Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_pilon, 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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 43
Found at i:2677177 original size:118 final size:117
Alignment explanation
Indices: 2676969--2677316 Score: 499
Period size: 117 Copynumber: 3.0 Consensus size: 117
2676959 GCGATGTCAG
* * * *
2676969 TCCACTTCATTCTGTGATGGAATC--ACCAAGGTTGTACAAGTTCTTCTCATTATGAACTT-TT-
1 TCCACCTCTTTCTGTGATGGAATCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
** *
2677030 TCCCTCGCCGAATGAGTTATTCTCATTATGAACTTTCCACTGGAAATGTTGA
66 TCCCTCGTTGAATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA
* *
2677082 TCCACCTCTTTCTGTGATGGAATCGAACAAAATGTTGAACAAGTTCTCCTCATTATGAACTTCTT
1 TCCACCTCTTTCTGTGATGGAATCGAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
* * *
2677147 CTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGA
65 CTCCCTCGTTGAATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA
*
2677200 TCCACCTCCTTT-TATGATGGAATCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
1 TCCACCT-CTTTCTGTGATGGAATCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
* * *
2677264 CTCCCTCGTTGTATGAGCTATTCTCATTATGAACTCTCCACTGAAAATGTTGA
65 CTCCCTCGTTGAATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA
2677317 GAAAAGGTTG
Statistics
Matches: 209, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
113 22 0.11
115 2 0.01
116 29 0.14
117 84 0.40
118 68 0.33
119 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (117 bp):
TCCACCTCTTTCTGTGATGGAATCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
TCCCTCGTTGAATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA
Found at i:2677334 original size:91 final size:91
Alignment explanation
Indices: 2677228--2677481 Score: 400
Period size: 91 Copynumber: 2.8 Consensus size: 91
2677218 GGAATCGAAC
* *
2677228 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGTATGAGCTATTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTA
*
2677293 TGAACTCTCCACTGAAAATGTTGAGA
66 TGAACTCTCCAATGAAAATGTTGAGA
* *
2677319 AAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCAATA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTA
* *
2677384 TGAACTCTCCAATGGAAATGTTGAGC
66 TGAACTCTCCAATGAAAATGTTGAGA
* *
2677410 CAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCCCCTCGTTGGATGAGTTATTCTCA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT---CCCTCGTTGGATGAGTTATTCTCA
2677475 TTATGAA
63 TTATGAA
2677482 TTTATTCTCC
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
91 119 0.80
94 30 0.20
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (91 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTA
TGAACTCTCCAATGAAAATGTTGAGA
Found at i:2677506 original size:41 final size:42
Alignment explanation
Indices: 2677422--2677522 Score: 177
Period size: 41 Copynumber: 2.4 Consensus size: 42
2677412 AGGTTGAACA
*
2677422 AGTTCTTCTCATTATGAATTTCTTCTCCCCCCTCGTTGGATG
1 AGTTCTTCTCATTATGAATTTATTCTCCCCCCTCGTTGGATG
*
2677464 AGTTATTCTCATTATGAATTTATTCT-CCCCCTCGTTGGATG
1 AGTTCTTCTCATTATGAATTTATTCTCCCCCCTCGTTGGATG
2677505 AGTTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
2677523 CTCTCTATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 32 0.57
42 24 0.43
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.44
Consensus pattern (42 bp):
AGTTCTTCTCATTATGAATTTATTCTCCCCCCTCGTTGGATG
Found at i:2678213 original size:21 final size:22
Alignment explanation
Indices: 2678159--2678213 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
2678149 ATTTATCATG
2678159 TGTATGAAATGAT-AAAATGTA
1 TGTATGAAATGATGAAAATGTA
2678180 TGT-TGCAAA-GATGAAAAT-TCA
1 TGTATG-AAATGATGAAAATGT-A
2678201 TGTATG-AATGATG
1 TGTATGAAATGATG
2678214 GTTTTCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
20 8 0.28
21 19 0.66
22 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.33
Consensus pattern (22 bp):
TGTATGAAATGATGAAAATGTA
Found at i:2678600 original size:59 final size:54
Alignment explanation
Indices: 2678416--2678605 Score: 192
Period size: 51 Copynumber: 3.5 Consensus size: 54
2678406 AGATACCTTT
* * * *
2678416 AAAATTAGGCTTAGCTTCTTTCAAAAATTCATTTAAAAACATCAAGAAACCCCTA
1 AAAATCAGGCTTAGTTTCTTTTAAAAATTCA-TTGAAAACATCAAGAAACCCCTA
* *
2678471 AAAACCAGGCTTAGTTTC---TAAATA-TCATTTGAAAACATCAAGAAACCCCTA
1 AAAATCAGGCTTAGTTTCTTTTAAAAATTCA-TTGAAAACATCAAGAAACCCCTA
* ** *
2678522 AAAATTAGGCTTAAATTCTTTTAAGAAATTCATTGAGAATCATCATCAAGAAACCCCTG
1 AAAATCAGGCTTAGTTTCTTTTAA-AAATTCATTGA-AA--A-CATCAAGAAACCCCTA
2678581 AAAATCAGGCTTAGTTTC-TTTAAAA
1 AAAATCAGGCTTAGTTTCTTTTAAAA
2678606 TCTTTCTTTT
Statistics
Matches: 111, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
51 40 0.36
52 4 0.04
54 3 0.03
55 21 0.19
56 5 0.05
57 2 0.02
58 6 0.05
59 30 0.27
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (54 bp):
AAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGAAAACATCAAGAAACCCCTA
Found at i:2679936 original size:15 final size:16
Alignment explanation
Indices: 2679913--2679945 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2679903 TTTGGTTGGC
*
2679913 TTCTTGTGTTC-TTGA
1 TTCTGGTGTTCATTGA
2679928 TTCTGGTGTTCATTGA
1 TTCTGGTGTTCATTGA
2679944 TT
1 TT
2679946 TGATGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TTCTGGTGTTCATTGA
Found at i:2680594 original size:9 final size:9
Alignment explanation
Indices: 2680582--2680637 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
2680572 ATTTGATTGA
*
2680582 TTTTCTTTC
1 TTTTTTTTC
2680591 TTTTTTTTC
1 TTTTTTTTC
* *
2680600 TGTTTTTCTA
1 T-TTTTTTTC
2680610 TTTTTTTTC
1 TTTTTTTTC
2680619 TTTTTTATGTC
1 TTTTTT-T-TC
2680630 TTTTTTTT
1 TTTTTTTT
2680638 GCTATATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 22 0.56
10 9 0.23
11 8 0.21
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2680616 original size:11 final size:10
Alignment explanation
Indices: 2680582--2680637 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 10
2680572 ATTTGATTGA
2680582 TTTTCTTTCTT
1 TTTTCTTT-TT
*
2680593 TTTT-TTCTGT
1 TTTTCTT-TTT
2680603 TTTTCTATTTT
1 TTTTCT-TTTT
2680614 TTTTCTTTTT
1 TTTTCTTTTT
*
2680624 TATGTCTTTTT
1 T-TTTCTTTTT
2680635 TTT
1 TTT
2680638 GCTATATCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 13 0.35
11 23 0.62
12 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:2680633 original size:19 final size:19
Alignment explanation
Indices: 2680591--2680636 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2680581 ATTTTCTTTC
*
2680591 TTTTTTTTCTGTTTTTCTA
1 TTTTTTTTCTGTTTTTATA
*
2680610 TTTTTTTTCT-TTTTTATG
1 TTTTTTTTCTGTTTTTATA
2680628 TCTTTTTTT
1 T-TTTTTTT
2680637 TGCTATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (19 bp):
TTTTTTTTCTGTTTTTATA
Found at i:2680633 original size:28 final size:28
Alignment explanation
Indices: 2680581--2680634 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2680571 TATTTGATTG
* *
2680581 ATTTTCTTTCTTTTTTTTCTGTTTTTCT
1 ATTTTCTTTCTTTTTTATCTCTTTTTCT
* *
2680609 ATTTTTTTTCTTTTTTATGTCTTTTT
1 ATTTTCTTTCTTTTTTATCTCTTTTT
2680635 TTTGCTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.80
Consensus pattern (28 bp):
ATTTTCTTTCTTTTTTATCTCTTTTTCT
Found at i:2684710 original size:51 final size:51
Alignment explanation
Indices: 2684649--2684762 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 51
2684639 AAAATAAGAA
* * *
2684649 TGGCCAAAATGCAAGAAAATAAAGGT-TAGTAGCTAAATCAGAAA-TAAATAG
1 TGGCCAAAATGCAA-AAAATAAA-ATATAGTAGCTAAATCAAAAATTAAAAAG
*
2684700 TGGCCAAAATGCAAAAATTAAAATACTAGTAGCTAAATCAAAAATTAAAAAG
1 TGGCCAAAATGCAAAAAATAAAATA-TAGTAGCTAAATCAAAAATTAAAAAG
* *
2684752 TGACTAAAATG
1 TGGCCAAAATG
2684763 AATAAATTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 1 0.02
50 7 0.13
51 31 0.57
52 15 0.28
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.21
Consensus pattern (51 bp):
TGGCCAAAATGCAAAAAATAAAATATAGTAGCTAAATCAAAAATTAAAAAG
Found at i:2690665 original size:19 final size:19
Alignment explanation
Indices: 2690641--2690690 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2690631 TAATTTGAGA
***
2690641 AAAATCAATTTAGTTTTTT
1 AAAATCAATTTACAGTTTT
2690660 AAAATCAATTTACAGTTTT
1 AAAATCAATTTACAGTTTT
2690679 AAAATCAATTTA
1 AAAATCAATTTA
2690691 ATTGATTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (19 bp):
AAAATCAATTTACAGTTTT
Found at i:2697120 original size:16 final size:16
Alignment explanation
Indices: 2697099--2697137 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2697089 AATTTAGTGA
2697099 AACCGAAAGTAACACG
1 AACCGAAAGTAACACG
* *
2697115 AACCGAAATTAACCCG
1 AACCGAAAGTAACACG
2697131 AACCGAA
1 AACCGAA
2697138 TTTTAACCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.08
Consensus pattern (16 bp):
AACCGAAAGTAACACG
Found at i:2697186 original size:32 final size:32
Alignment explanation
Indices: 2697128--2697190 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2697118 CGAAATTAAC
**
2697128 CCGAACCGAATTTTAACCCATTTGAAAGCAAA
1 CCGAACCGAATTTTAACCCACATGAAAGCAAA
*
2697160 CCGAACTGAA-TTTAACCCGACATGAAAGCAA
1 CCGAACCGAATTTTAACCC-ACATGAAAGCAA
2697191 CCAGAACAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.19
Consensus pattern (32 bp):
CCGAACCGAATTTTAACCCACATGAAAGCAAA
Found at i:2697970 original size:32 final size:32
Alignment explanation
Indices: 2697907--2697983 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
2697897 GACTCGACCT
*
2697907 AATATTGACCCGACCCAAAATATAACAGATCC
1 AATATTGACCCGAACCAAAATATAACAGATCC
* *
2697939 GATATTGACCTGAACCAAAA-ATCAATC-GATCC
1 AATATTGACCCGAACCAAAATAT-AA-CAGATCC
*
2697971 AATATTGATCCGA
1 AATATTGACCCGA
2697984 GCCGAAAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 2 0.05
32 34 0.92
33 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.22
Consensus pattern (32 bp):
AATATTGACCCGAACCAAAATATAACAGATCC
Found at i:2698002 original size:32 final size:29
Alignment explanation
Indices: 2697907--2698002 Score: 68
Period size: 32 Copynumber: 3.0 Consensus size: 29
2697897 GACTCGACCT
* *
2697907 AATATTGACCCGACCCAAAATATAACAGATCC
1 AATATTGA-CCGA-CCAAAA-ACAACTGATCC
*
2697939 GATATTGACCTGAACCAAAAATCAA-TCGATCC
1 AATATTGACC-G-ACCAAAAA-CAACT-GATCC
2697971 AATATTGATCCGAGCCGAAAAACAACTGATCC
1 AATATTGA-CCGA-CC-AAAAACAACTGATCC
2698003 GATAATCACC
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
31 4 0.08
32 39 0.75
33 9 0.17
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (29 bp):
AATATTGACCGACCAAAAACAACTGATCC
Found at i:2700252 original size:148 final size:148
Alignment explanation
Indices: 2700070--2700364 Score: 536
Period size: 148 Copynumber: 2.0 Consensus size: 148
2700060 AAATACTCAA
*
2700070 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTT
