Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, whole genome shotgun sequence
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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 5 of 13
Found at i:2731093 original size:41 final size:41
Alignment explanation
Indices: 2731036--2731118 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2731026 GCTTGAGGCT
2731036 ACTGGATTCTTTCTAGATTTTTCAGTGCAAATTTTGCTGTA
1 ACTGGATTCTTTCTAGATTTTTCAGTGCAAATTTTGCTGTA
2731077 ACTGGATTCTTTCTAGATTTTTCAGTGCAAATTTTGCTGTA
1 ACTGGATTCTTTCTAGATTTTTCAGTGCAAATTTTGCTGTA
2731118 A
1 A
2731119 TCAGTAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (41 bp):
ACTGGATTCTTTCTAGATTTTTCAGTGCAAATTTTGCTGTA
Found at i:2733470 original size:2 final size:2
Alignment explanation
Indices: 2733463--2733493 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2733453 TGTGGGTGTC
2733463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2733494 TAGTTGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2737232 original size:2 final size:2
Alignment explanation
Indices: 2737225--2737258 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2737215 AAAAGAAAAA
*
2737225 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2737259 TTCCAGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2738007 original size:2 final size:2
Alignment explanation
Indices: 2738000--2738039 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2737990 TTCAAAAGGA
* *
2738000 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2738040 AGAATACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2738175 original size:2 final size:2
Alignment explanation
Indices: 2738168--2738197 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2738158 TAGGACATAT
2738168 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
2738198 GAAATCCCTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2745700 original size:2 final size:2
Alignment explanation
Indices: 2745693--2745717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2745683 TTACATGATC
2745693 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
2745718 ATAAAGAAAA
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:2745899 original size:15 final size:14
Alignment explanation
Indices: 2745877--2745906 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2745867 TAATTTCTAA
2745877 TTTTTTTTATTTTT
1 TTTTTTTTATTTTT
2745891 TTTTATTTTATTTTT
1 TTTT-TTTTATTTTT
2745906 T
1 T
2745907 CATTCTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTATTTTT
Found at i:2751221 original size:2 final size:2
Alignment explanation
Indices: 2751177--2751203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2751167 AATGGTACTC
2751177 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 T
2751204 TCTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2775224 original size:6 final size:6
Alignment explanation
Indices: 2775204--2775267 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
2775194 CGATCCCGGG
* * * * * *
2775204 CCTTTGC CCTCTC CCTATC CCTTTC TCTGTC CCTCTC CCTTTC CTTTTC
1 CCTTT-C CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC
*
2775253 CCTTTC CCTGTC CCT
1 CCTTTC CCTTTC CCT
2775268 CTCCTTGCTC
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 42 0.91
7 4 0.09
ACGTcount: A:0.02, C:0.50, G:0.05, T:0.44
Consensus pattern (6 bp):
CCTTTC
Found at i:2775257 original size:30 final size:30
Alignment explanation
Indices: 2775221--2775284 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
2775211 CCTCTCCCTA
* *
2775221 TCCCTTTCTCTGTCCCTCTCCCTTTC-CTTT
1 TCCCTTTCCCTGTCCCTCT-CCTTGCTCTTT
2775251 TCCCTTTCCCTGTCCCTCTCCTTGCTCTTT
1 TCCCTTTCCCTGTCCCTCTCCTTGCTCTTT
2775281 TCCC
1 TCCC
2775285 CACCCGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.00, C:0.48, G:0.05, T:0.47
Consensus pattern (30 bp):
TCCCTTTCCCTGTCCCTCTCCTTGCTCTTT
Found at i:2775272 original size:24 final size:24
Alignment explanation
Indices: 2775204--2775273 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
2775194 CGATCCCGGG
*
2775204 CCTTTGCCCTCTCCCTATCCCTTTC
1 CCTTT-CCCTCTCCCTATCCTTTTC
* * *
2775229 TCTGTCCCTCTCCCTTTCCTTTTC
1 CCTTTCCCTCTCCCTATCCTTTTC
* *
2775253 CCTTTCCCTGTCCCTCTCCTT
1 CCTTTCCCTCTCCCTATCCTT
2775274 GCTCTTTTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 34 0.92
25 3 0.08
ACGTcount: A:0.01, C:0.50, G:0.04, T:0.44
Consensus pattern (24 bp):
CCTTTCCCTCTCCCTATCCTTTTC
Found at i:2780032 original size:13 final size:12
Alignment explanation
Indices: 2779999--2780042 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
2779989 TTTCTTTATA
*
2779999 TAATTAATATGAT
1 TAATTAAAAT-AT
2780012 TAAATTAAAATAT
1 T-AATTAAAATAT
2780025 ATAATTAAAATAT
1 -TAATTAAAATAT
2780038 TAATT
1 TAATT
2780043 TATTATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 14 0.50
14 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TAATTAAAATAT
Found at i:2792019 original size:6 final size:6
Alignment explanation
Indices: 2792005--2792063 Score: 59
Period size: 6 Copynumber: 9.3 Consensus size: 6
2791995 CCAACATGAA
2792005 TTTTCT TTTT-T TTTTCTT TTTTCT TTTTCT TTTTCAGT TTTGTCT TTTAT-T
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTC--T TTT-TCT TTT-TCT
2792056 TTTTCT TT
1 TTTTCT TT
2792064 CTTTTTGTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
5 6 0.13
6 23 0.50
7 11 0.24
8 4 0.09
9 2 0.04
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:2796776 original size:19 final size:18
Alignment explanation
Indices: 2796751--2796792 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2796741 TTATTTAAAA
* *
2796751 ATATTAAAATAATTTTTT
1 ATATTTAAATAAGTTTTT
*
2796769 ATATTTAATTAAGTTTTT
1 ATATTTAAATAAGTTTTT
2796787 ATATTT
1 ATATTT
2796793 TTATTTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATATTTAAATAAGTTTTT
Found at i:2798337 original size:40 final size:40
Alignment explanation
Indices: 2798262--2798337 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
2798252 GCTTAAGTAA
*
2798262 TTTTATTAAATTTAAAATATTTATTTAAGTTAATTTAAAT
1 TTTTATTAAATTTAAAATATTTAATTAAGTTAATTTAAAT
* *
2798302 TTTTATTTGAATTT-AAATA-TTAATTGAGTTGAATTT
1 TTTTA-TTAAATTTAAAATATTTAATTAAGTT-AATTT
2798338 TGAACTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 9 0.29
40 15 0.48
41 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (40 bp):
TTTTATTAAATTTAAAATATTTAATTAAGTTAATTTAAAT
Found at i:2804834 original size:41 final size:42
Alignment explanation
Indices: 2804789--2804877 Score: 171
Period size: 41 Copynumber: 2.1 Consensus size: 42
2804779 GGACCAATCC
2804789 TATTTATCCTTCTAGAGAAACTACTCGGTTTTAGA-TTTTTT
1 TATTTATCCTTCTAGAGAAACTACTCGGTTTTAGATTTTTTT
2804830 TATTTATCCTTCTAGAGAAACTACTCGGTTTTAGATTTTTTT
1 TATTTATCCTTCTAGAGAAACTACTCGGTTTTAGATTTTTTT
2804872 TATTTA
1 TATTTA
2804878 ATTTCTTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 35 0.74
42 12 0.26
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (42 bp):
TATTTATCCTTCTAGAGAAACTACTCGGTTTTAGATTTTTTT
Found at i:2805057 original size:33 final size:33
Alignment explanation
Indices: 2805015--2805110 Score: 183
Period size: 33 Copynumber: 2.9 Consensus size: 33
2805005 AGCCCTCCTT
2805015 TCAAAGCAACCATCCCATAATATTATTATTCTA
1 TCAAAGCAACCATCCCATAATATTATTATTCTA
2805048 TCAAAGCAACCATCCCATAATATTATTATTCTA
1 TCAAAGCAACCATCCCATAATATTATTATTCTA
*
2805081 TCAAAGCAACCATCCCATAATATTTTTATT
1 TCAAAGCAACCATCCCATAATATTATTATT
2805111 ATTCTTCTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (33 bp):
TCAAAGCAACCATCCCATAATATTATTATTCTA
Found at i:2807539 original size:17 final size:17
Alignment explanation
Indices: 2807519--2807552 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2807509 AAAGTAACTT
2807519 TTTTAAAAAAATAAAAA
1 TTTTAAAAAAATAAAAA
* *
2807536 TTTTTAAAATATAAAAA
1 TTTTAAAAAAATAAAAA
2807553 AAATTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAATAAAAA
