TATAAATTTTATATTAATATT
*
634986 TATATATTTTATAATTAA-ATT
1 TATAAATTTTAT-ATTAATATT
635007 TA
1 TA
635009 AATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATAAATTTTATATTAATATT
Found at i:635038 original size:27 final size:28
Alignment explanation
Indices: 634987--635040 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
634977 ATTAATTTTT
*
634987 ATATATTTTATAATTAAATTTAAATAAAA
1 ATATATTTTATAATT-AATTAAAATAAAA
*
635016 ATATATTTTATTATT-ATTAAAATAA
1 ATATATTTTATAATTAATTAAAATAA
635041 TAATTCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
29 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATATTTTATAATTAATTAAAATAAAA
Found at i:636048 original size:2 final size:2
Alignment explanation
Indices: 636037--636065 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
636027 CCCACTATTC
636037 TA TA TA -A 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
636066 CACACATCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:636376 original size:2 final size:2
Alignment explanation
Indices: 636350--636398 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
636340 TACTTGGAGG
* * * *
636350 TA TA TG TA TA TG TA TA CA AA 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
636392 TA TA TA T
1 TA TA TA T
636399 TTGCAGCAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:638883 original size:52 final size:52
Alignment explanation
Indices: 638818--638922 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
638808 TTAATTACCA
* *
638818 ATACCCTCTTTCTTCTTACTTTCCGAAGTCAAAAATAACTTTAAATCCTTAG
1 ATACCCTCTTTCTTCTTACCTTCCGAACTCAAAAATAACTTTAAATCCTTAG
638870 ATACCCTCTTTCTTCTTACCTTCCGAACTCAAAAATAACTTTAAATCCTTAG
1 ATACCCTCTTTCTTCTTACCTTCCGAACTCAAAAATAACTTTAAATCCTTAG
638922 A
1 A
638923 GCCGACATTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (52 bp):
ATACCCTCTTTCTTCTTACCTTCCGAACTCAAAAATAACTTTAAATCCTTAG
Found at i:638972 original size:2 final size:2
Alignment explanation
Indices: 638965--638994 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
638955 TTTTCTTGTC
638965 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
638995 TATTTAAGGG
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:642048 original size:2 final size:2
Alignment explanation
Indices: 642031--642066 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
642021 ATGCAGGTTT
642031 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
642067 TAAAGGAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:642261 original size:18 final size:18
Alignment explanation
Indices: 642235--642271 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
642225 TATATTTTAT
*
642235 AAAATTAAAAATTAATTA
1 AAAAATAAAAATTAATTA
*
642253 AAAAATAAAAATTATTTA
1 AAAAATAAAAATTAATTA
642271 A
1 A
642272 TTTTGATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATAAAAATTAATTA
Found at i:645377 original size:2 final size:2
Alignment explanation
Indices: 645370--645394 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
645360 TAGGTTCCTA
645370 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
645395 CAGTATCTCT
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:650747 original size:17 final size:17
Alignment explanation
Indices: 650711--650748 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
650701 TATATATATT
*
650711 TAAATATTTATTAAATA
1 TAAATATTTATTAAAAA
650728 TAAATATTT-TTAAAAAA
1 TAAATATTTATT-AAAAA
650745 TAAA
1 TAAA
650749 GAGTTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATTTATTAAAAA
Found at i:651025 original size:39 final size:39
Alignment explanation
Indices: 650976--651051 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 39
650966 TTATTCAATT
*
650976 ATAATGTAATTAAT-ATATTATTATTGTTT-TATTTTATTG
1 ATAATATAATTAATAATA-T-TTATTGTTTGTATTTTATTG
651015 ATAATATAATTAATAATATTTATTGTTTGTATTTTAT
1 ATAATATAATTAATAATATTTATTGTTTGTATTTTAT
651052 ATCTAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 9 0.26
39 22 0.65
40 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (39 bp):
ATAATATAATTAATAATATTTATTGTTTGTATTTTATTG
Found at i:651938 original size:13 final size:14
Alignment explanation
Indices: 651922--651960 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
651912 TTTGTGTCTG
651922 ATAT-AATTTTTAA
1 ATATAAATTTTTAA
* *
651935 ATATAAATATTGAA
1 ATATAAATTTTTAA
651949 ATATAAATTTTT
1 ATATAAATTTTT
651961 CTGGTATCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
ATATAAATTTTTAA
Found at i:657016 original size:21 final size:19
Alignment explanation
Indices: 656979--657020 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
656969 ATATAAAATA
*
656979 AATTTAAATTAATTATATT
1 AATTTAAATTAAATATATT
656998 AATTTAATATTTAAATATATT
1 AATTTAA-A-TTAAATATATT
657019 AA
1 AA
657021 AATATCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTAAATTAAATATATT
Found at i:664937 original size:21 final size:21
Alignment explanation
Indices: 664911--664963 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