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
* * * *
2700135 GAATTGAATTGAATTTTTGAGTTTTTGTTTAAATTTAATTATAAATATTTATTATATTATAATAT
66 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
2700200 TATTTGATTCTAATTTAG
131 TATTTGATTCTAATTTAG
*
2700218 TTCAGTTTATAAAATAGTTTACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
2700283 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
66 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
2700348 TATTTGATTCTAATTTA
131 TATTTGATTCTAATTTA
2700365 AATAGTTTTT
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 141 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (148 bp):
TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTTAG
Found at i:2700880 original size:34 final size:34
Alignment explanation
Indices: 2700841--2700934 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 34
2700831 ATTGATTATG
** *
2700841 AATTTGGGGTTGGGCATGTAATTGAGTATTTTAA
1 AATTTGGGGTTTAGAATGTAATTGAGTATTTTAA
* **
2700875 AATTTGAGGTTTAGAATGTAATTGAAGTATTTTGG
1 AATTTGGGGTTTAGAATGTAATTG-AGTATTTTAA
2700910 AATTTGGGGTTTAGAATGTAATTGA
1 AATTTGGGGTTTAGAATGTAATTGA
2700935 TGATTATGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
34 21 0.40
35 31 0.60
ACGTcount: A:0.30, C:0.01, G:0.28, T:0.41
Consensus pattern (34 bp):
AATTTGGGGTTTAGAATGTAATTGAGTATTTTAA
Found at i:2704878 original size:21 final size:21
Alignment explanation
Indices: 2704852--2705009 Score: 80
Period size: 21 Copynumber: 7.9 Consensus size: 21
2704842 ATATAGAATT
2704852 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
* * *
2704873 TGTCCCAAATGACCACATAGA
1 TGTCCCGAAGGACCACATATA
*
2704894 TTTCCCGAAGGACCAC-----
1 TGTCCCGAAGGACCACATATA
** *
2704910 --TCCTTAAGGATCACATATA
1 TGTCCCGAAGGACCACATATA
* * * *
2704929 TATTCCAAAGGA-CAAATATA
1 TGTCCCGAAGGACCACATATA
* * *
2704949 TGTCCCGAAGAACCATATAAA
1 TGTCCCGAAGGACCACATATA
* * * **
2704970 TGTTCCAAATGATTACATATA
1 TGTCCCGAAGGACCACATATA
*
2704991 TATCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
2705010 GTACCCTCGA
Statistics
Matches: 96, Mismatches: 33, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
14 11 0.11
20 15 0.16
21 70 0.73
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:2709355 original size:15 final size:14
Alignment explanation
Indices: 2709334--2709367 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2709324 CATGGAGTCT
2709334 CATATCTCATTATCA
1 CATATCTCA-TATCA
*
2709349 TATATCTCATATCA
1 CATATCTCATATCA
2709363 CATAT
1 CATAT
2709368 TCTTGTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (14 bp):
CATATCTCATATCA
Found at i:2713552 original size:26 final size:26
Alignment explanation
Indices: 2713523--2713576 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2713513 ATCGAAGTAT
2713523 TAATACACATAAGGTCGTGCCCGCCA
1 TAATACACATAAGGTCGTGCCCGCCA
* * *
2713549 TAATACACATAAGTTTGTGCCCTCCA
1 TAATACACATAAGGTCGTGCCCGCCA
2713575 TA
1 TA
2713577 TGCATTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCGCCA
Found at i:2714672 original size:21 final size:22
Alignment explanation
Indices: 2714648--2714693 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
2714638 AGGGTATTGA
2714648 TACTTC-TATAGGGAGTATCAG
1 TACTTCATATAGGGAGTATCAG
*
2714669 TAC-TCATATAGGGAGTATCGG
1 TACTTCATATAGGGAGTATCAG
2714690 TACT
1 TACT
2714694 ACCTTTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (22 bp):
TACTTCATATAGGGAGTATCAG
Found at i:2720559 original size:23 final size:22
Alignment explanation
Indices: 2720526--2720587 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
2720516 TTTGGTGCAG
*
2720526 AGGGAATCGATACCCCCGTTCAA
1 AGGGAACCGAT-CCCCCGTTCAA
* * *
2720549 AGGGAACCGATTCCCCTTTGAA
1 AGGGAACCGATCCCCCGTTCAA
*
2720571 GGGGAACCGATTCCCCC
1 AGGGAACCGA-TCCCCC
2720588 CCACAGGGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (22 bp):
AGGGAACCGATCCCCCGTTCAA
Found at i:2727065 original size:11 final size:11
Alignment explanation
Indices: 2727049--2727084 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2727039 AAAGAATGTT
2727049 AAATTAAAAAA
1 AAATTAAAAAA
2727060 AAATTAAAAAA
1 AAATTAAAAAA
*
2727071 ATATTAAATAAA
1 AAATTAAA-AAA
2727083 AA
1 AA
2727085 GAGGAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:2728535 original size:26 final size:26
Alignment explanation
Indices: 2728502--2728685 Score: 153
Period size: 26 Copynumber: 7.1 Consensus size: 26
2728492 TTCAAAAATG
*
2728502 TTTT-AAAACTATATATTATATATGT
1 TTTTAAAAACTATATATTATATATAT
2728527 TTTTAAAAACTATATATTATATATAT
1 TTTTAAAAACTATATATTATATATAT
* * * *
2728553 GTTTTGAAAATTATATAATATATATGT
1 -TTTTAAAAACTATATATTATATATAT
* *
2728580 TTTCAAAACCTATATATTATATATAT
1 TTTTAAAAACTATATATTATATATAT
* * * *
2728606 ATATATATA-TATATATATATATATAT
1 TTTTAAAAACTATATAT-TATATATAT
* * * * *
2728632 ATATATATA-TATATATT-TA-AAAT
1 TTTTAAAAACTATATATTATATATAT
2728655 GTTTTCAAAAACTATATATTATATATAT
1 -TTTT-AAAAACTATATATTATATATAT
2728683 TTT
1 TTT
2728686 CAGAAATGTT
Statistics
Matches: 128, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.02
24 4 0.03
25 15 0.12
26 76 0.59
27 27 0.21
28 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (26 bp):
TTTTAAAAACTATATATTATATATAT
Found at i:2728575 original size:53 final size:52
Alignment explanation
Indices: 2728499--2728605 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 52
2728489 GCTTTCAAAA
* *
2728499 ATGTTTTAAAACTATATATTATATATGTTTTTAAAAACTATATATTATATAT
1 ATGTTTTAAAACTATATAATATATATGTTTTCAAAAACTATATATTATATAT
* *
2728551 ATGTTTTGAAAATTATATAATATATATGTTTTCAAAACCTATATATTATATAT
1 ATGTTTT-AAAACTATATAATATATATGTTTTCAAAAACTATATATTATATAT
2728604 AT
1 AT
2728606 ATATATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 7 0.14
53 43 0.86
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (52 bp):
ATGTTTTAAAACTATATAATATATATGTTTTCAAAAACTATATATTATATAT
Found at i:2728595 original size:2 final size:2
Alignment explanation
Indices: 2728590--2728647 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
2728580 TTTCAAAACC
2728590 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2728631 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2728648 TTAAAATGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2728621 original size:53 final size:53
Alignment explanation
Indices: 2728506--2728633 Score: 150
Period size: 53 Copynumber: 2.4 Consensus size: 53
2728496 AAAATGTTTT
* * * * *
2728506 AAAACTATATATTATATATGTTTTTAAAAACTATATATTATATATATGTTTTG
1 AAAATTATATAATATATATGTTTTCAAAAACTATATATTATATATATATTATG
*
2728559 AAAATTATATAATATATATGTTTTCAAAACCTATATATTATATATATATATAT-
1 AAAATTATATAATATATATGTTTTCAAAAACTATATATTATATATATAT-TATG
*
2728612 ATATATATATATATATATATAT
1 A-AAAT-TATATA-ATATATAT
2728634 ATATATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 45 0.70
54 5 0.08
55 6 0.09
56 8 0.12
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (53 bp):
AAAATTATATAATATATATGTTTTCAAAAACTATATATTATATATATATTATG
Found at i:2728627 original size:77 final size:78
Alignment explanation
Indices: 2728496--2728682 Score: 197
Period size: 77 Copynumber: 2.4 Consensus size: 78
2728486 ATAGCTTTCA
* * * * *
2728496 AAAATGTTTT-AAAACTATATATTATATATGTTTTTAAAAACTATATATTATATATATGTTTTGA
1 AAAATGTTTTCAAAACTATATATTATATATATATATAAAAACTATATATTATATATAT-ATAT-A
2728560 AA-AT-TATATA-AT
64 AATATATATATATAT
* * *
2728572 ATATATGTTTTCAAAACCTATATATTATATATATATATATATA-TATATA-TATATATATATATA
1 A-AAATGTTTTCAAAA-CTATATATTATATATATATATAAAAACTATATATTATATATATATATA
* *
2728635 TATATATATATATTT
64 AATATATATATATAT
2728650 AAAATGTTTTCAAAAACTATATATTATATATAT
1 AAAATGTTTTC-AAAACTATATATTATATATAT
2728683 TTTCAGAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
75 2 0.02
76 5 0.05
77 49 0.53
78 16 0.17
79 21 0.23
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (78 bp):
AAAATGTTTTCAAAACTATATATTATATATATATATAAAAACTATATATTATATATATATATAAA
TATATATATATAT
Found at i:2728671 original size:34 final size:37
Alignment explanation
Indices: 2728629--2728899 Score: 283
Period size: 36 Copynumber: 7.3 Consensus size: 37
2728619 TATATATATA
2728629 TATATATATATATATATATTT-AAAATGTTTTCAAAAAC
1 TATATAT-TATATATAT-TTTCAAAATGTTTTCAAAAAC
2728667 TATATATTATATATATTTTCAGAAATGTTTT-AAAAA-
1 TATATATTATATATATTTTCA-AAATGTTTTCAAAAAC
* * * *
2728703 TATCTATTATATTTGTTTTCAAAATGTTTTAAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
2728740 TATATATTATATATATGTTTTCAAAATGTTTTC-AAAAC
1 TATATATTATATATA--TTTTCAAAATGTTTTCAAAAAC
2728778 TATATA--ATATATATTTTCAAAATGTTTTC-AAAAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
* *** *
2728812 TATATAATATATATATTTTCGAAAACCAATTTCTAAAAAT
1 TATATATTATATATATTTTC-AAAA-TGTTTTC-AAAAAC
* *
2728852 TATATATTATAT-T-TTTTCAAAAAATATTTTCAAAAAA
1 TATATATTATATATATTTTC--AAAATGTTTTCAAAAAC
2728889 T-TATATTATAT
1 TATATATTATAT
2728900 TAATACATAT
Statistics
Matches: 204, Mismatches: 16, Indels: 28
0.82 0.06 0.11
Matches are distributed among these distances:
34 27 0.13
35 9 0.04
36 55 0.27
37 37 0.18
38 41 0.20
39 20 0.10
40 15 0.07
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:2728738 original size:73 final size:71
Alignment explanation
Indices: 2728630--2728835 Score: 258
Period size: 73 Copynumber: 2.8 Consensus size: 71
2728620 ATATATATAT
2728630 ATATATATATATATATATTT-AAAATGTTTTCAAAAACTATATATTATATATATTTTCAGAAATG
1 ATATATA-ATATATAT-TTTCAAAATGTTTT-AAAAACTATATATTATATATATTTTCAGAAATG
2728694 TTTT-AAAA
63 TTTTCAAAA
* * *
2728702 ATATCTATTATATTTGTTTTCAAAATGTTTTAAAAAACTATATATTATATATATGTTTTCA-AAA
1 ATA--TATAATATATATTTTCAAAATGTTTT-AAAAACTATATATTATATATA--TTTTCAGAAA
2728766 TGTTTTCAAAA
61 TGTTTTCAAAA
* * *
2728777 CTATATAATATATATTTTCAAAATGTTTTCAAAACTATATAATATATATATTTTC-GAAA
1 ATATATAATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAGAAA
2728836 ACCAATTTCT
Statistics
Matches: 117, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
70 8 0.07
72 25 0.21
73 60 0.51
74 12 0.10
75 12 0.10
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (71 bp):
ATATATAATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAGAAATGTTT
TCAAAA
Found at i:2728863 original size:38 final size:40
Alignment explanation
Indices: 2728807--2728899 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 40
2728797 AAATGTTTTC
* * * *
2728807 AAAACTATATAATATATATATTTTCGAAAACCAATTTCTA
1 AAAATTATATAATATATATATTTTCAAAAAACAATTTCAA
* * *
2728847 AAAATTATAT-AT-TATATTTTTTCAAAAAATATTTTCAA
1 AAAATTATATAATATATATATTTTCAAAAAACAATTTCAA
*
2728885 AAAATTATATTATAT
1 AAAATTATATAATAT
2728900 TAATACATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 30 0.68
39 4 0.09
40 10 0.23
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (40 bp):
AAAATTATATAATATATATATTTTCAAAAAACAATTTCAA