Found at i:2829136 original size:33 final size:33
Alignment explanation
Indices: 2829094--2829165 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
2829084 CTCTGGACCT
2829094 ATGAACAGTTACACATTAGCTTCAAAGTCAACC
1 ATGAACAGTTACACATTAGCTTCAAAGTCAACC
*
2829127 ATGAACAGTTACACATTAGCTTCAGAGTCAACC
1 ATGAACAGTTACACATTAGCTTCAAAGTCAACC
2829160 ATGAAC
1 ATGAAC
2829166 TCCAGCGGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (33 bp):
ATGAACAGTTACACATTAGCTTCAAAGTCAACC
Found at i:2831867 original size:17 final size:18
Alignment explanation
Indices: 2831845--2831884 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2831835 ATTTTTAAAT
*
2831845 TAAATAAATAAA-AATAA
1 TAAATAAACAAATAATAA
2831862 TAAATAAACAAATAATAA
1 TAAATAAACAAATAATAA
2831880 -AAATA
1 TAAATA
2831885 TTAACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAAACAAATAATAA
Found at i:2831874 original size:15 final size:13
Alignment explanation
Indices: 2831847--2831884 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2831837 TTTTAAATTA
2831847 AATAAATAAAAAT
1 AATAAATAAAAAT
*
2831860 AATAAATAAACA-
1 AATAAATAAAAAT
2831872 AAT-AATAAAAAT
1 AATAAATAAAAAT
2831884 A
1 A
2831885 TTAACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 7 0.32
12 4 0.18
13 11 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:2831874 original size:21 final size:22
Alignment explanation
Indices: 2831840--2831884 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2831830 TTTTTATTTT
*
2831840 TAAATTAAATAAATAA-AAATAA
1 TAAATTAAACAAATAATAAA-AA
2831862 TAAA-TAAACAAATAATAAAAA
1 TAAATTAAACAAATAATAAAAA
2831883 TA
1 TA
2831885 TTAACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAATTAAACAAATAATAAAAA
Found at i:2840594 original size:2 final size:2
Alignment explanation
Indices: 2840542--2840574 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2840532 TTTAATTTTG
2840542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2840575 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2845015 original size:28 final size:28
Alignment explanation
Indices: 2844977--2845045 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2844967 GAAGTTTAGT
* *
2844977 TATAAAAATTTATTTAATTTAA-AAAATA
1 TATAAAAATTTATTCAATATAATAAAA-A
2845005 TATAAAAATTTGATTCAATATAATAAAAA
1 TATAAAAATTT-ATTCAATATAATAAAAA
2845034 -ATAAAAATTTAT
1 TATAAAAATTTAT
2845046 AATAAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.05
28 21 0.57
29 10 0.27
30 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
TATAAAAATTTATTCAATATAATAAAAA
Found at i:2845568 original size:12 final size:12
Alignment explanation
Indices: 2845547--2845588 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2845537 CACGGCGTCG
2845547 TTTC-CTCTCTC
1 TTTCTCTCTCTC
*
2845558 TCTCTCTCTCTC
1 TTTCTCTCTCTC
*
2845570 TTTCTCTTTCTC
1 TTTCTCTCTCTC
2845582 TTTCTCT
1 TTTCTCT
2845589 TTCTGTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 3 0.11
12 24 0.89
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCTCTCTCTC
Found at i:2845589 original size:6 final size:6
Alignment explanation
Indices: 2845554--2845592 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2845544 TCGTTTCCTC
* *
2845554 TCTCTC TCTCTC TCTCTT TCTCTT TCTCTT TCTCTT TCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCT
2845593 GTCTTGACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
TCTCTT
Found at i:2849316 original size:17 final size:18
Alignment explanation
Indices: 2849296--2849329 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2849286 TAATTAAAGA
*
2849296 AAAAAATTAAT-TTTAAT
1 AAAAAATAAATATTTAAT
2849313 AAAAAATAAATATTTAA
1 AAAAAATAAATATTTAA
2849330 ATTTATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAATAAATATTTAAT
Found at i:2849535 original size:64 final size:65
Alignment explanation
Indices: 2849420--2849549 Score: 156
Period size: 64 Copynumber: 2.0 Consensus size: 65
2849410 CATAAATAAG
** * *
2849420 TCTTAACGTAAAACTGTAACAATTAACGTAAAAATTTATAAACGTAGAATAACTAAAT-TTTAAA
1 TCTTAACGTAAAACTGTAACAATTAACGTAAAAATCAATAAACGTAAAATAAATAAATATTTAAA
** * * *
2849484 TCTTAACGTAAATGTGTGAGAATTAACGTAACAAATCAATTAA-GTAAAATAAATAAATATTTAA
1 TCTTAACGTAAAACTGTAACAATTAACGTAA-AAATCAATAAACGTAAAATAAATAAATATTTAA
2849548 A
65 A
2849549 T
1 T
2849550 TTATATTCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
64 40 0.73
65 15 0.27
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (65 bp):
TCTTAACGTAAAACTGTAACAATTAACGTAAAAATCAATAAACGTAAAATAAATAAATATTTAAA
Found at i:2849625 original size:15 final size:15
Alignment explanation
Indices: 2849597--2849629 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2849587 ATTTTAATTT
2849597 TTAAATAAAGAATAA
1 TTAAATAAAGAATAA
2849612 TTAAGATAAA-AATAA
1 TTAA-ATAAAGAATAA
2849627 TTA
1 TTA
2849630 TAGTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
TTAAATAAAGAATAA
Found at i:2849646 original size:234 final size:230
Alignment explanation
Indices: 2849381--2850183 Score: 755
Period size: 234 Copynumber: 3.3 Consensus size: 230
2849371 TTTAATTTTT
* *
2849381 TAATAAAAATAATTATAGTTCAAAATTGACATAAATAAGTCTTAACGTAAAACTGTAACAATTAA
1 TAATAAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTTAACGTAAAACTGTAACAATTGA
* *
2849446 CGTAAAAATTTATAAACGT-AGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAATTAA
66 CGTAAAAATTTATAAACGTGA-AATAACTAAATTTTAAATCTTAACGTAAATGTGTAAAAATTAA
* * *
2849510 CGTAACAAATCAATTAAGTAAAATAAATAAATATTTAAATTTATATTCTTAAACTAAAAGTGTTC
130 CGTAACAAGTCAATTAAGTAAAATAAATAAATATTTAAATATAT-TTCTTAAACTAAAAGTATTC
2849575 AACGATATATAAATTTTAATTTTTAAATAAAGAATAA
194 AACGATATATAAATTTTAATTTTTAAATAAAGAATAA
* *
2849612 TTAAGATAAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTTAA-GATAAAATTGTAATAA
1 -T-A-ATAAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTTAACG-TAAAACTGTAACAA
* * *
2849676 TTGACGTAAACATTTATAAACGTGAAATAATTAAATTTTAAATCTTAACGTAAATATGTAAAAAT
62 TTGACGTAAAAATTTATAAACGTGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTAAAAAT
*
2849741 TAACGTAATAAGTCAATTAAGTAAAAAAATTTAATTTTTATGAAAAATAAATATTTAAATATATT
127 TAACGTAACAAGTCAATTAAGT------A---AA-----AT---AAATAAATATTTAAATATATT
* * * *
2849806 TTTTAGATTAAAAGTATTTAACGATATATAAATTTTAATTTTTAAATAAAGAATAA
175 TCTTAAACTAAAAGTATTCAACGATATATAAATTTTAATTTTTAAATAAAGAATAA
* ** * * * * * * *
2849862 TAATTATTATTATTATAATTTAAAATTGATATAAATAAATCTTGACGTAAAACTATAACAGTTGA
1 TAATAAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTTAACGTAAAACTGTAACAATTGA
* * * * *
2849927 CGCAAAAACTTATAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTAATAGTTAAC
66 CGTAAAAATTTATAAACGTGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTAAAAATTAAC
* *
2849992 GTAGCAAGTTAATTAAGTAAATAAATTTTAATTTTAGTGAAAAATAAATATTTAAATATATATTC
131 GTAACAAGTCAATTAAG----T--A----AA----A-T---AAATAAATATTTAAATATAT-TTC
** ** * * * *
2850057 TGGAGTTAAATGTATTTAACGATATATAAATTTTAATTTTTATATAAAAAATAA
177 TTAAACTAAAAGTATTCAACGATATATAAATTTTAATTTTTAAATAAAGAATAA
* * * * *
2850111 TAATAACAAAAATAGTTATAGTTTAAAATTGATATAGATAAATCTTGACGTAAAACTGTAACAAT
1 TAAT---AAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTTAACGTAAAACTGTAACAAT
*
2850176 TGATGTAA
63 TGACGTAA
2850184 NNNNNNNNNN
Statistics
Matches: 480, Mismatches: 59, Indels: 44
0.82 0.10 0.08
Matches are distributed among these distances:
232 1 0.00
233 2 0.00
234 131 0.27
235 1 0.00
240 1 0.00
243 2 0.00
247 128 0.27
248 33 0.07
249 54 0.11
250 52 0.11
251 20 0.04
252 55 0.11
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (230 bp):
TAATAAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTTAACGTAAAACTGTAACAATTGA
CGTAAAAATTTATAAACGTGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTAAAAATTAAC
GTAACAAGTCAATTAAGTAAAATAAATAAATATTTAAATATATTTCTTAAACTAAAAGTATTCAA
CGATATATAAATTTTAATTTTTAAATAAAGAATAA
Found at i:2850008 original size:247 final size:248
Alignment explanation
Indices: 2849534--2850178 Score: 837
