Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold174
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 15
Found at i:551283 original size:31 final size:33
Alignment explanation
Indices: 551231--551340 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 33
551221 TTAATACATG
* *
551231 TATAATATAAATATATAAATATTTTAAATTTTA
1 TATAATATAAATATATAAATATATTAAAATTTA
*
551264 TATAATA-AAAT-TATTAATATATTAAAA-TT-
1 TATAATATAAATATATAAATATATTAAAATTTA
*
551293 TATAATA-AAA-ATA-AAATATATT-AAATATGA
1 TATAATATAAATATATAAATATATTAAAAT-TTA
*
551323 TTATAATATAAAAATATA
1 -TATAATATAAATATATA
551341 CGAATATAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
27 3 0.05
28 8 0.12
29 13 0.20
30 2 0.03
31 20 0.31
32 7 0.11
33 10 0.16
34 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
TATAATATAAATATATAAATATATTAAAATTTA
Found at i:551298 original size:17 final size:17
Alignment explanation
Indices: 551263--551316 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
551253 TTTAAATTTT
551263 ATATAATAAAATTATTA
1 ATATAATAAAATTATTA
*
551280 ATATATTAAAATT-TATA
1 ATATAATAAAATTAT-TA
*
551297 ATAAAAATAAAATATATTA
1 AT-ATAATAAAAT-TATTA
551316 A
1 A
551317 ATATGATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 16 0.53
18 8 0.27
19 4 0.13
20 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAATAAAATTATTA
Found at i:551554 original size:4 final size:4
Alignment explanation
Indices: 551538--551646 Score: 128
Period size: 4 Copynumber: 27.2 Consensus size: 4
551528 TTTCAAAAAA
* * * * * * *
551538 ATAT ATGT ATAT ATAT ACAT ATAC ATAC ATAT ATAT ACAT ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
551586 ATAT ATAT ATAT ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
551634 ATAT ATAT ATAT A
1 ATAT ATAT ATAT A
551647 GCCTTCCCTT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 93 1.00
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:551645 original size:10 final size:10
Alignment explanation
Indices: 551538--551646 Score: 128
Period size: 10 Copynumber: 10.9 Consensus size: 10
551528 TTTCAAAAAA
*
551538 ATATATGTAT
1 ATATATATAT
*
551548 ATATATACAT
1 ATATATATAT
* *
551558 ATACATACAT
1 ATATATATAT
*
551568 ATATATACAT
1 ATATATATAT
* *
551578 ATACATACAT
1 ATATATATAT
551588 ATATATATAT
1 ATATATATAT
* *
551598 ATACATACAT
1 ATATATATAT
*
551608 ACATATATAT
1 ATATATATAT
551618 ATATATATAT
1 ATATATATAT
551628 ATATATATAT
1 ATATATATAT
551638 ATATATATA
1 ATATATATA
551647 GCCTTCCCTT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 86 1.00
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (10 bp):
ATATATATAT
Found at i:551646 original size:20 final size:20
Alignment explanation
Indices: 551546--551640 Score: 145
Period size: 20 Copynumber: 4.8 Consensus size: 20
551536 AAATATATGT
*
551546 ATATATATACATATACATAC
1 ATATATATATATATACATAC
*
551566 ATATATATACATATACATAC
1 ATATATATATATATACATAC
551586 ATATATATATATATACATAC
1 ATATATATATATATACATAC
* * *
551606 ATACATATATATATATATAT
1 ATATATATATATATACATAC
551626 ATATATATATATATA
1 ATATATATATATATA
551641 TATATAGCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATATATATATATACATAC
Found at i:554882 original size:12 final size:12
Alignment explanation
Indices: 554865--554889 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
554855 TTTTGTAACG
554865 ACTGGTAATCAT
1 ACTGGTAATCAT
554877 ACTGGTAATCAT
1 ACTGGTAATCAT
554889 A
1 A
554890 TCGCGTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ACTGGTAATCAT
Found at i:555587 original size:2 final size:2
Alignment explanation
Indices: 555580--555613 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
555570 AATTATAGCA
555580 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
555614 CCTTTGCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:555849 original size:91 final size:92
Alignment explanation
Indices: 555694--555876 Score: 341
Period size: 91 Copynumber: 2.0 Consensus size: 92
555684 GCCAACAGTT
555694 TTCAGATGATTTTGTGGGTTAATTTCCTTATTTTCTCTTTGGCCGTACGTTTTTT-GGGGGGGGG
1 TTCAGATGATTTTGTGGGTTAATTTCCTTATTTTCTCTTTGGCCGTACGTTTTTTGGGGGGGGGG
555758 GGGGGTGCTGTTATTGTTTGTTGATGA
66 GGGGGTGCTGTTATTGTTTGTTGATGA
*
555785 TTCAGATGATTTTGTGGGTTAATTTCCTTATTTTCTCTTTGGCCGTACGTTTTTTTTGGGGGGGG
1 TTCAGATGATTTTGTGGGTTAATTTCCTTATTTTCTCTTTGGCCGTACG-TTTTTTGGGGGGGGG
555850 GGGGGGTGCTGTTATTGTTTGTTGATG
65 GGGGGGTGCTGTTATTGTTTGTTGATG
555877 CATTATCATA
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
91 49 0.54
92 6 0.07
93 35 0.39
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.47
Consensus pattern (92 bp):
TTCAGATGATTTTGTGGGTTAATTTCCTTATTTTCTCTTTGGCCGTACGTTTTTTGGGGGGGGGG
GGGGGTGCTGTTATTGTTTGTTGATGA
Found at i:566956 original size:13 final size:13
Alignment explanation
Indices: 566938--566967 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
566928 TTTTTTTTAA
566938 AATATTTATATTT
1 AATATTTATATTT
566951 AATATTTATATTT
1 AATATTTATATTT
566964 AATA
1 AATA
566968 CATATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:567697 original size:20 final size:20
Alignment explanation
Indices: 567672--567716 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
567662 CTATTTGAAT
*
567672 AATTTAATTAATTAAAT-ATA
1 AATTTAAATAATT-AATCATA
*
567692 AATTTAAATACTTAATCATA
1 AATTTAAATAATTAATCATA
567712 AATTT
1 AATTT
567717 TTTTAATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAAATAATTAATCATA
Found at i:569890 original size:15 final size:15
Alignment explanation
Indices: 569861--569903 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
569851 ATGTCACAAT
**
569861 TTAAAAATAAAAAAA
1 TTAAAAATATTAAAA
*
569876 TTATAAATATTAAAA
1 TTAAAAATATTAAAA
*
569891 TTAAAAATTTTAA
1 TTAAAAATATTAA
569904 TTTATTGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAAATATTAAAA
Found at i:571721 original size:14 final size:15
Alignment explanation
Indices: 571702--571733 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
571692 CATATTTTTG
571702 TTTATTTTAA-TTAT
1 TTTATTTTAATTTAT
571716 TTTATTTTAATTTAT
1 TTTATTTTAATTTAT
571731 TTT
1 TTT
571734 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTAATTTAT
Found at i:573496 original size:21 final size:20
Alignment explanation
Indices: 573462--573518 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
573452 AATTAAAGAT
* *
573462 AAATATGAATAAATAATTTA
1 AAATATAAATAAATAATATA
*
573482 ATAATATAAAAAAATTAATATA
1 A-AATATAAATAAA-TAATATA
573504 AAATATTAAATAAAT
1 AAATA-TAAATAAAT
573519 CTGATGGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATATAAATAAATAATATA
Found at i:573600 original size:27 final size:27
Alignment explanation
Indices: 573566--573623 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
573556 TACTATCGAG
*
573566 AAAATAATAAAAATATAAATAAA-AATA
1 AAAATAAT-AAAATATAAAAAAATAATA
*
573593 AAAATAATAAAATTTAAAAAAATAATA
1 AAAATAATAAAATATAAAAAAATAATA
573620 AAAA
1 AAAA
573624 ATTTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (27 bp):
AAAATAATAAAATATAAAAAAATAATA
Found at i:573764 original size:16 final size:16
Alignment explanation
