Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold485
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: 999764
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 6 of 8
Found at i:587847 original size:24 final size:24
Alignment explanation
Indices: 587820--587870 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
587810 CAGATTTATG
*
587820 TATTTATATTATT-TTTTTAAATTA
1 TATTTATA-TATTATATTTAAATTA
* *
587844 TATTTTTATATTATATTTATATTA
1 TATTTATATATTATATTTAAATTA
587868 TAT
1 TAT
587871 AATTTATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTATATATTATATTTAAATTA
Found at i:587871 original size:13 final size:13
Alignment explanation
Indices: 587815--587877 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
587805 ATATACAGAT
*
587815 TTATGTATTTATA
1 TTATATATTTATA
* * *
587828 TTATTTTTTTAAA
1 TTATATATTTATA
*
587841 TTATATTTTTATA
1 TTATATATTTATA
587854 -T-TATATTTATA
1 TTATATATTTATA
587865 TTATATAATTTAT
1 TTATAT-ATTTAT
587878 TAGAAAATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
11 9 0.22
12 2 0.05
13 24 0.59
14 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:590954 original size:16 final size:16
Alignment explanation
Indices: 590917--590954 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
590907 TATCTTTAAT
590917 TATTATTATTAAATTA
1 TATTATTATTAAATTA
*
590933 -AGTTATTATTAAGTTA
1 TA-TTATTATTAAATTA
590949 TATTAT
1 TATTAT
590955 ACTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 1 0.05
16 17 0.89
17 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TATTATTATTAAATTA
Found at i:592356 original size:17 final size:17
Alignment explanation
Indices: 592315--592357 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
592305 TTTTATAAAA
**
592315 ATTATTTTATTATTTTT
1 ATTATTTTAAAATTTTT
592332 ATGT-TTTTAAAATTTTT
1 AT-TATTTTAAAATTTTT
592349 ATTATTTTA
1 ATTATTTTA
592358 TATATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTATTTTAAAATTTTT
Found at i:592369 original size:16 final size:16
Alignment explanation
Indices: 592348--592396 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
592338 TTAAAATTTT
592348 TATTATTTTATATATA
1 TATTATTTTATATATA
*
592364 TATTATTTTGATATTTA
1 TATTATTTT-ATATATA
* *
592381 AATTTTTTTATA-ATA
1 TATTATTTTATATATA
592396 T
1 T
592397 TTTTTTACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 13 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTATTTTATATATA
Found at i:592684 original size:14 final size:14
Alignment explanation
Indices: 592665--592700 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
592655 AATTTATTAA
592665 TATATTTATATGA-T
1 TATATTTATAT-ATT
592679 TATATTTATATATT
1 TATATTTATATATT
592693 TATATTTA
1 TATATTTA
592701 ATTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TATATTTATATATT
Found at i:592710 original size:14 final size:13
Alignment explanation
Indices: 592656--592710 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
592646 ATTTTTTTAA
592656 ATTTATTA-ATAT
1 ATTTATTATATAT
592668 ATTTA-TATGATTAT
1 ATTTATTAT-A-TAT
*
592682 ATTTATATATTTAT
1 ATTTAT-TATATAT
592696 ATTTAATTATATAT
1 ATTT-ATTATATAT
592710 A
1 A
592711 AATATAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
11 2 0.06
12 5 0.14
13 1 0.03
14 22 0.63
15 2 0.06
16 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
ATTTATTATATAT
Found at i:592710 original size:22 final size:21
Alignment explanation
Indices: 592664--592710 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
592654 AAATTTATTA
*
592664 ATATATTTATATGATTATATTT
1 ATATATTTATAT-ATTATATAT
592686 ATATATTTATAT-TTA-ATTAT
1 ATATATTTATATATTATA-TAT
592706 ATATA
1 ATATA
592711 AATATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.43
22 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATATTTATATATTATATAT
Found at i:593047 original size:2 final size:2
Alignment explanation
Indices: 593040--593064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
593030 TTATTACGTA
593040 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
593065 ATGTTATCAT
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:594015 original size:19 final size:19
Alignment explanation
Indices: 593991--594052 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
593981 TTTTGAATTT
593991 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
594010 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
594031 CATA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
594050 CAA
1 CAA
594053 TGTATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:594058 original size:13 final size:13
Alignment explanation
Indices: 594040--594064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
594030 ACATAAGTGT
594040 TGTATCGATACAA
1 TGTATCGATACAA
594053 TGTATCGATACA
1 TGTATCGATACA
594065 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:594060 original size:32 final size:32
Alignment explanation
Indices: 594019--594091 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
594009 ACAAACAGAA
594019 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
594051 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
594083 AATGTATCG
1 AATGTATCG
594092 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:594077 original size:19 final size:18
Alignment explanation
Indices: 594021--594083 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
594011 AAACAGAAAA
594021 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
594040 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
594053 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
594072 TGTATCGATACA
1 TGTATCGATACA
594084 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:596566 original size:52 final size:52
Alignment explanation
Indices: 596499--596894 Score: 278
Period size: 52 Copynumber: 7.6 Consensus size: 52
596489 TTAAGTTTCT
* * *
596499 CAATTGTTC-ATAATCGGGGATATTCCAACCCCGGTTTTATTTTCAAAATAC
1 CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
* * * * *
596550 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
* * * * * *
596603 CAATTTTTC-ACAATTGAGGATACTCCAACCTC-G--TTATTTCATCAGGGATACTC
1 CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTT--TCA---AAACAC
*** * * * * *
596656 CAA--CCCCGT-TACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
1 CAATTTTTC-TATA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
* * *
596710 TAATTTCTC-ATAATCGGGGATACTCTAACCCCGGTTTTA-TTTCTAAAACAC
1 CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
* *
596761 TAATTTTTC-ACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
* * * *
596812 CAATTTTTCTTTAATCGGGGATACTCCAACTCTGATTTTA-TTTCAAAAAACAC
1 CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTTC--AAAACAC
* *
596865 CAATTTTTC-ACAATCGAGGATACTCCAACC
1 CAATTTTTCTATAATCGGGGATACTCCAACC
596895 TCGTTATTTC
Statistics
Matches: 267, Mismatches: 54, Indels: 47
0.73 0.15 0.13
Matches are distributed among these distances:
49 6 0.02
50 4 0.01
51 91 0.34
52 94 0.35
53 39 0.15
54 5 0.02
55 2 0.01
56 17 0.06
57 3 0.01
59 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
CAATTTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
Found at i:596643 original size:31 final size:28
Alignment explanation
Indices: 596620--596691 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
596610 TCACAATTGA
*
596620 GGATACTCCAACCTCGTTATTTCATCAG
1 GGATACTCCAACCCCGTTATTTCATCAG