Period size: 247 Copynumber: 2.6 Consensus size: 248
2849524 TAAGTAAAAT
* * * * * *
2849534 AAATAAATATTTAAATTTATATTCTTAAACTAAAAGTGTTCAACGATATATAAATTTTAATTTTT
1 AAATAAATATTTAAATATAT-TTTTTAGATTAAAAGTATTTAACGATATATAAATTTTAATTTTT
* * * *
2849599 AAATAAAGAATAATTAAGATAAAAATAATTATAGTTTAAAATTGACATAAATAAGTCTT-AAGAT
65 AAATAAAGAATAA-T-A-ATAAAAATTATTATAGTTTAAAATTGATATAAATAAATCTTGACG-T
* * * * * *
2849663 AAAATTGTAATAATTGACGTAAACATTTATAAACGTGAAATAATTAAATTTTAAATCTTAACGTA
126 AAAACTGTAACAATTGACGCAAAAACTTATAAACGTGAAATAACTAAATTTTAAATCTTAACGTA
*
2849728 AATATGTAAAAATTAACGTAATAAGTCAATTAAGTAAA-AAAATTTAATTTTTA-TGAA
191 AATATGTAAAAATTAACGTAACAAGTCAATTAAGTAAATAAAATTTAA-TTTTAGTGAA
2849785 AAATAAATATTTAAATATATTTTTTAGATTAAAAGTATTTAACGATATATAAATTTTAATTTTTA
1 AAATAAATATTTAAATATATTTTTTAGATTAAAAGTATTTAACGATATATAAATTTTAATTTTTA
* ** *
2849850 AATAAAGAATAATAATTATTATTATTATAATTTAAAATTGATATAAATAAATCTTGACGTAAAAC
66 AATAAAGAATAATAATAAAAATTATTATAGTTTAAAATTGATATAAATAAATCTTGACGTAAAAC
* * * *
2849915 TATAACAGTTGACGCAAAAACTTATAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATGT
131 TGTAACAATTGACGCAAAAACTTATAAACGTGAAATAACTAAATTTTAAATCTTAACGTAAATAT
* * * * *
2849980 GTAATAGTTAACGTAGCAAGTTAATTAAGTAAATAAATTTTAATTTTAGTGAA
196 GTAAAAATTAACGTAACAAGTCAATTAAGTAAATAAAATTTAATTTTAGTGAA
* * * *
2850033 AAATAAATATTTAAATATATATTCTGGAGTTAAATGTATTTAACGATATATAAATTTTAATTTTT
1 AAATAAATATTTAAATATATTTTTTAGA-TTAAAAGTATTTAACGATATATAAATTTTAATTTTT
* * * *
2850098 ATATAAAAAATAATAATAACAAAAATAGTTATAGTTTAAAATTGATATAGATAAATCTTGACGTA
65 AAATAAAGAATAATAAT-A-AAAATTA-TTATAGTTTAAAATTGATATAAATAAATCTTGACGTA
2850163 AAACTGTAACAATTGA
127 AAACTGTAACAATTGA
2850179 TGTAANNNNN
Statistics
Matches: 343, Mismatches: 44, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
247 128 0.37
248 40 0.12
249 51 0.15
250 52 0.15
251 23 0.07
252 49 0.14
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.38
Consensus pattern (248 bp):
AAATAAATATTTAAATATATTTTTTAGATTAAAAGTATTTAACGATATATAAATTTTAATTTTTA
AATAAAGAATAATAATAAAAATTATTATAGTTTAAAATTGATATAAATAAATCTTGACGTAAAAC
TGTAACAATTGACGCAAAAACTTATAAACGTGAAATAACTAAATTTTAAATCTTAACGTAAATAT
GTAAAAATTAACGTAACAAGTCAATTAAGTAAATAAAATTTAATTTTAGTGAA
Found at i:2850561 original size:24 final size:24
Alignment explanation
Indices: 2850534--2850579 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2850524 TTAATTAAAA
*
2850534 TTTTAATATTAAAA-AAATAATATT
1 TTTTAAT-TTAAAATAAAAAATATT
2850558 TTTTAATTTAAAATAAAAAATA
1 TTTTAATTTAAAATAAAAAATA
2850580 AAATAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTAATTTAAAATAAAAAATATT
Found at i:2860944 original size:20 final size:22
Alignment explanation
Indices: 2860919--2860958 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
2860909 CTGGATATGG
2860919 CTTCCA-GTTCCTC-ACAGGCT
1 CTTCCATGTTCCTCAACAGGCT
*
2860939 CTTCCATTTTCCTCAACAGG
1 CTTCCATGTTCCTCAACAGG
2860959 AAGAGAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (22 bp):
CTTCCATGTTCCTCAACAGGCT
Found at i:2863518 original size:11 final size:11
Alignment explanation
Indices: 2863487--2863518 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2863477 TTGGTTCCTT
*
2863487 AAAAAAAAACC
1 AAAAAAAAAGC
2863498 AAAAAAAAAGC
1 AAAAAAAAAGC
2863509 AAAAAAAAAG
1 AAAAAAAAAG
2863519 AATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:2867908 original size:139 final size:141
Alignment explanation
Indices: 2867656--2867929 Score: 435
Period size: 139 Copynumber: 2.0 Consensus size: 141
2867646 ATATAAGTTT
* * *
2867656 AAAATATTAAACCTATTTCTTTACTTGTATTTTTTTCTCTTTTTTAGTTCATCTACCAATGATAA
1 AAAATATTAAACCTAGTTCTTTACTTGTATTTTTTTCTCTGTTTTAGTTCATCTACCAATGACAA
* * *
2867721 TTTTTCTACGTGGCATATCTACCTGTATAGCTAATCTAATGCCTATATATTGAATTCTTAAATTT
66 TTTTTCTACGTGGCATATCTACCCGTACAGCTAATCTAATACCTATATATTGAATTCTTAAATTT
2867786 AATTTAATTTA
131 AATTTAATTTA
* * *
2867797 AAAATATTAAATCTAGTTCTTTATTTGTA-TTTTTT-TCTGTTTTAGTTTATCTACCAATGACAA
1 AAAATATTAAACCTAGTTCTTTACTTGTATTTTTTTCTCTGTTTTAGTTCATCTACCAATGACAA
*
2867860 TTTTTCTACGTTGCATATCTACCCGTACAGCTAATCTAATACCTATATATTGAATTCTTAAATTT
66 TTTTTCTACGTGGCATATCTACCCGTACAGCTAATCTAATACCTATATATTGAATTCTTAAATTT
*
2867925 GATTT
131 AATTT
2867930 TCTATATTTC
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
139 90 0.74
140 6 0.05
141 26 0.21
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.48
Consensus pattern (141 bp):
AAAATATTAAACCTAGTTCTTTACTTGTATTTTTTTCTCTGTTTTAGTTCATCTACCAATGACAA
TTTTTCTACGTGGCATATCTACCCGTACAGCTAATCTAATACCTATATATTGAATTCTTAAATTT
AATTTAATTTA
Found at i:2868126 original size:26 final size:26
Alignment explanation
Indices: 2868091--2868152 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
2868081 TTTAAAATTA
* * * *
2868091 AAAAAT-AAAAATTTATATTTTATTT
1 AAAAATAAAAAAATTATATATCATTC
2868116 AAAAATAAAAAAATTATATATCATTC
1 AAAAATAAAAAAATTATATATCATTC
2868142 AATAAATAAAA
1 AA-AAATAAAA
2868153 TGTTAAGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.19
26 17 0.55
27 8 0.26
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATAAAAAAATTATATATCATTC
Found at i:2877926 original size:11 final size:11
Alignment explanation
Indices: 2877910--2877936 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2877900 ATAAAATACG
2877910 AATTTAAAATA
1 AATTTAAAATA
2877921 AATTTAAAATA
1 AATTTAAAATA
2877932 AATTT
1 AATTT
2877937 GTATAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:2890029 original size:24 final size:24
Alignment explanation
Indices: 2889997--2890061 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 24
2889987 ATAAAGACAC
2889997 ATTTGATTAAAAAT-AAAAATAAAA
1 ATTT-ATTAAAAATAAAAAATAAAA
2890021 ATTTAATTAAATATAATAAAAAATAAAA
1 ATTT-ATT-AA-A-AATAAAAAATAAAA
2890049 ATTTATTAAAAAT
1 ATTTATTAAAAAT
2890062 TTTAAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 10 0.28
25 3 0.08
26 3 0.08
27 6 0.17
28 14 0.39
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATTTATTAAAAATAAAAAATAAAA
Found at i:2895143 original size:17 final size:18
Alignment explanation
Indices: 2895111--2895146 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
2895101 GTTGAAATTT
2895111 TTTAATAAATATTTTTTA
1 TTTAATAAATATTTTTTA
2895129 TTTAATAAA-ATTTTTTA
1 TTTAATAAATATTTTTTA
2895146 T
1 T
2895147 AATTGGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATAAATATTTTTTA
Found at i:2895339 original size:9 final size:9
Alignment explanation
Indices: 2895325--2895371 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
2895315 ACCTTTGTTC
*
2895325 CTTTCTCAT
1 CTTTCTCTT
2895334 CTTTCT-TT
1 CTTTCTCTT
2895342 CTTTCTCTT
1 CTTTCTCTT
*
2895351 CTTTTTC-T
1 CTTTCTCTT
*
2895359 CTTTTTCTT
1 CTTTCTCTT
2895368 CTTT
1 CTTT
2895372 TTTCTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 15 0.44
9 19 0.56
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (9 bp):
CTTTCTCTT
Found at i:2895345 original size:17 final size:16
Alignment explanation
Indices: 2895325--2895378 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
2895315 ACCTTTGTTC
*
2895325 CTTTCTCATCTTTCTTT
1 CTTTCTCTTCTTT-TTT
2895342 CTTTCTCTTCTTTTTCT
1 CTTTCTCTTCTTTTT-T
*
2895359 CTTTTTCTTCTTTTTT
1 CTTTCTCTTCTTTTTT
2895375 CTTT
1 CTTT
2895379 TTTTTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 7 0.21
17 27 0.79
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (16 bp):
CTTTCTCTTCTTTTTT
Found at i:2895372 original size:9 final size:9
Alignment explanation
Indices: 2895335--2895382 Score: 55
Period size: 8 Copynumber: 5.3 Consensus size: 9
2895325 CTTTCTCATC
2895335 TTTCTTTCTT
1 TTTC-TTCTT
*
2895345 TCTCTTCTT
1 TTTCTTCTT
2895354 TTTC-TCTT
1 TTTCTTCTT
2895362 TTTCTTCTTT
1 TTTCTTC-TT
2895372 TTTCTT-TT
1 TTTCTTCTT
2895380 TTT
1 TTT
2895383 TTGATAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 13 0.38
9 10 0.29
10 11 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:2896112 original size:2 final size:2