Indices: 573739--573775 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
573729 AACAACCAAC
*
573739 TAATTTTTAATTAAAT
1 TAATTCTTAATTAAAT
573755 TAATTCTTAATTAAAT
1 TAATTCTTAATTAAAT
573771 TAATT
1 TAATT
573776 TAAACAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTCTTAATTAAAT
Found at i:573943 original size:87 final size:89
Alignment explanation
Indices: 573811--573995 Score: 311
Period size: 87 Copynumber: 2.1 Consensus size: 89
573801 TTAATCAATG
573811 CAAATATCACCAACAAAAAAAAAAAAGTGATTAATGCTCAAGTGCCCTATTATCTAAGCATATCA
1 CAAATATCACCAAC-AAAAAAAAAAAGTGATTAATGCTCAAGTGCCCTATTATCTAAGCATATCA
* *
573876 ATCAATTATTAACTAACATGGAAGT
65 ATCAATGATTAACTAACATGGAAGA
*
573901 CAAATATCACCAAC-AAAAAAAAAAGTGA-TAATTCTCAAGTGCCCTATTATCTAAGCATATCAA
1 CAAATATCACCAACAAAAAAAAAAAGTGATTAATGCTCAAGTGCCCTATTATCTAAGCATATCAA
*
573964 TCAATGGTTAACTAACATGGAAGA
66 TCAATGATTAACTAACATGGAAGA
573988 CAAATATC
1 CAAATATC
573996 TCCATTTAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
87 63 0.69
88 14 0.15
90 14 0.15
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.25
Consensus pattern (89 bp):
CAAATATCACCAACAAAAAAAAAAAGTGATTAATGCTCAAGTGCCCTATTATCTAAGCATATCAA
TCAATGATTAACTAACATGGAAGA
Found at i:575926 original size:25 final size:26
Alignment explanation
Indices: 575889--575941 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
575879 ATATTTTACG
**
575889 TATATTTAAAAATAAATATCAAATTT
1 TATATTTAAAAATAAATAAAAAATTT
* *
575915 TATATTT-TAAATATATAAAAAATTT
1 TATATTTAAAAATAAATAAAAAATTT
575940 TA
1 TA
575942 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TATATTTAAAAATAAATAAAAAATTT
Found at i:576917 original size:29 final size:30
Alignment explanation
Indices: 576823--576922 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 30
576813 TTGATGAGTT
* * *
576823 TAAAAATTTATTTTATTATTAAAAATAATAT
1 TAAAAATATATTTTATTATT-TAAATAATAA
* * *
576854 TAAAAATTTATTATTTTTTTAATTAAAT-TTAAA
1 TAAAAA--TA-TATTTTATTATTTAAATAAT-AA
576887 TAAAAATAT-TTTTATTATTTAAATAATAA
1 TAAAAATATATTTTATTATTTAAATAATAA
*
576916 TATAAAT
1 TAAAAAT
576923 TAATTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 21 0.39
30 2 0.04
31 8 0.15
32 1 0.02
33 12 0.22
34 10 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAAAATATATTTTATTATTTAAATAATAA
Found at i:577678 original size:15 final size:15
Alignment explanation
Indices: 577660--577706 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 15
577650 TGATAAGTGT
577660 AATTTTTATAAATTA
1 AATTTTTATAAATTA
*
577675 AA--TTT-TAAATAA
1 AATTTTTATAAATTA
577687 AATTTTTATAAATTTA
1 AATTTTTATAAA-TTA
577703 AATT
1 AATT
577707 GATTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 8 0.31
13 3 0.12
14 3 0.12
15 6 0.23
16 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTTATAAATTA
Found at i:577713 original size:15 final size:14
Alignment explanation
Indices: 577695--577725 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
577685 AAAATTTTTA
577695 TAAATTTAAATTGAT
1 TAAATTTAAATT-AT
577710 TAAATTTAAATTAT
1 TAAATTTAAATTAT
577724 TA
1 TA
577726 TTTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TAAATTTAAATTAT
Found at i:577762 original size:22 final size:22
Alignment explanation
Indices: 577734--577781 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
577724 TATTTTTATT
*
577734 TAAATTTAATTATA-AAAATATA
1 TAAATTTAATAATATAAAATA-A
577756 TAAATTTAATAATATAAAATAA
1 TAAATTTAATAATATAAAATAA
577778 TAAA
1 TAAA
577782 ATAAATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATAATATAAAATAA
Found at i:578424 original size:15 final size:14
Alignment explanation
Indices: 578396--578431 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
578386 CGATTTAATT
578396 AATAAAAATAAAAA
1 AATAAAAATAAAAA
*
578410 AATAATAAATTAAAA
1 AATAA-AAATAAAAA
578425 AATAAAA
1 AATAAAA
578432 CAAAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:579714 original size:3 final size:3
Alignment explanation
Indices: 579706--579731 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
579696 GTTGGTAAAA
579706 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
579732 CCCTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:580827 original size:20 final size:18
Alignment explanation
Indices: 580802--580842 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
580792 TTTTTTTTAA
580802 AATTTAAATTAATTTATTTT
1 AATTTAAATT-A-TTATTTT
580822 AATTTAAATTATTATTTT
1 AATTTAAATTATTATTTT
580840 AAT
1 AAT
580843 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTAAATTATTATTTT
Found at i:581292 original size:15 final size:14
Alignment explanation
Indices: 581272--581303 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
581262 AAGATAAAAA
581272 AAAATTTAAAATATT
1 AAAATTTAAAAT-TT
581287 AAAATTTAAAATTT
1 AAAATTTAAAATTT
581301 AAA
1 AAA
581304 TATATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTTAAAATTT
Found at i:581295 original size:7 final size:7
Alignment explanation
Indices: 581272--581303 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
581262 AAGATAAAAA
581272 AAAATTT
1 AAAATTT
581279 AAAATATT
1 AAAAT-TT
581287 AAAATTT
1 AAAATTT
581294 AAAATTT
1 AAAATTT
581301 AAA
1 AAA
581304 TATATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:583874 original size:18 final size:18
Alignment explanation
Indices: 583844--583882 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
583834 ATAAGTATAC
*
583844 TTATAATTTATAATATTT
1 TTATAATTTATAATAGTT
583862 TTAT-ATTTAATAATAGTT
1 TTATAATTT-ATAATAGTT
583880 TTA
1 TTA
583883 CAATCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATAATTTATAATAGTT
Found at i:585133 original size:16 final size:16
Alignment explanation
Indices: 585112--585153 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
585102 AAATATAAAT
585112 TATTTAT-TCATATTAA
1 TATTTATAT-ATATTAA
*
585128 TATTTATATATTTTAA
1 TATTTATATATATTAA
585144 TATTTA-ATAT
1 TATTTATATAT
585154 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 19 0.79
17 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTATATATATTAA
Found at i:587750 original size:11 final size:10
Alignment explanation
Indices: 587668--587754 Score: 61
Period size: 10 Copynumber: 8.4 Consensus size: 10
587658 ATATTTTACA
*
587668 AAATAAATTA
1 AAATAAATTT
* *
587678 AAAAATAATAT
1 AAATA-AATTT
*
587689 AAATAAATCT
1 AAATAAATTT
587699 AAATAAATTT
1 AAATAAATTT
*
587709 AAACTACCTATTT
1 AAA-TA--AATTT
*
587722 --ATAAATAT
1 AAATAAATTT
587730 AAATAAATTT
1 AAATAAATTT
587740 AAATAAAATTT
1 AAAT-AAATTT
587751 AAAT
1 AAAT
587755 TTTATATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
8 3 0.05
10 33 0.55
11 20 0.33
13 4 0.07
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATAAATTT
Found at i:587766 original size:25 final size:25
Alignment explanation
Indices: 587737--587785 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
587727 TATAAATAAA
* *
587737 TTTAAATAAAATTTAAATTTTATAT
1 TTTAAATAAAATTAAAATTATATAT
*
587762 TTTAATTAAAATTAAAATTATATA
1 TTTAAATAAAATTAAAATTATATA
587786 AATATAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAAATAAAATTAAAATTATATAT
Found at i:587838 original size:27 final size:27