**
596648 GGATACTCCAACCCCGTTACCTC--CGAGG
1 GGATACTCCAACCCCGTTATTTCATC-A-G
596676 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
596692 GCTTTATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 37 0.95
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCATCAG
Found at i:596740 original size:51 final size:51
Alignment explanation
Indices: 596674--596894 Score: 271
Period size: 51 Copynumber: 4.3 Consensus size: 51
596664 TTACCTCCGA
* * * *
596674 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTAATTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCATAATC
* * *
596725 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCATAATC
* * *
596776 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTC-ATAATC
* * * * * *
596828 GGGGATACTCCAACTCTGATTTTATTTCAAAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTC-CAAAACACTAATTTTTCATAATC
*
596880 GAGGATACTCCAACC
1 GGGGATACTCCAACC
596895 TCGTTATTTC
Statistics
Matches: 146, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
51 85 0.58
52 45 0.31
53 16 0.11
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCATAATC
Found at i:596800 original size:102 final size:104
Alignment explanation
Indices: 596674--596894 Score: 302
Period size: 102 Copynumber: 2.1 Consensus size: 104
596664 TTACCTCCGA
* ** *
596674 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTAATTTCTC-ATAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCTATAATCGGGGATACTCCAA
* * *
596738 CCCCGGTTTTATTTC-TAAAACACTAATTTTTCACAATC
66 CCCCGATTTTATTTCAAAAAACACCAATTTTTCACAATC
* * * *
596776 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTTAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCTATAATCGGGGATACTCCAA
* *
596841 CTCTGATTTTATTTCAAAAAACACCAATTTTTCACAATC
66 CCCCGATTTTATTTCAAAAAACACCAATTTTTCACAATC
*
596880 GAGGATACTCCAACC
1 GGGGATACTCCAACC
596895 TCGTTATTTC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
102 39 0.38
103 29 0.28
104 35 0.34
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (104 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCTATAATCGGGGATACTCCAA
CCCCGATTTTATTTCAAAAAACACCAATTTTTCACAATC
Found at i:596913 original size:28 final size:28
Alignment explanation
Indices: 596877--596951 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
596867 ATTTTTCACA
* **
596877 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTACCTC
*
596905 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCTCGTTACCTC
***
596933 CGAGGGGATACTCCAACCT
1 ATCGGGGATACTCCAACCT
596952 TGGCTTTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTACCTC
Found at i:596980 original size:262 final size:262
Alignment explanation
Indices: 596500--597004 Score: 884
Period size: 262 Copynumber: 1.9 Consensus size: 262
596490 TAAGTTTCTC
* * *
596500 AATTGTTCATAATCGGGGATATTCCAACCCCGGTTTTATTTTCAAAATACCAATTTTCCTTTAAT
1 AATTGTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAAT
* *
596565 CGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCA
66 CGGGGATACTCCAACTCCGATTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCA
596630 ACCTCGTTATTTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCT
131 ACCTCGTTATTTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCT
*
596695 TTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCTAACCCCGGTTTTATTTCTAAAACA
196 TTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
596760 CT
261 CT
* *
596762 AATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTTAAT
1 AATTGTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAAT
*
596827 CGGGGATACTCCAACTCTGATTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCA
66 CGGGGATACTCCAACTCCGATTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCA
* **
596892 ACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCTTGGCT
131 ACCTCGTTATTTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCT
* *
596957 TTATTTCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
196 TTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCG
597005 TTATTTCCGA
Statistics
Matches: 229, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
262 229 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (262 bp):
AATTGTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAAT
CGGGGATACTCCAACTCCGATTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCA
ACCTCGTTATTTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCT
TTATTTCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
CT
Found at i:597014 original size:79 final size:78
Alignment explanation
Indices: 596907--597109 Score: 228
Period size: 79 Copynumber: 2.6 Consensus size: 78
596897 GTTATTTCAT
** * *
596907 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCTTGGCTTTATTTCCAAAAT-A
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC-CGACTTTATTTCC-AAATCA
* * *
596971 TTGATTTCTCATAAT
64 TCGATTTCTCACAAC
* * * *
596986 TGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGACTTTATTTCCAAATCAT
*
597051 CGATTTTTCACAAC
65 CGATTTCTCACAAC
* * * *
597065 CGGAGATGCTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCC
597110 CGTTATTATC
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 6 0.06
79 96 0.92
80 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGACTTTATTTCCAAATCATC
GATTTCTCACAAC
Found at i:598694 original size:17 final size:16
Alignment explanation
Indices: 598662--598695 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
598652 TTAAAGTAAA
598662 TATTTTTATAATATTT
1 TATTTTTATAATATTT
* *
598678 TATTTTTTTAATAATT
1 TATTTTTATAATATTT
598694 TA
1 TA
598696 AATAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTATAATATTT
Found at i:606551 original size:26 final size:24
Alignment explanation
Indices: 606522--606586 Score: 62
Period size: 26 Copynumber: 2.7 Consensus size: 24
606512 TAAATTTTTT
*
606522 TATTAAAAATTTATT-GTGAATGATAA
1 TATTAAAAATTTATTAGT--ATCAT-A
*
606548 TATTTAAAA-TTATTAGTATCATA
1 TATTAAAAATTTATTAGTATCATA
*
606571 TATTAAAAATTAATTA
1 TATTAAAAATTTATTA
606587 CCAAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 9 0.27
24 9 0.27
25 5 0.15
26 10 0.30
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (24 bp):
TATTAAAAATTTATTAGTATCATA
Found at i:606861 original size:13 final size:11
Alignment explanation
Indices: 606840--606873 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
606830 TTTTTATATC
606840 AAAATTTAAATA
1 AAAATTTAAA-A
606852 AAATATTTAAAA
1 AAA-ATTTAAAA
606864 AAAATTTAAA
1 AAAATTTAAA
606874 CCACAATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 7 0.33
13 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:607019 original size:19 final size:19
Alignment explanation
Indices: 606970--607118 Score: 69
Period size: 18 Copynumber: 8.5 Consensus size: 19
606960 AAATATAAAT
*
606970 TTTATATA-TTTATGTTATA
1 TTTATATATTTTA-ATTATA
*
606989 TTTAAATA-TTTAATTATA
1 TTTATATATTTTAATTATA
607007 TTTATATATTTT-A-TA-A
1 TTTATATATTTTAATTATA
* *
607023 TTATATAAATATTAA-TATA
1 TT-TATATATTTTAATTATA
* *
607042 TTAATA-ATTTTTATTATA
1 TTTATATATTTTAATTATA
*
607060 --TA-A-AATTTAA--ATA
1 TTTATATATTTTAATTATA
* *
607073 TTTATAT-GTTTATATAATA
1 TTTATATATTTTA-ATTATA
*
607092 -TT-TATATTTTAATTATT
1 TTTATATATTTTAATTATA
607109 TTTATATATT
1 TTTATATATT
607119 ATATTTGTGG
Statistics
Matches: 100, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.03
15 8 0.08
16 9 0.09
17 23 0.23
18 31 0.31
19 26 0.26