Alignment explanation
Indices: 2896105--2896138 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2896095 GATAGTTTGG
*
2896105 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2896139 GAGGGTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2897849 original size:15 final size:15
Alignment explanation
Indices: 2897829--2897860 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2897819 TAATATTATA
2897829 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
2897844 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
2897859 AT
1 AT
2897861 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:2897931 original size:54 final size:50
Alignment explanation
Indices: 2897828--2897944 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 50
2897818 ATAATATTAT
* *
2897828 AATTAAAAT-AAA-AAATATTAAAATAAAATATATAATATAAGAATTAGA
1 AATTAAAATAAAATAAATATAAAAATAAAATATATAATATAAGAATAAGA
*
2897876 AATTAAAATAAAATAAATATCAAAAATTAAAATTTATATAATATAGGTAA-AAGA
1 AATTAAAATAAAATAAATAT-AAAAA-TAAAA--TATATAATATAAG-AATAAGA
*
2897930 AATTACAATAAAATA
1 AATTAAAATAAAATA
2897945 TGTAATATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
48 9 0.16
49 3 0.05
50 6 0.10
51 4 0.07
52 5 0.09
54 29 0.50
55 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (50 bp):
AATTAAAATAAAATAAATATAAAAATAAAATATATAATATAAGAATAAGA
Found at i:2897998 original size:40 final size:40
Alignment explanation
Indices: 2897925--2898003 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
2897915 AATATAGGTA
* * *
2897925 AAAGAAATTACAATAAAATATGTAATATGAAAAATTATATG
1 AAAGAAATGACAATAAAATATATAACATGAAAAA-TATATG
* *
2897966 AAAGAAATGA-AATAAAATATATGACATTAAAAATATAT
1 AAAGAAATGACAATAAAATATATAACATGAAAAATATAT
2898004 TTAAGAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 5 0.15
40 19 0.58
41 9 0.27
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (40 bp):
AAAGAAATGACAATAAAATATATAACATGAAAAATATATG
Found at i:2898170 original size:46 final size:45
Alignment explanation
Indices: 2898120--2898212 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 45
2898110 AAAGAACTTA
* *
2898120 TAAATCAAACGCAATGTTATCTTCTTTGCATTTTAATCATTATATT
1 TAAATCAAACGCAATGTTATCTTCCTTACATTTTAATCATTAT-TT
*
2898166 TAAATCAAACGTAATGTTATCTTCCTTACATTTTAATCATTATTT
1 TAAATCAAACGCAATGTTATCTTCCTTACATTTTAATCATTATTT
2898211 TA
1 TA
2898213 CTTGTATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 4 0.09
46 40 0.91
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (45 bp):
TAAATCAAACGCAATGTTATCTTCCTTACATTTTAATCATTATTT
Found at i:2908077 original size:3 final size:3
Alignment explanation
Indices: 2908071--2908104 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2908061 TATCTTTTGC
2908071 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2908105 TAATTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2916150 original size:157 final size:155
Alignment explanation
Indices: 2915864--2916174 Score: 487
Period size: 157 Copynumber: 2.0 Consensus size: 155
2915854 CACATCAAAT
*
2915864 TTCACATTATCCCAATAATATGACAGAAGCTAACACCCTACAGCAAATTTCCAGTCATTTCTAGA
1 TTCACATTATCCCAATAATATGACACAAGCTAACACCCTACAGCAAATTTCCAGTCATTTCTAGA
* * ** *
2915929 TTTTACGATCTGTATAATTAATGTGCATCACTCAATAAAATAAAATACTAGGAAAAGAGTATCTG
66 CTTTACAATCTGTATAACCAATGTGCATCACTCAATAAAATAAAATACTAGGAAAAGAGCATCTG
*
2915994 ATGAGTGGATATCAATGTAAAATCG
131 ATGAGTGGATAGCAATGTAAAATCG
* * **
2916019 TTCACATTATCCCAATAATTTGAGACAAGCTAACACCCTACACAGCAAATTTCCAGTTGTTTCTA
1 TTCACATTATCCCAATAATATGACACAAGCTAACACCCT--ACAGCAAATTTCCAGTCATTTCTA
*
2916084 GACTTTCCAATCTGTATAACCAATGTGCATCACTCAATAAAATAAAATACTAGGAAAAGAGCATC
64 GACTTTACAATCTGTATAACCAATGTGCATCACTCAATAAAATAAAATACTAGGAAAAGAGCATC
*
2916149 TGATGAGTGGATGGCAATGTAAAATC
129 TGATGAGTGGATAGCAATGTAAAATC
2916175 ATCCAGAATA
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
155 36 0.26
157 105 0.74
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (155 bp):
TTCACATTATCCCAATAATATGACACAAGCTAACACCCTACAGCAAATTTCCAGTCATTTCTAGA
CTTTACAATCTGTATAACCAATGTGCATCACTCAATAAAATAAAATACTAGGAAAAGAGCATCTG
ATGAGTGGATAGCAATGTAAAATCG
Found at i:2921123 original size:2 final size:2
Alignment explanation
Indices: 2921116--2921141 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2921106 GAGTAGATTA
2921116 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
2921142 TTGCAAAAGA
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:2923267 original size:27 final size:28
Alignment explanation
Indices: 2923206--2923268 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
2923196 TAAAAATATA
2923206 ATTTTTA-TAAAATATTAAAATTTTGAC
1 ATTTTTATTAAAATATTAAAATTTTGAC
** * *
2923233 A-TAATATTAAAATTTTAAAATTTT-AT
1 ATTTTTATTAAAATATTAAAATTTTGAC
2923259 ATTTTTATTA
1 ATTTTTATTA
2923269 TATTTAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTTTTATTAAAATATTAAAATTTTGAC
Found at i:2923360 original size:17 final size:19
Alignment explanation
Indices: 2923338--2923372 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2923328 CTTAATTAAA
2923338 ATATAATT-TATT-ATTTT
1 ATATAATTATATTCATTTT
2923355 ATATAATTATATTCATTT
1 ATATAATTATATTCATTT
2923373 AAACTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATAATTATATTCATTTT
Found at i:2923419 original size:30 final size:30
Alignment explanation
Indices: 2923248--2923443 Score: 96
Period size: 30 Copynumber: 6.4 Consensus size: 30
2923238 ATTAAAATTT
* * * *
2923248 TAAAATTTTATATTTTTATTAT-ATTTAAT
1 TAAATTTTTATATTTTTATTCTAAATTAAA
* *
2923277 TATATTTTT-TATATTTTATTTTAAATTAAA
1 TAAATTTTTATAT-TTTTATTCTAAATTAAA
* * *
2923307 TAATTTTTTATTATTAATTA-TCTTAATTAAAA
1 TAAATTTTTA-TATT-TTTATTCTAAATT-AAA
* * **
2923339 TATAATTTATTAT-TTTATATAAT-TATATTCATT
1 TA-AATTT-TTATATTT-T-TATTCTAAATT-AAA
* * *
2923372 TAAACTTTTAAACTTTTATTCTAAATTAAA
1 TAAATTTTTATATTTTTATTCTAAATTAAA
* * *
2923402 TAAATTTTTATATTTTTATTTTGAATCAAA
1 TAAATTTTTATATTTTTATTCTAAATTAAA
*
2923432 TAAATATTTATA
1 TAAATTTTTATA
2923444 ATTAATTATT
Statistics
Matches: 123, Mismatches: 31, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
28 3 0.02
29 15 0.12
30 51 0.41
31 16 0.13
32 20 0.16
33 14 0.11
34 4 0.03
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
TAAATTTTTATATTTTTATTCTAAATTAAA
Found at i:2923470 original size:17 final size:16
Alignment explanation
Indices: 2923417--2923475 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
2923407 TTTTATATTT
*
2923417 TTATTTTGAATCAAATAA
1 TTATTTT-AATTAAAT-A
* *
2923435 ATATTTATAATTAATTA
1 TTATTT-TAATTAAATA
2923452 TTATTTTAATTAAAATA
1 TTATTTTAATT-AAATA
2923469 TTATTTT
1 TTATTTT
2923476 TTACTTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 5 0.15
17 17 0.50
18 11 0.32
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATTTTAATTAAATA
Found at i:2923483 original size:19 final size:20
Alignment explanation
Indices: 2923448--2923505 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
2923438 TTTATAATTA
2923448 ATTATTATTTTAATTAAAAT
1 ATTATTATTTTAATTAAAAT
* *
2923468 ATTATT-TTTTACTTAATAT
1 ATTATTATTTTAATTAAAAT
*
2923487 ATTAATATATTATAATTAA
1 ATT-AT-TATTTTAATTAA
2923506 TAATGATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 14 0.45
20 8 0.26
21 1 0.03
22 8 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTATTTTAATTAAAAT
Found at i:2923502 original size:10 final size:8
Alignment explanation
Indices: 2923480--2923574 Score: 60
Period size: 8 Copynumber: 12.0 Consensus size: 8
2923470 TATTTTTTAC
2923480 TTAATATA
1 TTAATATA
2923488 TTAATATA
1 TTAATATA
2923496 TT-ATA-A
1 TTAATATA
2923502 TTAATAATGA
1 TTAAT-AT-A
*
2923512 TATAACATA
1 T-TAATATA
*
2923521 TTAACATA
1 TTAATATA
2923529 TT-ATA-A
1 TTAATATA
2923535 TTAATGATGA
1 TTAAT-AT-A
2923545 TATAATATA
1 T-TAATATA
2923554 TT-A-AT-
1 TTAATATA
2923559 TTAATATA
1 TTAATATA
*
2923567 ATAATATA
1 TTAATATA
2923575 ATTTTTTATT
Statistics
Matches: 71, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