Found at i:2728883 original size:13 final size:13
Alignment explanation
Indices: 2728865--2728889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2728855 ATATTATATT
2728865 TTTTCAAAAAATA
1 TTTTCAAAAAATA
2728878 TTTTCAAAAAAT
1 TTTTCAAAAAAT
2728890 TATATTATAT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAAATA
Found at i:2729605 original size:85 final size:84
Alignment explanation
Indices: 2729462--2729933 Score: 613
Period size: 85 Copynumber: 5.6 Consensus size: 84
2729452 ATCGACAGTC
* * ** * *
2729462 TTTGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGCTACAAATTTGACATGCCCTTGAGTTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGTTGAA
*
2729527 TGGAATCGAACTCGAAGGT
66 TGTAATCGAACTCGAAGGT
* * * * *
2729546 ATTTGTTGACAGATAACCATTATCGCCTTGAGTTATGCTGTAAATTGGATATGTCCTTGAGCTGA
1 -TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGTTGA
* *
2729611 ATGAAATCGAACTCAAAGGTT
65 ATGTAATCGAACTCGAAGG-T
* * * * * *
2729632 TTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTCGATATGTCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGTTGAA
*
2729697 TGTAATCAAACTCGAAGGTT
66 TGTAATCGAACTCGAAGG-T
* * *
2729717 TTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATATCCTTGAGTTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGTTGAA
2729782 TGTAATCGAACTCGAAGGT
66 TGTAATCGAACTCGAAGGT
* * *
2729801 TTTGGTTGACAGATAACCCTTCCCGCCTTGAACTATACTGTAAATTTGATATG-CCTTTGAGTTG
1 TTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCC-TTGAGTTG
*
2729865 AATGTAATCAAACTCGAAGGT
64 AATGTAATCGAACTCGAAGGT
* *
2729886 TTTGGTTGACATATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTG
1 TTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
2729934 CTGGGAGATA
Statistics
Matches: 340, Mismatches: 44, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
84 6 0.02
85 333 0.98
86 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (84 bp):
TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGTTGAA
TGTAATCGAACTCGAAGGT
Found at i:2729913 original size:255 final size:255
Alignment explanation
Indices: 2729462--2729931 Score: 683
Period size: 255 Copynumber: 1.8 Consensus size: 255
2729452 ATCGACAGTC
* * * *
2729462 TTTGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGCTACAAATTTGACATGCCCTTGAGTTGAA
1 TTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTACAAATTTGACATACCCTTGAGTTGAA
* ** *
2729527 TGGAATCGAACTCGAAGGTATTTGTTGACAGATAACCATTATCGCCTTGAGTTATGCTGTAAATT
66 TGGAATCGAACTCGAAGGTATTTGTTGACAGATAACCATTACCGCCTTGAACTATACTGTAAATT
* *
2729592 GGATATGTCCTTGAGCTGAATGAAATCGAACTCAAAGGTTTTTATTGACAGATAACCCTTCTCGC
131 GGATATGTCCTTGAGCTGAATGAAATCAAACTCAAAGGTTTTGATTGACAGATAACCCTTCTCGC
2729657 CTTGAGTTATGCTATAAATTCGATATGTCTTTGAGCTGAATGTAATCAAACTCGAAGGTT
196 CTTGAGTTATGCTATAAATTCGATATGTCTTTGAGCTGAATGTAATCAAACTCGAAGGTT
* ** * *
2729717 TTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATATCCTTGAGTTGAA
1 TTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTACAAATTTGACATACCCTTGAGTTGAA
* * *
2729782 TGTAATCGAACTCGAAGGT-TTTGGTTGACAGATAACCCTTCCCGCCTTGAACTATACTGTAAAT
66 TGGAATCGAACTCGAAGGTATTT-GTTGACAGATAACCATTACCGCCTTGAACTATACTGTAAAT
* * * * * *
2729846 TTGATATG-CCTTTGAGTTGAATGTAATCAAACTCGAAGGTTTTGGTTGACATATAACCCTTCTC
130 TGGATATGTCC-TTGAGCTGAATGAAATCAAACTCAAAGGTTTTGATTGACAGATAACCCTTCTC
*
2729910 GCCTTGAGTTATGCTGTAAATT
194 GCCTTGAGTTATGCTATAAATT
2729932 TGCTGGGAGA
Statistics
Matches: 188, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
254 5 0.03
255 183 0.97
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (255 bp):
TTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTACAAATTTGACATACCCTTGAGTTGAA
TGGAATCGAACTCGAAGGTATTTGTTGACAGATAACCATTACCGCCTTGAACTATACTGTAAATT
GGATATGTCCTTGAGCTGAATGAAATCAAACTCAAAGGTTTTGATTGACAGATAACCCTTCTCGC
CTTGAGTTATGCTATAAATTCGATATGTCTTTGAGCTGAATGTAATCAAACTCGAAGGTT
Found at i:2735307 original size:12 final size:12
Alignment explanation
Indices: 2735290--2735319 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2735280 TTAATCGCAA
*
2735290 AAATTAAAATTT
1 AAATTAAAACTT
2735302 AAATTAAAACTT
1 AAATTAAAACTT
2735314 AAATTA
1 AAATTA
2735320 CCCAATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAAACTT
Found at i:2735426 original size:23 final size:23
Alignment explanation
Indices: 2735373--2735427 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2735363 GAAAAAGTCA
* *
2735373 AAAAATAATGTTAAATAAAAAAAT
1 AAAAA-AATATTAAATAAAAAAAG
*
2735397 AAAAAAATATTAAATAAAAAGAG
1 AAAAAAATATTAAATAAAAAAAG
2735420 AAGAAAAA
1 AA-AAAAA
2735428 GGCTAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (23 bp):
AAAAAAATATTAAATAAAAAAAG
Found at i:2735526 original size:18 final size:17
Alignment explanation
Indices: 2735497--2735559 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
2735487 AGTGAAAATG
2735497 AAAT-AATAAAAAAGAA
1 AAATAAATAAAAAAGAA
* *
2735513 AAATGAATTAAAAAATAA
1 AAAT-AAATAAAAAAGAA
* *
2735531 TAATAAATAAAAAGGAA
1 AAATAAATAAAAAAGAA
2735548 AAATAAA-AAAAA
1 AAATAAATAAAAA
2735560 TAACAGAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 9 0.24
17 16 0.42
18 13 0.34
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (17 bp):
AAATAAATAAAAAAGAA
Found at i:2736627 original size:21 final size:23
Alignment explanation
Indices: 2736602--2736651 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 23
2736592 GGTCCGAATG
*
2736602 AAAAACAAAAAGA-AT-TAATAA
1 AAAAACAAAAAAACATATAATAA
2736623 AAAAACAAAAAAACATATAATAA
1 AAAAACAAAAAAACATATAATAA
2736646 ATAAAA
1 A-AAAA
2736652 ATAAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 7 0.28
24 4 0.16
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (23 bp):
AAAAACAAAAAAACATATAATAA
Found at i:2736735 original size:26 final size:25
Alignment explanation
Indices: 2736706--2736756 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2736696 TATAAAACTA
2736706 TATATTATAAAAAATGTTTTCAAAAC
1 TATATTAT-AAAAATGTTTTCAAAAC
* *
2736732 TATATTATATATATGTTTTCAAAAC
1 TATATTATAAAAATGTTTTCAAAAC
2736757 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (25 bp):
TATATTATAAAAATGTTTTCAAAAC
Found at i:2736767 original size:36 final size:36
Alignment explanation
Indices: 2736716--2736943 Score: 190
Period size: 36 Copynumber: 5.8 Consensus size: 36
2736706 TATATTATAA
*
2736716 AAAATGTTTTCAAAACTATATTATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATTATATATATGTTTTC
* * *
2736752 AAAACGTTTTAAAAACAATATAATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATTATATATATGTTTTC
* *
2736788 AAAAATGTTTTAAAAAACTATATATTATATATATATATATATATATTT
1 -AAAATGTTTT-AAAAAC-------TATAT-TATATATATGT-T-TTC
*
2736836 AAAATGTTTTCAAAAACTATATTATATATATATATATATTC
1 AAAATGTTTT-AAAAACTATA-T-TATATATATGT-T-TTC
*
2736877 AAAAATGTTTT-AAAATTATA-TATTATATATGTTTTC
1 -AAAATGTTTTAAAAACTATATTA-TATATATGTTTTC
2736913 AAAATGTTTTTAAAAACTATATTATATATAT
1 AAAATG-TTTTAAAAACTATATTATATATAT
2736944 ATATATATAT
Statistics
Matches: 160, Mismatches: 14, Indels: 35
0.77 0.07 0.17
Matches are distributed among these distances:
35 6 0.04
36 39 0.24
37 27 0.17
38 16 0.10
40 12 0.08
41 18 0.11
42 10 0.06
45 4 0.03
46 9 0.06
47 17 0.11
48 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATTATATATATGTTTTC
Found at i:2736843 original size:47 final size:46
Alignment explanation
Indices: 2736789--2736990 Score: 172
Period size: 45 Copynumber: 4.7 Consensus size: 46
2736779 TATGTTTTCA
2736789 AAAATGTTTTAAAAAACTATATATTATATATATATATATATAT-ATTT
1 AAAATGTTTT-AAAAACTATATATTATATATATATATATAT-TCATTT
2736836 AAAATGTTTTCAAAAAC--TATATTATATATATATATATATTCA---
1 AAAATGTTTT-AAAAACTATATATTATATATATATATATATTCATTT
*
2736878 AAAATGTTTT-AAAA-T-TATA-TAT-TATATATGT-T-TTC----
1 AAAATGTTTTAAAAACTATATATTATATATATATATATATTCATTT
2736913 AAAATGTTTTTAAAAACTATATTATATATATATATATATATATGT--TTT
1 AAAATG-TTTTAAAAACTATA-TAT-TATATATATATATATAT-TCATTT
* * *
2736961 CAAATGTTTTCAAAACTATATAATATATAT
1 AAAATGTTTTAAAAACTATATATTATATAT
2736991 TTAAAATGTT
Statistics
Matches: 133, Mismatches: 6, Indels: 34
0.77 0.03 0.20
Matches are distributed among these distances:
35 6 0.05
36 7 0.05
37 5 0.04
38 9 0.07
39 5 0.04
40 10 0.08
42 13 0.10
43 8 0.06
44 2 0.02
45 31 0.23
46 3 0.02
47 29 0.22
48 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (46 bp):
AAAATGTTTTAAAAACTATATATTATATATATATATATATTCATTT
Found at i:2736917 original size:77 final size:75
Alignment explanation
Indices: 2736817--2737107 Score: 251
Period size: 77 Copynumber: 3.8 Consensus size: 75
2736807 ATATATTATA
*
2736817 TATATATATATATATATTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTCAAAAA
1 TATATAT-TATATATTTTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTCAAAAA
2736882 TGTTTTAAAAT
65 TGTTTTAAAAT
*
2736893 TATATATTATATATGTTTTCAAAATGTTTTTAAAAACTATATTATATATATATATATATAT-ATG
1 TATATATTATATAT-TTTT-AAAATGTTTTCAAAAACTATATTATATATATATATATAT-TCA--
* *
2736957 TTTTCAAATGTTTTCAAAAC
61 ----AAAATGTTTT-AAAAT
*
2736977 TATATA--ATATATATTTAAAATGTTTTC-AAAACTATA-TA-ATATATATAT-T-TTCGAAAAC
1 TATATATTATATATTTTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTC-AAAA-
*
2737035 CACT-TTCTAAAAAT
64 -A-TGTT-TTAAAAT
* * * *
2737049 TATATATTATAT-TTTTTCAAAAAATATTTTTAAAAATTATACTATATATATATATATAT
1 TATATATTATATATTTTT---AAAATGTTTTCAAAAACTATATTATATATATATATATAT
2737108 ATATAATATA
Statistics
Matches: 176, Mismatches: 13, Indels: 47
0.75 0.06 0.20
Matches are distributed among these distances:
70 2 0.01
72 13 0.07
73 6 0.03
74 5 0.03
75 8 0.05
76 21 0.12
77 57 0.32
78 5 0.03
79 19 0.11
80 11 0.06
81 4 0.02
82 6 0.03
83 9 0.05
84 10 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (75 bp):
TATATATTATATATTTTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTCAAAAAT
GTTTTAAAAT
Found at i:2736998 original size:32 final size:32
Alignment explanation
Indices: 2736943--2737022 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 32
2736933 ATTATATATA
* *
2736943 TATATATATATATGTTTTCAAATGTTTTCAAAAC
1 TATATA-ATATAT-ATTTAAAATGTTTTCAAAAC
2736977 TATATAATATATATTTAAAATGTTTTCAAAAC
1 TATATAATATATATTTAAAATGTTTTCAAAAC
2737009 TATATAATATATAT
1 TATATAATATATAT
2737023 ATTTTCGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 32 0.73
33 6 0.14
34 6 0.14
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATAATATATATTTAAAATGTTTTCAAAAC
Found at i:2737019 original size:79 final size:76
Alignment explanation
Indices: 2736819--2737024 Score: 242
Period size: 81 Copynumber: 2.7 Consensus size: 76
2736809 ATATTATATA
2736819 TATATATATATATATTTAAAATGTTTTCAAAA--ACTATAT-TATATATATATATATATTCAAAA
1 TATATATATATATATTTAAAATGTTTTCAAAACTA-TATATATATATATATATATATATTCAAAA
*
2736881 ATGTTTTAAAAT
65 ATGTTTTAAAAC
* *
2736893 TATATATTATATATGTTTTCAAAATGTTTTTAAAAACTATATTATATATATATATATATATATGT