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTATATATTTTAATTATA
Found at i:607092 original size:58 final size:57
Alignment explanation
Indices: 607006--607117 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 57
606996 ATTTAATTAT
*
607006 ATTTATATATTTTATAATTATATAAATATTAATATATTAATAATTTTTATTATATAAA
1 ATTTAAATATTTTATAATTATATAAATATTAATATATTAATAATTTTTA-TATATAAA
** * * *
607064 ATTTAAATATTTATATGTTTATAT-AATATTTATATTTTAATTATTTTTATATAT
1 ATTTAAATATTT-TATAATTATATAAATATTAATATATTAATAATTTTTATATAT
607118 TATATTTGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 5 0.11
58 33 0.70
59 9 0.19
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (57 bp):
ATTTAAATATTTTATAATTATATAAATATTAATATATTAATAATTTTTATATATAAA
Found at i:607114 original size:17 final size:19
Alignment explanation
Indices: 607069--607115 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
607059 ATAAAATTTA
607069 AATATTTATATGTTTATAT
1 AATATTTATATGTTTATAT
607088 AATATTTATAT-TTTA-AT
1 AATATTTATATGTTTATAT
* *
607105 TATTTTTATAT
1 AATATTTATAT
607116 ATTATATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
AATATTTATATGTTTATAT
Found at i:608202 original size:74 final size:78
Alignment explanation
Indices: 608072--608224 Score: 208
Period size: 74 Copynumber: 2.0 Consensus size: 78
608062 ATTTGTTTTC
* *
608072 AAAATGTTGTTAAGTTCTTGAGATGCAATTATGTTTTTTTGGTTTAGACTTTGAGTGCTTTGAAA
1 AAAATGTTGTTAAGTTCCTGAGATACAATTATGTTTTTTT-GTTT--ACTTTGAGTGCTTTGAAA
*
608137 TGTATGTTTAATTTGT
63 TGTATGTATAATTTGT
608153 AAAATGTTGTTAAGTTCCTGAGATACAA-T-T-TTTTTTT-TTT-CTCTTGAGTGCTTTGAAATG
1 AAAATGTTGTTAAGTTCCTGAGATACAATTATGTTTTTTTGTTTACT-TTGAGTGCTTTGAAATG
608213 TATGTATAATTT
65 TATGTATAATTT
608225 CTTTCTCTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
73 2 0.03
74 28 0.41
76 3 0.04
78 7 0.10
79 1 0.01
80 1 0.01
81 26 0.38
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (78 bp):
AAAATGTTGTTAAGTTCCTGAGATACAATTATGTTTTTTTGTTTACTTTGAGTGCTTTGAAATGT
ATGTATAATTTGT
Found at i:610122 original size:44 final size:44
Alignment explanation
Indices: 610072--610161 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
610062 TCTAGATCCC
610072 TAACCAAAGTGCTGAGTAGGGTTGCCAAGTTGTCAGAATCAGGA
1 TAACCAAAGTGCTGAGTAGGGTTGCCAAGTTGTCAGAATCAGGA
610116 TAACCAAAGTGCTGAGTAGGGTTGCCAAGTTGTCAGAATCAGGA
1 TAACCAAAGTGCTGAGTAGGGTTGCCAAGTTGTCAGAATCAGGA
610160 TA
1 TA
610162 TCCTTTCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (44 bp):
TAACCAAAGTGCTGAGTAGGGTTGCCAAGTTGTCAGAATCAGGA
Found at i:610143 original size:21 final size:21
Alignment explanation
Indices: 610075--610143 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
610065 AGATCCCTAA
610075 CCAAAGTGCTGAGTAGGGTTG
1 CCAAAGTGCTGAGTAGGGTTG
* * * **
610096 CC-AAGTTGTCAGAATCAGGATAA
1 CCAAAG-TG-CTGAGT-AGGGTTG
610119 CCAAAGTGCTGAGTAGGGTTG
1 CCAAAGTGCTGAGTAGGGTTG
610140 CCAA
1 CCAA
610144 GTTGTCAGAA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 8 0.24
23 8 0.24
24 3 0.09
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (21 bp):
CCAAAGTGCTGAGTAGGGTTG
Found at i:612929 original size:22 final size:20
Alignment explanation
Indices: 612902--612950 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
612892 AATACTTATT
612902 AATTATATATAATATTTAAAAA
1 AATTATATATAATA--TAAAAA
612924 AATTAT-TA-AATATAAAAA
1 AATTATATATAATATAAAAA
612942 AATTA-ATAT
1 AATTATATAT
612951 CCGTCTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
18 13 0.52
20 4 0.16
21 2 0.08
22 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATATATAATATAAAAA
Found at i:614004 original size:22 final size:22
Alignment explanation
Indices: 613979--614028 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
613969 TATCGAATTA
*
613979 TATTTTAAAATATAAATTTCGG
1 TATTTTAAAATATAAAGTTCGG
*
614001 TATTTTAAAGTATAAAGTTCGG
1 TATTTTAAAATATAAAGTTCGG
*
614023 TGTTTT
1 TATTTT
614029 TAACTCGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (22 bp):
TATTTTAAAATATAAAGTTCGG
Found at i:614362 original size:15 final size:13
Alignment explanation
Indices: 614333--614357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614323 TTGTTTAAAG
614333 TTTTTAAAATTTA
1 TTTTTAAAATTTA
614346 TTTTTAAAATTT
1 TTTTTAAAATTT
614358 TTATTAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAAAATTTA
Found at i:624928 original size:54 final size:54
Alignment explanation
Indices: 624869--625033 Score: 132
Period size: 54 Copynumber: 3.1 Consensus size: 54
624859 AGACACTAGA
624869 AACTTACTTATCAACATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCAT
1 AACTTACTTATCAACATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCAT
** ***** * *
624923 AACTTA-TT-T-TGCATTTTCAACCTAA-C-TGCA-AAGCAT-GATAGA-GA-CACT
1 AACTTACTTATCAACATTTT-GGTGGAAGCATACAGAGGCATGGAT-GATGATCA-T
624971 AGAAACTTACTTATCAACATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCAT
1 ---AACTTACTTATCAACATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCAT
625028 AACTTA
1 AACTTA
625034 TTTTGCATTT
Statistics
Matches: 78, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
47 2 0.03
48 6 0.08
49 7 0.09
50 3 0.04
51 13 0.17
52 5 0.06
53 5 0.06
54 19 0.24
55 3 0.04
56 7 0.09
57 6 0.08
58 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (54 bp):
AACTTACTTATCAACATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCAT
Found at i:624939 original size:51 final size:51
Alignment explanation
Indices: 624883--625044 Score: 120
Period size: 51 Copynumber: 3.1 Consensus size: 51
624873 TACTTATCAA
624883 CATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCATAACTTATTTTG
1 CATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCATAACTTATTTTG
***** * * **
624934 CATTTTCAACCTAA-C-TGCA-AAGCAT-GATAGA-GA-CACTAGAAACTTACTTATCAA
1 CATTTT-GGTGGAAGCATACAGAGGCATGGAT-GATGATCA-T---AACTTA-TT-T-TG
624988 CATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCATAACTTATTTTG
1 CATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCATAACTTATTTTG
625039 CATTTT
1 CATTTT
625045 CATATAAAAG
Statistics
Matches: 78, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
47 2 0.03
48 6 0.08
49 7 0.09
50 3 0.04
51 19 0.24
52 5 0.06
53 5 0.06
54 13 0.17
55 3 0.04
56 7 0.09
57 6 0.08
58 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (51 bp):
CATTTTGGTGGAAGCATACAGAGGCATGGATGATGATCATAACTTATTTTG
Found at i:625019 original size:105 final size:105
Alignment explanation
Indices: 624837--625046 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
624827 AGTAATATCC
624837 ACCTAACTGCAAAGCATGATAGAGACACTAGAAACTTACTTATCAACATTTTGGTGGAAGCATAC
1 ACCTAACTGCAAAGCATGATAGAGACACTAGAAACTTACTTATCAACATTTTGGTGGAAGCATAC
624902 AGAGGCATGGATGATGATCATAACTTATTTTGCATTTTCA
66 AGAGGCATGGATGATGATCATAACTTATTTTGCATTTTCA
624942 ACCTAACTGCAAAGCATGATAGAGACACTAGAAACTTACTTATCAACATTTTGGTGGAAGCATAC
1 ACCTAACTGCAAAGCATGATAGAGACACTAGAAACTTACTTATCAACATTTTGGTGGAAGCATAC
625007 AGAGGCATGGATGATGATCATAACTTATTTTGCATTTTCA
66 AGAGGCATGGATGATGATCATAACTTATTTTGCATTTTCA
625047 TATAAAAGAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (105 bp):
ACCTAACTGCAAAGCATGATAGAGACACTAGAAACTTACTTATCAACATTTTGGTGGAAGCATAC
AGAGGCATGGATGATGATCATAACTTATTTTGCATTTTCA
Found at i:628203 original size:19 final size:19
Alignment explanation
Indices: 628160--628215 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
628150 TTGTTAAATT
*
628160 TTTAATTAAATTAATATC-A
1 TTTAATTTAA-TAATATCAA