Alignment explanation
Indices: 587784--587838 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
587774 TAAAATTATA
*
587784 TAAATATAAATAATATTTCAACCACTC
1 TAAATATAAATAATATTACAACCACTC
* *
587811 TAAATATAAATAATATTACCACCGCTC
1 TAAATATAAATAATATTACAACCACTC
587838 T
1 T
587839 TAATTCTAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAATATAAATAATATTACAACCACTC
Found at i:588436 original size:31 final size:33
Alignment explanation
Indices: 588401--588463 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
588391 CTTTCATTTT
* * *
588401 AATTAAATTTAATAATT-TT-AAATATAATATA
1 AATTAAATATAAAAATTATTAAAAAATAATATA
588432 AATTAAATATAAAAATTATTAAAAAATAATAT
1 AATTAAATATAAAAATTATTAAAAAATAATAT
588464 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 15 0.56
32 2 0.07
33 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AATTAAATATAAAAATTATTAAAAAATAATATA
Found at i:588477 original size:14 final size:13
Alignment explanation
Indices: 588448--588473 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
588438 ATATAAAAAT
588448 TATTAAAAAATAA
1 TATTAAAAAATAA
588461 TATTAAAAAATAA
1 TATTAAAAAATAA
588474 ATATAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TATTAAAAAATAA
Found at i:588696 original size:23 final size:22
Alignment explanation
Indices: 588670--588716 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
588660 CAATTGATTG
*
588670 ATATTTATAAATATTAAATAAAA
1 ATATGTATAAA-ATTAAATAAAA
**
588693 ATATGTATAAAATTATTTAAAA
1 ATATGTATAAAATTAAATAAAA
588715 AT
1 AT
588717 TATTAACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATGTATAAAATTAAATAAAA
Found at i:589250 original size:16 final size:16
Alignment explanation
Indices: 589221--589255 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
589211 TGTTTAAATT
589221 TTTTATTTATTTTATA
1 TTTTATTTATTTTATA
589237 TTTT-TTTATATTTATA
1 TTTTATTTAT-TTTATA
589253 TTT
1 TTT
589256 AAATGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTTATA
Found at i:591194 original size:11 final size:12
Alignment explanation
Indices: 591154--591213 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
591144 TAATATCATA
591154 TTTATATTATTTT
1 TTTATATTA-TTT
*
591167 TTTAATATTATAT
1 TTT-ATATTATTT
591180 TTTA-ATTATTT
1 TTTATATTATTT
*
591191 TTTATATCATATT
1 TTTATATTAT-TT
*
591204 TATATATTAT
1 TTTATATTAT
591214 ATTTAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 10 0.26
12 5 0.13
13 18 0.46
14 6 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:591212 original size:25 final size:25
Alignment explanation
Indices: 591143--591234 Score: 97
Period size: 25 Copynumber: 3.9 Consensus size: 25
591133 ATTTTATAAA
591143 TTAATATCATATTTATATTATT-TTT
1 TTAATATCATATTTATA-TATTATTT
*
591168 TTAATATTATATTT-TA-ATTATTT
1 TTAATATCATATTTATATATTATTT
* *
591191 TTTATATCATATTTATATATTATAT
1 TTAATATCATATTTATATATTATTT
*
591216 TTAA-ATTATA-TTAT-TATTA
1 TTAATATCATATTTATATATTA
591235 AACAAAAGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
22 8 0.14
23 19 0.33
24 9 0.16
25 22 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTAATATCATATTTATATATTATTT
Found at i:591223 original size:11 final size:11
Alignment explanation
Indices: 591167--591227 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
591157 ATATTATTTT
591167 TTTAATATTATA
1 TTTAA-ATTATA
* *
591179 TTTTAATTATTT
1 TTTAAATTA-TA
* *
591191 TTTATATCATA
1 TTTAAATTATA
591202 TTTATATATTATA
1 TTTA-A-ATTATA
591215 TTTAAATTATA
1 TTTAAATTATA
591226 TT
1 TT
591228 ATTATTAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
11 17 0.45
12 12 0.32
13 9 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTAAATTATA
Found at i:591224 original size:18 final size:18
Alignment explanation
Indices: 591171--591232 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
591161 TATTTTTTTA
*
591171 ATATTATATTTTAATTAT
1 ATATTATATTTAAATTAT
* * * *
591189 TTTTTATA-TCATATTTAT
1 ATATTATATTTA-AATTAT
591207 ATATTATATTTAAATTAT
1 ATATTATATTTAAATTAT
591225 ATTATTAT
1 A-TATTAT
591233 TAAACAAAAG
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
17 1 0.03
18 23 0.72
19 8 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTATATTTAAATTAT
Found at i:591638 original size:28 final size:28
Alignment explanation
Indices: 591607--591661 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
591597 TAAAATGTAA
* *
591607 TTTAATTTA-ATTTATAAAATTTAAAAAT
1 TTTAATTTATAATT-TAAAATATAAAAAT
*
591635 TTTATTTTATAATTTAAAATATAAAAA
1 TTTAATTTATAATTTAAAATATAAAAA
591662 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTAATTTATAATTTAAAATATAAAAAT
Found at i:591650 original size:21 final size:22
Alignment explanation
Indices: 591610--591653 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
591600 AATGTAATTT
591610 AATTTAATTTATAAAATTTAAA
1 AATTTAATTTATAAAATTTAAA
* *
591632 AATTTTATTT-TATAATTTAAA
1 AATTTAATTTATAAAATTTAAA
591653 A
1 A
591654 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTAATTTATAAAATTTAAA
Found at i:592075 original size:32 final size:32
Alignment explanation
Indices: 592011--592075 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
592001 TAAATTATTA
**
592011 TTTAATAATAAAAAATAAAATTTTATTTAAAT
1 TTTAATAATAAAAAATAAAATTTTATAAAAAT
*
592043 TTTAAT-ATAAAATATATAAATTTTATAAAAAT
1 TTTAATAATAAAAAATA-AAATTTTATAAAAAT
592075 T
1 T
592076 ATATTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTAATAATAAAAAATAAAATTTTATAAAAAT
Found at i:592842 original size:12 final size:12
Alignment explanation
Indices: 592822--592850 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
592812 CAGTTATATA
592822 AATAT-AATTAT
1 AATATAAATTAT
592833 AATATAAATTAT
1 AATATAAATTAT
592845 AATATA
1 AATATA
592851 TCATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATAAATTAT
Found at i:592894 original size:29 final size:30
Alignment explanation
Indices: 592826--592894 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
592816 TATATAAATA
592826 TAATTATAATATAAATTATAATATATCATAT
1 TAATTAT-ATATAAATTATAATATATCATAT
** *
592857 TAAACATATATAAA-TATATTATATCATAT
1 TAATTATATATAAATTATAATATATCATAT
*
592886 TTATTATAT
1 TAATTATAT
592895 TATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 20 0.62
30 7 0.22
31 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATTATATATAAATTATAATATATCATAT
Found at i:592922 original size:18 final size:18
Alignment explanation
Indices: 592882--592931 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
592872 ATATTATATC
*
592882 ATATTTATTATATTATTT
1 ATATTTATTAAATTATTT
*
592900 TTATTTATTAAATGTA-TT
1 ATATTTATTAAAT-TATTT
592918 ATATTT-TT-AATTAT
1 ATATTTATTAAATTAT
592932 ATTTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 2 0.07
18 18 0.67
19 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
ATATTTATTAAATTATTT
Found at i:595159 original size:2 final size:2
Alignment explanation
Indices: 595147--595191 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
595137 TTGTAAAAGC
595147 AT AT A- 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
595188 AT AT
1 AT AT