1 TATATA-TATATAT-ATTT-AAAATG-TTTTCAAAACTATA-TATATATATATATATATATA--T
***
2736958 TTTCAAATGTTTTCAAAAC
59 TCAAAAATGTTTT-AAAAC
2736977 TATATA-ATATATATTTAAAATGTTTTCAAAACTATATA-ATATATATAT
1 TATATATATATATATTTAAAATGTTTTCAAAACTATATATATATATATAT
2737025 TTTCGAAAAC
Statistics
Matches: 113, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
74 6 0.05
75 7 0.06
76 3 0.03
77 16 0.14
78 10 0.09
79 15 0.13
80 10 0.09
81 19 0.17
82 6 0.05
83 11 0.10
84 10 0.09
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (76 bp):
TATATATATATATATTTAAAATGTTTTCAAAACTATATATATATATATATATATATATTCAAAAA
TGTTTTAAAAC
Found at i:2737048 original size:156 final size:157
Alignment explanation
Indices: 2736819--2737111 Score: 422
Period size: 156 Copynumber: 1.9 Consensus size: 157
2736809 ATATTATATA
2736819 TATATATATATATATTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTCAAAAATG
1 TATATATATATATATTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTCAAAAATG
* * *
2736884 TTTTAAAATTATATATTATATATGTTTTC-AAAATGTTTTTAAAAACTATATTATATATATATAT
66 TTTAAAAATTATATATTATAT-T-TTTTCAAAAATATTTTTAAAAACTATACTATATATATATAT
2736948 ATATATATGTTTTCAAATGTTTTCAAAAC
129 ATATATATGTTTTCAAATGTTTTCAAAAC
2736977 TATATA-ATATATATTTAAAATGTTTTC-AAAACTATA-TA-ATATATATAT-T-TTCGAAAACC
1 TATATATATATATATTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTC-AAAA--
*
2737036 ACT-TTCTAAAAATTATATATTATATTTTTTCAAAAAATATTTTTAAAAATTATACTATATATAT
63 A-TGTT-TAAAAATTATATATTATATTTTTTC-AAAAATATTTTTAAAAACTATACTATATATAT
2737100 ATATATATATAT
125 ATATATATATAT
2737112 AATATAAATA
Statistics
Matches: 124, Mismatches: 4, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
152 3 0.02
153 5 0.04
154 15 0.12
155 6 0.05
156 68 0.55
157 21 0.17
158 6 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (157 bp):
TATATATATATATATTTAAAATGTTTTCAAAAACTATATTATATATATATATATATTCAAAAATG
TTTAAAAATTATATATTATATTTTTTCAAAAATATTTTTAAAAACTATACTATATATATATATAT
ATATATGTTTTCAAATGTTTTCAAAAC
Found at i:2737131 original size:13 final size:13
Alignment explanation
Indices: 2737100--2737149 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2737090 CTATATATAT
* *
2737100 ATATATATATATA
1 ATATAAATAAATA
2737113 ATATAAATAAATA
1 ATATAAATAAATA
2737126 ATATAAA-AAATA
1 ATATAAATAAATA
*
2737138 AAATAAAATAAA
1 ATAT-AAATAAA
2737150 AACAAATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 8 0.25
13 21 0.66
14 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAAATAAATA
Found at i:2737143 original size:17 final size:16
Alignment explanation
Indices: 2737117--2737151 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2737107 TATATAATAT
*
2737117 AAATAAATAATATAAA
1 AAATAAATAAAATAAA
2737133 AAATAAAATAAAATAAA
1 AAAT-AAATAAAATAAA
2737150 AA
1 AA
2737152 CAAATTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAATAAAATAAA
Found at i:2739247 original size:12 final size:12
Alignment explanation
Indices: 2739230--2739256 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2739220 ATAAAATATA
2739230 TAAAAATATTTT
1 TAAAAATATTTT
2739242 TAAAAATATTTT
1 TAAAAATATTTT
2739254 TAA
1 TAA
2739257 TGTTTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:2741443 original size:45 final size:45
Alignment explanation
Indices: 2741392--2741488 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
2741382 GTTTTGAGCT
* * * *
2741392 ACGGCTTGAGAAGATGATTCGGTGTTGGTGACGGAGGCTTCAGCA
1 ACGGCTTGAGAAGATGATCCGGTGTTGGCGACGGAGACATCAGCA
*
2741437 ACGGCTTGAGATGATGATCCGGTGTTGGCGACGGAGACATCAGCA
1 ACGGCTTGAGAAGATGATCCGGTGTTGGCGACGGAGACATCAGCA
2741482 ACGGCTT
1 ACGGCTT
2741489 CTGATGATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (45 bp):
ACGGCTTGAGAAGATGATCCGGTGTTGGCGACGGAGACATCAGCA
Found at i:2741495 original size:45 final size:45
Alignment explanation
Indices: 2741392--2741514 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
2741382 GTTTTGAGCT
* * * * * *
2741392 ACGGCTTGAGAAGATGATTCGGTGTTGGTGACGGAGGCTTCAGCA
1 ACGGCTTCAGATGATGATCCGGTGTTGGCGACGGAGACATCAGCA
*
2741437 ACGGCTTGAGATGATGATCCGGTGTTGGCGACGGAGACATCAGCA
1 ACGGCTTCAGATGATGATCCGGTGTTGGCGACGGAGACATCAGCA
* *
2741482 ACGGCTTC---TGATGATCTGGTGTTGGAGACGGAG
1 ACGGCTTCAGATGATGATCCGGTGTTGGCGACGGAG
2741515 CATAACAGCG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 23 0.33
45 47 0.67
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (45 bp):
ACGGCTTCAGATGATGATCCGGTGTTGGCGACGGAGACATCAGCA
Found at i:2742855 original size:14 final size:14
Alignment explanation
Indices: 2742836--2742862 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2742826 ATTTATTTTT
2742836 TAATTATATTTATA
1 TAATTATATTTATA
2742850 TAATTATATTTAT
1 TAATTATATTTAT
2742863 TGTTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:2743019 original size:21 final size:21
Alignment explanation
Indices: 2742990--2743034 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2742980 ATATAAAAAA
2742990 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
2743011 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
2743032 TTA
1 TTA
2743035 AAATAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:2744623 original size:2 final size:2
Alignment explanation
Indices: 2744616--2744743 Score: 111
Period size: 2 Copynumber: 62.5 Consensus size: 2
2744606 AACAACTAGA
2744616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2744658 AT AA ACT AT AT AT AT -T AT AT AGT TT AC AT AT GA- ACT AT AT GT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT -AT A-T AT AT AT
* *
2744700 AT AA ACT AT AT AT A- ACT AT AT AT AT AA ACT AT AT A- AT AT AT
1 AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT
2744741 AT A
1 AT A
2744744 GTTTAATAGT
Statistics
Matches: 103, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
1 4 0.04
2 92 0.89
3 7 0.07
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2744688 original size:29 final size:29
Alignment explanation
Indices: 2744616--2744888 Score: 120
Period size: 33 Copynumber: 8.5 Consensus size: 29
2744606 AACAACTAGA
* *
2744616 ATATATATATATATATATA-TATATATAT
1 ATATATATATACATATAAACTATATATAT
*
2744644 ATATATATATATATATAAACTATATATAT
1 ATATATATATACATATAAACTATATATAT
* *
2744673 -TATATAGTTTACATATGAACTATATGTATAAACT
1 ATATATA-TATACATATAAACTATA--TAT--A-T
*
2744707 ATATATAACTATATATATAAACTATATAATAT
1 ATATAT-A-TATACATATAAACTATAT-ATAT
*
2744739 ATATAGTTTAATAGTTTACATATGAACTATATATAT
1 ATATA---T-ATA---TACATATAAACTATATATAT
* *
2744775 AAACTATATAGTTTACGTATAAACTATATATAT
1 --A-TATATA-TATACATATAAACTATATATAT
* *
2744808 AGTTTAT-TAATGAACTATATAAACTATTTATAT
1 A-TATATAT-AT--AC-ATATAAACTATATATAT
** * *
2744841 AGTATATACTATGTATATAAACTATTGTTTAT
1 A-TATATA-TATACATATAAACTA-TATATAT
*
2744873 ATTTATATACTACATA
1 ATATATATA-TACATA
2744889 CTATAGTTGA
Statistics
Matches: 191, Mismatches: 26, Indels: 53
0.71 0.10 0.20
Matches are distributed among these distances:
28 24 0.13
29 24 0.13
30 3 0.02
31 27 0.14
32 14 0.07
33 41 0.21
34 6 0.03
35 12 0.06
36 21 0.11
37 14 0.07
38 1 0.01
39 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (29 bp):
ATATATATATACATATAAACTATATATAT
Found at i:2744753 original size:73 final size:73
Alignment explanation
Indices: 2744621--2744784 Score: 230
Period size: 73 Copynumber: 2.3 Consensus size: 73
2744611 CTAGAATATA
* *
2744621 TATATATATATA-TATATATATATATATATATATATATATAAACTATATATATTATATAGTTTAC
1 TATATATATAAACTATATATATATATATATATAAATATATAAACTATATATATTATATAGTTTAC
2744685 ATATGAAC
66 ATATGAAC
*
2744693 TATATGTATAAACTATATATA-ACTATATATATAAACTATAT-AA-TATATATAGTT-TAATAGT
1 TATATATATAAACTATATATATA-TATATATATAAA-TATATAAACTATATATA-TTAT-ATAGT
2744754 TTACATATGAAC
62 TTACATATGAAC
2744766 TATATATATAAACTATATA
1 TATATATATAAACTATATA
2744785 GTTTACGTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
72 20 0.24
73 58 0.70
74 5 0.06
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (73 bp):
TATATATATAAACTATATATATATATATATATAAATATATAAACTATATATATTATATAGTTTAC
ATATGAAC
Found at i:2744809 original size:65 final size:66
Alignment explanation
Indices: 2744643--2744813 Score: 190
Period size: 73 Copynumber: 2.5 Consensus size: 66
2744633 TATATATATA
* * *
2744643 TATATATATATATATATAAACTATATATAT--TAT-ATAGTTTACATATGAACTATATGTATAAA
1 TATATATATATACATATAAACTATATATATAGTTTAATAGTTTACATATGAACTATATATATAAA
2744705 C
66 C
*
2744706 TATATATAACTATATATATAAACTATATAATATATATAGTTTAATAGTTTACATATGAACTATAT
1 TATATAT-A-TATACATATAAAC----T-ATATATATAGTTTAATAGTTTACATATGAACTATAT
2744771 ATATAAAC
59 ATATAAAC
*
2744779 TATATAGT-T-TACGTATAAACTATATATATAGTTTA
1 TATATA-TATATACATATAAACTATATATATAGTTTA
2744814 TTAATGAACT
Statistics
Matches: 93, Mismatches: 4, Indels: 20
0.79 0.03 0.17
Matches are distributed among these distances:
63 7 0.08
64 1 0.01
65 27 0.29
66 1 0.01
69 1 0.01
70 17 0.18
71 1 0.01
72 2 0.02
73 35 0.38
74 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (66 bp):
TATATATATATACATATAAACTATATATATAGTTTAATAGTTTACATATGAACTATATATATAAA
C
Found at i:2744851 original size:18 final size:18
Alignment explanation
Indices: 2744825--2744859 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2744815 TAATGAACTA
*
2744825 TATAAACTATTTATATAG
1 TATAAACTATGTATATAG
*
2744843 TATATACTATGTATATA
1 TATAAACTATGTATATA
2744860 AACTATTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
TATAAACTATGTATATAG
Found at i:2745188 original size:18 final size:18
Alignment explanation
Indices: 2745165--2745270 Score: 94
Period size: 18 Copynumber: 5.9 Consensus size: 18
2745155 ATAAAAACTA
* *
2745165 TATATATAAAGTATATGG
1 TATATATAAACTATATAG
2745183 TATATATAAACTATATAG
1 TATATATAAACTATATAG
*
2745201 TATATATAAACTATACA-
1 TATATATAAACTATATAG
** *
2745218 T-TATAT-AGTTCAT-TAA
1 TATATATAAACT-ATATAG
*
2745234 TATATATAAACTATATAA
1 TATATATAAACTATATAG
2745252 TATATATATAACATATATA
1 TATATATA-AAC-TATATA
2745271 TTAATTTTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
15 3 0.04
16 8 0.11
17 8 0.11
18 45 0.62
19 3 0.04
20 6 0.08
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.41
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:2745199 original size:13 final size:13
Alignment explanation
Indices: 2745142--2745180 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2745132 ATACTTTTGC
*
2745142 ATATGAACTATAT
1 ATATAAACTATAT
*
2745155 ATAAAAACTATAT
1 ATATAAACTATAT
*
2745168 ATATAAAGTATAT
1 ATATAAACTATAT
2745181 GGTATATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:2745302 original size:69 final size:69
Alignment explanation
Indices: 2745164--2745302 Score: 151
Period size: 69 Copynumber: 2.0 Consensus size: 69
2745154 TATAAAAACT
* ** * *
2745164 ATATATATAAAGTATATGGTATATATAAACTATATAGTATATATAAACTATACATTATATAGTTC