664901 TGCCTGTCTC
664911 AAAATATGA-AAAAATTTATAT
1 AAAATATGATAAAAATTT-TAT
*
664932 AAAATATGATAAAAATTTTCT
1 AAAATATGATAAAAATTTTAT
664953 AAAATAT-ATAA
1 AAAATATGATAA
664964 GCTCTACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.13
21 18 0.60
22 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
AAAATATGATAAAAATTTTAT
Found at i:666896 original size:13 final size:13
Alignment explanation
Indices: 666878--666902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
666868 TGTTATCATG
666878 AGTTACTTAAGAC
1 AGTTACTTAAGAC
666891 AGTTACTTAAGA
1 AGTTACTTAAGA
666903 GGGGATATTC
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AGTTACTTAAGAC
Found at i:669171 original size:19 final size:21
Alignment explanation
Indices: 669122--669175 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
669112 TTTCAACAAT
669122 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* * *
669143 ATGCATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
669162 TTGTATCGATACAA
1 TTGTATCGATACAA
669176 TGTATCGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:673377 original size:27 final size:26
Alignment explanation
Indices: 673334--673397 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 26
673324 ATTAAAATAT
* * *
673334 ATAA-ATATATAATAATATTTTAAAA
1 ATAATATAAATAAAAATATTATAAAA
673359 ATAATTATAAATAAAAATATTATAAAA
1 ATAA-TATAAATAAAAATATTATAAAA
673386 ATAATATAAATA
1 ATAATATAAATA
673398 TACAAATGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.12
26 8 0.24
27 22 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAATATAAATAAAAATATTATAAAA
Found at i:673380 original size:15 final size:16
Alignment explanation
Indices: 673354--673384 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
673344 AATAATATTT
673354 TAAAAATAATTATAAA
1 TAAAAATAATTATAAA
673370 TAAAAAT-ATTATAAA
1 TAAAAATAATTATAAA
673385 AATAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAATAATTATAAA
Found at i:673834 original size:13 final size:12
Alignment explanation
Indices: 673786--673831 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
673776 AATAATTTTA
673786 AAAATAATAAGAT
1 AAAATAATAA-AT
*
673799 GAAATAATAAAGT
1 AAAATAATAAA-T
673812 AAAATAAT-AAT
1 AAAATAATAAAT
673823 AAAATAATA
1 AAAATAATA
673832 TAAAATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 9 0.31
12 3 0.10
13 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:673834 original size:16 final size:16
Alignment explanation
Indices: 673801--673834 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
673791 AATAAGATGA
*
673801 AATAATAAAGTAAAAT
1 AATAATAAAATAAAAT
*
673817 AATAATAAAATAATAT
1 AATAATAAAATAAAAT
673833 AA
1 AA
673835 AATTATGTTA
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAATAAAATAAAAT
Found at i:675656 original size:19 final size:20
Alignment explanation
Indices: 675623--675661 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
675613 GTGATCTAAA
675623 GGTCATTATATTCTTTATTG
1 GGTCATTATATTCTTTATTG
675643 GGTCATTA-ATTCTTTATTG
1 GGTCATTATATTCTTTATTG
675662 ACTAGGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (20 bp):
GGTCATTATATTCTTTATTG
Found at i:681606 original size:2 final size:2
Alignment explanation
Indices: 681599--681623 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
681589 TGATTTGTTT
681599 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
681624 TCTGCTTTCT
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:684803 original size:2 final size:2
Alignment explanation
Indices: 684796--684834 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
684786 AAAGAAAAAT
*
684796 AG AG AG AG AG AG AG AG AG AG AG CA- AG CG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG A
684835 ACTAACCGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:686146 original size:22 final size:23
Alignment explanation
Indices: 686121--686169 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
686111 TAATTGTATA
*
686121 TAAATTAAAATTTATAT-TTTAT
1 TAAATTAAAATTTAAATATTTAT
* *
686143 TAAA-TATATTTTAAATATTTAT
1 TAAATTAAAATTTAAATATTTAT
686165 TAAAT
1 TAAAT
686170 ATATAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTAAAATTTAAATATTTAT
Found at i:686158 original size:11 final size:12
Alignment explanation
Indices: 686134--686173 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
686124 ATTAAAATTT
*
686134 ATATTTTATTAA
1 ATATATTATTAA
686146 ATATATT-TTAA
1 ATATATTATTAA
686157 ATAT-TTATTAA
1 ATATATTATTAA
686168 ATATAT
1 ATATAT
686174 AAATAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 16 0.64
12 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATATTATTAA
Found at i:686171 original size:20 final size:20
Alignment explanation
Indices: 686138--686188 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
686128 AAATTTATAT
686138 TTTATTAAATATATTTTAAAT-A
1 TTTATTAAATATA---TAAATAA
686160 TTTATTAAATATATAAATAA
1 TTTATTAAATATATAAATAA
686180 TTTATTAAA
1 TTTATTAAA