*
628179 -TAAATTTAATAATATCAA
1 TTTAATTTAATAATATCAA
*
628197 TTTAATTTAATGATATCAA
1 TTTAATTTAATAATATCAA
628216 AATAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.23
18 8 0.26
19 16 0.52
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTAATTTAATAATATCAA
Found at i:628221 original size:19 final size:19
Alignment explanation
Indices: 628181--628221 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
628171 TAATATCATA
**
628181 AATTTAATAATATCAATTT
1 AATTTAATAATATCAAAAT
*
628200 AATTTAATGATATCAAAAT
1 AATTTAATAATATCAAAAT
628219 AAT
1 AAT
628222 ATAAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTAATAATATCAAAAT
Found at i:628278 original size:2 final size:2
Alignment explanation
Indices: 628273--628299 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
628263 CTGGCACATG
628273 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
628300 CCACAAACTA
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:628662 original size:14 final size:14
Alignment explanation
Indices: 628643--628670 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
628633 TTTTTTGATT
628643 TTAAATATATTTTA
1 TTAAATATATTTTA
628657 TTAAATATATTTTA
1 TTAAATATATTTTA
628671 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:629080 original size:17 final size:18
Alignment explanation
Indices: 629047--629082 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
629037 AAGAGGTTAA
629047 ATTTAATTATGATTTTTT
1 ATTTAATTATGATTTTTT
*
629065 ATTTATTTAT-ATTTTTT
1 ATTTAATTATGATTTTTT
629082 A
1 A
629083 AAATTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTAATTATGATTTTTT
Found at i:629225 original size:2 final size:2
Alignment explanation
Indices: 629218--629252 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
629208 AAATAAATAA
629218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
629253 CATTTATCAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:629360 original size:5 final size:5
Alignment explanation
Indices: 629350--629426 Score: 56
Period size: 5 Copynumber: 16.2 Consensus size: 5
629340 AATAATTTTA
* * * *
629350 AATAT AATAT AAAAT ATTAT -AT-T AATAT AATAT -ATTT GATA- AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* *
629396 AAAAAT AATAT AATA- AATAT AATAT GATAT A
1 -AATAT AATAT AATAT AATAT AATAT AATAT A
629427 TTTACGAGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
3 1 0.02
4 13 0.24
5 37 0.67
6 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:629377 original size:18 final size:18
Alignment explanation
Indices: 629354--629399 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
629344 ATTTTAAATA
629354 TAATATAAAATATTAT-AT
1 TAATATAAAATATT-TGAT
*
629372 TAATATAATATATTTGAT
1 TAATATAAAATATTTGAT
*
629390 AAATATAAAA
1 TAATATAAAA
629400 ATAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TAATATAAAATATTTGAT
Found at i:629395 original size:24 final size:23
Alignment explanation
Indices: 629348--629430 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 23
629338 CGAATAATTT
*
629348 TAAATATAATATAAAATA-TT-A
1 TAAATATAATATAATATATTTAA
*
629369 T--AT-TAATATAATATATTTGA
1 TAAATATAATATAATATATTTAA
*
629389 TAAATATAA-A-AATA-ATATAA
1 TAAATATAATATAATATATTTAA
*
629409 TAAATATAATATGATATATTTA
1 TAAATATAATATAATATATTTA
629431 CGAGAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
18 11 0.22
19 4 0.08
20 15 0.31
21 6 0.12
22 6 0.12
23 7 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATATAATATAATATATTTAA
Found at i:632303 original size:2 final size:2
Alignment explanation
Indices: 632296--632323 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
632286 CACAAACATT
632296 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
632324 CTATCTATAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:637516 original size:18 final size:18
Alignment explanation
Indices: 637495--637536 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
637485 TTTCTATGAA
* *
637495 TTTTAGTATAAATATTAT
1 TTTTAATATAAATATTAG
637513 TTTTAATATAAATATTAG
1 TTTTAATATAAATATTAG
637531 TTTTAA
1 TTTTAA
637537 CAACATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTAATATAAATATTAG
Found at i:637556 original size:4 final size:4
Alignment explanation
Indices: 637547--637576 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
637537 CAACATTTAC
637547 AATA AATA AATA AATA AATA AATGA AATA A
1 AATA AATA AATA AATA AATA AAT-A AATA A
637577 TTATAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:641460 original size:28 final size:28
Alignment explanation
Indices: 641428--641483 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
641418 CATACACTAA
*
641428 TATTATATTTATATTTA-TTTTTATATTT
1 TATTATATTT-TAATTATTTTTTATATTT
641456 TATTATATTTTAATTATTTTTTATATTT
1 TATTATATTTTAATTATTTTTTATATTT
641484 ACTGACATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (28 bp):
TATTATATTTTAATTATTTTTTATATTT
Found at i:641461 original size:10 final size:10
Alignment explanation
Indices: 641428--641483 Score: 59
Period size: 9 Copynumber: 6.0 Consensus size: 10
641418 CATACACTAA
641428 TATTATATTT
1 TATTATATTT
641438 ATATT-TA-TT
1 -TATTATATTT
641447 T-TTATATTT
1 TATTATATTT
641456 TATTATATTT
1 TATTATATTT
*
641466 TAAT-TATTT
1 TATTATATTT
641475 T-TTATATTT
1 TATTATATTT
641484 ACTGACATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 16 0.41
10 13 0.33
11 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTATATTT
Found at i:642779 original size:34 final size:34
Alignment explanation
Indices: 642740--642807 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
642730 CCATTATGTC
* *
642740 TTTTTAGCATAATAAGATTACTTTTTATAAACTG
1 TTTTTAGCAGAATAAAATTACTTTTTATAAACTG
*
642774 TTTTTAGCAGAATAAAATTACTTTTTATACACTG
1 TTTTTAGCAGAATAAAATTACTTTTTATAAACTG
642808 AATCTGCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (34 bp):
TTTTTAGCAGAATAAAATTACTTTTTATAAACTG
Found at i:643804 original size:85 final size:85
Alignment explanation
Indices: 643657--643826 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
643647 TCTCCATCAT
* *
643657 TCTTGCTCTAGTCTATCTTGATACAATGCTAATTGCAGTTATGGATCCAAGTAATTATTGTTCAT
1 TCTTGCTATAGTCTATCTTGATACAATGCTAATTGCAGTTATGGATCCAAGTAATTAATGTTCAT
643722 AAGATTTCTAATGCAAAGAA
66 AAGATTTCTAATGCAAAGAA
* *
643742 TCTTGCTATAGTCTATCTTGCTACAGTGCTAATTGCAGTTATGGATCCAAGTAATTAATGTTCAT
1 TCTTGCTATAGTCTATCTTGATACAATGCTAATTGCAGTTATGGATCCAAGTAATTAATGTTCAT
*
643807 GAGATTTCTAATGCAAAGAA
66 AAGATTTCTAATGCAAAGAA
643827 CCCACCGGAG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (85 bp):
TCTTGCTATAGTCTATCTTGATACAATGCTAATTGCAGTTATGGATCCAAGTAATTAATGTTCAT
AAGATTTCTAATGCAAAGAA
Found at i:643872 original size:22 final size:22
Alignment explanation
Indices: 643833--643878 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
643823 AGAACCCACC
* *
643833 GGAGTGGCAACTATAA-GGCAT
1 GGAGTGGCAACCAAAAGGGCAT
643854 GGAGTGAGCAACCAAAAGGGCAT
1 GGAGTG-GCAACCAAAAGGGCAT
643877 GG
1 GG
643879 TATTGCTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 7 0.33
ACGTcount: A:0.35, C:0.15, G:0.37, T:0.13
Consensus pattern (22 bp):
GGAGTGGCAACCAAAAGGGCAT
Found at i:644288 original size:16 final size:16
Alignment explanation
Indices: 644267--644297 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
644257 TGGTAGAAGA
*
644267 CTTAAACATGCTTAAG
1 CTTAAACATACTTAAG
644283 CTTAAACATACTTAA
1 CTTAAACATACTTAA
