Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012313.1 Corchorus olitorius cultivar O-4 contig12346, 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: 99555
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6546 original size:33 final size:33
Alignment explanation
Indices: 6509--6687 Score: 243
Period size: 33 Copynumber: 5.5 Consensus size: 33
6499 ACGTGGGGGC
*
6509 GTCCCTAGGGGGCGCCCCACCACGGGGGGAGGG
1 GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
6542 GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
1 GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
6575 GTCCCCAGGGGGCGCCCCACCAC-GGGGGAGGG
1 GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
** * *
6607 GTCCCCAGGGGGCGCCCCACCACAAGGGAAGGC
1 GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
** * ** * *
6640 GTCCCCAACGGGAGCCCGGCCACGGGGTGAGGC
1 GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
6673 GTCCCCAGGGGGCGC
1 GTCCCCAGGGGGCGC
6688 TTAGCCCATG
Statistics
Matches: 129, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
32 32 0.25
33 97 0.75
ACGTcount: A:0.14, C:0.37, G:0.45, T:0.04
Consensus pattern (33 bp):
GTCCCCAGGGGGCGCCCCACCACGGGGGGAGGG
Found at i:6624 original size:65 final size:65
Alignment explanation
Indices: 6506--6687 Score: 247
Period size: 65 Copynumber: 2.8 Consensus size: 65
6496 CAGACGTGGG
* ** *
6506 GGCGTCCCTAGGGGGCGCCCCACCACGGGGGGAGGGGTCCCCAGGGGGCGCCCCACCACGGGGGG
1 GGCGTCCCCAGGGGGCGCCCCACCAC-GGGGGAGGGGTCCCCAGGGGGCGCCCCACCACAAGGGA
6571 A
65 A
*
6572 GGGGTCCCCAGGGGGCGCCCCACCACGGGGGAGGGGTCCCCAGGGGGCGCCCCACCACAAGGGAA
1 GGCGTCCCCAGGGGGCGCCCCACCACGGGGGAGGGGTCCCCAGGGGGCGCCCCACCACAAGGGAA
** * ** *
6637 GGCGTCCCCAACGGGAGCCCGGCCACGGGGTGAGGCGTCCCCAGGGGGCGC
1 GGCGTCCCCAGGGGGCGCCCCACCACGGGG-GAGGGGTCCCCAGGGGGCGC
6688 TTAGCCCATG
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 60 0.58
66 43 0.42
ACGTcount: A:0.14, C:0.37, G:0.45, T:0.04
Consensus pattern (65 bp):
GGCGTCCCCAGGGGGCGCCCCACCACGGGGGAGGGGTCCCCAGGGGGCGCCCCACCACAAGGGAA
Found at i:6678 original size:98 final size:98
Alignment explanation
Indices: 6509--6687 Score: 250
Period size: 98 Copynumber: 1.8 Consensus size: 98
6499 ACGTGGGGGC
* ** * * ** *
6509 GTCCCTAGGGGGCGCCCCACCACGGGGGGAGGGGTCCCCAGGGGGCGCCCCACCACGGGGGGAGG
1 GTCCCCAGGGGGCGCCCCACCACAAGGGAAGGCGTCCCCAACGGGAGCCCCACCACGGGGGGAGG
*
6574 GGTCCCCAGGGGGCGCCCCACCACGGGGGAGGG
66 CGTCCCCAGGGGGCGCCCCACCACGGGGGAGGG
** *
6607 GTCCCCAGGGGGCGCCCCACCACAAGGGAAGGCGTCCCCAACGGGAGCCCGGCCACGGGGTGAGG
1 GTCCCCAGGGGGCGCCCCACCACAAGGGAAGGCGTCCCCAACGGGAGCCCCACCACGGGGGGAGG
6672 CGTCCCCAGGGGGCGC
66 CGTCCCCAGGGGGCGC
6688 TTAGCCCATG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
98 69 1.00
ACGTcount: A:0.14, C:0.37, G:0.45, T:0.04
Consensus pattern (98 bp):
GTCCCCAGGGGGCGCCCCACCACAAGGGAAGGCGTCCCCAACGGGAGCCCCACCACGGGGGGAGG
CGTCCCCAGGGGGCGCCCCACCACGGGGGAGGG
Found at i:9607 original size:147 final size:145
Alignment explanation
Indices: 9316--9598 Score: 394
Period size: 147 Copynumber: 1.9 Consensus size: 145
9306 GTATTAGTAG
* * *
9316 AAGTAATCCTTATCGGACCATCTCTTCCCCAAATATTATTTAGAATCCATTGCATTTGGCTGATA
1 AAGTAATCCTTATCGGACCATCTCTTCCCCAAATATTATTTAGAATCCATTGCATCTGGCTAAGA
* * *
9381 TTTGAAATTTTGCCTAGAAATTGTAGAGCAACCATAATTATGCCACTCCATTATAACATCTTAAA
66 TTTGAAATTTTGCCTAGAAACTGTAGAGCAACCAGAATTATGCCACTCCATTATAACATCGTAAA
9446 CATCTTCTAAAGCCC
131 CATCTTCTAAAGCCC
* *
9461 AAGTAATCCTTATCGGACCACATCTCTTCCCCAAATATTATTTAGAATCCTTTTCATCCT-GCTA
1 AAGTAATCCTTATCGGA-C-CATCTCTTCCCCAAATATTATTTAGAATCCATTGCAT-CTGGCTA
* *
9525 AGATTTG-AATTTTGCCTAGAAACTGTAGAGTAA-C-GAATTATGCCTCTCTTTCATTATAACAT