5 2 0.03
6 9 0.13
7 12 0.17
8 29 0.41
9 4 0.06
10 8 0.11
11 7 0.10
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (8 bp):
TTAATATA
Found at i:2923522 original size:33 final size:33
Alignment explanation
Indices: 2923485--2923572 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
2923475 TTTACTTAAT
2923485 ATATTAATATATTATAATTAATAATGATATAAC
1 ATATTAATATATTATAATTAATAATGATATAAC
* * *
2923518 ATATTAACATATTATAATTAATGATGATATAAT
1 ATATTAATATATTATAATTAATAATGATATAAC
* *
2923551 ATATTAATTTAATATAA-TAATA
1 ATATTAATATATTATAATTAATA
2923573 TAATTTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 4 0.08
33 44 0.92
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (33 bp):
ATATTAATATATTATAATTAATAATGATATAAC
Found at i:2923565 original size:18 final size:18
Alignment explanation
Indices: 2923544--2923578 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2923534 ATTAATGATG
2923544 ATATAAT-ATATTAATTTA
1 ATATAATAATA-TAATTTA
2923562 ATATAATAATATAATTT
1 ATATAATAATATAATTT
2923579 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAATAATATAATTTA
Found at i:2923648 original size:15 final size:15
Alignment explanation
Indices: 2923625--2923654 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2923615 AAATATAACA
2923625 TAATAAATAATATTT
1 TAATAAATAATATTT
*
2923640 TAATTAATAATATTT
1 TAATAAATAATATTT
2923655 AATCAATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAAATAATATTT
Found at i:2923720 original size:25 final size:24
Alignment explanation
Indices: 2923687--2923743 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
2923677 TTTATTTGAT
* *
2923687 TTAAAATAAAAATATAAAATTTTA
1 TTAAAATAAAAAAATAAAACTTTA
2923711 TTAAATATAAAAAAATAAAACTTTA
1 TTAAA-ATAAAAAAATAAAACTTTA
2923736 TTTAAAAT
1 -TTAAAAT
2923744 TTTTTAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 5 0.17
25 19 0.66
26 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TTAAAATAAAAAAATAAAACTTTA
Found at i:2930725 original size:71 final size:73
Alignment explanation
Indices: 2930599--2930734 Score: 197
Period size: 71 Copynumber: 1.9 Consensus size: 73
2930589 CCAAATGACA
* * * *
2930599 CTACACTAAAAGCTATCTGGAAAAATAAAAAACCGTTTCATTTGATTGCCTGTCCTGAGAGCACA
1 CTACACTAAAAGCCATCTAGAAAAATAAAAAACCGTTTCATTAGAATGCCTGTCCTGAGAGCACA
2930664 AAAAAAAG
66 AAAAAAAG
*
2930672 CTACACTAAAAGCCATC-AGAAAAA-AAGAAAA-GGTTTCATTAGAATGCCTGTCCTGAGAGCAC
1 CTACACTAAAAGCCATCTAGAAAAATAA-AAAACCGTTTCATTAGAATGCCTGTCCTGAGAGCAC
2930734 A
65 A
2930735 CAATAAAGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
71 31 0.54
72 10 0.18
73 16 0.28
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (73 bp):
CTACACTAAAAGCCATCTAGAAAAATAAAAAACCGTTTCATTAGAATGCCTGTCCTGAGAGCACA
AAAAAAAG
Found at i:2933066 original size:46 final size:46
Alignment explanation
Indices: 2932999--2933094 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
2932989 ATAATTTAGC
2932999 TAGATTCAGTGAGAGGAATTATGTACAATGACACTAGATGGAGTCA
1 TAGATTCAGTGAGAGGAATTATGTACAATGACACTAGATGGAGTCA
*
2933045 TAGATTCAGTGAGAGGAATTATGTACAATGACACTAGATGGGGTCA
1 TAGATTCAGTGAGAGGAATTATGTACAATGACACTAGATGGAGTCA
2933091 TAGA
1 TAGA
2933095 GAGAAAAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.26
Consensus pattern (46 bp):
TAGATTCAGTGAGAGGAATTATGTACAATGACACTAGATGGAGTCA
Found at i:2935089 original size:2 final size:2
Alignment explanation
Indices: 2935082--2935113 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2935072 TATCACATTA
*
2935082 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2935114 TATTTAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2940575 original size:22 final size:22
Alignment explanation
Indices: 2940550--2940605 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2940540 TTTTTTTTTT
*
2940550 TAATTTTTTAAA-AATATAATAA
1 TAATTTTTTAAATAATA-AAAAA
2940572 TAATTTTTTAAATTAATAAAAAA
1 TAATTTTTTAAA-TAATAAAAAA
*
2940595 GAATTTTTTAA
1 TAATTTTTTAA
2940606 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 12 0.40
23 14 0.47
24 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAATTTTTTAAATAATAAAAAA
Found at i:2940588 original size:19 final size:21
Alignment explanation
Indices: 2940550--2940590 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2940540 TTTTTTTTTT
2940550 TAATTTTTTAAAAATATAATAA
1 TAATTTTTT-AAAATATAATAA
2940572 TAATTTTTT-AAAT-TAATAA
1 TAATTTTTTAAAATATAATAA
2940591 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
22 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTTTTTAAAATATAATAA
Found at i:2941294 original size:195 final size:194
Alignment explanation
Indices: 2941090--2941465 Score: 581
Period size: 195 Copynumber: 1.9 Consensus size: 194
2941080 AAGTTAATAA
2941090 TTTTTTAAAATATTATGTCATTTTTTAAAAATAAATAAAAATTAGAGTAAAATACGCTAACATCT
1 TTTTTTAAAATATTATGTCATTTTTTAAAAATAAATAAAAATTAGAGTAAAATACGCTAACATCT
* * * * * *
2941155 CAATTTTTAACTATAATTAAACATGAGTTCATTAATTTTCAAAATGAATATTCTATTCTAAAAAA
66 CAATTTTTAACGACAACTAAACATAAGTTCATTAATTTTCAAAATGAATATTCCACTCT-AAAAA
2941220 AATATTTTCGTTGGACAAATAAGTTTTGTCACTACTCAACTGTCAATACTTCGAATTTAAGAATT
130 AATATTTTCGTTGGACAAATAAGTTTTGTCACTACTCAACTGTCAATACTTCGAATTTAAGAATT
*
2941285 TTTTTTAAAATATTATGTCATTTTTTAAAAATAAATAAAAATTAGAGTAAAATACTCTAACATCT
1 TTTTTTAAAATATTATGTCATTTTTTAAAAATAAATAAAAATTAGAGTAAAATACGCTAACATCT
** * *
2941350 CAATTTTTAACGACAACTAAATGTAAGTTTATTAATTTTCAAAATGAATATTCCACTCTAAAAGA
66 CAATTTTTAACGACAACTAAACATAAGTTCATTAATTTTCAAAATGAATATTCCACTCTAAAAAA
* * * ** * *
2941415 ATATTTTTGTTTGATATTTAATTTTTGTCATTACTCAACTGTCAATACTTC
131 ATATTTTCGTTGGACAAATAAGTTTTGTCACTACTCAACTGTCAATACTTC
2941466 TATTAATTTG
Statistics
Matches: 163, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
194 49 0.30
195 114 0.70
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (194 bp):
TTTTTTAAAATATTATGTCATTTTTTAAAAATAAATAAAAATTAGAGTAAAATACGCTAACATCT
CAATTTTTAACGACAACTAAACATAAGTTCATTAATTTTCAAAATGAATATTCCACTCTAAAAAA
ATATTTTCGTTGGACAAATAAGTTTTGTCACTACTCAACTGTCAATACTTCGAATTTAAGAATT
Found at i:2941650 original size:26 final size:23
Alignment explanation
Indices: 2941597--2941639 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2941587 GCTCTTGTTT
* *
2941597 GTGCTCCCTTAAGGAGCATCGTA
1 GTGCTCCCCTAAGGAACATCGTA
2941620 G-GCTCCCCTAAGGAACATCG
1 GTGCTCCCCTAAGGAACATCG
2941640 ATATAGTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (23 bp):
GTGCTCCCCTAAGGAACATCGTA
Found at i:2944451 original size:2 final size:2
Alignment explanation
Indices: 2944444--2944475 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2944434 ATAATTGACA
*
2944444 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2944476 GGTATGCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2947616 original size:23 final size:23
Alignment explanation
Indices: 2947573--2947618 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2947563 TGAAAGGGAG
* *
2947573 CAAATAAACAAGAGGGGAGGAAA
1 CAAATAAACAAGAGAGCAGGAAA
2947596 CAAAGTAAACAAG-GAGCAGGAAA
1 CAAA-TAAACAAGAGAGCAGGAAA
2947619 GCTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.57, C:0.11, G:0.28, T:0.04
Consensus pattern (23 bp):
CAAATAAACAAGAGAGCAGGAAA
Found at i:2954546 original size:5 final size:5
Alignment explanation
Indices: 2954538--2954573 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
2954528 ACTATAGACT
* *
2954538 AGAAA AGAAA AGAAA GGAAA CGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
2954574 TGTTAAACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:2955694 original size:1 final size:1
Alignment explanation
Indices: 2955597--2955674 Score: 138
Period size: 1 Copynumber: 78.0 Consensus size: 1
2955587 AAACCCCACC
* *
2955597 GGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2955662 GGGGGGGGGGGGG
1 GGGGGGGGGGGGG
2955675 AAAAAAAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:2960555 original size:2 final size:2
Alignment explanation