644298 TTATAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (16 bp):
CTTAAACATACTTAAG
Found at i:648744 original size:16 final size:16
Alignment explanation
Indices: 648719--648780 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
648709 TATGTTATAT
*
648719 ATTTAATTAAAATTTA
1 ATTTATTTAAAATTTA
648735 ATTTATTTAAAATTTA
1 ATTTATTTAAAATTTA
* *
648751 ACTATATTTTAAATTTA
1 A-TTTATTTAAAATTTA
*
648768 TTTTATATTAAAA
1 ATTTAT-TTAAAA
648781 AGTAAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 20 0.53
17 18 0.47
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATTTAAAATTTA
Found at i:648764 original size:17 final size:16
Alignment explanation
Indices: 648725--648767 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
648715 ATATATTTAA
*
648725 TTAAAATTTAATTTAT
1 TTAAAATTTAATATAT
648741 TTAAAATTTAACTATAT
1 TTAAAATTTAA-TATAT
*
648758 TTTAAATTTA
1 TTAAAATTTA
648768 TTTTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATTTAATATAT
Found at i:653387 original size:13 final size:13
Alignment explanation
Indices: 653369--653393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
653359 ACAGAGATCA
653369 AATGTATCGATAT
1 AATGTATCGATAT
653382 AATGTATCGATA
1 AATGTATCGATA
653394 CATTCTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:654447 original size:42 final size:42
Alignment explanation
Indices: 654388--654519 Score: 149
Period size: 42 Copynumber: 3.1 Consensus size: 42
654378 TAGCCCTCAA
* * *
654388 AGAGAAAGAAGAGATATGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATATGAGGGATGATAGGAGGAGAGATAAG
* *
654430 AGAGATAGTAGAGATATGATGGATGATAGAAGGAGAGATAAG
1 AGAGATAGTAGAGATATGAGGGATGATAGGAGGAGAGATAAG
* * * * * *
654472 AGAGATAATAGAGAAAGGAGGGATGACAGGAAGAGGAGAGAAG
1 AGAGATAGTAGAGATATGAGGGATGATAGGAGGA-GAGATAAG
654515 A-AGAT
1 AGAGAT
654520 GGAAGATTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 68 0.89
43 8 0.11
ACGTcount: A:0.47, C:0.01, G:0.39, T:0.13
Consensus pattern (42 bp):
AGAGATAGTAGAGATATGAGGGATGATAGGAGGAGAGATAAG
Found at i:660473 original size:29 final size:31
Alignment explanation
Indices: 660440--660499 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
660430 GTATAACATC
*
660440 TTATTAAATGTAATA-ATTAATAATT-TTAT
1 TTATTAAATGTAATATATTAAAAATTGTTAT
* *
660469 TTATTATATTTAATATATTAAAAATTGTTAT
1 TTATTAAATGTAATATATTAAAAATTGTTAT
660500 ATATAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 9 0.35
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TTATTAAATGTAATATATTAAAAATTGTTAT
Found at i:660512 original size:30 final size:29
Alignment explanation
Indices: 660450--660522 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
660440 TTATTAAATG
* * *
660450 TAATAATTAATAATTTTATTTATTATATT
1 TAATAATTAAAAATTTTATATATAATATT
660479 TAATATATTAAAAATTGTTATATATAATA-T
1 TAATA-ATTAAAAATT-TTATATATAATATT
660509 TAATAACTTAAAAA
1 TAATAA-TTAAAAA
660523 AATTTAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 6 0.16
30 22 0.58
31 10 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TAATAATTAAAAATTTTATATATAATATT
Found at i:661330 original size:5 final size:5
Alignment explanation
Indices: 661313--661345 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
661303 TATTAAATAA
661313 TAATT TAAATT TAATT TAATT TAATT TAATT TA
1 TAATT T-AATT TAATT TAATT TAATT TAATT TA
661346 TAAGGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TAATT
Found at i:664214 original size:20 final size:21
Alignment explanation
Indices: 664189--664235 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 21
664179 TTAAGTTCGT
664189 TCAAGAG-CTAGAAAATATAA
1 TCAAGAGACTAGAAAATATAA
664209 TCAAGAGACAACTAGAAAATATAA
1 TCAAGAG---ACTAGAAAATATAA
664233 TCA
1 TCA
664236 TATCGTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
24 16 0.70
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (21 bp):
TCAAGAGACTAGAAAATATAA
Found at i:667227 original size:19 final size:20
Alignment explanation
Indices: 667179--667229 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
667169 GAAAATAAGT
667179 TTAAATATTAAATACATTAC
1 TTAAATATTAAATACATTAC
*
667199 TT-GATATTAAATA-ATTA-
1 TTAAATATTAAATACATTAC
*
667216 TTAAATATTTAATA
1 TTAAATATTAAATA
667230 AATATATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 10 0.37
20 2 0.07
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAAATATTAAATACATTAC
Found at i:668330 original size:3 final size:3
Alignment explanation
Indices: 668316--668350 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
668306 ATTGATATGG
*
668316 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
668351 AAATTGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:668571 original size:21 final size:21
Alignment explanation
Indices: 668547--668586 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
668537 TTTTTAATTT
668547 AAAT-TTAATTATAAAAATATA
1 AAATATTAA-TATAAAAATATA
668568 AAATATTAATATAAAAATA
1 AAATATTAATATAAAAATA
668587 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATTAATATAAAAATATA
Found at i:668595 original size:19 final size:21
Alignment explanation
Indices: 668550--668598 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
668540 TTAATTTAAA
668550 TTTAATTATAAAAATATAAAAT
1 TTTAA-TATAAAAATATAAAAT
* *
668572 ATTAATAT-AAAA-ATAATAT
1 TTTAATATAAAAATATAAAAT
668591 TTTAATAT
1 TTTAATAT
668599 TATTTTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 4 0.17
21 3 0.12
22 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAATATAAAAATATAAAAT
Found at i:669224 original size:15 final size:16
Alignment explanation
Indices: 669199--669241 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
669189 AAATATTAAA
669199 TTAAAACTT-AAATAAT
1 TTAAAA-TTAAAATAAT
669215 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
669231 TTAAAA-TAAAA
1 TTAAAATTAAAA
669242 AAAATAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAATTAAAATAAT
Found at i:673371 original size:25 final size:27
Alignment explanation
Indices: 673337--673403 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
673327 GTGTCAATTT
*
673337 ATATAATATAAATCAT-TAAT-TTTTAA
1 ATATTATATAAAT-ATATAATATTTTAA
673363 AT-TTATATAAATATATAATATTTTAA
1 ATATTATATAAATATATAATATTTTAA
673389 ATATTAT-TAAA-ATAT
1 ATATTATATAAATATAT
673404 GTAAAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 2 0.05
25 17 0.46
26 14 0.38
27 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTATATAAATATATAATATTTTAA
Found at i:674528 original size:17 final size:17
Alignment explanation
Indices: 674506--674539 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
674496 ATTTTTATAT
*
674506 TTTTAATTAAAAGAAAG
1 TTTTAAGTAAAAGAAAG
674523 TTTTAAGTAAAAGAAAG
1 TTTTAAGTAAAAGAAAG
674540 AAAGAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (17 bp):
TTTTAAGTAAAAGAAAG
Found at i:677936 original size:3 final size:3
Alignment explanation
Indices: 677928--677956 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
677918 ATGTGACTAA
677928 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
677957 TTTACCTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:678837 original size:10 final size:9
Alignment explanation
Indices: 678800--678836 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
678790 TTCTTTGAAG
*
678800 ATTTTTATA
1 ATTTTTAAA
*
678809 CTTTTTAAA
1 ATTTTTAAA
678818 ATTTTTAAA
1 ATTTTTAAA
678827 ATTTTTAAA
1 ATTTTTAAA
678836 A
1 A