686189 AATTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.18
20 10 0.36
22 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATTAAATATATAAATAA
Found at i:686191 original size:22 final size:22
Alignment explanation
Indices: 686138--686191 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
686128 AAATTTATAT
* *
686138 TTTATTAAATATATTTTAAATA
1 TTTATTAAAAATATTATAAATA
686160 TTTATT--AAATA-TATAAATAA
1 TTTATTAAAAATATTATAAAT-A
686180 TTTATTAAAAAT
1 TTTATTAAAAAT
686192 TAATTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 6 0.22
20 11 0.41
22 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATTAAAAATATTATAAATA
Found at i:686426 original size:22 final size:23
Alignment explanation
Indices: 686401--686449 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
686391 TAATTACATA
*
686401 TAAATTAAAATTTATAT-TTTAT
1 TAAATTAAAATTTAAATATTTAT
* *
686423 TAAA-TATATTTTAAATATTTAT
1 TAAATTAAAATTTAAATATTTAT
686445 TAAAT
1 TAAAT
686450 GTATAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTAAAATTTAAATATTTAT
Found at i:686429 original size:28 final size:30
Alignment explanation
Indices: 686388--686444 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
686378 TCAGTTTGAG
*
686388 TTTTAATTACATATAAATTAAA-ATTTATA
1 TTTTAATTAAATATAAATTAAATATTTATA
**
686417 TTTT-ATTAAATATATTTTAAATATTTAT
1 TTTTAATTAAATATAAATTAAATATTTAT
686445 TAAATGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTAATTAAATATAAATTAAATATTTATA
Found at i:686438 original size:11 final size:11
Alignment explanation
Indices: 686418--686472 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
686408 AAATTTATAT
686418 TTTATTAAATA
1 TTTATTAAATA
686429 TATT-TTAAATA
1 T-TTATTAAATA
686440 TTTATT-AA-A
1 TTTATTAAATA
*
686449 TGTA-TAAATAA
1 TTTATTAAAT-A
686460 TTTATTAAATA
1 TTTATTAAATA
686471 TT
1 TT
686473 AATTTTACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
8 1 0.03
9 6 0.17
10 4 0.11
11 18 0.50
12 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TTTATTAAATA
Found at i:686459 original size:280 final size:281
Alignment explanation
Indices: 685902--686477 Score: 974
Period size: 280 Copynumber: 2.1 Consensus size: 281
685892 ATTTATTTTA
* *
685902 ATTAAAAATTAATTTAACAAACTTATTTACTGATTGAATGAATTGATCCACCTCAAAAATCAAAA
1 ATTAAAAATTAATTTAACAAAATTATTTACTGATTGAATGAATCGATCCACCTCAAAAATCAAAA
* *
685967 TGAAAGTTTAGTTGATCCGATTCATTTTCTCAATATATACTGAATATATGTTTCTGTTTCATTCA
66 TAAAAGTTTAGTTGATCCGATTCATTTTCTCAATATATACTGAATATATGTTTCTATTTCATTCA
* * * *
686032 ATCGTTTTTTTTCTGTTTTAGTTGAATTTAAGTTTAATTTGAGTTTAAGTGAATTTTACTTGAGC
131 ATCGTTTTTTCTCTGTTTTAATTGAATATAAGTTTAATTTGAGTTTAAGTGAATTTTACTTGAGA
* **
686097 TTCATTTTGAGTTTTAATTGTATATAAATTAAAATTTATATTTTATTAAATATATTTTAAATATT
196 TTCAGTTTGAGTTTTAATTACATATAAATTAAAATTTATATTTTATTAAATATATTTTAAATATT
686162 TATTAAATATATAAATAATTT
261 TATTAAATATATAAATAATTT
* * *
686183 ATTAAAAATTAATTTAATAAAATTATTTACTGATTGAATGAATCGATTCACGTCAAAAATCAAAA
1 ATTAAAAATTAATTTAACAAAATTATTTACTGATTGAATGAATCGATCCACCTCAAAAATCAAAA
*
686248 TAAAAGTTTAGTTGATCCGATTCATTTTCTCAATATATACTGAATGTATGTTTCTATTTCATTCA
66 TAAAAGTTTAGTTGATCCGATTCATTTTCTCAATATATACTGAATATATGTTTCTATTTCATTCA
* *
686313 ATC-TTTTTTCTCTGTTTTAATTGAATATAGGTTTAATTTGAGTTTAAGTGGATTTTACTTGAGA
131 ATCGTTTTTTCTCTGTTTTAATTGAATATAAGTTTAATTTGAGTTTAAGTGAATTTTACTTGAGA
686377 TTCAGTTTGAGTTTTAATTACATATAAATTAAAATTTATATTTTATTAAATATATTTTAAATATT
196 TTCAGTTTGAGTTTTAATTACATATAAATTAAAATTTATATTTTATTAAATATATTTTAAATATT
*
686442 TATTAAATGTATAAATAATTT
261 TATTAAATATATAAATAATTT
*
686463 ATTAAATATTAATTT
1 ATTAAAAATTAATTT
686478 TACTGATTTG
Statistics
Matches: 276, Mismatches: 19, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
280 151 0.55
281 125 0.45
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (281 bp):
ATTAAAAATTAATTTAACAAAATTATTTACTGATTGAATGAATCGATCCACCTCAAAAATCAAAA
TAAAAGTTTAGTTGATCCGATTCATTTTCTCAATATATACTGAATATATGTTTCTATTTCATTCA
ATCGTTTTTTCTCTGTTTTAATTGAATATAAGTTTAATTTGAGTTTAAGTGAATTTTACTTGAGA
TTCAGTTTGAGTTTTAATTACATATAAATTAAAATTTATATTTTATTAAATATATTTTAAATATT
TATTAAATATATAAATAATTT
Found at i:686528 original size:9 final size:9
Alignment explanation
Indices: 686509--686602 Score: 59
Period size: 9 Copynumber: 10.0 Consensus size: 9
686499 TAATAATAAA
686509 AAATTAATT
1 AAATTAATT
686518 -AATTAAATT
1 AAATT-AATT
686527 AAAATT--TT
1 -AAATTAATT
686535 AAATTAATT
1 AAATTAATT
*
686544 AAAAATAATT
1 -AAATTAATT
686554 AAAATTAATTGT
1 -AAATTAA-T-T
* *
686566 ATATTAACT
1 AAATTAATT
686575 AAATTAATT
1 AAATTAATT
*
686584 AAATCAATTT
1 AAATTAA-TT
*
686594 TAATTAATT
1 AAATTAATT
686603 TTTTAATTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.07
8 6 0.09
9 22 0.33
10 22 0.33
11 11 0.16
12 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (9 bp):
AAATTAATT
Found at i:686545 original size:26 final size:27
Alignment explanation
Indices: 686509--686559 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
686499 TAATAATAAA
**
686509 AAATTAATTAATTA-AATTAAAATTTT