Indices: 2960548--2960574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2960538 TACATGACAT
2960548 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2960575 GTAAGTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2961032 original size:5 final size:5
Alignment explanation
Indices: 2961022--2961048 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2961012 AGGGAGAAGA
2961022 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
2961049 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2965196 original size:2 final size:2
Alignment explanation
Indices: 2965189--2965230 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2965179 ACAAAAGTTG
*
2965189 AT AT AT AT AT AT AT AT AC 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
2965231 GTTTGTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2966195 original size:2 final size:2
Alignment explanation
Indices: 2966188--2966215 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2966178 AAATAAAAAG
2966188 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2966216 AAAGAGAAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2968936 original size:3 final size:3
Alignment explanation
Indices: 2968928--2968966 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
2968918 TTGCTTCAAT
2968928 TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
2968967 CCCCATGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2968950 original size:14 final size:13
Alignment explanation
Indices: 2968931--2968966 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
2968921 CTTCAATTTC
2968931 TTCTTCTTCTTCTT
1 TTCTTCTTCTTC-T
2968945 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
2968958 TTCTTCTTC
1 TTCTTCTTC
2968967 CCCCATGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCTTCTTCTTCT
Found at i:2978527 original size:2 final size:2
Alignment explanation
Indices: 2978514--2978552 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2978504 GGCATGAGTA
*
2978514 AT AT AT AC 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
2978553 AAGTCAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2983268 original size:1 final size:1
Alignment explanation
Indices: 2983262--2983287 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2983252 AATATGTTCC
2983262 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
2983288 GTTATTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2985498 original size:155 final size:155
Alignment explanation
Indices: 2985284--2985592 Score: 582
Period size: 155 Copynumber: 2.0 Consensus size: 155
2985274 AAGAATATTC
* *
2985284 TTCTCCTTTAAAATTTTGACTAGAAGATGGCAAATGACTTAATTTTCTGATCAAACAAACAGCAG
1 TTCTCCTTGAAAAATTTGACTAGAAGATGGCAAATGACTTAATTTTCTGATCAAACAAACAGCAG
2985349 ACTCTATAAAGTTAGGTAAAGTACTTAGAAAAAAACATAAAAAACAAATTCTAACTTTTTCCCTC
66 ACTCTATAAAGTTAGGTAAAGTACTTAGAAAAAAACATAAAAAACAAATTCTAACTTTTTCCCTC
*
2985414 CTTGAAGTTAAGTAATTTTTGGTTT
131 CTTGAAGTTAAGTAATTATTGGTTT
2985439 TTCTCCTTGAAAAATTTGACTAGAAGATGGCAAATGACTTAATTTTCTGATCAAACAAACAGCAG
1 TTCTCCTTGAAAAATTTGACTAGAAGATGGCAAATGACTTAATTTTCTGATCAAACAAACAGCAG
*
2985504 ACTCTATAAAGTTAGGTAACGTACTTAGAAAAAAACATAAAAAACAAATTCTAACTTTTTCCCTC
66 ACTCTATAAAGTTAGGTAAAGTACTTAGAAAAAAACATAAAAAACAAATTCTAACTTTTTCCCTC
2985569 CTTGAAGTTAAGTAATTATTGGTT
131 CTTGAAGTTAAGTAATTATTGGTT
2985593 CACATTCTTG
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 150 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (155 bp):
TTCTCCTTGAAAAATTTGACTAGAAGATGGCAAATGACTTAATTTTCTGATCAAACAAACAGCAG
ACTCTATAAAGTTAGGTAAAGTACTTAGAAAAAAACATAAAAAACAAATTCTAACTTTTTCCCTC
CTTGAAGTTAAGTAATTATTGGTTT
Found at i:2987183 original size:23 final size:24
Alignment explanation
Indices: 2987155--2987204 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
2987145 AAATATTACA
2987155 AAATTA-TATTATATT-AATATATT
1 AAATTATTATT-TATTAAATATATT
2987178 AAATTATTATTTATTAAAATATATT
1 AAATTATTATTTATT-AAATATATT
2987203 AA
1 AA
2987205 CAAATCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.42
24 4 0.17
25 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATTATTATTTATTAAATATATT
Found at i:2988861 original size:18 final size:17
Alignment explanation
Indices: 2988835--2988887 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
2988825 AATTTTTATA
*
2988835 ATTAATAATTAATTAATT
1 ATTATTAATTAATTAA-T
2988853 ATTATTAATTAA--AAT
1 ATTATTAATTAATTAAT
* *
2988868 ATTATTTATTAATTTAT
1 ATTATTAATTAATTAAT
2988885 ATT
1 ATT
2988888 TACATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 12 0.40
16 2 0.07
17 5 0.17
18 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTAATTAATTAAT
Found at i:2996788 original size:102 final size:103
Alignment explanation
Indices: 2996606--2996806 Score: 314
Period size: 102 Copynumber: 1.9 Consensus size: 103
2996596 GCTCTTCAAT
*
2996606 CAAAATTATGAGAATGTGAATTGAAATTTGAAAACACTATCCTGGTTGTTTACAATCTTAGTGGT
1 CAAAATTATGAGAATGTGAATTGAAATTTG---A-ACTATCCTGGTTGTTTACAATCTTAGTGGG
*
2996671 AAACAGAACAGGGTTCTTTGCACATTCCTTCCATACTTCAGC
62 AAACAGAACAGGGTTCTTAGCACATTCCTTCCATACTTCAGC
*
2996713 CAAAATTATGAGAATGTGAATTGAAATTTG-ACTATCCTGGTTGTTTACAATCTTAGTGGGAAAT
1 CAAAATTATGAGAATGTGAATTGAAATTTGAACTATCCTGGTTGTTTACAATCTTAGTGGGAAAC
* *
2996777 AGAATAGGGTTCTTAGCGCATTCCTTCCAT
66 AGAACAGGGTTCTTAGCACATTCCTTCCAT
2996807 TATTTATTGA
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
102 59 0.66
107 30 0.34
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (103 bp):
CAAAATTATGAGAATGTGAATTGAAATTTGAACTATCCTGGTTGTTTACAATCTTAGTGGGAAAC
AGAACAGGGTTCTTAGCACATTCCTTCCATACTTCAGC
Found at i:3001864 original size:22 final size:21
Alignment explanation
Indices: 3001788--3001867 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 21
3001778 AATTTATAAG
3001788 ATTTTTTATA--AAAAAATATA
1 ATTTTTTATATTAAAAAAT-TA
* *
3001808 ACTTTTTATATGAAAAATATT-
1 ATTTTTTATATTAAAAA-ATTA
3001829 ATTTTTT-TAGTTAAAAAATGTA
1 ATTTTTTATA-TTAAAAAAT-TA
*
3001851 ATTTTTTATTTTAAAAA
1 ATTTTTTATATTAAAAA
3001868 TACACTTACA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 13 0.27
21 13 0.27
22 20 0.41
23 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTTTTATATTAAAAAATTA
Found at i:3001866 original size:21 final size:21
Alignment explanation
Indices: 3001788--3001869 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
3001778 AATTTATAAG
*
3001788 ATTTTTTA-TAAAAAAATATA
1 ATTTTTTATTTAAAAAATATA
* * *
3001808 ACTTTTTATATGAAAAATATTA
1 ATTTTTTATTTAAAAAATA-TA
* * *
3001830 TTTTTTTAGTTAAAAAATGTA
1 ATTTTTTATTTAAAAAATATA
*
3001851 ATTTTTTATTTTAAAAATA
1 ATTTTTTATTTAAAAAATA
3001870 CACTTACACA
Statistics
Matches: 46, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
20 7 0.15
21 24 0.52
22 15 0.33
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTTTTATTTAAAAAATATA
Found at i:3009001 original size:6 final size:6
Alignment explanation
Indices: 3008990--3009016 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3008980 AAAAATGTCA
3008990 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
3009017 GAAAAGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:3012058 original size:17 final size:17
Alignment explanation
Indices: 3012023--3012063 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3012013 TCTCTTCTAT
*
3012023 TTTTAATTTTATATTTA
1 TTTTAATTTTATATATA
3012040 TTTTAATTTT-TAGTATA
1 TTTTAATTTTATA-TATA
3012057 -TTTAATT
1 TTTTAATT
3012064 ATTTCTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTATATATA
Found at i:3020886 original size:14 final size:14
Alignment explanation
Indices: 3020869--3020898 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3020859 CATTAATTTT
3020869 AATTACTTAAATTA
1 AATTACTTAAATTA
3020883 AATTACTTAAATTA
1 AATTACTTAAATTA
3020897 AA
1 AA
3020899 CTCACACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTACTTAAATTA
Found at i:3028802 original size:21 final size:21