1 ATATATATAAACTATATAATATATATAAACTATATAGTATATATAAACTAAACATTATATAGTTA
2745229 ATTA
66 ATTA
* *
2745233 ATATATATAAACTATATAATATATATATAACATATATATTA-ATTTTAATA-TAAACA-TATATA
1 ATATATATAAACTATATAATATATATA-AAC-TATATAGTATA-TATAA-ACTAAACATTATATA
2745295 -TTAATTA
62 GTTAATTA
2745302 A
1 A
2745303 AAGAATTGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
69 31 0.53
70 10 0.17
71 17 0.29
72 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (69 bp):
ATATATATAAACTATATAATATATATAAACTATATAGTATATATAAACTAAACATTATATAGTTA
ATTA
Found at i:2745675 original size:10 final size:10
Alignment explanation
Indices: 2745660--2745694 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2745650 TCTTTAGAAA
2745660 TTCATATGTG
1 TTCATATGTG
* *
2745670 TTCATATTTT
1 TTCATATGTG
2745680 TTCATATGTG
1 TTCATATGTG
2745690 TTCAT
1 TTCAT
2745695 CCCAAAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (10 bp):
TTCATATGTG
Found at i:2745941 original size:110 final size:112
Alignment explanation
Indices: 2745783--2746031 Score: 276
Period size: 112 Copynumber: 2.2 Consensus size: 112
2745773 TTTCAACCCT
* * * *
2745783 TGTTCATCATTGTTCTTCC-CAAAAACCCTTCTTTGATCTTCACAAACACCAAAATCC-AAA-CC
1 TGTTCATCCTAGTTCTTCCTC--AAACCATTATTTGATCTTCACAAACACCAAAA-CCTAAACCC
* * * *
2745845 ATT-TTGTGTTTTT-TATCAAACACCAAAAAAATCAACCCTTGTTCATCCA
63 ATTCATGT-TTTTTCGATCAAACACCAAAAAAATAAACCCTTATTCATCCA
2745894 TGTTCATCCTAGTTCTTCCTCAAACCATTATTTGATCTTCACAAACACCAAAACCTAAACCCATT
1 TGTTCATCCTAGTTCTTCCTCAAACCATTATTTGATCTTCACAAACACCAAAACCTAAACCCATT
* * * * *
2745959 CATGTTTTTTCGATCAAGCACCCAAAAATTAAACCCTTATTCATTCG
66 CATGTTTTTTCGATCAAACACCAAAAAAATAAACCCTTATTCATCCA
* *
2746006 TGTTCATCC-ATTTTCTTCCTGAAACC
1 TGTTCATCCTA-GTTCTTCCTCAAACC
2746032 CTTACAAACA
Statistics
Matches: 117, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
109 2 0.02
110 33 0.28
111 28 0.24
112 54 0.46
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (112 bp):
TGTTCATCCTAGTTCTTCCTCAAACCATTATTTGATCTTCACAAACACCAAAACCTAAACCCATT
CATGTTTTTTCGATCAAACACCAAAAAAATAAACCCTTATTCATCCA
Found at i:2746219 original size:6 final size:6
Alignment explanation
Indices: 2746177--2746307 Score: 77
Period size: 6 Copynumber: 22.0 Consensus size: 6
2746167 TATTTAGATA
* * * * * * *
2746177 AAACCC TAACCC TAACCC TAACCC TAACCT TAACCC AAACCC AAAACC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * * * * *
2746225 AAACCT AAAACC AAACCC AAACCC -GATCC AGATCCC AAACCC GAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC A-AACCC AAACCC AAACCC
* * * * *
2746273 GAACCC GAACCC GAACCC GAACCC -AACTC AAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
2746308 GAATCCGAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
5 7 0.07
6 93 0.90
7 3 0.03
ACGTcount: A:0.41, C:0.46, G:0.05, T:0.08
Consensus pattern (6 bp):
AAACCC
Found at i:2746283 original size:18 final size:18
Alignment explanation
Indices: 2746178--2746325 Score: 91
Period size: 18 Copynumber: 8.3 Consensus size: 18
2746168 ATTTAGATAA
* * *
2746178 AACCCTAACCCTAACCCT
1 AACCCGAACCCAAACCCG
* ** *
2746196 AACCCTAACCTTAACCCA
1 AACCCGAACCCAAACCCG
* * **
2746214 AACCCAAAACCAAACCTA
1 AACCCGAACCCAAACCCG
* *
2746232 AAACCAAACCCAAACCCG
1 AACCCGAACCCAAACCCG
* * *
2746250 ATCCAGATCCCAAACCCG
1 AACCCGAACCCAAACCCG
*
2746268 AACCCGAACCCGAACCCG
1 AACCCGAACCCAAACCCG
* *
2746286 AACCCGAACCC-AACTCA
1 AACCCGAACCCAAACCCG
* * *
2746303 AACCCGAATCCGAATCCG
1 AACCCGAACCCAAACCCG
2746321 AACCC
1 AACCC
2746326 AAATCCAAGC
Statistics
Matches: 103, Mismatches: 26, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
17 14 0.14
18 89 0.86
ACGTcount: A:0.40, C:0.45, G:0.07, T:0.08
Consensus pattern (18 bp):
AACCCGAACCCAAACCCG
Found at i:2746331 original size:12 final size:12
Alignment explanation
Indices: 2746238--2746325 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
2746228 CCTAAAACCA
*
2746238 AACCCAAACCCG
1 AACCCGAACCCG
* * * *
2746250 ATCCAGATCCCA
1 AACCCGAACCCG
2746262 AACCCGAACCCG
1 AACCCGAACCCG
2746274 AACCCGAACCCG
1 AACCCGAACCCG
2746286 AACCCGAACCC-
1 AACCCGAACCCG
* *
2746297 AACTCAAACCCG
1 AACCCGAACCCG
* *
2746309 AATCCGAATCCG
1 AACCCGAACCCG
2746321 AACCC
1 AACCC
2746326 AAATCCAAGC
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
11 9 0.15
12 50 0.85
ACGTcount: A:0.36, C:0.47, G:0.11, T:0.06
Consensus pattern (12 bp):
AACCCGAACCCG
Found at i:2748938 original size:20 final size:20
Alignment explanation
Indices: 2748913--2748993 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
2748903 CAATAGTTGG
*
2748913 TGCTTGATTCTGCTTGATAT
1 TGCTTGATTCTACTTGATAT
* ** *
2748933 TGCTTGATTATGTTTTATAT
1 TGCTTGATTCTACTTGATAT
* * *
2748953 TGTTTGCTTCTATTTGATAT
1 TGCTTGATTCTACTTGATAT
2748973 TGCTTGATTCTACTTGATAT
1 TGCTTGATTCTACTTGATAT
2748993 T
1 T
2748994 TGTAAGAGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.17, C:0.11, G:0.16, T:0.56
Consensus pattern (20 bp):
TGCTTGATTCTACTTGATAT
Found at i:2749115 original size:23 final size:23
Alignment explanation
Indices: 2749085--2749162 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
2749075 CCGAATGCAG
2749085 GATGCTTGCTGAATTGATGCAAT
1 GATGCTTGCTGAATTGATGCAAT
*
2749108 GATGCTTGCTGAATTGAAGCAAT
1 GATGCTTGCTGAATTGATGCAAT
* * *
2749131 AATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATGCAAT
2749154 GATGCTTGC
1 GATGCTTGC
2749163 CGGTTGCTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATGCAAT
Found at i:2749756 original size:13 final size:13
Alignment explanation
Indices: 2749737--2749774 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2749727 TAATTTAATG
2749737 ATTATAAATAA-A
1 ATTATAAATAAGA
2749749 ATTTATAACATAAGA
1 A-TTATAA-ATAAGA
2749764 ATTATAAATAA
1 ATTATAAATAA
2749775 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:2749784 original size:19 final size:19
Alignment explanation
Indices: 2749760--2749799 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2749750 TTTATAACAT
2749760 AAGAATT-ATAAATAATATA
1 AAGAATTGA-AAATAATATA
*
2749779 AAGAATTGAAATTAATATA
1 AAGAATTGAAAATAATATA
2749798 AA
1 AA
2749800 AACTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
AAGAATTGAAAATAATATA
Found at i:2749978 original size:16 final size:16
Alignment explanation
Indices: 2749959--2749997 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2749949 TGAGTAAATT
*
2749959 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
2749975 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
2749991 ACAGGTC
1 ACAGGTC
2749998 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:2762391 original size:55 final size:55
Alignment explanation
Indices: 2762332--2762814 Score: 678
Period size: 55 Copynumber: 8.8 Consensus size: 55
2762322 AGACTTGAAA
* * *
2762332 AATCTTCA-AATAACGGGTCTGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCATAA-AACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAAC
* * * *
2762387 AATCTTCATAAAACGGGTCTGCTCCCTATTCTTTCGGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * *
2762442 AACCTTCAACAAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
2762498 AATCTTCATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAAC
* *
2762553 AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAT
1 AATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
2762609 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
2762664 AATCTTCAT-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * *
2762718 AATCTTCATAAAACGGGTCCACTCTCTATTCCTACAGAGAGTATAGGACTCG---
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
2762770 -ATCTTCA-ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAG
1 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
2762815 GGCTCGATCT
Statistics
Matches: 392, Mismatches: 28, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
50 1 0.00
51 39 0.10
54 57 0.15
55 193 0.49
56 99 0.25
57 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (55 bp):
AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:2762503 original size:111 final size:111
Alignment explanation
Indices: 2762332--2762814 Score: 707
Period size: 111 Copynumber: 4.4 Consensus size: 111
2762322 AGACTTGAAA
* * * *
2762332 AATCTTCAA-ATAACGGGTCTGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCA
1 AATCTTCAACAAAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCA
* * *
2762395 TAAAACGGGTCTGCTCCCTATTCTTTCGGAGAGTATAGAACTCGAAC
65 TAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
2762442 AACCTTCAACAAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAT
1 AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAT
*
2762507 AAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
66 AAAACGGGTCCGCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAAC
*
2762553 AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAT
1 AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAT
*
2762618 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
66 AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
2762664 AATCTTC-A-TAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAT
1 AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAT
* * * *
2762727 AAAACGGGTCCACTCTCTATTCCTACAGAGAGTATAGGACTCG---
66 AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
2762770 -ATCTTCAAC-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAG
1 AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
2762815 GGCTCGATCT
Statistics
Matches: 345, Mismatches: 22, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
105 6 0.02
106 35 0.10
109 93 0.27
110 11 0.03
111 194 0.56
112 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (111 bp):
AATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAT
AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:2762629 original size:166 final size:163
Alignment explanation
Indices: 2762332--2762814 Score: 708
Period size: 166 Copynumber: 2.9 Consensus size: 163
2762322 AGACTTGAAA
*
2762332 AATCTTCA-AATAACGGGTCTGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAT
1 AATCTTCATAA-AACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAT
* * * * * *
2762396 AAAACGGGTCTGCTCCCTATTCTTTCGGAGAGTATAGAACTCGAACAACCTTCAACAAAATGGGT
65 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA-AATCTTC-A-AAAACGGGT
2762461 CCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
127 CCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
2762498 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAAC
1 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTC-AT
2762563 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATAAAACGGGTC
65 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA-AATCTTCA-AAAACGGGTC
2762628 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