1 AAATTAATTAAAAATAATTAAAATTTT
686535 AAATTAATTAAAAATAATTAAAATT
1 AAATTAATTAAAAATAATTAAAATT
686560 AATTGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATTAATTAAAAATAATTAAAATTTT
Found at i:686598 original size:15 final size:14
Alignment explanation
Indices: 686578--686623 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
686568 ATTAACTAAA
686578 TTAATTAAATCAATT
1 TTAATT-AATCAATT
*
686593 TTAATTAAT--TTT
1 TTAATTAATCAATT
686605 TTAATTTAATCAATT
1 TTAA-TTAATCAATT
686620 TTAA
1 TTAA
686624 CCAAATTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 6 0.23
13 5 0.19
14 3 0.12
15 12 0.46
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAATTAATCAATT
Found at i:686848 original size:15 final size:16
Alignment explanation
Indices: 686817--686894 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 16
686807 TTTATGATGG
*
686817 ATATA-AAAATATAAT
1 ATATATAAAATATTAT
686832 ATATATAAAAT-TTAT
1 ATATATAAAATATTAT
*
686847 ATAATATAAATTATTA-
1 AT-ATATAAAATATTAT
686863 ATATATAATAATTAATTA-
1 ATATATAA-AA-T-ATTAT
*
686881 AAATATAAAATATT
1 ATATATAAAATATT
686895 TTAAATATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
15 19 0.36
16 17 0.32
17 6 0.11
18 11 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATAAAATATTAT
Found at i:686853 original size:18 final size:17
Alignment explanation
Indices: 686832--686891 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
686822 AAAATATAAT
686832 ATATATAAAATTTA-T-
1 ATATATAAAATTTATTA
686847 ATA-ATATAAA-TTATTA
1 ATATATA-AAATTTATTA
*
686863 ATATATAATAATTAATTA
1 ATATATAA-AATTTATTA
*
686881 AAATATAAAAT
1 ATATATAAAAT
686892 ATTTTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.16
15 7 0.19
16 4 0.11
17 8 0.22
18 12 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATAAAATTTATTA
Found at i:686920 original size:37 final size:36
Alignment explanation
Indices: 686862--686931 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
686852 ATAAATTATT
686862 AATATATAATAATTAATTAAAATATAAAATATTTTA
1 AATATATAATAATTAATTAAAATATAAAATATTTTA
* *
686898 AATATTATTATAATATAA-TAAAATATAAATTATT
1 AATA-TATAATAAT-TAATTAAAATATAAAATATT
686932 AAATTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 4 0.13
37 23 0.77
38 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
AATATATAATAATTAATTAAAATATAAAATATTTTA
Found at i:688557 original size:5 final size:5
Alignment explanation
Indices: 688527--688719 Score: 53
Period size: 5 Copynumber: 38.6 Consensus size: 5
688517 TTTAATATTT
* * *
688527 TTATA TTTATA TCATA TT-TA -TATA TTTTA TTATA TTATAA TTATA TTTAAA
1 TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA -TTATA
* * * * * * *
688578 ATATT TTATA TT-TA TATAAA TTTTA ATATA ATA-A TAAT- TTATA TTATA
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA
* * ** * * *
688626 TAAAA TT-TA AAATA TT-TA TTTTA TT-T- TTATA TTTTA TATATT TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA
* * * *
688673 TTATA TTTTATA TTATC TTATAA TAATA TTATC TAATA TTACTA TTA
1 TTATA --TTATA TTATA TTAT-A TTATA TTATA TTATA TTA-TA TTA
688720 CTAGTTGAAA
Statistics
Matches: 132, Mismatches: 38, Indels: 34
0.65 0.19 0.17
Matches are distributed among these distances:
3 3 0.02
4 19 0.14
5 78 0.59
6 27 0.20
7 5 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:688572 original size:29 final size:26
Alignment explanation
Indices: 688516--688591 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 26
688506 AAATGTAAAA
*
688516 ATTT-AATATTTTTATATTTATATCAT
1 ATTTAAATA-TTTTATATTTAAATCAT
* *
688542 ATTTATATATTTTATTATATTATAATTAT
1 ATTTAAATATTTTA-TAT-TTA-AATCAT
688571 ATTTAAAATATTTTATATTTA
1 ATTT-AAATATTTTATATTTA
688592 TATAAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 9 0.22
27 6 0.15
28 6 0.15
29 11 0.27
30 9 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTAAATATTTTATATTTAAATCAT
Found at i:688573 original size:21 final size:20
Alignment explanation
Indices: 688521--688594 Score: 63
Period size: 19 Copynumber: 4.0 Consensus size: 20
688511 TAAAAATTTA
688521 ATATTT-TTATATTTATATC
1 ATATTTATTATATTTATATC
*
688540 ATATTTA-TATATTT-TATT
1 ATATTTATTATATTTATATC
*
688558 ATATTATAATTATATTTA-A-A
1 ATATT-T-ATTATATTTATATC
688578 ATA-TT-TTATATTTATAT
1 ATATTTATTATATTTATAT
688595 AAATTTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
16 9 0.20
17 1 0.02
18 9 0.20
19 15 0.33
20 4 0.09
21 8 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTATTATATTTATATC
Found at i:688586 original size:16 final size:17
Alignment explanation
Indices: 688516--688674 Score: 73
Period size: 16 Copynumber: 9.2 Consensus size: 17
688506 AAATGTAAAA
688516 ATTTAAT-AT-TTTTAT
1 ATTTAATAATATTTTAT
*
688531 ATTTATATCATATTTATAT
1 ATTTA-ATAATATTT-TAT
* *
688550 ATTTTATTATATTATAATTAT
1 A-TTTA--ATAATAT-TTTAT
688571 ATTTAA-AATATTTTAT
1 ATTTAATAATATTTTAT
688587 ATTTATATAA-ATTTTA-
1 ATTTA-ATAATATTTTAT
* *
688603 ATATAATAATAATTTAT
1 ATTTAATAATATTTTAT
* *
688620 A-TTATATAAAATTTAAAAT