678837 AATTATATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:679271 original size:10 final size:10
Alignment explanation
Indices: 679256--679288 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
679246 CAAAAGTTCC
*
679256 TATATATATA
1 TATATATACA
679266 TATATATACA
1 TATATATACA
679276 TATATATACA
1 TATATATACA
679286 TAT
1 TAT
679289 GTTATAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATACA
Found at i:679847 original size:2 final size:2
Alignment explanation
Indices: 679840--679870 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
679830 ATCTCTGTTA
*
679840 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
679871 CTTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:681297 original size:18 final size:19
Alignment explanation
Indices: 681274--681321 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
681264 TTAAATTACT
681274 ATTATAAATATATT-TT-TA
1 ATTATAAATAT-TTATTCTA
681292 ATTATAGTAATATTTATTCTA
1 ATTATA--AATATTTATTCTA
681313 ATTATAAAT
1 ATTATAAAT
681322 TATAACTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.23
19 5 0.19
20 7 0.27
21 8 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATAAATATTTATTCTA
Found at i:686108 original size:22 final size:22
Alignment explanation
Indices: 686083--686125 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
686073 ATTTTTTATT
686083 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
*
686105 TAAATATTGATATAAAAATAT
1 TAAATATTAATATAAAAATAT
686126 TTTAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:687542 original size:21 final size:20
Alignment explanation
Indices: 687501--687543 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
687491 TATATTTAAT
*
687501 TTTTTCTTTATTTTTTCCTC
1 TTTTTCTTTATTTTATCCTC
687521 TTTTTCTTTTCATTTTAT-CTC
1 TTTTTC-TTT-ATTTTATCCTC
687542 TT
1 TT
687544 CCTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCTTTATTTTATCCTC
Found at i:688376 original size:68 final size:68
Alignment explanation
Indices: 688298--688425 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 68
688288 TTAGAGAGAT
* * *
688298 GTATTGAATTTTGTCATGAGAAATTCTTGCTACGATTAAATAAAAAACGGGAATGAGTTTATACG
1 GTATTGAATTTTATCATGAGAAATGCTTGCAACGATTAAATAAAAAACGGGAATGAGTTTATACG
688363 GAG
66 GAG
*
688366 GTATTTAATTTTATCATGAGAAATGCTTGCAACGATTAAATAAAAAACGGGAATGAGTTT
1 GTATTGAATTTTATCATGAGAAATGCTTGCAACGATTAAATAAAAAACGGGAATGAGTTT
688426 CAAGGGTGTC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (68 bp):
GTATTGAATTTTATCATGAGAAATGCTTGCAACGATTAAATAAAAAACGGGAATGAGTTTATACG
GAG
Found at i:692972 original size:25 final size:26
Alignment explanation
Indices: 692935--692991 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
692925 ATGTTAATAT
**
692935 TTAATTAATTATGATAATTTAAAAAA
1 TTAATTAATTATGATAAAGTAAAAAA
*
692961 TTAATTTA-TATGATAAAGTAAAAAA
1 TTAATTAATTATGATAAAGTAAAAAA
692986 TTAATT
1 TTAATT
692992 CATGGAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (26 bp):
TTAATTAATTATGATAAAGTAAAAAA
Found at i:693557 original size:14 final size:14
Alignment explanation
Indices: 693506--693558 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
693496 ATTTGAGTTT
*
693506 TTTTAAAATATATA
1 TTTTAAAATATAAA
*
693520 TTTT-GAATATAAA
1 TTTTAAAATATAAA
* * *
693533 TATGAATATATAAA
1 TTTTAAAATATAAA
693547 TTTTAAAATATA
1 TTTTAAAATATA
693559 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (14 bp):
TTTTAAAATATAAA
Found at i:696882 original size:27 final size:31
Alignment explanation
Indices: 696820--696882 Score: 71
Period size: 30 Copynumber: 2.1 Consensus size: 31
696810 TAAATTACTA
* *
696820 TTAATTTATTAAAATAATATTTTTATTTAAAT
1 TTAATTTATTAAAATAATATTTTTA-TAAAAC
696852 TTAA-TTA-TAAAATAAT-TTTTTA-AAAAC
1 TTAATTTATTAAAATAATATTTTTATAAAAC
696879 TTAA
1 TTAA
696883 AATATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 7 0.24
29 6 0.21
30 9 0.31
31 3 0.10
32 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATTTATTAAAATAATATTTTTATAAAAC
Found at i:697947 original size:13 final size:14
Alignment explanation
Indices: 697929--697966 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
697919 TTATCAAAAT
697929 AATATTATT-TTAA
1 AATATTATTATTAA
697942 AATATT-TTATTAA
1 AATATTATTATTAA
697955 AATATTATTATT
1 AATATTATTATT
697967 TTGTTACGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 16 0.70
14 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:698338 original size:25 final size:23
Alignment explanation
Indices: 698301--698365 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
698291 TAAATTTTCA
* *
698301 TTAAATTAATATTTTTATTAATT
1 TTAAATTATTATTTTTAATAATT
* *
698324 TATAATGTTATTATTGTTAATAATT
1 T-TAA-ATTATTATTTTTAATAATT
698349 TTAAATTATTATATTTT
1 TTAAATTATTAT-TTTT
698366 GAAAAACTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 8 0.24
24 9 0.27
25 16 0.48
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
TTAAATTATTATTTTTAATAATT
Found at i:709065 original size:2 final size:2
Alignment explanation
Indices: 709058--709083 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
709048 AAAGCAATTA
709058 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
709084 GGTACCTGCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:710193 original size:19 final size:18
Alignment explanation
Indices: 710155--710196 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
710145 ATTTACATTG
710155 ATAAT-AAAATTAAATAA
1 ATAATAAAAATTAAATAA
*
710172 ATAATAAAAATATAATTAA
1 ATAATAAAAAT-TAAATAA
710191 ATAATA
1 ATAATA
710197 CAATAGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 12 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAAAAATTAAATAA
Found at i:710196 original size:13 final size:13
Alignment explanation
Indices: 710155--710196 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 13
710145 ATTTACATTG
*
710155 ATAATAAAATTAA
1 ATAATATAATTAA
710168 ATAA-ATAA-TAA
1 ATAATATAATTAA
710179 A-AATATAATTAA
1 ATAATATAATTAA
710191 ATAATA
1 ATAATA
710197 CAATAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.08
11 8 0.32
12 7 0.28
13 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATATAATTAA
Found at i:710870 original size:18 final size:17
Alignment explanation
Indices: 710849--710900 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
710839 TTTTATTTAT
710849 TATTAAATTTATATAAAA
1 TATT-AATTTATATAAAA
* *
710867 TATTATTTTATTATTAAA
1 TATTAATTTA-TATAAAA
* *
710885 TAATAATTTAAATAAA
1 TATTAATTTATATAAA
710901 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAATTTATATAAAA
Found at i:710958 original size:23 final size:22
Alignment explanation
Indices: 710932--710974 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
710922 TTCATCTAAA
*
710932 ATTAACTCAAATAAATTAATCTT
1 ATTAAATCAAATAAA-TAATCTT
*
710955 ATTAAATTAAATAAATAATC
1 ATTAAATCAAATAAATAATC
710975 AAATTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTAAATCAAATAAATAATCTT
Found at i:714070 original size:2 final size:2
Alignment explanation
Indices: 714063--714089 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
714053 TCCCTCTAAC
714063 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
714090 GTATCAGTGC
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:716193 original size:29 final size:29
Alignment explanation
Indices: 716158--716223 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
716148 TATAAAATTT
* *
716158 ATATTATCTTATATAAAAATATATTATATA