595192 CATAATGGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:596480 original size:15 final size:15
Alignment explanation
Indices: 596462--596508 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
596452 TATTTTATAA
*
596462 TAAATTAATTTAATT
1 TAAATTAAATTAATT
596477 TAAATTAAATTAATT
1 TAAATTAAATTAATT
* * *
596492 AAAATTTAATAAATT
1 TAAATTAAATTAATT
596507 TA
1 TA
596509 TAAATATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATTAAATTAATT
Found at i:598591 original size:20 final size:17
Alignment explanation
Indices: 598565--598612 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 17
598555 TTTTGAATTT
598565 AATAAAAATAATATATTAA
1 AATAAAAATAAT-TA-TAA
598584 ACATAAAAA-AATTATAA
1 A-ATAAAAATAATTATAA
598601 AATAATAAATAA
1 AATAA-AAATAA
598613 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 4 0.15
19 4 0.15
20 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAAATAATTATAA
Found at i:598608 original size:19 final size:20
Alignment explanation
Indices: 598564--598615 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
598554 TTTTTGAATT
*
598564 TAATAAAAATAATATATTAAA
1 TAATAAAAA-AATATATAAAA
*
598585 -CATAAAAAAAT-TATAAAA
1 TAATAAAAAAATATATAAAA
*
598603 TAATAAATAAATA
1 TAATAAAAAAATA
598616 ATTTTTATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 6 0.24
19 12 0.48
20 7 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATAAAAAAATATATAAAA
Found at i:600429 original size:11 final size:11
Alignment explanation
Indices: 600415--600474 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 11
600405 GTGATTTTTA
*
600415 TAAATTTAATT
1 TAAATTTAAAT
600426 TAAA-TTAAAT
1 TAAATTTAAAT
*
600436 TAAATTTAAAA
1 TAAATTTAAAT
* *
600447 TAATTTTTAA-
1 TAAATTTAAAT
600457 T-AATTTAAAT
1 TAAATTTAAAT
600467 T-AATTTAA
1 TAAATTTAA
600475 TACTCATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
9 6 0.15
10 18 0.44
11 17 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:601599 original size:28 final size:25
Alignment explanation
Indices: 601547--601633 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 25
601537 AATAATTTAG
* *
601547 AATTTTATATAATATAATTTGTAATT
1 AATTTTATATAATATAATATATAA-T
*
601573 TATTTTATATAATATCTAATATATAAT
1 AATTTTATATAATA--TAATATATAAT
*
601600 AATTTT-TAT-ATAATAATGTA-AAT
1 AATTTTATATAAT-ATAATATATAAT
601623 AATTTT-TATAA
1 AATTTTATATAA
601634 ATACTTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
23 12 0.23
24 7 0.13
25 2 0.04
26 17 0.33
27 6 0.12
28 8 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (25 bp):
AATTTTATATAATATAATATATAAT
Found at i:601613 original size:21 final size:22
Alignment explanation
Indices: 601589--601636 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
601579 ATATAATATC
601589 TAATATAT-AATAATTTTTATA
1 TAATATATAAATAATTTTTATA
*
601610 TAATAATGTAAATAATTTTTATA
1 TAAT-ATATAAATAATTTTTATA
601633 -AATA
1 TAATA
601637 CTTAAAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 6 0.25
23 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATATATAAATAATTTTTATA
Found at i:603532 original size:18 final size:18
Alignment explanation
Indices: 603512--603582 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
603502 AAATAAAAAT
*
603512 AAATAATTATATTATAATA
1 AAATAA-TATAATATAATA
603531 AAATAATATAATATAAT-
1 AAATAATATAATATAATA
**
603548 TTATAA-ATAATAT-ATA
1 AAATAATATAATATAATA
* *
603564 AATTTATATAATATTAATA
1 AAATAATATAATA-TAATA
603583 TATTTAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
15 2 0.05
16 9 0.22
17 10 0.24
18 11 0.27
19 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATAATATAATATAATA
Found at i:603544 original size:21 final size:21
Alignment explanation
Indices: 603508--603584 Score: 56
Period size: 23 Copynumber: 3.7 Consensus size: 21
603498 TTAAAAATAA
*
603508 AAATAA-ATAATTATATTATAAT
1 AAATAATATAA-TATAATAT-AT
*
603530 AAAATAATATAATATAATTTAT
1 -AAATAATATAATATAATATAT
603552 AAATAATAT-ATA-AAT-T-T
1 AAATAATATAATATAATATAT
*
603569 ATATAATATTAATATA
1 AAATAATA-TAATATA
603585 TTTAATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 8 0.17
18 2 0.04
19 6 0.13
20 4 0.09
21 9 0.19
22 2 0.04
23 12 0.26
24 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAATATAATATAATATAT
Found at i:603545 original size:23 final size:21
Alignment explanation
Indices: 603507--603588 Score: 75
Period size: 19 Copynumber: 4.0 Consensus size: 21
603497 TTTAAAAATA
603507 AAAATAA-ATAATTATATTATAAT
1 AAAATAATATAA-TATATT-T-AT
603530 AAAATAATATAATATAATTTAT
1 AAAATAATATAATAT-ATTTAT
*
603552 -AAATAATAT-ATAAATTTAT
1 AAAATAATATAATATATTTAT
*
603571 ATAAT-AT-TAATATATTTA
1 AAAATAATATAATATATTTA
603589 ATATAAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
18 1 0.02
19 16 0.31
20 6 0.12
21 9 0.17
22 2 0.04
23 11 0.21
24 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATAATATAATATATTTAT
Found at i:603547 original size:5 final size:5
Alignment explanation
Indices: 603510--603594 Score: 51
Period size: 5 Copynumber: 17.8 Consensus size: 5
603500 AAAAATAAAA
*
603510 ATAA- ATAATT ATATT ATAAT A-AA- ATAAT ATAAT ATAATTT ATAA-
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAA--T ATAAT
* *
603554 ATAAT AT-AT A-AAT -TTAT ATAAT ATTAAT AT-AT TTAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAA
603595 ATTTTTAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
3 1 0.02
4 22 0.35
5 27 0.43
6 8 0.13
7 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:603598 original size:11 final size:10
Alignment explanation
Indices: 603533--603594 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 10
603523 TTATAATAAA
*
603533 ATAATATAAT
1 ATAATTTAAT
*
603543 ATAATTTATAA
1 ATAATTTA-AT
*
603554 ATAATAT-AT
1 ATAATTTAAT
603563 A-AATTT-AT
1 ATAATTTAAT
603571 ATAATATTAAT
1 ATAAT-TTAAT
603582 AT-ATTTAAT
1 ATAATTTAAT
603591 ATAA
1 ATAA
603595 ATTTTTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
8 7 0.17
9 12 0.29
10 12 0.29
11 11 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:603860 original size:17 final size:14
Alignment explanation
Indices: 603828--603856 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
603818 TCCATTAGAT
603828 TTTTTTTTATTTAA
1 TTTTTTTTATTTAA
603842 TTTTTTTTATTTAA
1 TTTTTTTTATTTAA
603856 T
1 T
603857 AATTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTATTTAA
Found at i:604697 original size:4 final size:4
Alignment explanation
Indices: 604675--604718 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
604665 TAAATTCATA
* * * *
604675 ATAT AAAT ATGT ATGT ATAT ATAT GTAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
604719 GGTTACATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:604698 original size:14 final size:14
Alignment explanation
Indices: 604675--604718 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
604665 TAAATTCATA
*
604675 ATATAAATATGTAT
1 ATATATATATGTAT
*
604689 GTATATATATGTAT
1 ATATATATATGTAT
*
604703 ATATATATATATAT
1 ATATATATATGTAT
604717 AT
1 AT
604719 GGTTACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:604699 original size:10 final size:10
Alignment explanation