1 ATTTA-ATAATATTT--TAT
**
688639 ATTT-ATTTTATTTTTAT
1 ATTTAATAATA-TTTTAT
*
688656 ATTTTAT-ATATTTTAT
1 ATTTAATAATATTTTAT
688672 ATT
1 ATT
688675 ATATTTTATA
Statistics
Matches: 111, Mismatches: 16, Indels: 33
0.69 0.10 0.21
Matches are distributed among these distances:
15 9 0.08
16 31 0.28
17 29 0.26
18 11 0.10
19 10 0.09
20 10 0.09
21 10 0.09
22 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAATAATATTTTAT
Found at i:688662 original size:7 final size:7
Alignment explanation
Indices: 688642--688686 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
688632 TTAAAATATT
688642 TATTTTA
1 TATTTTA
688649 T-TTTTA
1 TATTTTA
688655 TATTTTA
1 TATTTTA
688662 TATATTT-
1 TAT-TTTA
*
688669 TATATTA
1 TATTTTA
688676 TATTTTA
1 TATTTTA
688683 TATT
1 TATT
688687 ATCTTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 8 0.24
7 22 0.67
8 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTTTA
Found at i:688688 original size:17 final size:17
Alignment explanation
Indices: 688527--688694 Score: 75
Period size: 17 Copynumber: 10.0 Consensus size: 17
688517 TTTAATATTT
*
688527 TTATA-TTTATATCATA
1 TTATATTTTATATTATA
688543 TTTATATATTT-TATTATA
1 -TTATAT-TTTATATTATA
*
688561 TTATA-ATTATATT-TA
1 TTATATTTTATATTATA
**
688576 AAATATTTTATATT-TA
1 TTATATTTTATATTATA
*
688592 TATAAATTTTA-A-TATAA
1 T-TATATTTTATATTAT-A
* *
688609 TAATAATTTATATTATA
1 TTATATTTTATATTATA
* * *
688626 TAAAATTTAAAATATT-TA
1 TTATATTT--TATATTATA
* *
688644 TTTTATTTTTATATTTTA
1 TTATA-TTTTATATTATA
688662 -TATATTTTATATTATA
1 TTATATTTTATATTATA
* * *
688678 TTTTATATTATCTTATA
1 TTATATTTTATATTATA
688695 ATAATATTAT
Statistics
Matches: 114, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.07
16 32 0.28
17 48 0.42
18 15 0.13
19 11 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTTATATTATA
Found at i:690155 original size:3 final size:3
Alignment explanation
Indices: 690140--690173 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
690130 GCTTGTTTAT
*
690140 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
690174 CATAATTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:693477 original size:22 final size:22
Alignment explanation
Indices: 693452--693496 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
693442 ATTTTATTTT
693452 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAATT-TAAAAATATA
*
693474 TAAATATTAATTTAAAATTATA
1 TAAATATTAATTTAAAAATATA
693496 T
1 T
693497 TTGAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATATTAATTTAAAAATATA
Found at i:696359 original size:2 final size:2
Alignment explanation
Indices: 696352--696388 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
696342 AAAACTTGCT
696352 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
696389 TATATATATA
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:698373 original size:15 final size:14
Alignment explanation
Indices: 698317--698377 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 14
698307 CTCATATTAT
698317 ATTTTTAAAATTTAA
1 ATTTTTAAAATTT-A
*
698332 ATTTTATAAAA-AT-
1 ATTTT-TAAAATTTA
698345 ATTTTTAAAAAATTTA
1 ATTTTT--AAAATTTA
698361 ATTTTTAATAATTTA
1 ATTTTTAA-AATTTA
698376 AT
1 AT
698378 AAATTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
12 1 0.03
13 5 0.13
14 6 0.16
15 15 0.39
16 11 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTTAAAATTTA
Found at i:699152 original size:2 final size:2
Alignment explanation
Indices: 699145--699183 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
699135 TAAGTCATAC
699145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
699184 ACAAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:701081 original size:2 final size:2
Alignment explanation
Indices: 701074--701099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
701064 ATAAAGAAGG
701074 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
701100 GAATAAATAA
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:701408 original size:13 final size:12
Alignment explanation
Indices: 701381--701419 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
701371 TAATGATAAA
701381 TATAATGAATAT
1 TATAATGAATAT
*
701393 TATAATGATTTAT
1 TATAATGA-ATAT
*
701406 TATAATAAATAT
1 TATAATGAATAT
701418 TA
1 TA
701420 ATTATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (12 bp):
TATAATGAATAT
Found at i:701627 original size:2 final size:2
Alignment explanation
Indices: 701620--701648 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
701610 TTGAAGACAC
701620 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 T
701649 GGAGTGAGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:702201 original size:2 final size:2
Alignment explanation
Indices: 702194--702236 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
702184 TGTCCTCACT
702194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
702236 T
1 T
702237 GCACCATTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:702633 original size:31 final size:30