128 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
2762664 AATCTTCAT-AAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAT
1 AATCTTCATAAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAT
* * * *
2762727 AAAACGGGTCCACTCTCTATTCCTACAGAGAGTATAGGACTCG---ATCTTCAACAAACGTGTCC
65 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCAA-AAACGGGTCC
*
2762789 GCTCCCTATTCCTTCAGAGAGTATAG
129 GCTCTCTATTCCTTCAGAGAGTATAG
2762815 GGCTCGATCT
Statistics
Matches: 295, Mismatches: 18, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
159 1 0.00
160 41 0.14
164 41 0.14
165 46 0.16
166 116 0.39
167 50 0.17
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (163 bp):
AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA
AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCAAAAACGGGTCCGC
TCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:2762879 original size:37 final size:37
Alignment explanation
Indices: 2762838--2762918 Score: 162
Period size: 37 Copynumber: 2.2 Consensus size: 37
2762828 TAAAATAAGT
2762838 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
2762875 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
2762912 TTGCTTC
1 TTGCTTC
2762919 GAAGGTCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:2764211 original size:17 final size:17
Alignment explanation
Indices: 2764189--2764326 Score: 77
Period size: 17 Copynumber: 7.8 Consensus size: 17
2764179 CCTCCTTTAA
2764189 TTTCTCTTTTTTTCATT
1 TTTCTCTTTTTTTCATT
2764206 TTTCTC-TTTTTTCATT
1 TTTCTCTTTTTTTCATT
* **
2764222 TTTCAT-TTTTTCTCCCCT
1 TTTC-TCTTTTT-TTCATT
* *
2764240 TTTC-CATTTTTTCTTCT
1 TTTCTCTTTTTTTCAT-T
* *
2764257 TTTTTTTTTCTTTTCATT
1 TTTCTCTTT-TTTTCATT
* *
2764275 TTT-TCCATCATTTTTCTTT
1 TTTCT-C-T-TTTTTTCATT
*
2764294 TTTCTCATTTTTTCATTT
1 TTTCTCTTTTTTTCA-TT
2764312 TTTCTCTTTTATTTC
1 TTTCTCTTTT-TTTC
2764327 TTCTTCAAGC
Statistics
Matches: 90, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
16 16 0.18
17 26 0.29
18 24 0.27
19 22 0.24
20 2 0.02
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTCTTTTTTTCATT
Found at i:2764261 original size:19 final size:19
Alignment explanation
Indices: 2764220--2764307 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 19
2764210 TCTTTTTTCA
* *
2764220 TTTTT-CATTTTTTCTCCC
1 TTTTTCCATTTTTTCTTCT
*
2764238 CTTTTCCATTTTTTCTTCT
1 TTTTTCCATTTTTTCTTCT
2764257 TTTTT---TTTTCTT-TTCAT
1 TTTTTCCATTTT-TTCTTC-T
**
2764274 TTTTTCCATCATTT-TTCT
1 TTTTTCCATTTTTTCTTCT
2764292 TTTTTCTCATTTTTTC
1 TTTTTC-CATTTTTTC
2764308 ATTTTTTCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
16 7 0.13
17 8 0.15
18 11 0.20
19 26 0.48
20 2 0.04
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTCCATTTTTTCTTCT
Found at i:2764279 original size:36 final size:35
Alignment explanation
Indices: 2764239--2764331 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 35
2764229 TTTTCTCCCC
* **
2764239 TTTTCCATTTTTTCTTCTTTTTTTTTTCTTTTCATT
1 TTTTCCATTTTTTCTTCTTTTCTCATT-TTTTCATT
2764275 TTTTCCATCATTTTTCTT-TTTTCTCATTTTTTCATT
1 TTTTCCAT--TTTTTCTTCTTTTCTCATTTTTTCATT
*
2764311 TTTTCTCTTTTATTTCTTCTT
1 TTTTC-CATTT-TTTCTTCTT
2764332 CAAGCAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
35 2 0.04
36 27 0.56
37 11 0.23
38 8 0.17
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (35 bp):
TTTTCCATTTTTTCTTCTTTTCTCATTTTTTCATT
Found at i:2764296 original size:46 final size:49
Alignment explanation
Indices: 2764188--2764315 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 49
2764178 CCCTCCTTTA
*
2764188 ATTTCTCTTTTTTTCATTTTTCTCTTTTTTCATTTTTCATTTTTTCTCCC
1 ATTTTTCTTTTTTTCATTTTTCTCTTTTTTCA-TTTTCATTTTTTCTCCC
* * * *
2764238 CTTTTCCATTTTTTC-TTCTTT-T-TTTTTTC-TTTTCATTTTTTC-CATC
1 ATTTTTCTTTTTTTCATT-TTTCTCTTTTTTCATTTTCATTTTTTCTC-CC
2764284 ATTTTTCTTTTTTCTCATTTTT-TCATTTTTTC
1 ATTTTTCTTTTTT-TCATTTTTCTC-TTTTTTC
2764316 TCTTTTATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
45 1 0.02
46 24 0.38
47 6 0.09
48 9 0.14
49 10 0.16
50 14 0.22
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (49 bp):
ATTTTTCTTTTTTTCATTTTTCTCTTTTTTCATTTTCATTTTTTCTCCC
Found at i:2764313 original size:19 final size:19
Alignment explanation
Indices: 2764267--2764315 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
2764257 TTTTTTTTTC
2764267 TTTTCATTTTTTCCATCAT
1 TTTTCATTTTTTCCATCAT
2764286 TTTTC-TTTTTT-C-TCATT
1 TTTTCATTTTTTCCATCA-T
2764303 TTTTCATTTTTTC
1 TTTTCATTTTTTC
2764316 TCTTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.11
17 7 0.26
18 12 0.44
19 5 0.19
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCATTTTTTCCATCAT
Found at i:2774031 original size:45 final size:47
Alignment explanation
Indices: 2773966--2774063 Score: 146
Period size: 45 Copynumber: 2.1 Consensus size: 47
2773956 TGTTATCCAC
*
2773966 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
2774012 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
2774059 AAAAA
1 AAAAA
2774064 ACGAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 28 0.60
46 8 0.17
47 11 0.23
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:2783482 original size:42 final size:42
Alignment explanation
Indices: 2783435--2783885 Score: 469
Period size: 42 Copynumber: 10.8 Consensus size: 42
2783425 AAATTGTGGA
* * * *
2783435 GTTTATTAAAAAAATGCCGTTAAGGTTCATGACTATCGCGGC
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
** * * *
2783477 GTTTATTACAAAAACGCCGCTAAATTGTATGACTATAGAGGC
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* * * * * *
2783519 GTTTATCACAAAAACGCTGCTAAGGTGCATAACTATGGTGGT
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* * * *
2783561 GTTTATTAGAAAAACGCCACTAAGGTGCATGACTATCGCCGT
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* * *
2783603 GTTTATTACAAAAACACCGCTAAGGTGCATGACTATTGCGAC
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* * * *
2783645 TTTTATTACAAAAATGCCGTTAAGGTGCATGACTATCGCAGC
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* * *
2783687 GTTTATTACAAAAACGCCACTAATGTGCATGACTATCACGGC
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* *
2783729 GTTTATTACAAAAACGCCTG-TAAGGTTCATGACTATTGCGGC
1 GTTTATTACAAAAACGCC-GCTAAGGTGCATGACTATCGCGGC
* *
2783771 ATTTA-T-CAGAAAACGCCGCTAAGGAT-CATGACTATTGCGGC
1 GTTTATTACA-AAAACGCCGCTAAGG-TGCATGACTATCGCGGC
* * * * * **
2783812 GTTTATTACAAAAACACTGCTAAAGAGCATTACTATTACGGC
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
* *
2783854 GTTTATTACAAAAACGACGCTAAGGTTCATGA
1 GTTTATTACAAAAACGCCGCTAAGGTGCATGA
2783886 ATATTGATAA
Statistics
Matches: 335, Mismatches: 67, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
40 3 0.01
41 33 0.10
42 297 0.89
43 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (42 bp):
GTTTATTACAAAAACGCCGCTAAGGTGCATGACTATCGCGGC
Found at i:2783907 original size:29 final size:29
Alignment explanation
Indices: 2783865--2783920 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2783855 TTTATTACAA
*
2783865 AAACGACGCTAAGGTTCATGAATATTGAT
1 AAACGACGCTAAGGTGCATGAATATTGAT
* *
2783894 AAACGCCGCTAAGGTGCATGACTATTG
1 AAACGACGCTAAGGTGCATGAATATTG
2783921 TGGCGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (29 bp):
AAACGACGCTAAGGTGCATGAATATTGAT
Found at i:2788106 original size:14 final size:14
Alignment explanation
Indices: 2788087--2788114 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2788077 TTTGATTCCT
2788087 TCCTATTCCATGTG
1 TCCTATTCCATGTG
2788101 TCCTATTCCATGTG
1 TCCTATTCCATGTG
2788115 AAGAAGACAT
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:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
TCCTATTCCATGTG
Found at i:2789395 original size:28 final size:28
Alignment explanation
Indices: 2789355--2789418 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
2789345 GTGGAATTAG
*
2789355 AAATATCCTACATAAAAAATAGCATAAT
1 AAATATCTTACATAAAAAATAGCATAAT
2789383 AAATATCTTACATAAAAAATAGCATAAT
1 AAATATCTTACATAAAAAATAGCATAAT
2789411 AAATATCT
1 AAATATCT
2789419 AAACAAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (28 bp):
AAATATCTTACATAAAAAATAGCATAAT
Found at i:2790628 original size:16 final size:16
Alignment explanation
Indices: 2790609--2790642 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2790599 ACATATGGAT
2790609 GATTGAAGACTTTTTA
1 GATTGAAGACTTTTTA
*
2790625 GATTGTAGACTTTTTA
1 GATTGAAGACTTTTTA
2790641 GA
1 GA
2790643 GTCGACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (16 bp):
GATTGAAGACTTTTTA
Found at i:2791225 original size:32 final size:32
Alignment explanation
Indices: 2791117--2791244 Score: 120
Period size: 32 Copynumber: 4.1 Consensus size: 32
2791107 TCACAAGATT
*
2791117 AAAATTGTTAAGCTCGATTCAAACTCTAAATC
1 AAAATTGTTAAGCTCGATTCAAACTCGAAATC
* * ** * *
2791149 AAAATT-TTAGAGTTTGAGAC-CA-T-GAACTC
1 AAAATTGTTA-AGCTCGATTCAAACTCGAAATC
*
2791178 CAAATATGTTAAGCTCGATTCAAACTCGAAATC
1 AAAAT-TGTTAAGCTCGATTCAAACTCGAAATC
* *
2791211 AAAATTGTTAAGCTCGATTCGAACTCAAAATC
1 AAAATTGTTAAGCTCGATTCAAACTCGAAATC
2791243 AA
1 AA
2791245 TGGTATTTTC
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
29 8 0.11
30 8 0.11
31 8 0.11
32 40 0.55
33 9 0.12
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (32 bp):
AAAATTGTTAAGCTCGATTCAAACTCGAAATC
Found at i:2791418 original size:18 final size:19
Alignment explanation
Indices: 2791397--2791438 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2791387 CTTTTAAAGC
*
2791397 AAAATTAGA-TTTTGAAAA
1 AAAATTAAAGTTTTGAAAA
2791415 AAAA-TAAAGTTTTGAAAA
1 AAAATTAAAGTTTTGAAAA
*
2791433 ATAATT
1 AAAATT
2791439 TTGACCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 16 0.80
19 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAATTAAAGTTTTGAAAA
Found at i:2793764 original size:80 final size:80
Alignment explanation
Indices: 2793522--2793987 Score: 729
Period size: 80 Copynumber: 5.8 Consensus size: 80
2793512 CTTGCCCTCA
* * *
2793522 GCACACAGCAAAAAGGGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAG
1 GCACACAGC--AAA-GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAG
* *
2793586 ATCCGTAGGGTTACCTTAA
62 GTCCGTAGGGTTACCTTAT
* * *
2793605 GCACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGG-CCTACCTAAGACATCCTTAGGTCC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
*
2793669 GTAAGGTTACCTTAT
66 GTAGGGTTACCTTAT
* * *
2793684 GCACACATCAAAGGGAACCAACATAAGGATATACCTTAGGACCTACCCAAGATATCCTTAGGTCC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
2793749 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
* *
2793764 GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAGGATATTCTTAGGTCC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
2793829 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