1 ATATTATATTATATAAAAATA-AATATATA
*
716188 AT-TTATATTTTATAAAAATAAATATATA
1 ATATTATATTATATAAAAATAAATATATA
716216 ATATTATA
1 ATATTATA
716224 ATGTTAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.28
29 21 0.66
30 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATTATATTATATAAAAATAAATATATA
Found at i:717821 original size:11 final size:11
Alignment explanation
Indices: 717807--717837 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
717797 TGTATTCATG
717807 TTATATTTATA
1 TTATATTTATA
*
717818 TTATATTTTTA
1 TTATATTTATA
717829 TTATATTTA
1 TTATATTTA
717838 AAGTATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTTATA
Found at i:722198 original size:18 final size:16
Alignment explanation
Indices: 722171--722253 Score: 63
Period size: 15 Copynumber: 5.4 Consensus size: 16
722161 AAATATTTTA
722171 AAAT-TTATATAATAT
1 AAATATTATATAATAT
722186 AAATTATTA-AT-ATATT
1 AAA-TATTATATAATA-T
722202 AAATATTATATAATTAT
1 AAATATTATATAA-TAT
*
722219 AAAATATTTTA-AATAT
1 -AAATATTATATAATAT
*
722235 AATTA-TA-ATAA-AT
1 AAATATTATATAATAT
722248 AAATAT
1 AAATAT
722254 ACTAATTGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
13 7 0.13
14 3 0.05
15 15 0.27
16 12 0.22
17 7 0.13
18 11 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTATATAATAT
Found at i:722198 original size:32 final size:33
Alignment explanation
Indices: 722152--722226 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
722142 CGATGTGACG
* *
722152 TAAATATATAAATATTTTAAA-ATTTATATAA-TA
1 TAAAT-TATTAATATATTAAATA-TTATATAATTA
722185 TAAATTATTAATATATTAAATATTATATAATTA
1 TAAATTATTAATATATTAAATATTATATAATTA
*
722218 TAAAATATT
1 TAAATTATT
722227 TTAAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 21 0.57
33 16 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAAATTATTAATATATTAAATATTATATAATTA
Found at i:722207 original size:27 final size:28
Alignment explanation
Indices: 722177--722242 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
722167 TTTAAAATTT
*
722177 ATATAATATAAATTAT-TAATATATTAA
1 ATATAATATAAATTATAAAATATATTAA
* *
722204 ATATTATAT-AATTATAAAATATTTTAA
1 ATATAATATAAATTATAAAATATATTAA
722231 ATATAATTATAA
1 ATATAA-TATAA
722243 TAAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.19
27 22 0.69
28 3 0.09
29 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATAATATAAATTATAAAATATATTAA
Found at i:722245 original size:25 final size:27
Alignment explanation
Indices: 722194--722254 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
722184 ATAAATTATT
*
722194 AATATATTAAATATTATATAATTATAA
1 AATATATTAAATATTATATAATAATAA
* *
722221 AATATTTTAAATATAATTATAATAA-ATA
1 AATATATTAAATATTA-TATAATAATA-A
722249 AATATA
1 AATATA
722255 CTAATTGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATATTAAATATTATATAATAATAA
Found at i:723180 original size:2 final size:2
Alignment explanation
Indices: 723175--723204 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
723165 ATATATAGGT
723175 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
723205 GGTTCTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:725520 original size:16 final size:16
Alignment explanation
Indices: 725494--725534 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
725484 AAAAATGTCT
*
725494 TTTTCAAAAGAAAATTA
1 TTTT-AAAAGAAAAATA
725511 TTTTAAAAGAAAAATA
1 TTTTAAAAGAAAAATA
*
725527 ATTTAAAA
1 TTTTAAAA
725535 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (16 bp):
TTTTAAAAGAAAAATA
Found at i:725892 original size:20 final size:20
Alignment explanation
Indices: 725867--725908 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
725857 AGTTTAAATT
725867 ATTATTTAAT-AATAATAAAA
1 ATTATTTAATAAAT-ATAAAA
*
725887 ATTATTTATTAAATATAAAA
1 ATTATTTAATAAATATAAAA
725907 AT
1 AT
725909 ATAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTATTTAATAAATATAAAA
Found at i:731436 original size:22 final size:22
Alignment explanation
Indices: 731402--731447 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
731392 TAAATTTATT
*
731402 TGAGTTGATTTATTTATTAGAA
1 TGAGTTGATTTATTTATTAAAA
731424 TGAGATTGA-TTATTTATTAAAA
1 TGAG-TTGATTTATTTATTAAAA
731446 TG
1 TG
731448 TTGAGTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (22 bp):
TGAGTTGATTTATTTATTAAAA
Found at i:734349 original size:2 final size:2
Alignment explanation
Indices: 734336--734393 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
734326 GGCTACCATT
* *
734336 TC TC TC TT TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
734378 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
734394 AGGGTTCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:737151 original size:15 final size:17
Alignment explanation
Indices: 737133--737194 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 17
737123 ATTTATTATA
737133 TTTATAT-TTAA-AATT
1 TTTATATATTAATAATT
737148 TTTATATATTAATAA--
1 TTTATATATTAATAATT
* *
737163 TTTATGATA-TAATTATA
1 TTTAT-ATATTAATAATT
737180 TTTATATAATTAATA
1 TTTATAT-ATTAATA
737195 TAAAAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
15 17 0.45
16 9 0.24
17 8 0.21
18 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTATATATTAATAATT
Found at i:737218 original size:14 final size:14
Alignment explanation
Indices: 737143--737230 Score: 56
Period size: 14 Copynumber: 6.3 Consensus size: 14
737133 TTTATATTTA
*
737143 AAATTTTTATATAT
1 AAATTATTATATAT
* *
737157 TAATAATT-TATGAT
1 AAATTATTATAT-AT
*
737171 ATAATTA-TATTTAT
1 A-AATTATTATATAT
* *
737185 ATAATTAATATA-AA
1 A-AATTATTATATAT
737199 AAATTATTATATAT
1 AAATTATTATATAT
* *
737213 AAATTATCAAATAT
1 AAATTATTATATAT
737227 AAAT
1 AAAT
737231 AGACATGACC
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
13 12 0.21
14 36 0.63
15 9 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (14 bp):
AAATTATTATATAT
Found at i:738838 original size:14 final size:14
Alignment explanation
Indices: 738819--738848 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
738809 TCTGGCAGTT
*
738819 GGCACCAGTTGCAA
1 GGCACCAGTCGCAA
738833 GGCACCAGTCGCAA
1 GGCACCAGTCGCAA
738847 GG
1 GG
738849 GAAGGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.30, G:0.33, T:0.10
Consensus pattern (14 bp):
GGCACCAGTCGCAA
Found at i:739256 original size:44 final size:45
Alignment explanation
Indices: 739165--739310 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 45
739155 TTTTAAATTT
* *
739165 TTTAAAATTTATTTTCATATATTTATATTTTATAATTAATAAAAAA
1 TTTAAAAATTATTTTCA-ATATTAATATTTTATAATTAATAAAAAA
* **
739211 TTTAAAAATTATTTTC-ATATTAATA-TTTATATATTATTATTAAA
1 TTTAAAAATTATTTTCAATATTAATATTTTATA-ATTAATAAAAAA
* * *
739255 TTTAAATAAAAATATTTTTAATTATTAAATATTAATTTTAATTAAT-AAAAA
1 TTT--A-AAAATTATTTTCAA-TATT-AATATT--TTATAATTAATAAAAAA
739306 TTTAA
1 TTTAA
739311 TTTATTTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 6 0.08
44 20 0.25
46 16 0.20
47 10 0.13
48 2 0.03
49 5 0.06
50 4 0.05
51 7 0.09
52 5 0.06
53 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (45 bp):
TTTAAAAATTATTTTCAATATTAATATTTTATAATTAATAAAAAA
Found at i:739288 original size:36 final size:36
Alignment explanation
Indices: 739248--739345 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 36
739238 TATATATTAT
*
739248 TATTAAATTTAAATAAAAATATTTTTAA-TTA-TTAAA
1 TATTAAATTTAAATAAAAA-A-ATTTAATTTATTTAAA
* *
739284 TATTAATTTTAATTAATAAAAATTTAATTTATTTAAA
1 TATTAAATTTAAATAA-AAAAATTTAATTTATTTAAA
* *