Indices: 604681--604719 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
604671 CATAATATAA
*
604681 ATATGTATGT
1 ATATATATGT
604691 ATATATATGT
1 ATATATATGT
*
604701 ATATATATAT
1 ATATATATGT
604711 ATATATATG
1 ATATATATG
604720 GTTACATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (10 bp):
ATATATATGT
Found at i:605218 original size:18 final size:17
Alignment explanation
Indices: 605193--605226 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
605183 AATATAATGT
*
605193 TATTATTATAAATTATG
1 TATTATTAAAAATTATG
605210 TATTAATTAAAAATTAT
1 TATT-ATTAAAAATTAT
605227 AGTCGTACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTATTAAAAATTATG
Found at i:606056 original size:15 final size:15
Alignment explanation
Indices: 606026--606055 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
606016 AAAATATTAA
606026 ATTTATTTAAATTTT
1 ATTTATTTAAATTTT
606041 ATTTAATTTAAATTT
1 ATTT-ATTTAAATTT
606056 AAATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTATTTAAATTTT
Found at i:606418 original size:21 final size:21
Alignment explanation
Indices: 606372--606418 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
606362 AAACAACTAA
606372 AATTT-TAAAAATAAAAAATC
1 AATTTATAAAAATAAAAAATC
* * * *
606392 ATTTTATAAATATAAATATTC
1 AATTTATAAAAATAAAAAATC
606413 AATTTA
1 AATTTA
606419 CGTAATTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTATAAAAATAAAAAATC
Found at i:606755 original size:21 final size:21
Alignment explanation
Indices: 606719--606773 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 21
606709 TTAAAAAATT
606719 AAATATAAATTAAATAATTTTAATA
1 AAATAT-AA-TAAAT-A-TTTAATA
606744 TTAAATATAATAAATATTTAATA
1 --AAATATAATAAATATTTAATA
606767 AAATATA
1 AAATATA
606774 TATTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 7 0.25
23 7 0.25
24 1 0.04
25 5 0.18
26 2 0.07
27 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATAATAAATATTTAATA
Found at i:606778 original size:16 final size:16
Alignment explanation
Indices: 606740--606786 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
606730 AAATAATTTT
* *
606740 AATATTAAATATAATA
1 AATATTTAATAAAATA
606756 AATATTTAATAAAATA
1 AATATTTAATAAAATA
* *
606772 TATATTTAATTAAAT
1 AATATTTAATAAAAT
606787 TGTATAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTTAATAAAATA
Found at i:607190 original size:16 final size:16
Alignment explanation
Indices: 607171--607205 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
607161 TTTACATATC
*
607171 TAAATATTTATTATTT
1 TAAATATATATTATTT
*
607187 TAAATATATATTTTTT
1 TAAATATATATTATTT
607203 TAA
1 TAA
607206 CAAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAAATATATATTATTT
Found at i:608889 original size:3 final size:3
Alignment explanation
Indices: 608881--608906 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
608871 CCATGGCAAT
608881 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
608907 TGGGCAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:611129 original size:20 final size:18
Alignment explanation
Indices: 611104--611140 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
611094 GTAAATGAAG
611104 GTTTATTTAATTTAATTTAA
1 GTTTATTT-ATTT-ATTTAA
611124 GTTTATTTATTTATTTA
1 GTTTATTTATTTATTTA
611141 TTTGTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
GTTTATTTATTTATTTAA
Found at i:611500 original size:29 final size:29
Alignment explanation
Indices: 611443--611501 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
611433 AATATAATTT
* *
611443 TTTTATAAATAATTGATTGAAATTTTAAA
1 TTTTATAAATAATTGATAGAAATTATAAA
611472 TTTTATAAATAGATT-A-AGAAATTAATAAA
1 TTTTATAAATA-ATTGATAGAAATT-ATAAA
611501 T
1 T
611502 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 6 0.23
29 17 0.65
30 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (29 bp):
TTTTATAAATAATTGATAGAAATTATAAA
Found at i:611874 original size:2 final size:2
Alignment explanation
Indices: 611867--611910 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
611857 TTAATTTGAT
611867 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
611909 TA
1 TA
611911 CGTGCGTTGG
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):
TA
Found at i:612100 original size:3 final size:3
Alignment explanation
Indices: 612092--612118 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
612082 ATTTTACCAT
612092 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
612119 ATATATTAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:612143 original size:12 final size:11
Alignment explanation
Indices: 612096--612144 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
612086 TACCATTAAT
612096 AATAATAATAA
1 AATAATAATAA
612107 TAATAATAATAA
1 -AATAATAATAA
*
612119 ATATATTAA-AA
1 A-ATAATAATAA
612130 AATAATGAATAA
1 AATAAT-AATAA
612142 AAT
1 AAT
612145 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.12
11 6 0.19
12 22 0.69
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:613890 original size:13 final size:13
Alignment explanation
Indices: 613872--613908 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
613862 AAATATAAAT
613872 TATTATTAAATTA
1 TATTATTAAATTA
613885 TATTATTAAATTA
1 TATTATTAAATTA
613898 TATTATTAAAT
1 TATTATTAAAT
613909 AAGTGTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTATTAAATTA
Found at i:614437 original size:20 final size:20
Alignment explanation
Indices: 614412--614452 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
614402 TTTTTGGATT
614412 TTTCAAAACCTTAATTAAAA
1 TTTCAAAACCTTAATTAAAA
614432 TTTCAAAACCTTAATTAAAA
1 TTTCAAAACCTTAATTAAAA
614452 T
1 T
614453 AAAATCTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTCAAAACCTTAATTAAAA
Found at i:615602 original size:19 final size:20
Alignment explanation
Indices: 615578--615615 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
615568 AAAAAATCTT
615578 TAAA-TTTTATAATTTTATC
1 TAAATTTTTATAATTTTATC
*
615597 TAAATTTTTATATTTTTAT
1 TAAATTTTTATAATTTTAT
615616 TATATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATTTTTATAATTTTATC
Found at i:615822 original size:29 final size:30
Alignment explanation
Indices: 615757--615824 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
615747 GATATAATGA
* *
615757 CTTATTTAGATACGAATCAAAAGATAAAGC
1 CTTATTTGGATACGAATCAAAACATAAAGC
615787 CTTATTTGGATAC-AAT-AAATACATAAAAG-
1 CTTATTTGGATACGAATCAAA-ACAT-AAAGC
615816 CTTATTTGG
1 CTTATTTGG
615825 TAAAGTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 3 0.09
29 15 0.44
30 16 0.47
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (30 bp):
CTTATTTGGATACGAATCAAAACATAAAGC
Found at i:616885 original size:29 final size:30
Alignment explanation
Indices: 616838--616895 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
616828 AATAATCATC
*
616838 TTTAATAAATGAAAAATTATCTTTAAAAAT
1 TTTAATAAATAAAAAATTATCTTTAAAAAT
*
616868 TTTAAT-AATAAAAAATTATGTTTAAAAA
1 TTTAATAAATAAAAAATTATCTTTAAAAA
616896 CATGAGGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTAATAAATAAAAAATTATCTTTAAAAAT
Found at i:620394 original size:5 final size:5
Alignment explanation