*
2793844 GCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
2793909 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
* *
2793924 GCACACATCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTC
2793988 TGTAAGGACT
Statistics
Matches: 357, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
79 63 0.18
80 281 0.79
81 4 0.01
83 9 0.03
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (80 bp):
GCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
GTAGGGTTACCTTAT
Found at i:2799945 original size:17 final size:18
Alignment explanation
Indices: 2799913--2799947 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2799903 TGACCGGTCA
2799913 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
2799931 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
2799948 GTTGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:2799997 original size:29 final size:30
Alignment explanation
Indices: 2799955--2800036 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 30
2799945 ACCGTTGACC
*
2799955 GGTGCTATTTTGGTAAATAATTCA-GTTTT
1 GGTGCTATTCTGGTAAATAATTCAGGTTTT
*
2799984 GGTGCTAATCTGGTAAATAATT-AGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGGTTTT
*
2800013 GGTGCTATTCTGGTAATTAATTCA
1 GGTGCTATTCTGGTAAATAATTCA
2800037 AAATGGGTGC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
28 1 0.02
29 45 0.96
30 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.44
Consensus pattern (30 bp):
GGTGCTATTCTGGTAAATAATTCAGGTTTT
Found at i:2800077 original size:30 final size:29
Alignment explanation
Indices: 2800013--2800081 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
2800003 ATTAGGTTTT
* *
2800013 GGTGCTATTCTGGTAATTAATTCAAAATG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
* *
2800042 GGTGCTATTTTGGTAATTATTTTTAAAAAG
1 GGTGCTATTTTGGTAATTA-ATTCAAAAAG
2800072 GGTGCTATTT
1 GGTGCTATTT
2800082 GTGTAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCAAAAAG
Found at i:2806759 original size:17 final size:18
Alignment explanation
Indices: 2806723--2806761 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2806713 GACCGGTCAC
*
2806723 GACCCGACCCGACCCGTT
1 GACCAGACCCGACCCGTT
*
2806741 GACCAGACCCGA-TCGTT
1 GACCAGACCCGACCCGTT
2806758 GACC
1 GACC
2806762 GTTGACCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.44, G:0.23, T:0.13
Consensus pattern (18 bp):
GACCAGACCCGACCCGTT
Found at i:2806850 original size:29 final size:29
Alignment explanation
Indices: 2806770--2806850 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
2806760 CCGTTGACCA
*
2806770 GTGCTATTCTGGTAAATAATTCAGTTTTG
1 GTGCTATTCTGGTAAATAATTCGGTTTTG
* *
2806799 GTGCTAATCTAGTAAATAATTCGGTTTTG
1 GTGCTATTCTGGTAAATAATTCGGTTTTG
*
2806828 GTGCTATTCTGGTAATTAATTCG
1 GTGCTATTCTGGTAAATAATTCG
2806851 AAATGGGTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (29 bp):
GTGCTATTCTGGTAAATAATTCGGTTTTG
Found at i:2806894 original size:29 final size:29
Alignment explanation
Indices: 2806827--2806894 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
2806817 ATTCGGTTTT
* * *
2806827 GGTGCTATTCTGGTAATTAATTCGAAATG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
* *
2806856 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
2806885 GGTGCTATTT
1 GGTGCTATTT
2806895 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCAAAAAG
Found at i:2808637 original size:80 final size:80
Alignment explanation
Indices: 2808504--2808875 Score: 620
Period size: 80 Copynumber: 4.7 Consensus size: 80
2808494 AGGGGGTTAC
* **
2808504 AACCAACCTAAGGATATACCTTGGG-CCTACCCAAGACATCCTTAGGTTTGTAGGGTTACCTTAT
1 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
* * *
2808568 GCACACAGCACATGG
66 GCACACAACAAAGGG
2808583 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
1 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
2808648 GCACACAACAAAGGG
66 GCACACAACAAAGGG
2808663 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
1 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
*
2808728 GCACACAGCAAAGGG
66 GCACACAACAAAGGG
* * *
2808743 AACCAACCTAAGGATATGCCTTGGGACCTACCCAAGATATCCTTAGGGCTGTAGGGTTACCTTAT
1 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
*
2808808 GCACACAACAAAGAG
66 GCACACAACAAAGGG
* *
2808823 AACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
1 AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
2808876 AGGACCTATA
Statistics
Matches: 277, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
79 25 0.09
80 252 0.91
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
AACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
GCACACAACAAAGGG
Found at i:2815118 original size:42 final size:41
Alignment explanation
Indices: 2815016--2815118 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 41
2815006 CCTACTTCAT
* *
2815016 AAATCATCCTAAAACTTCAATACCTACTGCATAAGCTACTAA
1 AAATCAT-CTTAAACTTCAATACCTACTGCATAAGCTACCAA
* ** *
2815058 AACT-ATTCCTCCAACTTCAATACCTATTGCATAAGCTACCAA
1 AAATCA-T-CTTAAACTTCAATACCTACTGCATAAGCTACCAA
2815100 AAATCATCTTAAACCTTCA
1 AAATCATCTTAAA-CTTCA
2815119 TCCATATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
41 5 0.10
42 44 0.88
43 1 0.02
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (41 bp):
AAATCATCTTAAACTTCAATACCTACTGCATAAGCTACCAA
Found at i:2816106 original size:16 final size:19
Alignment explanation
Indices: 2816093--2816147 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2816083 AGAAAAAAGG
2816093 AAAAAATAATAAAATGAGT
1 AAAAAATAATAAAATGAGT
* * *
2816112 AAAAAATAAAAACAATAAAT
1 AAAAAATAATAA-AATGAGT
*
2816132 AAAATA-AATAAAATGA
1 AAAAAATAATAAAATGA
2816148 TAACGTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 4 0.14
19 15 0.52
20 10 0.34
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAAATAATAAAATGAGT
Found at i:2816189 original size:16 final size:17
Alignment explanation
Indices: 2816160--2816201 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2816150 ACGTAAATAA
2816160 AAAAACAAAACAAA-AT
1 AAAAACAAAACAAACAT
* *
2816176 AAAAATAAAGCAAACAT
1 AAAAACAAAACAAACAT
2816193 -AAAACAAAA
1 AAAAACAAAA
2816202 ATAAAACCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.79, C:0.12, G:0.02, T:0.07
Consensus pattern (17 bp):
AAAAACAAAACAAACAT
Found at i:2816194 original size:11 final size:11
Alignment explanation
Indices: 2816161--2816208 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
2816151 CGTAAATAAA
*
2816161 AAAAC-AAAAC
1 AAAACAAAAAT
*
2816171 AAAATAAAAAT
1 AAAACAAAAAT
* *
2816182 AAAGCAAACAT
1 AAAACAAAAAT
2816193 AAAACAAAAAT
1 AAAACAAAAAT
2816204 AAAAC
1 AAAAC
2816209 CAAGGAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 4 0.13
11 26 0.87
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.08
Consensus pattern (11 bp):
AAAACAAAAAT
Found at i:2816276 original size:23 final size:22
Alignment explanation
Indices: 2816233--2816275 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2816223 AATTAACTAG
*
2816233 AAAAAAGAAATAAGAATAAAAC
1 AAAAAAAAAATAAGAATAAAAC
2816255 AAAAAAAATAATAA-AATAAAA
1 AAAAAAAA-AATAAGAATAAAA
2816276 AGGTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAAAAAAAATAAGAATAAAAC
Found at i:2816346 original size:7 final size:7
Alignment explanation
Indices: 2816334--2816417 Score: 55
Period size: 7 Copynumber: 11.1 Consensus size: 7
2816324 AATGTAAGAA
2816334 AAAAAAT
1 AAAAAAT
2816341 AAAAAAT
1 AAAAAAT
2816348 ATTATAATAAT
1 A--A-AA-AAT
2816359 AAAAAAT
1 AAAAAAT
2816366 AAAAAAT
1 AAAAAAT
*
2816373 AGTAAAAAC
1 A--AAAAAT
* *
2816382 ATAGAAT
1 AAAAAAT
2816389 AAAAAAT
1 AAAAAAT
2816396 GATAAAAAT
1 -A-AAAAAT
2816405 --AAAAT
1 AAAAAAT
2816410 AAAAAAT
1 AAAAAAT
2816417 A
1 A
2816418 TATATACATA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
5 5 0.08
7 33 0.54
8 3 0.05
9 14 0.23
10 2 0.03
11 4 0.07
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (7 bp):
AAAAAAT
Found at i:2816362 original size:23 final size:21
Alignment explanation
Indices: 2816332--2816418 Score: 79
Period size: 25 Copynumber: 3.9 Consensus size: 21
2816322 AAAATGTAAG
2816332 AAAA-AAAATAAAAAATATTA
1 AAAATAAAATAAAAAATATTA
*
2816352 TAATAATAAAAAATAAAAAATAGTAA
1 -AA-AAT--AAAATAAAAAATA-TTA
*
2816378 AAACATAGAATAAAAAATGA-TA
1 AAA-ATAAAATAAAAAAT-ATTA
2816400 AAAATAAAATAAAAAATAT
1 AAAATAAAATAAAAAATAT
2816419 ATATACATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
20 1 0.02
21 15 0.28
22 6 0.11
23 11 0.20
24 2 0.04
25 17 0.31
26 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (21 bp):
AAAATAAAATAAAAAATATTA
Found at i:2816402 original size:22 final size:21
Alignment explanation
Indices: 2816361--2816433 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
2816351 ATAATAATAA
2816361 AAAATAAAAAATAGTAAAAACAT
1 AAAATAAAAAATA-T-AAAACAT
*
2816384 AGAATAAAAAATGATAAAA-AT
1 AAAATAAAAAAT-ATAAAACAT
*
2816405 AAAATAAAAAATATATATACAT
1 AAAATAAAAAATATA-AAACAT
*
2816427 ATAATAA
1 AAAATAA
2816434 TGAGAGAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.07
21 15 0.35
22 12 0.28
23 12 0.28
24 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAATAAAAAATATAAAACAT
Found at i:2818367 original size:84 final size:84
Alignment explanation
Indices: 2818265--2818813 Score: 643
Period size: 84 Copynumber: 6.5 Consensus size: 84
2818255 GAATGGAATT
* * * *
2818265 GAACTCGAAGGTTTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGATGTGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
* * *
2818330 CTTTGAGCTGAGTGTAATC
66 CTTGGAGCTGAGCGTAGTC
* * *
2818349 GAACTCGAAGGTCTTTTGTTGG-ATGATATCCCTTATCGCCTTGAGCTATGCTGCAAATGATGTG
1 GAACTCGAAGGTCTTTTGTTGGCA-GATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* *
2818413 CCTTTGAGCTGAGCGTAGTT
65 CCTTGGAGCTGAGCGTAGTC
* *
2818433 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAT-CCTTGAGTTATGCTGCAAATGATATG
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT-TGCCTTGAGCTATGCTGCAAATGATGTG
* *
2818497 CCTTTGAGCTGAGCTTAGTC
65 CCTTGGAGCTGAGCGTAGTC
* * * * * *
2818517 GAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATTGCCTTGAGCTATGTTACAAATTATGAGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
*
2818582 CTTGGAGCTGAGCATAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * *
2818601 GAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
* *
2818666 CTTGGAGTTGAACGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * ** * *
2818685 GAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTACCTTGAACTATATTGTAAATGATATGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
* *
2818750 CTTGGGGCTGAGCGTAGTT
66 CTTGGAGCTGAGCGTAGTC
* * * * * * *
2818769 AAACTCGAAGGTATTTTATTGACAAATAGCCCTTCTTGCATTGAG
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