Alignment explanation
Indices: 702576--702636 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
702566 AATTATATTC
* *
702576 AAATATTTTTTAAACTTAAATATTAAATAT
1 AAATATTTTTAAAAATTAAATATTAAATAT
702606 AAATATTTTTAAAAAATTAAA-ATTTAAATAT
1 AAATATTTTT-AAAAATTAAATA-TTAAATAT
702637 CATAAATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATATTTTTAAAAATTAAATATTAAATAT
Found at i:703621 original size:25 final size:24
Alignment explanation
Indices: 703588--703669 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 24
703578 TTACATTAAA
*
703588 ATTATTATTTTATGATTATAATATTT
1 ATTA-TATTTTAT-ATAATAATATTT
*
703614 TTTATA-TTTATA-AATAATATTT
1 ATTATATTTTATATAATAATATTT
* * * *
703636 ATTATAATTAATTATGATAATATCT
1 ATTATATTTTA-TATAATAATATTT
703661 ATTATATTT
1 ATTATATTT
703670 AATCGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
22 14 0.30
23 4 0.09
24 7 0.15
25 18 0.39
26 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTATATTTTATATAATAATATTT
Found at i:704196 original size:9 final size:9
Alignment explanation
Indices: 704184--704233 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
704174 GGAGAAGGAG
704184 AAGAAAGAA
1 AAGAAAGAA
704193 AAGAAAGAA
1 AAGAAAGAA
704202 AAGAAAGAA
1 AAGAAAGAA
704211 AAGAAAGAA
1 AAGAAAGAA
* *
704220 AACAAGGAA
1 AAGAAAGAA
704229 AAGAA
1 AAGAA
704234 GACCGAGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (9 bp):
AAGAAAGAA
Found at i:704197 original size:18 final size:18
Alignment explanation
Indices: 704139--704234 Score: 71
Period size: 18 Copynumber: 5.7 Consensus size: 18
704129 CAAGAAGACA
704139 AAAGAAAAGAAGGAGAAG
1 AAAGAAAAGAAGGAGAAG
704157 ---GATAAAG-AGGAGAAG
1 AAAGA-AAAGAAGGAGAAG
*
704172 -AAG--GAGAAGGAGAAG
1 AAAGAAAAGAAGGAGAAG
* *
704187 AAAGAAAAGAAAGAAAAG
1 AAAGAAAAGAAGGAGAAG
* * *
704205 AAAGAAAAGAAAGAAAAC
1 AAAGAAAAGAAGGAGAAG
*
704223 AAGGAAAAGAAG
1 AAAGAAAAGAAG
704235 ACCGAGAACA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
14 2 0.03
15 18 0.28
16 7 0.11
17 1 0.02
18 36 0.56
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (18 bp):
AAAGAAAAGAAGGAGAAG
Found at i:704206 original size:27 final size:27
Alignment explanation
Indices: 704139--704234 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 27
704129 CAAGAAGACA
* *
704139 AAAGAAAAGAAGGAGAAGGATAA-AGAGG
1 AAAGAAAAGAAGGAGAA-GA-AAGAAAAG
*
704167 AGAAGAAGGAGAAGGAGAAGAAAGAAAAG
1 A-AAGAA-AAGAAGGAGAAGAAAGAAAAG
* * *
704196 AAAGAAAAGAAAGAAAAGAAAGAAAAC
1 AAAGAAAAGAAGGAGAAGAAAGAAAAG
*
704223 AAGGAAAAGAAG
1 AAAGAAAAGAAG
704235 ACCGAGAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
27 27 0.48
28 8 0.14
29 11 0.20
30 10 0.18
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (27 bp):
AAAGAAAAGAAGGAGAAGAAAGAAAAG
Found at i:704381 original size:16 final size:16
Alignment explanation
Indices: 704360--704407 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
704350 TGGTGTGAAA
704360 TTATATTTAAAATATT
1 TTATATTTAAAATATT
704376 TTATATTTATATAA-ATT
1 TTATATTTA-A-AATATT
*
704393 TTAATATATAAAATA
1 TT-ATATTTAAAATA
704408 ACTCATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 11 0.41
17 8 0.30
18 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:707829 original size:18 final size:19
Alignment explanation
Indices: 707807--707875 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
707797 TTAAAAAAAT
707807 TATATTTATATAAATTTTAA
1 TATATTTATATAAATTTT-A
* **
707827 TATATTAATAATTTATTTTA
1 TATATTTAT-ATAAATTTTA
707847 TATATTT-TAATAAA-TTTA
1 TATATTTAT-ATAAATTTTA
707865 TATATTTATAT
1 TATATTTATAT
707876 TATATTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 13 0.32
19 6 0.15
20 15 0.37
21 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTTATATAAATTTTA
Found at i:707856 original size:22 final size:22
Alignment explanation
Indices: 707820--707888 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 22
707810 ATTTATATAA
*
707820 ATTTTA-ATATATTAATAATTT
1 ATTTTATATATTTTAATAATTT
707841 ATTTTATATATTTTAATAA---
1 ATTTTATATATTTTAATAATTT
*
707860 A-TTTATATATTTATATTATATTT
1 ATTTTATATATTT-TAATA-ATTT
707883 ATTTTA
1 ATTTTA
707889 GTTTTTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 11 0.28
19 5 0.13
20 1 0.03
21 6 0.15
22 11 0.28
23 1 0.03
24 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTATATATTTTAATAATTT
Found at i:707872 original size:31 final size:30
Alignment explanation
Indices: 707804--707880 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
707794 TTATTAAAAA
* *
707804 AATTATATTTATATAAATTTTAATATATTAAT
1 AATT-TATTT-TATATATTTTAATAAATTAAT
*
707836 AATTTATTTTATATATTTTAATAAATTTAT
1 AATTTATTTTATATATTTTAATAAATTAAT
*
707866 ATATTTATATTATAT
1 A-ATTTATTTTATAT
707881 TTATTTTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.47
31 17 0.43
32 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
AATTTATTTTATATATTTTAATAAATTAAT
Found at i:712878 original size:16 final size:17
Alignment explanation