Indices: 620359--620387 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
620349 TTATTTTTAA
620359 ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
620388 ATTATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:622538 original size:19 final size:18
Alignment explanation
Indices: 622516--622555 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
622506 AGATTTAGTA
* *
622516 ATTTATGTATTTGTATTAT
1 ATTTATATATTT-TATAAT
622535 ATTTATATATTTTATAAT
1 ATTTATATATTTTATAAT
622553 ATT
1 ATT
622556 ATAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTATATATTTTATAAT
Found at i:623126 original size:18 final size:17
Alignment explanation
Indices: 623102--623150 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
623092 TGATTTAATT
623102 ATAAAAATAAAAATCAAA
1 ATAAAAATAAAAAT-AAA
*
623120 GTAAAAATAAAAATAAA
1 ATAAAAATAAAAATAAA
623137 ATAAAAATAAAAAT
1 ATAAAAATAAAAAT
623151 GATATATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
ATAAAAATAAAAATAAA
Found at i:623131 original size:5 final size:6
Alignment explanation
Indices: 623102--623150 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
623092 TGATTTAATT
* *
623102 ATAAAA ATAAAA ATCAAA GTAAAA ATAAAA AT-AAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
623149 AT
1 AT
623151 GATATATTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:625407 original size:16 final size:16
Alignment explanation
Indices: 625386--625419 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
625376 CCTTAATCAG
625386 TAGCACTATATGAGTT
1 TAGCACTATATGAGTT
625402 TAGCACTATATGAGTT
1 TAGCACTATATGAGTT
625418 TA
1 TA
625420 TCATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (16 bp):
TAGCACTATATGAGTT
Found at i:633784 original size:417 final size:417
Alignment explanation
Indices: 633010--633848 Score: 1678
Period size: 417 Copynumber: 2.0 Consensus size: 417
633000 TTTTTTTTAA
633010 GCTTTGTTTTTAGGTTGTGTTTCTCTAAAAAAATTTTTGTTTTTGTTTTTGTGCTTTGTGCTTAG
1 GCTTTGTTTTTAGGTTGTGTTTCTCTAAAAAAATTTTTGTTTTTGTTTTTGTGCTTTGTGCTTAG
633075 TATGCTTTAATTTATATGCTGATTTTTCTTTTGAAACCTTGAGTTTTGTTTAATATTTTGGAATA
66 TATGCTTTAATTTATATGCTGATTTTTCTTTTGAAACCTTGAGTTTTGTTTAATATTTTGGAATA
633140 CCTTGTAAGTTTTAGATACATCTTTGTGTTGAGTTTTAATGCTTGAGAGATATAAGCATGATTAG
131 CCTTGTAAGTTTTAGATACATCTTTGTGTTGAGTTTTAATGCTTGAGAGATATAAGCATGATTAG
633205 TGATTTTTTTTCTTTAAAAATATATATGATAGTGTCCCATTAGTTTGTTAATTGAGAAATGCACA
196 TGATTTTTTTTCTTTAAAAATATATATGATAGTGTCCCATTAGTTTGTTAATTGAGAAATGCACA
633270 AAGACTTAATGCAAAATTAAGCGTTCAAGTGAGCTTTTGAACCTATGAGCAATTCATAAATTTTG
261 AAGACTTAATGCAAAATTAAGCGTTCAAGTGAGCTTTTGAACCTATGAGCAATTCATAAATTTTG
633335 CTCCATTTTCTTTGGTTGAGTGATATCAAACATGGTGTGTTTATTCTAGAACTTGCTTGTGAATG
326 CTCCATTTTCTTTGGTTGAGTGATATCAAACATGGTGTGTTTATTCTAGAACTTGCTTGTGAATG
633400 CATTTTGAGACCACATTTTGGATTGAT
391 CATTTTGAGACCACATTTTGGATTGAT
633427 GCTTTGTTTTTAGGTTGTGTTTCTCTAAAAAAATTTTTGTTTTTGTTTTTGTGCTTTGTGCTTAG
1 GCTTTGTTTTTAGGTTGTGTTTCTCTAAAAAAATTTTTGTTTTTGTTTTTGTGCTTTGTGCTTAG
633492 TATGCTTTAATTTATATGCTGATTTTTCTTTTGAAACCTTGAGTTTTGTTTAATATTTTGGAATA
66 TATGCTTTAATTTATATGCTGATTTTTCTTTTGAAACCTTGAGTTTTGTTTAATATTTTGGAATA
633557 CCTTGTAAGTTTTAGATACATCTTTGTGTTGAGTTTTAATGCTTGAGAGATATAAGCATGATTAG
131 CCTTGTAAGTTTTAGATACATCTTTGTGTTGAGTTTTAATGCTTGAGAGATATAAGCATGATTAG
633622 TGATTTTTTTTCTTTAAAAATATATATGATAGTGTCCCATTAGTTTGTTAATTGAGAAATGCACA
196 TGATTTTTTTTCTTTAAAAATATATATGATAGTGTCCCATTAGTTTGTTAATTGAGAAATGCACA
633687 AAGACTTAATGCAAAATTAAGCGTTCAAGTGAGCTTTTGAACCTATGAGCAATTCATAAATTTTG
261 AAGACTTAATGCAAAATTAAGCGTTCAAGTGAGCTTTTGAACCTATGAGCAATTCATAAATTTTG
633752 CTCCATTTTCTTTGGTTGAGTGATATCAAACATGGTGTGTTTATTCTAGAACTTGCTTGTGAATG
326 CTCCATTTTCTTTGGTTGAGTGATATCAAACATGGTGTGTTTATTCTAGAACTTGCTTGTGAATG
633817 CATTTTGAGACCACATTTTGGATTGAT
391 CATTTTGAGACCACATTTTGGATTGAT
633844 GCTTT
1 GCTTT
633849 AATATGATAA
Statistics
Matches: 422, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
417 422 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (417 bp):
GCTTTGTTTTTAGGTTGTGTTTCTCTAAAAAAATTTTTGTTTTTGTTTTTGTGCTTTGTGCTTAG
TATGCTTTAATTTATATGCTGATTTTTCTTTTGAAACCTTGAGTTTTGTTTAATATTTTGGAATA
CCTTGTAAGTTTTAGATACATCTTTGTGTTGAGTTTTAATGCTTGAGAGATATAAGCATGATTAG
TGATTTTTTTTCTTTAAAAATATATATGATAGTGTCCCATTAGTTTGTTAATTGAGAAATGCACA
AAGACTTAATGCAAAATTAAGCGTTCAAGTGAGCTTTTGAACCTATGAGCAATTCATAAATTTTG
CTCCATTTTCTTTGGTTGAGTGATATCAAACATGGTGTGTTTATTCTAGAACTTGCTTGTGAATG
CATTTTGAGACCACATTTTGGATTGAT
Found at i:634066 original size:1 final size:1
Alignment explanation
Indices: 634056--634140 Score: 71
Period size: 1 Copynumber: 85.0 Consensus size: 1
634046 TGGCAATTGG
* * * ** * * ** *
634056 AAAAAGAAAAAAAACAAAACAAAAAAAAGGAAAAACAAAAAAAAAACAAAAAAAAGGAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
634121 AAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
634141 GTGAAGATTT
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.87, C:0.07, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:634141 original size:30 final size:29
Alignment explanation
Indices: 634054--634139 Score: 133
Period size: 29 Copynumber: 3.0 Consensus size: 29
634044 CATGGCAATT
634054 GGAAAAAGAA-AAAAAACAAAACAAAAAAAA
1 GGAAAAA-AACAAAAAA-AAAACAAAAAAAA
634084 GG--AAAAACAAAAAAAAAACAAAAAAAA
1 GGAAAAAAACAAAAAAAAAACAAAAAAAA
634111 GGAAAAAAACAAAAAAAAAACAAAAAAAA
1 GGAAAAAAACAAAAAAAAAACAAAAAAAA
634140 AGTGAAGATT
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.32
28 9 0.17
29 25 0.47
30 2 0.04
ACGTcount: A:0.85, C:0.07, G:0.08, T:0.00
Consensus pattern (29 bp):
GGAAAAAAACAAAAAAAAAACAAAAAAAA
Found at i:636719 original size:30 final size:30
Alignment explanation
Indices: 636675--636736 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
636665 CGAAATTAAT
* * *
636675 TTAAGTGATTTAATTTATTAATAA-TAAAAA
1 TTAAATGATATAATTTAATAA-AACTAAAAA
636705 TTAAATGATATAATTTAATAAAACTAAAAA
1 TTAAATGATATAATTTAATAAAACTAAAAA
636735 TT
1 TT
636737 TATAACTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
TTAAATGATATAATTTAATAAAACTAAAAA
Found at i:636980 original size:2 final size:2
Alignment explanation
Indices: 636975--637006 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
636965 TTTTCTTAAA
636975 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
637007 TAAGAAGGGG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:638437 original size:27 final size:26
Alignment explanation
Indices: 638376--638448 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
638366 ATAGTCTCTA
* *
638376 AATTTATATATTATTAATAAATTAAAT
1 AATTT-TATTTTATTAAAAAATTAAAT
*
638403 AATATTATTTTATTAAAAAATATAAAT
1 AATTTTATTTTATTAAAAAAT-TAAAT
638430 AATTTTATTTT-TTAAAAAA
1 AATTTTATTTTATTAAAAAA
638449 ATTTATTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTTTATTTTATTAAAAAATTAAAT
Found at i:640341 original size:30 final size:31
Alignment explanation
Indices: 640307--640364 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
640297 ACGTAATAAA
* *
640307 AATAATAAAAAAT-ATTTTTATTTTTAATTT
1 AATAATAAAAAATAATATTTATTGTTAATTT
*
640337 AATAATATAAAATAATATTTATTGTTAA
1 AATAATAAAAAATAATATTTATTGTTAA