Alignment explanation
Indices: 3028776--3028819 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3028766 TGGCTTAAAT
3028776 TTCGGCTTGTAACAAGTAGCA
1 TTCGGCTTGTAACAAGTAGCA
3028797 TTCGGCTTGTAACAAGTAGCA
1 TTCGGCTTGTAACAAGTAGCA
3028818 TT
1 TT
3028820 AAAACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGGCTTGTAACAAGTAGCA
Found at i:3029085 original size:32 final size:32
Alignment explanation
Indices: 3029044--3029109 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
3029034 GATGGGTCTT
3029044 TGGAATATGGGTTTTTCACCATCTATCAAGCA
1 TGGAATATGGGTTTTTCACCATCTATCAAGCA
3029076 TGGAATATGGGTTTTTCACCATCTATCAAGCA
1 TGGAATATGGGTTTTTCACCATCTATCAAGCA
3029108 TG
1 TG
3029110 TCTTTTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (32 bp):
TGGAATATGGGTTTTTCACCATCTATCAAGCA
Found at i:3031697 original size:24 final size:24
Alignment explanation
Indices: 3031665--3031720 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3031655 GCACACCAGC
3031665 TGCAGCATTTGAGGCTTTGCTACA
1 TGCAGCATTTGAGGCTTTGCTACA
3031689 TGCAGCATTTGAGGCTTTGCTACA
1 TGCAGCATTTGAGGCTTTGCTACA
3031713 TGCAGCAT
1 TGCAGCAT
3031721 CTTCCGCCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (24 bp):
TGCAGCATTTGAGGCTTTGCTACA
Found at i:3032893 original size:8 final size:8
Alignment explanation
Indices: 3032852--3032890 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
3032842 AAAAAATTGA
3032852 ATATATAC
1 ATATATAC
3032860 ATATATAC
1 ATATATAC
*
3032868 ATACATAC
1 ATATATAC
*
3032876 ATATATAT
1 ATATATAC
3032884 ATATATA
1 ATATATA
3032891 TATTACAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAC
Found at i:3033558 original size:81 final size:81
Alignment explanation
Indices: 3033473--3033760 Score: 276
Period size: 81 Copynumber: 3.5 Consensus size: 81
3033463 GTTATGTTAA
*
3033473 AAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTATATGTCATGGTTAAAAAAAATT
1 AAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTATATGTCATGGTTAAAAAAGATT
*
3033538 ATTACATGCTATGCTG
66 ATTACATGCTATGTTG
* * * * * **
3033554 AAAAAAAAAATTATTGTTATACATCATGAACAAAAATATATTGCATAT-T-ATGCCTAAAAAAGA
1 AAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTT--ATATGTCATGGTTAAAAAAGA
* *
3033617 TTATTACATGCCATATTG
64 TTATTACATGCTATGTTG
* * ** * * * * * *
3033635 AAAACAAATATTATTGTTATAGTTTATATATAAAAACATGTTACACGTCATAGTTAAAAAAGATT
1 AAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTATATGTCATGGTTAAAAAAGATT
* *
3033700 ATGACACG-TCATGTTG
66 ATTACATGCT-ATGTTG
* * *
3033716 AAAATAAAAATATTATTATTACATATCAAGTACAAAAACATGTTA
1 -AAA-AAAAATATTATTGTTACACATCATGTACAAAAACATGTTA
3033761 CATTTAAAAA
Statistics
Matches: 161, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
79 2 0.01
80 1 0.01
81 119 0.74
82 4 0.02
83 35 0.22
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (81 bp):
AAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTATATGTCATGGTTAAAAAAGATT
ATTACATGCTATGTTG
Found at i:3033803 original size:30 final size:28
Alignment explanation
Indices: 3033767--3033844 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
3033757 GTTACATTTA
*
3033767 AAAAAAATGTTTTTGTTACATATTATGTT
1 AAAAAAAT-TTTTTGTTACACATTATGTT
3033796 GAAAAAAATATTATTT-TTACACATTATGTT
1 -AAAAAAAT-TT-TTTGTTACACATTATGTT
*
3033826 TAAAAAA-TTTTTGTTACAC
1 AAAAAAATTTTTTGTTACAC
3033845 TTTAATACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.07
27 8 0.19
29 6 0.14
30 23 0.53
31 3 0.07
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (28 bp):
AAAAAAATTTTTTGTTACACATTATGTT
Found at i:3042594 original size:22 final size:23
Alignment explanation
Indices: 3042556--3042600 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3042546 CACATTGAGA
*
3042556 AATACAAAAAAATATTTTTCATT
1 AATACAAAAAAATATTTCTCATT
*
3042579 AATACAAAACAA-ATTTCTCATT
1 AATACAAAAAAATATTTCTCATT
3042601 GTGATTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (23 bp):
AATACAAAAAAATATTTCTCATT
Found at i:3045136 original size:21 final size:21
Alignment explanation
Indices: 3045092--3045136 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3045082 ATTAAATCTT
* *
3045092 AATCTAATATAATTTACATCA
1 AATCTAATATAAATAACATCA
3045113 AATCTAGATATAAATAACAT-A
1 AATCTA-ATATAAATAACATCA
3045134 AAT
1 AAT
3045137 AAATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (21 bp):
AATCTAATATAAATAACATCA
Found at i:3045510 original size:2 final size:2
Alignment explanation
Indices: 3045503--3045534 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3045493 TAGGTTCTCT
3045503 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
3045535 GAAACAATAA
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):
TA
Found at i:3055065 original size:2 final size:2
Alignment explanation
Indices: 3055060--3055094 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3055050 AAATTAGAAT
3055060 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 T
3055095 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3056063 original size:2 final size:2
Alignment explanation
Indices: 3056058--3056091 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3056048 TTTTTGAGAC
*
3056058 TA TA TA TA TA TA TA TA CA 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
3056092 AACCAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3056743 original size:5 final size:5
Alignment explanation
Indices: 3056690--3056741 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
3056680 ACATGAGGCC
* * *
3056690 TTTC- TTTCGT TTTCT ATTCC TTTCC TTTCT TTTCT TTTCT TTTCT TTT-T
1 TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
3056739 TTT
1 TTT
3056742 TTAATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 8 0.19
5 30 0.71
6 4 0.10
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:3059008 original size:29 final size:30
Alignment explanation
Indices: 3058973--3059038 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
3058963 ATTTTAAAAA
* *
3058973 TTTTATATTTTTATTAT-ATTTAATTAAAT
1 TTTTATATTTTTATTATAAATTAAATAAAT
*
3059002 TTTTATATTTTTATTTTAAATTAAATAAAT
1 TTTTATATTTTTATTATAAATTAAATAAAT
3059032 TTTTATA
1 TTTTATA
3059039 ATTAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTATATTTTTATTATAAATTAAATAAAT
Found at i:3059020 original size:21 final size:22
Alignment explanation
Indices: 3058972--3059023 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3058962 TATTTTAAAA
*
3058972 ATTTTATATTTTTATTATATTT
1 ATTTTAAATTTTTATTATATTT
* *
3058994 A-ATTAAATTTTTA-TATTTTT
1 ATTTTAAATTTTTATTATATTT
3059014 ATTTTAAATT
1 ATTTTAAATT
3059024 AAATAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 17 0.68
22 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTAAATTTTTATTATATTT
Found at i:3059064 original size:14 final size:15
Alignment explanation
Indices: 3059037--3059068 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3059027 TAAATTTTTA
3059037 TAATTAATAATTAAT
1 TAATTAATAATTAAT
3059052 TAATTAA-AATTAAT
1 TAATTAATAATTAAT
3059066 TAA
1 TAA
3059069 AATATTATTT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTAATAATTAAT
Found at i:3060955 original size:2 final size:2
Alignment explanation
Indices: 3060948--3060990 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3060938 TTGTAAAACT
3060948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3060988 TA T
1 TA T
3060991 TTTTTCCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3061476 original size:2 final size:2
Alignment explanation
Indices: 3061471--3061498 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3061461 AAAAGTAATA
3061471 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
3061499 GCATATCTTT
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:3062149 original size:3 final size:3
Alignment explanation
Indices: 3062141--3062170 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3062131 TTGGTTGTCA