Indices: 712857--712888 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
712847 ATCAAATTTT
712857 ATATAATAT-AATATAA
1 ATATAATATAAATATAA
712873 ATATAATATAAATATA
1 ATATAATATAAATATA
712889 CGAATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAATATAAATATAA
Found at i:713480 original size:16 final size:16
Alignment explanation
Indices: 713440--713485 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
713430 TGGATGATTA
*
713440 TTTAATATATTAATTG
1 TTTAATATTTTAATTG
* *
713456 TTTAATATTTTATTTT
1 TTTAATATTTTAATTG
*
713472 TTTAATATTATAAT
1 TTTAATATTTTAAT
713486 AATTCATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTAATATTTTAATTG
Found at i:714062 original size:22 final size:22
Alignment explanation
Indices: 714034--714077 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
714024 ATATTTTTTA
* * *
714034 TTTTTTATTTTTAAATTATAAT
1 TTTTTTATATTAAAAATATAAT
714056 TTTTTTATATTAAAAATATAAT
1 TTTTTTATATTAAAAATATAAT
714078 GACAGTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTTATATTAAAAATATAAT
Found at i:714485 original size:16 final size:17
Alignment explanation
Indices: 714443--714488 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
714433 ATAAAAATTT
714443 TATA-AAATATTAAAATA
1 TATATAAATA-TAAAATA
714460 TATATAAATATAAAATA
1 TATATAAATATAAAATA
*
714477 -ATTTAAATATAA
1 TATATAAATATAA
714489 TTATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.41
17 11 0.41
18 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TATATAAATATAAAATA
Found at i:715975 original size:87 final size:85
Alignment explanation
Indices: 715876--716039 Score: 249
Period size: 87 Copynumber: 1.9 Consensus size: 85
715866 CCAAGCTAAG
* * *
715876 TTTTAATATGATATTTTATAATTTGT-ATGAATTTAATTTAATTTGAATAATTATTTATTAAATA
1 TTTTAATATGATATTTTATAATTTGTAAAG-ATTTAATTTAA-ATAAATAATTATTTATTAAATA
715940 AAAATAATTTATATTAAGTTAAA
64 AAAAT-ATTTATATTAAGTTAAA
*
715963 TTTTAATATGATATTTTATAATTTTTAAAGATTTAATTTAAATAAATAATTATTTATTAAATAAA
1 TTTTAATATGATATTTTATAATTTGTAAAGATTTAATTTAAATAAATAATTATTTATTAAATAAA
*
716028 AATATTTTTATT
66 AATATTTATATT
716040 TAAATTTAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
85 8 0.11
86 25 0.35
87 36 0.51
88 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (85 bp):
TTTTAATATGATATTTTATAATTTGTAAAGATTTAATTTAAATAAATAATTATTTATTAAATAAA
AATATTTATATTAAGTTAAA
Found at i:716044 original size:20 final size:20
Alignment explanation
Indices: 715993--716044 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
715983 ATTTTTAAAG
715993 ATTTAATTTAAATAAATAATT
1 ATTT-ATTTAAATAAATAATT
716014 ATTTA-TTAAATAAA-AATAT
1 ATTTATTTAAATAAATAAT-T
*
716033 TTTTATTTAAAT
1 ATTTATTTAAAT
716045 TTAATTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 14 0.50
20 7 0.25
21 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTATTTAAATAAATAATT
Found at i:716064 original size:87 final size:87
Alignment explanation
Indices: 715886--716070 Score: 225
Period size: 86 Copynumber: 2.1 Consensus size: 87
715876 TTTTAATATG
* * *
715886 ATATTTTATAATTTGTATGAATTTAATTTAATTTGAATAATTATTTATTAAATAAAAATAATTTA
1 ATATTTTATAATTTGTAAGAATTTAATTTAATATAAATAATTATTTATTAAATAAAAATAATTTA
* * * *
715951 TATTAAGTTAAATTTTAATATG
66 TATTAAATTAAATTTAAAAATA
*
715973 ATATTTTATAATTTTTAA-AGATTTAATTTAA-ATAAATAATTATTTATTAAATAAAAAT-ATTT
1 ATATTTTATAATTTGTAAGA-ATTTAATTTAATATAAATAATTATTTATTAAATAAAAATAATTT
* *
716035 TTATTTAAATTTAATTATAAAAATA
65 ATA-TTAAATTAAATT-TAAAAATA
716060 ATATTTT-TAAT
1 ATATTTTATAAT
716071 AATAAAATTA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.07
86 40 0.47
87 39 0.46
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (87 bp):
ATATTTTATAATTTGTAAGAATTTAATTTAATATAAATAATTATTTATTAAATAAAAATAATTTA
TATTAAATTAAATTTAAAAATA
Found at i:716085 original size:18 final size:19
Alignment explanation
Indices: 716040--716108 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 19
716030 TATTTTTATT
* *
716040 TAAA-TTTAATTATAAAAA
1 TAAATTTTAATAATCAAAA
716058 TAATATTTTTAATAAT-AAAA
1 TAA-A-TTTTAATAATCAAAA
* *
716078 TTAATTTTTA-AATCAAAA
1 TAAATTTTAATAATCAAAA
*
716096 TAAATTTAAATAA
1 TAAATTTTAATAA
716109 ATTCGAATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.08
18 19 0.47
19 4 0.10
20 6 0.15
21 8 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATTTTAATAATCAAAA
Found at i:716086 original size:20 final size:21
Alignment explanation
Indices: 716044--716086 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
716034 TTTATTTAAA
*
716044 TTTAATTATAAAAATAATATT
1 TTTAATAATAAAAATAATATT
*
716065 TTTAATAATAAAATTAAT-TT
1 TTTAATAATAAAAATAATATT
716085 TT
1 TT
716087 AAATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATAATAAAAATAATATT
Found at i:716086 original size:50 final size:50
Alignment explanation
Indices: 715993--716110 Score: 118
Period size: 49 Copynumber: 2.3 Consensus size: 50
715983 ATTTTTAAAG
715993 ATTTAATTTAAATAAATAATTATTTATTAAATAAAAATATTTTTATTTAA
1 ATTTAATTTAAATAAATAATTATTTATTAAATAAAAATATTTTTATTTAA