63 AGATTTGAAATTTTGCCTAGAAACTGTAGAGCAACCAGAATTATGCCACTC---CATTATAACAT
9587 CGTAAACATCTT
125 CGTAAACATCTT
9599 TTGGAGCCCG
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
144 12 0.10
145 18 0.15
146 25 0.20
147 66 0.54
148 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (145 bp):
AAGTAATCCTTATCGGACCATCTCTTCCCCAAATATTATTTAGAATCCATTGCATCTGGCTAAGA
TTTGAAATTTTGCCTAGAAACTGTAGAGCAACCAGAATTATGCCACTCCATTATAACATCGTAAA
CATCTTCTAAAGCCC
Found at i:10014 original size:2 final size:2
Alignment explanation
Indices: 10007--10054 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
9997 AGTTAAATTA
* *
10007 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT CT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
10050 AT AT A
1 AT AT A
10055 AAAGTACGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11173 original size:15 final size:15
Alignment explanation
Indices: 11153--11184 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11143 AACTATCGTC
*
11153 TAGGTATGGTATTGA
1 TAGGTATAGTATTGA
11168 TAGGTATAGTATTGA
1 TAGGTATAGTATTGA
11183 TA
1 TA
11185 ACTTCTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (15 bp):
TAGGTATAGTATTGA
Found at i:12764 original size:15 final size:15
Alignment explanation
Indices: 12744--12775 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12734 AACTACCGTC
12744 TAGGTATGGTATTGA
1 TAGGTATGGTATTGA
12759 TAGGTATGGTATTGA
1 TAGGTATGGTATTGA
12774 TA
1 TA
12776 ACTTCTTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (15 bp):
TAGGTATGGTATTGA
Found at i:13907 original size:22 final size:22
Alignment explanation
Indices: 13881--13935 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
13871 ACTATAATAT
*
13881 CAAAAAATTATAGGGAGATTAA
1 CAAAAAATCATAGGGAGATTAA
** *
13903 CAAAATCTCATAGGGAGATTAT
1 CAAAAAATCATAGGGAGATTAA
13925 C-AAAAATCATA
1 CAAAAAATCATA
13936 TGAAGGTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.24
Consensus pattern (22 bp):
CAAAAAATCATAGGGAGATTAA
Found at i:13945 original size:21 final size:22
Alignment explanation
Indices: 13903--13972 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
13893 GGGAGATTAA
* ** *
13903 CAAAATCTCATAGGGAGATTAT
1 CAAAATATCATAGCAAGGTTAT
13925 CAAAA-ATCATATG-AAGGTTAT
1 CAAAATATCATA-GCAAGGTTAT
* *
13946 -AAAATTTCATAGCGAGGTTAT
1 CAAAATATCATAGCAAGGTTAT
13967 CAAAAT
1 CAAAAT
13973 TTAGCAGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.13
21 23 0.59
22 11 0.28
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (22 bp):
CAAAATATCATAGCAAGGTTAT
Found at i:13974 original size:22 final size:22
Alignment explanation
Indices: 13890--14000 Score: 95
Period size: 22 Copynumber: 5.1 Consensus size: 22
13880 TCAAAAAATT
* * *
13890 ATAGGGAGATTAACAAAATCTC
1 ATAGGGAGGTTATCAAAATTTC
* *
13912 ATAGGGAGATTATCAAAA-ATC
1 ATAGGGAGGTTATCAAAATTTC
* *
13933 ATATGAAGGTTAT-AAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
*
13954 ATAGCGAGGTTATCAAAATTT-
1 ATAGGGAGGTTATCAAAATTTC
*
13975 AGCAGGGTA-GTTATCAAAATTTC
1 A-TAGGG-AGGTTATCAAAATTTC
13998 ATA
1 ATA
14001 AAAATATTCA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
20 4 0.06
21 25 0.35
22 41 0.57
23 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (22 bp):
ATAGGGAGGTTATCAAAATTTC
Found at i:14023 original size:2 final size:2
Alignment explanation
Indices: 14016--14051 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14006 ATTCAATCGA
14016 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
14052 GACTTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17121 original size:181 final size:179