2818814 TTGTGTTGTA
Statistics
Matches: 399, Mismatches: 62, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
83 2 0.01
84 396 0.99
85 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (84 bp):
GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTC
Found at i:2819000 original size:124 final size:124
Alignment explanation
Indices: 2818838--2819424 Score: 782
Period size: 124 Copynumber: 4.7 Consensus size: 124
2818828 AACACAATAT
* * * * * * *
2818838 CCTTCTTCGTGAAGTTGAAATCGTTGAGGGCCCCTTCGTTGTGAATTTGAGCCTTAAATTGAATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * * *
2818903 TCCTTCATCGCGAAGTTGAAATCCAATTTGAAGATGAATGTTGCTGGTGGGCACGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTACTGGTGAGCACGATTC
* *** * *
2818962 TCTTCGTCGTGAAGTTGAAATTATGGAGGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTAGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * *
2819027 TCCTTCGTCGTGAAGTTGAAATCCAATATGAAGATGAATATTGCTGGTGGGCACGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTACTGGTGAGCACGATTC
* *
2819086 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTAATCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * *
2819151 TCCTTCGTCCTGAAGTTGAAATCCAATCTAAAGATTAATGTTACTGGTGAGCACAATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTACTGGTGAGCACGATTC
* * **
2819210 TCTTCGTCATGAAGTTGAAACCGTGGATGGCCCCTTTATTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * *
2819275 TCCTTCGTCGTGAAGTTGAAATCCAATCT-AGAGATAAATGTTACTGGTGAGTATGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTGA-AGATGAATGTTACTGGTGAGCACGATTC
* * *
2819334 CCTTCGTCAG-GAAATTGAAACCGTAGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAATTGGAT
1 CCTTCGTC-GTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGAT
* *
2819398 ATCCTTCGTCATGTAGTTGAAATCCAA
65 ATCCTTCGTCGTGAAGTTGAAATCCAA
2819425 ATATTTCGAG
Statistics
Matches: 412, Mismatches: 49, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
123 1 0.00
124 411 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (124 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
TCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTACTGGTGAGCACGATTC
Found at i:2819624 original size:43 final size:43
Alignment explanation
Indices: 2819563--2819682 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
2819553 AGATAGGCAT
* * *
2819563 GATATCCTTCGTCGTGGAGTTGAAATCGTGGATGTGTGGGAAC
1 GATATCCTCCATCGTGGAGTTGAAATCATGGATGTGTGGGAAC
* * * * *
2819606 GATATCCTCCATCATGGAGTTGAAATTATGGATTTGTGGGTAT
1 GATATCCTCCATCGTGGAGTTGAAATCATGGATGTGTGGGAAC
**
2819649 GATATCCTCTTTCGTGGAGTTGAAATCATGGATG
1 GATATCCTCCATCGTGGAGTTGAAATCATGGATG
2819683 GCTCATTCGT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.34
Consensus pattern (43 bp):
GATATCCTCCATCGTGGAGTTGAAATCATGGATGTGTGGGAAC
Found at i:2820928 original size:95 final size:93
Alignment explanation
Indices: 2820729--2820983 Score: 343
Period size: 95 Copynumber: 2.7 Consensus size: 93
2820719 GGCTAGCTGA
* * * *
2820729 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTTAAT-ATCATTGTATTATA
1 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAATCTTTATTGTATTATA
**
2820793 ATCACCTTTATCAGGCTAGCTGGATATT
66 ATCACCTTTATCAGGCTAGCTAAATATT
*
2820821 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAATCTTTATTGTAAATTA
1 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAATCTTTATTGT--ATTA
*
2820886 TAATCACCTTTATCAGGCTAGCTAAATCTT
64 TAATCACCTTTATCAGGCTAGCTAAATATT
* * * * *
2820916 ATCCATAAAGCCGAGGCA-TTTAACCAATTGCTTTAGAGGGATAGCTCAAGCTTTATTCTATATA
1 ATCCATAAAGCCG-GGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAATCTTTATTGTAT-TA
2820980 TAAT
64 TAAT
2820984 ATTATAATCT
Statistics
Matches: 144, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
92 47 0.33
93 8 0.06
94 6 0.04
95 80 0.56
96 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (93 bp):
ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAATCTTTATTGTATTATA
ATCACCTTTATCAGGCTAGCTAAATATT
Found at i:2821064 original size:18 final size:18
Alignment explanation
Indices: 2821041--2821080 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2821031 AACCTGTTAT
2821041 AGTCTAGGTGTTTTTGAA
1 AGTCTAGGTGTTTTTGAA
2821059 AGTCTAGGTGTTTTTGAA
1 AGTCTAGGTGTTTTTGAA
2821077 AGTC
1 AGTC
2821081 AAGGAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (18 bp):
AGTCTAGGTGTTTTTGAA
Found at i:2823714 original size:11 final size:11
Alignment explanation
Indices: 2823689--2823742 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
2823679 ATGATAACGT
*
2823689 AAATAAAAAACA
1 AAATAAAACA-A
*
2823701 AAATAAAATAA
1 AAATAAAACAA
*
2823712 AAATAAAGCAA
1 AAATAAAACAA
*
2823723 ACATAAAACAA
1 AAATAAAACAA
2823734 AAATAAAAC
1 AAATAAAAC
2823743 CAAGGGGGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (11 bp):
AAATAAAACAA
Found at i:2831388 original size:21 final size:21
Alignment explanation
Indices: 2831362--2831403 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2831352 AATTTTTAAT
2831362 AATAAAGGGATTCAAAAAAAA
1 AATAAAGGGATTCAAAAAAAA
*
2831383 AATAAAGGGATTCAACAAAAA
1 AATAAAGGGATTCAAAAAAAA
2831404 TTGCACCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (21 bp):
AATAAAGGGATTCAAAAAAAA
Found at i:2835422 original size:2 final size:2
Alignment explanation
Indices: 2835415--2835455 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2835405 AAAAATAATA
*
2835415 AT AT AT AT AT AT AA AT AT AT AT AT -T 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
2835456 CGGGTCAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2836920 original size:22 final size:22
Alignment explanation
Indices: 2836890--2836935 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2836880 AGTAAAAACC
*
2836890 AAAATTTATATAAGACAATAAA
1 AAAAATTATATAAGACAATAAA
* *
2836912 AAAAATTATATGATACAATAAA
1 AAAAATTATATAAGACAATAAA
2836934 AA
1 AA
2836936 TTTCTACGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAATTATATAAGACAATAAA
Found at i:2838359 original size:39 final size:41
Alignment explanation
Indices: 2838281--2838362 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 41
2838271 ATTAATTATA
2838281 TAATCTCAATTAAATTATATTTTATATATATTTTAAATTTT
1 TAATCTCAATTAAATTATATTTTATATATATTTTAAATTTT
*
2838322 TAATCTC-ATTAAATT-TATCTTT-TATAT-TTTTAAAATTT
1 TAATCTCAATTAAATTATAT-TTTATATATATTTTAAATTTT
2838360 TAA
1 TAA
2838363 GGTAATTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
38 13 0.33
39 8 0.21
40 11 0.28
41 7 0.18
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (41 bp):
TAATCTCAATTAAATTATATTTTATATATATTTTAAATTTT
Found at i:2838376 original size:38 final size:39
Alignment explanation
Indices: 2838288--2838376 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 39
2838278 ATATAATCTC
* *
2838288 AATTAAATTATATTTTATATATATTTTAAATTTTTAATCT
1 AATTAAATT-TATTTTATATATATTTTAAAATTTTAAGCT
* *
2838328 CATTAAATTTATCTTT-TATAT-TTTTAAAATTTTAAGGT
1 AATTAAATTTAT-TTTATATATATTTTAAAATTTTAAGCT
*
2838366 AATTATATTTA
1 AATTAAATTTA
2838377 AATTATTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 23 0.55
39 8 0.19
40 11 0.26
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (39 bp):
AATTAAATTTATTTTATATATATTTTAAAATTTTAAGCT
Found at i:2838479 original size:17 final size:16
Alignment explanation
Indices: 2838454--2838487 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2838444 TAAAATCATG
2838454 TTAATAAATAAATTAT
1 TTAATAAATAAATTAT
*
2838470 TTAATAAAATTAATTAT
1 TTAAT-AAATAAATTAT
2838487 T
1 T
2838488 GATCATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATAAATAAATTAT
Found at i:2839304 original size:29 final size:29
Alignment explanation
Indices: 2839271--2839359 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
2839261 AAATTTTGTC
*
2839271 TAGTGACTAAAATATAAGTTTTGAAAGTT
1 TAGTGACTAAAATATAAATTTTGAAAGTT
* * *
2839300 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAATTTTG-AAAGTT
** * * *
2839330 TAGAAACCAAAATTATAATTTTTAAAAGTT
1 TAGTGACTAAAA-TATAAATTTTGAAAGTT
2839360 ATATATTTTA
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 19 0.41
30 19 0.41
31 8 0.17
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.36
Consensus pattern (29 bp):
TAGTGACTAAAATATAAATTTTGAAAGTT
Found at i:2840901 original size:28 final size:28
Alignment explanation
Indices: 2840863--2840960 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 28
2840853 ATTCGAAGAA
2840863 TTTT-TTA-TAATGATTTTAAAGAATAG
1 TTTTATTATTAATGATTTTAAAGAATAG
* *
2840889 TTTTATTATTAATGA-TGT----AATAT
1 TTTTATTATTAATGATTTTAAAGAATAG
*
2840912 TTTTCGATGATTTAGAATGATTTTAAAGAATAG
1 TTTT--ATTA-TT--AATGATTTTAAAGAATAG
2840945 TTTTATTATTAATGAT
1 TTTTATTATTAATGAT
2840961 GTAATATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 22
0.66 0.07 0.27
Matches are distributed among these distances:
23 8 0.15
25 3 0.06
26 6 0.11
27 5 0.09
28 17 0.31
29 2 0.04
30 2 0.04
31 3 0.06
33 8 0.15
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (28 bp):
TTTTATTATTAATGATTTTAAAGAATAG
Found at i:2840938 original size:56 final size:57
Alignment explanation
Indices: 2840866--2840991 Score: 227
Period size: 56 Copynumber: 2.2 Consensus size: 57
2840856 CGAAGAATTT
*
2840866 TTTATAATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTT-TCGATGA
1 TTTAGAATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCGATGA
2840922 TTTAGAATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCGATGA
1 TTTAGAATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCGATGA
2840979 TTTAGAAATGATT
1 TTTAG-AATGATT
2840992 GAAAAATGTA
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
56 48 0.72
57 12 0.18
58 7 0.10
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.48
Consensus pattern (57 bp):
TTTAGAATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCGATGA
Found at i:2841073 original size:47 final size:47
Alignment explanation
Indices: 2840928--2841077 Score: 139
Period size: 47 Copynumber: 3.2 Consensus size: 47
2840918 ATGATTTAGA
2840928 ATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCG
1 ATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCG
* ** ** * * **
2840975 ATGA-TTTAGA-AAT-GATTGAAAAATGTATTCGAATG-AAT-TTTTTTATA
1 ATGATTTTAAAGAATAG-TTTTATTAT-TAAT-G-ATGTAATATTTTCT-CG
2841022 ATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCG
1 ATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCG
2841069 ATGATTTTA
1 ATGATTTTA
2841078 GAAATGATTA
Statistics
Matches: 75, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
44 1 0.01
45 8 0.11
46 16 0.21
47 25 0.33
48 16 0.21
49 8 0.11
50 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.47
Consensus pattern (47 bp):
ATGATTTTAAAGAATAGTTTTATTATTAATGATGTAATATTTTCTCG
Done.