640365 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
AATAATAAAAAATAATATTTATTGTTAATTT
Found at i:640516 original size:19 final size:21
Alignment explanation
Indices: 640494--640534 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
640484 TTTTAAATTT
640494 AATTCTATTTT-T-ATTTAAA
1 AATTCTATTTTATAATTTAAA
*
640513 AATTTTATTTTATAATTTAAA
1 AATTCTATTTTATAATTTAAA
640534 A
1 A
640535 TATATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTCTATTTTATAATTTAAA
Found at i:642876 original size:21 final size:20
Alignment explanation
Indices: 642852--642919 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
642842 TACATTTAAT
642852 TTTATATATTTAATATATTTA
1 TTTATAT-TTTAATATATTTA
*
642873 -TT-TATTTTATTATATTATA
1 TTTATATTTTAATATATT-TA
* *
642892 ATTATATTTTAAATATTTTTA
1 TTTATATTTT-AATATATTTA
642913 TTTATAT
1 TTTATAT
642920 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 10 0.26
19 5 0.13
20 4 0.10
21 14 0.36
22 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATATTTTAATATATTTA
Found at i:642909 original size:34 final size:32
Alignment explanation
Indices: 642871--642981 Score: 110
Period size: 33 Copynumber: 3.5 Consensus size: 32
642861 TTAATATATT
642871 TATTTATTTTATTATATTATAATTATATTTTAAA
1 TATTT-TTTTATTATATTATAA-TATATTTTAAA
*
642905 TA--TTTTTATT-TA-TATAA-AT-TTTAAAA
1 TATTTTTTTATTATATTATAATATATTTTAAA
*
642931 TATTTATATTT-TTATATCATAATATATTTTAAA
1 TATTT-T-TTTATTATATTATAATATATTTTAAA
642964 TATTTTTTATATTATATT
1 TATTTTTT-TATTATATT
642982 CATGTAATTG
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
26 8 0.13
27 2 0.03
28 1 0.02
29 8 0.13
30 7 0.11
31 13 0.21
32 5 0.08
33 17 0.27
34 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (32 bp):
TATTTTTTTATTATATTATAATATATTTTAAA
Found at i:642914 original size:26 final size:26
Alignment explanation
Indices: 642897--642946 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
642887 TTATAATTAT
*
642897 ATTTT-AAATATTTTTATTTATATAA
1 ATTTTAAAATATTTATATTTATATAA
*
642922 ATTTTAAAATATTTATATTTTTATA
1 ATTTTAAAATATTTATATTTATATA
642947 TCATAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTAAAATATTTATATTTATATAA
Found at i:642975 original size:9 final size:9
Alignment explanation
Indices: 642850--642976 Score: 70
Period size: 9 Copynumber: 14.3 Consensus size: 9
642840 TTTACATTTA
642850 ATTTTATAT
1 ATTTTATAT
*
642859 ATTTAATAT
1 ATTTTATAT
*
642868 A-TTTATTT
1 ATTTTATAT
642876 ATTTTATTAT
1 ATTTTA-TAT
*
642886 ATTATAATTAT
1 ATT-TTA-TAT
*
642897 ATTTTAAAT
1 ATTTTATAT
642906 ATTTT-TAT
1 ATTTTATAT
* *
642914 -TTATATAA
1 ATTTTATAT
*
642922 ATTTTA-AA
1 ATTTTATAT
642930 ATATTTATAT
1 AT-TTTATAT
642940 -TTTTATAT
1 ATTTTATAT
*
642948 CA--TAATAT
1 -ATTTTATAT
*
642956 ATTTTAAAT
1 ATTTTATAT
*
642965 ATTTTTTAT
1 ATTTTATAT
642974 ATT
1 ATT
642977 ATATTCATGT
Statistics
Matches: 90, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
7 4 0.04
8 26 0.29
9 43 0.48
10 8 0.09
11 9 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTTTATAT
Found at i:645534 original size:18 final size:18
Alignment explanation
Indices: 645511--645545 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
645501 ATATTTCTAT
* *
645511 TATATACATATATATTTA
1 TATATAAATATAAATTTA
645529 TATATAAATATAAATTT
1 TATATAAATATAAATTT
645546 TAAAATTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATAAATATAAATTTA
Found at i:646466 original size:16 final size:17
Alignment explanation
Indices: 646447--646489 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
646437 AAAAATTTAA
*
646447 ATTAAATTTAA-TTATT
1 ATTAAATTTAAGTTATC
646463 ATTAAATTTAAGTTATC
1 ATTAAATTTAAGTTATC
646480 A-TAAATTTAA
1 ATTAAATTTAA
646490 ATAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTAAATTTAAGTTATC
Found at i:646601 original size:24 final size:24
Alignment explanation
Indices: 646572--646657 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 24
646562 TTTTAATTTT
646572 AATTTAATTAAATATAAATAATTA
1 AATTTAATTAAATATAAATAATTA
*
646596 AATTTAAAATTAAATTTAAA-AATTA
1 AATTT--AATTAAATATAAATAATTA
* ** *
646621 AATTAAATT-TTTATTAAATAAATA
1 AATTTAATTAAATA-TAAATAATTA
*
646645 AATTTAATCAAAT
1 AATTTAATTAAAT
646658 TAATTTAAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
22 1 0.02
23 8 0.17
24 16 0.34
25 10 0.21
26 12 0.26
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTAATTAAATATAAATAATTA
Found at i:646602 original size:6 final size:6
Alignment explanation
Indices: 646559--646630 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
646549 TAATATTGAA
* * * *
646559 AAATTT TAATTT TAATTT -AA-TT AAATAT AAATAATT AAATTT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT--TT AAATTT AAATTT
*
646607 AAATTT AAAAATT AAA-TT AAATTT
1 AAATTT -AAATTT AAATTT AAATTT
646631 TTATTAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 2 0.04
5 9 0.17
6 33 0.61
7 5 0.09
8 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:646626 original size:12 final size:12
Alignment explanation
Indices: 646577--646627 Score: 66
Period size: 13 Copynumber: 4.0 Consensus size: 12
646567 ATTTTAATTT
646577 AATTAAATATAAA
1 AATTAAAT-TAAA
*
646590 TAATTAAATTTAA
1 -AATTAAATTAAA
646603 AATTAAATTTAAA
1 AATTAAA-TTAAA
646616 AATTAAATTAAA
1 AATTAAATTAAA
646628 TTTTTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 12 0.35
13 14 0.41
14 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTAAATTAAA
Found at i:647001 original size:2 final size:2
Alignment explanation
Indices: 646994--647022 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
646984 TTGGACACAA
646994 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
647023 AGATTTGGCA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:647214 original size:27 final size:27
Alignment explanation
Indices: 647160--647214 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
647150 ATTATAATTT
* *
647160 ATTACAATAATATTTATTATATTTAAA
1 ATTACAATAATATTTAATATATTAAAA
*
647187 ATTATAATAA-ATTTAATATGATTAAAA
1 ATTACAATAATATTTAATAT-ATTAAAA
647214 A
1 A
647215 CGTATTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
ATTACAATAATATTTAATATATTAAAA
Found at i:647858 original size:18 final size:19
Alignment explanation
Indices: 647835--647884 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
647825 AAAAATAATT
*
647835 AAAATATAATATT-ATATA
1 AAAATATAATATTGACATA
647853 AAAATATAAT-TTGACATA
1 AAAATATAATATTGACATA
*
647871 AATATATAAATATT
1 AAAATAT-AATATT
647885 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 20 0.74
19 3 0.11
20 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATATAATATTGACATA
Found at i:647907 original size:33 final size:33
Alignment explanation
Indices: 647868--647938 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
647858 ATAATTTGAC
* **
647868 ATAAATATATAAATATTTTTAAATTTATAT-AAT
1 ATAAATA-ATAAATATATCAAAATTTATATAAAT
*
647901 ATAAATAATTAATATATCAAAATTTATATAAAT
1 ATAAATAATAAATATATCAAAATTTATATAAAT
647934 ATAAA
1 ATAAA
647939 AAATTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
ATAAATAATAAATATATCAAAATTTATATAAAT
Found at i:647910 original size:18 final size:17