* * *
716043 ATTTAA-TTATAA-AAATAA-TATTT-TTAATAATAAAATTAATTTTTAAATCAA
1 ATTTAATTTA-AATAAATAATTATTTATT-A-AATAAAAAT-ATTTTT-ATTTAA
* *
716094 AATAAATTTAAATAAAT
1 ATTTAATTTAAATAAAT
716111 TCGAATCACG
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
47 2 0.04
48 6 0.11
49 17 0.30
50 14 0.25
51 10 0.18
52 7 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (50 bp):
ATTTAATTTAAATAAATAATTATTTATTAAATAAAAATATTTTTATTTAA
Found at i:716310 original size:22 final size:21
Alignment explanation
Indices: 716269--716316 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
716259 TTATTTCATA
*
716269 AATTTTA--AAATAATTATTT
1 AATTTTATTAAATAAATATTT
*
716288 ATTTTTATTAAATAAATATTTT
1 AATTTTATTAAATAAATA-TTT
716310 AATTTTA
1 AATTTTA
716317 AATGAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTTATTAAATAAATATTT
Found at i:716397 original size:19 final size:19
Alignment explanation
Indices: 716370--716418 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
716360 TGAATTAAAT
*
716370 TATTGTTATAATTATT-TTA
1 TATTTTTATAATT-TTATTA
716389 T-TTTATTATAATTTTATTA
1 TATTT-TTATAATTTTATTA
716408 TATTTTTATAA
1 TATTTTTATAA
716419 AATAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 19 0.73
20 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTATAATTTTATTA
Found at i:716402 original size:16 final size:16
Alignment explanation
Indices: 716369--716411 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
716359 TTGAATTAAA
* *
716369 TTATTGTTATAATTATT
1 TTATT-TTATTATAATT
716386 TTATTTTATTATAATT
1 TTATTTTATTATAATT
*
716402 TTATTATATT
1 TTATTTTATT
716412 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:716409 original size:30 final size:30
Alignment explanation
Indices: 716349--716409 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
716339 AAAAATTTTA
* *
716349 AATTTTTTTATTGAATTAAATTATTGTTAT
1 AATTATTTTATTGAATTAAATTATTATTAT
**
716379 AATTATTTTATTTTATTATAATT-TTATTAT
1 AATTATTTTATTGAATTA-AATTATTATTAT
716409 A
1 A
716410 TTTTTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
AATTATTTTATTGAATTAAATTATTATTAT
Found at i:717666 original size:35 final size:35
Alignment explanation
Indices: 717620--717691 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
717610 GGTATGGGTC
*
717620 ATTGTCGGCTGTAAATAATATCACATCTGCTTGCG
1 ATTGTCAGCTGTAAATAATATCACATCTGCTTGCG
717655 ATTGTCAGCTGTAAATAATATCACATCTGCTTGCG
1 ATTGTCAGCTGTAAATAATATCACATCTGCTTGCG
717690 AT
1 AT
717692 GAAGATGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (35 bp):
ATTGTCAGCTGTAAATAATATCACATCTGCTTGCG
Found at i:717987 original size:52 final size:52
Alignment explanation
Indices: 717929--718032 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
717919 AAAACTGTGT
717929 TCATATATACATATATATAAATTAAGCTTAGAAATGACTGGCGCATGAACCA
1 TCATATATACATATATATAAATTAAGCTTAGAAATGACTGGCGCATGAACCA
717981 TCATATATACATATATATAAATTAAGCTTAGAAATGACTGGCGCATGAACCA
1 TCATATATACATATATATAAATTAAGCTTAGAAATGACTGGCGCATGAACCA
718033 CTCTGTTGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (52 bp):
TCATATATACATATATATAAATTAAGCTTAGAAATGACTGGCGCATGAACCA
Found at i:728248 original size:15 final size:16
Alignment explanation
Indices: 728220--728253 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
728210 AAAAATGAGT
728220 ATACTGACACATACTC
1 ATACTGACACATACTC
*
728236 ATAC-GACATATACTC
1 ATACTGACACATACTC
728251 ATA
1 ATA
728254 TTAAATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
ATACTGACACATACTC
Found at i:729051 original size:3 final size:3
Alignment explanation
Indices: 729043--729067 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
729033 TTTTACTTAT
729043 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
729068 TTCCCCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:731506 original size:2 final size:2
Alignment explanation
Indices: 731499--731558 Score: 66
Period size: 2 Copynumber: 29.0 Consensus size: 2
731489 TTTCATATGC
* *
731499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT TT CAT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT
* *
731543 AC AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT
731559 TGGCTTTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:731805 original size:13 final size:13
Alignment explanation
Indices: 731776--731810 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
731766 AATATTTAAA
731776 TAAAAATATTAAGT
1 TAAAAA-ATTAAGT
*
731790 TAAAAAATTAATT
1 TAAAAAATTAAGT
731803 TAAAAAAT
1 TAAAAAAT
731811 AAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
TAAAAAATTAAGT
Found at i:731832 original size:17 final size:18
Alignment explanation
Indices: 731793--731831 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
731783 ATTAAGTTAA
731793 AAAATTAATTTAAAAAAT
1 AAAATTAATTTAAAAAAT
* *
731811 AAAATTTATTTAAAAATT
1 AAAATTAATTTAAAAAAT
731829 AAA
1 AAA
731832 TAGAGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTAATTTAAAAAAT
Done.