Alignment explanation
Indices: 16819--17168 Score: 583
Period size: 181 Copynumber: 1.9 Consensus size: 179
16809 GTCATTTAAT
*
16819 AAATATATTAAAAAAATTCTAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAAATAA
1 AAATATATTAAAAAAATTATAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAAATAA
* ** *
16884 AATAGTTATAAATGTATTAGATTTGATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATTGTAA
66 AATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATTATAA
* * *
16949 AAGTTTAAACAATGGCATTTAAGAAATATATTTGAAAAACAAGGGTAAG
131 AAATTTAAACAATGGCATTTAAGAAATATAATCGAAAAACAAGGGTAAG
*
16998 AAATATATTTAAAAAATTTATAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
1 AAATATA-TTAAAAAAATTATAATATATCTAA-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT
* *
17063 AAAATATTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTAT
64 AAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATTAT
17128 AAAAATTTAAACAATGGCATTTAAGAAATATAATCGAAAAA
129 AAAAATTTAAACAATGGCATTTAAGAAATATAATCGAAAAA
17169 TAAGCATATA
Statistics
Matches: 158, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
179 7 0.04
180 22 0.14
181 129 0.82
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (179 bp):
AAATATATTAAAAAAATTATAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAAATAA
AATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATTATAA
AAATTTAAACAATGGCATTTAAGAAATATAATCGAAAAACAAGGGTAAG
Found at i:17678 original size:30 final size:32
Alignment explanation
Indices: 17612--17678 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
17602 ATAAAAAAAC
*
17612 TCCCTTATGTTTTTCTTTTAGGACAAAATAAG
1 TCCCTTATGTTTTTCTTATAGGACAAAATAAG
* *
17644 -CCCTTATGTTTTT-TTATGGGATAAAAT-AG
1 TCCCTTATGTTTTTCTTATAGGACAAAATAAG
17673 TCCCTT
1 TCCCTT
17679 GCTGACATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 2 0.06
30 16 0.52
31 13 0.42
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (32 bp):
TCCCTTATGTTTTTCTTATAGGACAAAATAAG
Found at i:17851 original size:28 final size:31
Alignment explanation
Indices: 17811--17883 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
17801 CTTATTTTTG
* **
17811 AAACGTAAGGGATTA-ATTGT-CCTGAAA-A
1 AAACATAAGGGATTATATTGTCCCAAAAACA
*
17839 AAACATAAGGGATTATTTTGTCCCAAAAACA
1 AAACATAAGGGATTATATTGTCCCAAAAACA
17870 AAACATAAGGGATT
1 AAACATAAGGGATT
17884 TTTTTAGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 14 0.37
29 4 0.11
30 5 0.13
31 15 0.39
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (31 bp):
AAACATAAGGGATTATATTGTCCCAAAAACA
Found at i:22026 original size:24 final size:23
Alignment explanation
Indices: 21999--22044 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
21989 GATGAATTAA
*
21999 TCAATTAAGGGTGGGCACTCATGG
1 TCAATGAAGGGTGGGCAC-CATGG
*
22023 TCAATGATGGGTGGGCACCATG
1 TCAATGAAGGGTGGGCACCATG
22045 TAAAATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (23 bp):
TCAATGAAGGGTGGGCACCATGG
Found at i:25854 original size:11 final size:11
Alignment explanation
Indices: 25840--25877 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
25830 ATTCATAACA
25840 AATTTATAATT
1 AATTTATAATT
25851 AATTTATAATT
1 AATTTATAATT
25862 -ATTTGATAATT
1 AATTT-ATAATT
*
25873 TATTT
1 AATTT
25878 TATCTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:26166 original size:23 final size:23
Alignment explanation
Indices: 26140--26183 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
26130 TTAAATTTAA
*
26140 TATACTTATACCT-ATTTTATTTT
1 TATAATTATA-CTAATTTTATTTT
*
26163 TATAATTTTACTAATTTTATT
1 TATAATTATACTAATTTTATT
26184 AAGAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (23 bp):