739321 -ATTTAATTTAAATAAATTAAATTTA
1 TATTAAATTTAAATAAA-AAAATTTA
739346 TTAAATTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
35 6 0.12
36 37 0.73
37 8 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TATTAAATTTAAATAAAAAAATTTAATTTATTTAAA
Found at i:739295 original size:20 final size:21
Alignment explanation
Indices: 739270--739313 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
739260 ATAAAAATAT
* *
739270 TTTTAATTATTAAATA-TTAA
1 TTTTAATTAATAAAAATTTAA
739290 TTTTAATTAATAAAAATTTAA
1 TTTTAATTAATAAAAATTTAA
739311 TTT
1 TTT
739314 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAATTAATAAAAATTTAA
Found at i:739314 original size:20 final size:20
Alignment explanation
Indices: 739259--739331 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
739249 ATTAAATTTA
739259 AATAAAAATATT--TTTAATT
1 AATAAAAAT-TTAATTTAATT
* *
739278 ATTAAATA-TTAATTTTAATT
1 AATAAAAATTTAA-TTTAATT
739298 AATAAAAATTTAATTT-ATT
1 AATAAAAATTTAATTTAATT
739317 --T-AAAATTTAATTTAA
1 AATAAAAATTTAATTTAA
739332 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
16 12 0.27
17 4 0.09
19 9 0.20
20 16 0.36
21 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAAAAATTTAATTTAATT
Found at i:739336 original size:16 final size:16
Alignment explanation
Indices: 739302--739345 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
739292 TTAATTAATA
**
739302 AAAATTTAATTTATTT
1 AAAATTTAATTTAAAT
739318 AAAATTTAATTTAAAT
1 AAAATTTAATTTAAAT
*
739334 -AAATTAAATTTA
1 AAAATTTAATTTA
739346 TTAAATTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATTTAATTTAAAT
Found at i:740305 original size:7 final size:7
Alignment explanation
Indices: 740293--740319 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
740283 ATGTATCAAT
740293 AAATTTA
1 AAATTTA
740300 AAATTTA
1 AAATTTA
740307 AAATTTA
1 AAATTTA
740314 AAATTT
1 AAATTT
740320 TTTATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:740901 original size:3 final size:3
Alignment explanation
Indices: 740893--740943 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
740883 AAAATGAAGA
740893 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
740941 TAT
1 TAT
740944 CAGTTTTTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:741543 original size:22 final size:22
Alignment explanation
Indices: 741518--741570 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
741508 ATATTTTAAT
*
741518 AAATTATT-AATATATAAATATA
1 AAATT-TTAAATATATAAAAATA
*
741540 AAATTTTAAATATTTAAAAAT-
1 AAATTTTAAATATATAAAAATA
*
741561 AATTTTTAAA
1 AAATTTTAAA
741571 AAAATTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTTTAAATATATAAAAATA
Found at i:747547 original size:8 final size:8
Alignment explanation
Indices: 747526--747555 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
747516 TTTAATTTAA
747526 GCCCAAGT
1 GCCCAAGT
747534 GCCCCAAGT
1 G-CCCAAGT
747543 GCCCAAGT
1 GCCCAAGT
747551 GCCCA
1 GCCCA
747556 TCTTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.10
Consensus pattern (8 bp):
GCCCAAGT
Found at i:752425 original size:15 final size:14
Alignment explanation
Indices: 752407--752459 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
752397 TAAATAAATT
752407 ATATATACTTAAAAA
1 ATATATA-TTAAAAA
* *
752422 ATATATAATTTAAAT
1 ATATAT-ATTAAAAA
752437 ATATTATATTAAAAA
1 ATA-TATATTAAAAA
752452 ATA-ATATT
1 ATATATATT
752460 TAAGTAGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 5 0.16
15 23 0.72
16 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATATTAAAAA
Found at i:752987 original size:2 final size:2
Alignment explanation
Indices: 752980--753033 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
752970 AAGAAAGGAA
* ** **
752980 AT AT AT AT AT AT AT AT AT AT AT AT AC AT GC AT GC 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
753022 AT AT AT AT AT AT
1 AT AT AT AT AT AT
753034 GTAAAAGTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:753951 original size:2 final size:2
Alignment explanation
Indices: 753944--753981 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
753934 AGTCACATCA
753944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
753982 TTCTTCGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:754224 original size:2 final size:2
Alignment explanation
Indices: 754219--754258 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
754209 ATAAAAAACA
*
754219 AT AT AT GT 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
754259 TGCGAGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:754415 original size:23 final size:24
Alignment explanation
Indices: 754382--754431 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
754372 CTCTACTTTG
754382 ACACTCAAACAAATATCATTGTTC
1 ACACTCAAACAAATATCATTGTTC
754406 ACACT-AAACAAATATCATTGTTC
1 ACACTCAAACAAATATCATTGTTC
754429 ACA
1 ACA
754432 TTCTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (24 bp):
ACACTCAAACAAATATCATTGTTC
Found at i:762314 original size:44 final size:44
Alignment explanation
Indices: 762251--762336 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
762241 GTATCATTTT
* *
762251 TAAGATTATTATGGTGATTTAATTATTAGTAATCTTAAAGTAGA
1 TAAGATTATTATGGTGATTTAATCACTAGTAATCTTAAAGTAGA
* *
762295 TAAGATTATTAAT-GTGATTTAATCCCTAGTGATCTTAAAGTA
1 TAAGATTATT-ATGGTGATTTAATCACTAGTAATCTTAAAGTA
762337 CTATATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 35 0.95
45 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (44 bp):
TAAGATTATTATGGTGATTTAATCACTAGTAATCTTAAAGTAGA
Found at i:768489 original size:8 final size:8
Alignment explanation
Indices: 768461--768505 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
768451 TAATTAATGA
768461 AAATATTC
1 AAATATTC
768469 AAA-A-TC
1 AAATATTC
768475 AAAATATTC
1 -AAATATTC
768484 AAATATT-
1 AAATATTC
768491 AAATAATTC
1 AAAT-ATTC
768500 AAATAT
1 AAATAT
768506 GAAATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 2 0.06
7 8 0.25
8 16 0.50
9 6 0.19
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATATTC
Found at i:768494 original size:15 final size:15
Alignment explanation
Indices: 768460--768511 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
768450 ATAATTAATG
768460 AAAATATTCAAA-AT
1 AAAATATTCAAATAT
768474 CAAAATATTCAAATAT
1 -AAAATATTCAAATAT
*
768490 TAAATAATTCAAATAT
1 AAAAT-ATTCAAATAT
*
768506 GAAATA
1 AAAATA
768512 ATTTGAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 17 0.52
16 16 0.48
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAATATTCAAATAT
Found at i:768501 original size:16 final size:16
Alignment explanation
Indices: 768476--768514 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
768466 TTCAAAATCA
*
768476 AAAT-ATTCAAATATT
1 AAATAATTCAAATATG
768491 AAATAATTCAAATATG
1 AAATAATTCAAATATG
768507 AAATAATT
1 AAATAATT
768515 TGAATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATAATTCAAATATG
Found at i:771374 original size:26 final size:25
Alignment explanation
Indices: 771337--771398 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
771327 GATTATTATT
*
771337 TTTTAAA-TTTAATTTTAAAAT-ATA
1 TTTTAAATTTTAA-TGTAAAATAATA
771361 TTTTAAATTATTAATGTAAAATAATA
1 TTTTAAATT-TTAATGTAAAATAATA
771387 TTTTAATATTTT
1 TTTTAA-ATTTT
771399 TAAATAGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.21
25 8 0.24
26 15 0.45
27 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTAAATTTTAATGTAAAATAATA
Done.