Alignment explanation
Indices: 647888--647946 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
647878 AAATATTTTT
647888 AAATTTATATAATATAA
1 AAATTTATATAATATAA
*
647905 ATAA-TTA-AT-ATATCA
1 A-AATTTATATAATATAA
647920 AAATTTATATAAATATAA
1 AAATTTATAT-AATATAA
*
647938 AAAATTATA
1 AAATTTATA
647947 ATTATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 2 0.06
15 9 0.26
16 4 0.12
17 4 0.12
18 15 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTTATATAATATAA
Found at i:647957 original size:12 final size:12
Alignment explanation
Indices: 647940--647966 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
647930 AAATATAAAA
647940 AATTATAATTAT
1 AATTATAATTAT
647952 AATTATAATTAT
1 AATTATAATTAT
647964 AAT
1 AAT
647967 AAAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATAATTAT
Found at i:647964 original size:28 final size:27
Alignment explanation
Indices: 647926--647985 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
647916 ATCAAAATTT
647926 ATATAAATATAA-AAAATTATAATTATAA
1 ATATAAATATAATAAAA-TATAA-TATAA
* *
647954 TTATAATTATAATAAAATATAATATAA
1 ATATAAATATAATAAAATATAATATAA
647981 ATATA
1 ATATA
647986 TAAATTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.32
28 15 0.54
29 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATATAAATATAATAAAATATAATATAA
Found at i:648162 original size:3 final size:3
Alignment explanation
Indices: 648154--648193 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
648144 TGGTTTTGTT
648154 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
648194 AGTTTTAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:648267 original size:21 final size:22
Alignment explanation
Indices: 648238--648282 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
648228 AAAAAAAAAT
648238 AAAAAGGAA-AGAGAAGGAAGG
1 AAAAAGGAAGAGAGAAGGAAGG
* * *
648259 AAAATGGAAGAGAGAGGGGAGG
1 AAAAAGGAAGAGAGAAGGAAGG
648281 AA
1 AA
648283 GGAAAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (22 bp):
AAAAAGGAAGAGAGAAGGAAGG
Found at i:648347 original size:24 final size:24
Alignment explanation
Indices: 648320--648367 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
648310 GTATTCGTGC
*
648320 TATTTTTTTGTATTTTGTAT-TTTA
1 TATTTTTAT-TATTTTGTATGTTTA
*
648344 TATTTTTATTATTTTTTATGTTTA
1 TATTTTTATTATTTTGTATGTTTA
648368 AAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (24 bp):
TATTTTTATTATTTTGTATGTTTA
Found at i:649806 original size:16 final size:16
Alignment explanation
Indices: 649777--649829 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
649767 GACCTAGACA
*
649777 AAAATGATTCAAACTT
1 AAAATAATTCAAACTT
649793 AAAATAA-TCGAAACTT
1 AAAATAATTC-AAACTT
*
649809 AAAATAATTCAAAATT
1 AAAATAATTCAAACTT
649825 AAAAT
1 AAAAT
649830 GATTTGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.28
Consensus pattern (16 bp):
AAAATAATTCAAACTT
Found at i:651352 original size:2 final size:2
Alignment explanation
Indices: 651345--651383 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
651335 TTGACCAAAG
651345 TA TA 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 TA TA T
651384 GTGTGTGTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:662463 original size:1 final size:1
Alignment explanation
Indices: 662453--662550 Score: 79
Period size: 1 Copynumber: 98.0 Consensus size: 1
662443 TGGCAATTGG
* * * ** * * * *
662453 AAAAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAGAAAAAAGAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * *
662518 AAAAGGAAAAAAACAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
662551 GTGAAGATTT
Statistics
Matches: 75, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:662485 original size:30 final size:29
Alignment explanation
Indices: 662451--662539 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 29
662441 CATGGCAATT
662451 GGAAAAAGAAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAAAAA-AAAACAAAAAAAA
*
662481 GGAAAAAGAAAAAAGAAAAAAGAAAAAAAA
1 GGAAAAAGAAAAAA-AAAAAACAAAAAAAA
662511 --AACAAA-AAAAAGGAAAAAAACAAAAAAAA
1 GGAA-AAAGAAAAA--AAAAAAACAAAAAAAA
662540 AACAAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
28 7 0.13
29 17 0.32
30 27 0.51
31 2 0.04
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (29 bp):
GGAAAAAGAAAAAAAAAAAACAAAAAAAA
Found at i:662519 original size:41 final size:41
Alignment explanation
Indices: 662452--662550 Score: 139
Period size: 41 Copynumber: 2.4 Consensus size: 41
662442 ATGGCAATTG
662452 GAAAAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAGAA-AAAA
1 GAAAAA-AAAAAAAA-AAAACAAAAAAAAGGAAAAA-AACAAAA
*
662495 GAAAAAAGAAAAAAAAAACAAAAAAAAGGAAAAAAACAAAA
1 GAAAAAAAAAAAAAAAAACAAAAAAAAGGAAAAAAACAAAA
*
662536 -AAAAAACAAAAAAAA
1 GAAAAAAAAAAAAAAA
662551 GTGAAGATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
40 16 0.30
41 24 0.45
42 7 0.13
43 6 0.11
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (41 bp):
GAAAAAAAAAAAAAAAAACAAAAAAAAGGAAAAAAACAAAA
Found at i:662540 original size:29 final size:28
Alignment explanation
Indices: 662468--662551 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 28
662458 GAAAAAAAAC
*
662468 AAAACAAAAAAAAGGAA-AAAGAAAAAAGAA
1 AAAACAAAAAAAA--AACAAA-AAAAAGGAA
*
662498 AAAAGAAAAAAAAAACAAAAAAAAGGAAA
1 AAAACAAAAAAAAAACAAAAAAAAGG-AA
662527 AAAACAAAAAAAAAACAAAAAAAAG
1 AAAACAAAAAAAAAACAAAAAAAAG
662552 TGAAGATTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 8 0.16
29 29 0.59
30 12 0.24
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (28 bp):
AAAACAAAAAAAAAACAAAAAAAAGGAA
Found at i:666284 original size:3 final size:3
Alignment explanation
Indices: 666276--666322 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
666266 CAGCCCTAAC
*
666276 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
666323 TAAAGGCGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:668832 original size:13 final size:13
Alignment explanation
Indices: 668799--668839 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
668789 TCTTATATTC
668799 ATATCTAAATAT--
1 ATAT-TAAATATGA
*
668811 ATATCAAATATGA
1 ATATTAAATATGA
668824 ATATTAAATATGA
1 ATATTAAATATGA
668837 ATA
1 ATA
668840 ATAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 15 0.60
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (13 bp):
ATATTAAATATGA
Found at i:670190 original size:17 final size:17
Alignment explanation
Indices: 670168--670202 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
670158 AAAAAATTAA
* *
670168 ATATATTTATATCGAAT
1 ATATATTCATATCAAAT
670185 ATATATTCATATCAAAT
1 ATATATTCATATCAAAT
670202 A
1 A
670203 CTTACTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATATTCATATCAAAT
Found at i:674525 original size:17 final size:17
Alignment explanation
Indices: 674503--674546 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
674493 AAAAAATAAT
*
674503 ATTTATTATATATTAAA
1 ATTTATTAAATATTAAA
*
674520 ATTTATTAAATATTTAA
1 ATTTATTAAATATTAAA
*
674537 ATGTATTAAA
1 ATTTATTAAA
674547 AAATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTTATTAAATATTAAA
Done.