3062141 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3062171 GATTTGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3062710 original size:2 final size:2
Alignment explanation
Indices: 3062705--3062738 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3062695 CCACACAATG
3062705 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
3062739 GCATCAATTA
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:3064668 original size:12 final size:11
Alignment explanation
Indices: 3064645--3064694 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
3064635 ATAAAGTTAA
3064645 ATTTACAAAAAT
1 ATTTA-AAAAAT
3064657 ATTCTAAAAAAT
1 ATT-TAAAAAAT
3064669 A-TTAAAAAAT
1 ATTTAAAAAAT
*
3064679 ATTATTAAAAAT
1 ATT-TAAAAAAT
3064691 ATTT
1 ATTT
3064695 GTAATAGCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 9 0.26
11 3 0.09
12 20 0.59
13 2 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTTAAAAAAT
Found at i:3064676 original size:22 final size:23
Alignment explanation
Indices: 3064643--3064693 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
3064633 TAATAAAGTT
*
3064643 AAAT-TTACAAAAATATTCTAAA
1 AAATATTACAAAAATATTATAAA
*
3064665 AAATATTA-AAAAATATTATTAA
1 AAATATTACAAAAATATTATAAA
3064687 AAATATT
1 AAATATT
3064694 TGTAATAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATATTACAAAAATATTATAAA
Found at i:3074448 original size:60 final size:60
Alignment explanation
Indices: 3074347--3074460 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
3074337 GGTTAAATTA
* * * **
3074347 TCGGGTTGAAGTTGAATTGTTTTCTGGGGCTGGTCCATGGCCCATTAGCCATTATTTGTC
1 TCGGGTTGAAATTGAACTGCTTTCTGGGGCTAATCCATGGCCCATTAGCCATTATTTGTC
* * *
3074407 TCGGGTTGAAATTGAACTGCTTTCTTGGGCTAATCCTTGGCCCATTAGTCATTA
1 TCGGGTTGAAATTGAACTGCTTTCTGGGGCTAATCCATGGCCCATTAGCCATTA
3074461 ATTATTTGTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGGGTTGAAATTGAACTGCTTTCTGGGGCTAATCCATGGCCCATTAGCCATTATTTGTC
Found at i:3076867 original size:15 final size:15
Alignment explanation
Indices: 3076849--3076901 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3076839 AATTTACTTA
3076849 TTTTATTTTTAATAT
1 TTTTATTTTTAATAT
* *
3076864 TTTTAATTTTAAAAT
1 TTTTATTTTTAATAT
*
3076879 TTTTCTTTATTTAATAAT
1 TTTT-ATT-TTTAAT-AT
3076897 TTTTA
1 TTTTA
3076902 CTTGGTAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 5 0.17
18 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATTTTTAATAT
Found at i:3080133 original size:3 final size:3
Alignment explanation
Indices: 3080125--3080160 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3080115 AGGGTTTTAA
3080125 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3080161 CCCCTATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3084209 original size:31 final size:30
Alignment explanation
Indices: 3084165--3084224 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3084155 TAACAAAGAT
*
3084165 AGAAAAAGAATCTTAAACTAAATAAAATAA
1 AGAAAAAAAATCTTAAACTAAATAAAATAA
* *
3084195 AGAAAATAAAATCTTAACCTAACTAAAATA
1 AGAAAA-AAAATCTTAAACTAAATAAAATA
3084225 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (30 bp):
AGAAAAAAAATCTTAAACTAAATAAAATAA
Found at i:3100574 original size:7 final size:8
Alignment explanation
Indices: 3100521--3100600 Score: 52
Period size: 8 Copynumber: 9.2 Consensus size: 8
3100511 TATTATAATT
*
3100521 AAAATAAA
1 AAAATTAA
3100529 AAATATTAA
1 AAA-ATTAA
3100538 AAAATTAA
1 AAAATTAA
*
3100546 AATTATATAA
1 AA-AAT-TAA
*
3100556 TATAATTAA
1 -AAAATTAA
3100565 AAAATTAAA
1 AAAATT-AA
* *
3100574 ATAAAATAT
1 A-AAATTAA
*
3100583 ATAATTAA
1 AAAATTAA
3100591 AAAATTAA
1 AAAATTAA
3100599 AA
1 AA
3100601 TATAATATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
8 28 0.51
9 17 0.31
10 9 0.16
11 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAATTAA
Found at i:3100584 original size:26 final size:26
Alignment explanation
Indices: 3100517--3100686 Score: 140
Period size: 26 Copynumber: 6.5 Consensus size: 26
3100507 ATAATATTAT
3100517 AATTAAAATAAAA-A-AT-ATTAAAA
1 AATTAAAATAAAATATATAATTAAAA
* *
3100540 AATTAAAATTATATAATATAATTAAAA
1 AATTAAAATAAAAT-ATATAATTAAAA
3100567 AATTAAAATAAAATATATAATTAAAA
1 AATTAAAATAAAATATATAATTAAAA
* *
3100593 AATTAAAATATAATATATCAAATT--AT
1 AATTAAAATAAAATATAT--AATTAAAA
*
3100619 AATAAAAATAAAATATATAACATTAAAA
1 AATTAAAATAAAATATAT-A-ATTAAAA
* *
3100647 TATATT-TAAT-AAATA-ATATTATAAAA
1 -A-ATTAAAATAAAATATATAAT-TAAAA
3100673 AATTAAAAATAAAA
1 AATT-AAAATAAAA
3100687 AATAAATATA
Statistics
Matches: 119, Mismatches: 13, Indels: 26
0.75 0.08 0.16
Matches are distributed among these distances:
23 11 0.09
24 3 0.03
25 5 0.04
26 60 0.50
27 24 0.20
28 10 0.08
29 4 0.03
30 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
AATTAAAATAAAATATATAATTAAAA
Found at i:3100604 original size:50 final size:49
Alignment explanation
Indices: 3100517--3100686 Score: 152
Period size: 50 Copynumber: 3.3 Consensus size: 49
3100507 ATAATATTAT
3100517 AATTAAAATAAAA-A-AT-ATTAAAAAATTAAAATTATATAATATAATTAAAA
1 AATTAAAATAAAATATATAATTAAAAAATT-AAA--ATATAATAT-ATTAAAA
*
3100567 AATTAAAATAAAATATATAATTAAAAAATTAAAATATAATATATCAAATTA
1 AATTAAAATAAAATATATAATTAAAAAATTAAAATATAATATATTAAA--A
*
3100618 TAATAAAAATAAAATATATAACATTAAAATATATTTAATAA-ATAATAT-TATAAAA
1 -AATTAAAATAAAATATAT-A-ATTAAAA-A-A-TTAA-AATATAATATAT-TAAAA
3100673 AATTAAAAATAAAA
1 AATT-AAAATAAAA
3100687 AATAAATATA
Statistics
Matches: 102, Mismatches: 4, Indels: 23
0.79 0.03 0.18
Matches are distributed among these distances:
49 5 0.05
50 22 0.22
51 2 0.02
52 22 0.22
53 12 0.12
54 10 0.10
55 11 0.11
56 2 0.02
57 14 0.14
58 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (49 bp):
AATTAAAATAAAATATATAATTAAAAAATTAAAATATAATATATTAAAA
Found at i:3100633 original size:52 final size:51
Alignment explanation
Indices: 3100512--3100638 Score: 156
Period size: 52 Copynumber: 2.5 Consensus size: 51
3100502 ATTTTATAAT
3100512 ATTATAATTAAAATAAAA-A-AT-ATTAAAAAATTAAAATTATATAATATA
1 ATTATAATTAAAATAAAATATATAATTAAAAAATTAAAATTATATAATATA
*
3100560 ATTAAAAAATTAAAATAAAATATATAATTAAAAAATTAAAA-TATA-ATATATCAA
1 ATT--ATAATTAAAATAAAATATATAATTAAAAAATTAAAATTATATA-ATAT--A
*
3100614 ATTATAATAAAAATAAAATATATAA
1 ATTATAATTAAAATAAAATATATAA
3100639 CATTAAAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
48 3 0.04
50 14 0.21
51 2 0.03
52 30 0.44
53 15 0.22
54 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (51 bp):
ATTATAATTAAAATAAAATATATAATTAAAAAATTAAAATTATATAATATA
Found at i:3100689 original size:42 final size:42
Alignment explanation
Indices: 3100643--3100726 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
3100633 ATATAACATT
* *
3100643 AAAATATATTTAATAAA-TAATATTATAAAAAATTAAAAATAA
1 AAAATAAATATAATAAATTAATATTATAAAAAA-TAAAAATAA
* * * *
3100685 AAAATAAATATATTAAATTTATATTTTAATAAATAAAAATAA
1 AAAATAAATATAATAAATTAATATTATAAAAAATAAAAATAA
3100727 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 23 0.66
43 12 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (42 bp):
AAAATAAATATAATAAATTAATATTATAAAAAATAAAAATAA
Found at i:3106052 original size:21 final size:19
Alignment explanation
Indices: 3106026--3106064 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
3106016 CGAGTTTGGC
3106026 ATCGGATACTTCAAATATGAA
1 ATCGGA-ACTT-AAATATGAA
*
3106047 ATCGGACCTTAAATATGA
1 ATCGGAACTTAAATATGA
3106065 CCTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
ATCGGAACTTAAATATGAA
Found at i:3117902 original size:37 final size:37
Alignment explanation
Indices: 3117861--3117941 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
3117851 TGTGTAAATG
3117861 TGTTTGTGAATTCTTGGATCAATTAGTTGTGAATTGT
1 TGTTTGTGAATTCTTGGATCAATTAGTTGTGAATTGT
* *
3117898 TGTTTGTGAATTGTTGGATCAATTATTTGTGAATTGT
1 TGTTTGTGAATTCTTGGATCAATTAGTTGTGAATTGT
3117935 TGTTTGT
1 TGTTTGT
3117942 TGGTATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.20, C:0.04, G:0.25, T:0.52
Consensus pattern (37 bp):
TGTTTGTGAATTCTTGGATCAATTAGTTGTGAATTGT
Done.