TATAATTATACTAATTTTATTTT
Found at i:29104 original size:13 final size:13
Alignment explanation
Indices: 29088--29118 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29078 ACCATGTGGT
*
29088 AATACCCTATGTC
1 AATACCCTATGGC
29101 AATACCCTATGGC
1 AATACCCTATGGC
29114 AATAC
1 AATAC
29119 GTTCTCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (13 bp):
AATACCCTATGGC
Found at i:29355 original size:26 final size:26
Alignment explanation
Indices: 29313--29365 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
29303 TGTGACAGTT
*
29313 CCTGTGGCAAGACCCTATGGAAATAC
1 CCTGTGGCAACACCCTATGGAAATAC
*
29339 CCTGTGGCAACATCCTATGGAAATAC
1 CCTGTGGCAACACCCTATGGAAATAC
29365 C
1 C
29366 TTATACTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (26 bp):
CCTGTGGCAACACCCTATGGAAATAC
Found at i:30441 original size:31 final size:31
Alignment explanation
Indices: 30400--30460 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
30390 GTGTTCTATG
* *
30400 ATTTGCAAAAA-TCACATTTTTTTTTTCTTTT
1 ATTTGAAAAAATTC-CACTTTTTTTTTCTTTT
*
30431 ATTTGAAAAAATTCCCCTTTTTTTTTCTTT
1 ATTTGAAAAAATTCCACTTTTTTTTTCTTT
30461 CAAATTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (31 bp):
ATTTGAAAAAATTCCACTTTTTTTTTCTTTT
Found at i:31404 original size:46 final size:46
Alignment explanation
Indices: 31349--31682 Score: 386
Period size: 46 Copynumber: 7.4 Consensus size: 46
31339 GAATGCTTTG
*
31349 TAAGAAGCTACCATATAGAGAATTCTTTCTGAAGAAGGGTGCTCACA
1 TAAG-AGCTACCGTATAGAGAATTCTTTCTGAAGAAGGGTGCTCACA
* * *
31396 TAAGAGCTACCGTATAAAGTATTCTTTCTGAAAAAGGGTGCTCACA
1 TAAGAGCTACCGTATAGAGAATTCTTTCTGAAGAAGGGTGCTCACA
* * *
31442 TAAGAGCTACCATATAGAGTATTCTTTTTGAAGAAGGGTGCTCACA
1 TAAGAGCTACCGTATAGAGAATTCTTTCTGAAGAAGGGTGCTCACA
**
31488 TAAGAGCTACCGTATAGAGAATTCCTTT-TGAAGAAATGTGCTCACA
1 TAAGAGCTACCGTATAGAGAATT-CTTTCTGAAGAAGGGTGCTCACA
*
31534 TAAGAGCTA--G--T-----ATTCATTCTGAAGAAGGGTGCTCACA
1 TAAGAGCTACCGTATAGAGAATTCTTTCTGAAGAAGGGTGCTCACA
** * *
31571 TAAGAGCTACCACATAGA-ATATTTTTTTCTGAAGAAGGGTGCTCACG
1 TAAGAGCTACCGTATAGAGA-A-TTCTTTCTGAAGAAGGGTGCTCACA
* *
31618 TAAGAGCTAACGTATAGAGAATTCCTTT-TGAAGAAGTGTGCTCACA
1 TAAGAGCTACCGTATAGAGAATT-CTTTCTGAAGAAGGGTGCTCACA
*
31664 TAAGAGCTACTGTATAGAG
1 TAAGAGCTACCGTATAGAG
31683 TTTAAGATGC
Statistics
Matches: 246, Mismatches: 27, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
36 3 0.01
37 28 0.11
41 1 0.00
42 1 0.00
44 1 0.00
46 162 0.66
47 49 0.20
48 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
TAAGAGCTACCGTATAGAGAATTCTTTCTGAAGAAGGGTGCTCACA
Found at i:31603 original size:47 final size:47
Alignment explanation
Indices: 31550--31673 Score: 162
Period size: 47 Copynumber: 2.7 Consensus size: 47
31540 CTAGTATTCA
**
31550 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGA-ATATTTTT
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAGA-ATTCCT
* * **
31597 TTCTGAAGAAGGGTGCTCACGTAAGAGCTAACGTATAGAGAATTCCT
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAGAATTCCT
*
31644 TT-TGAAGAAGTGTGCTCACATAAGAGCTAC
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTAC
31674 TGTATAGAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
46 25 0.37
47 41 0.61
48 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (47 bp):
TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAGAATTCCT
Found at i:31645 original size:130 final size:129
Alignment explanation
Indices: 31413--31672 Score: 439
Period size: 130 Copynumber: 2.0 Consensus size: 129
31403 TACCGTATAA
* * *
31413 AGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTTTGAAGAAG
1 AGTATTCATTCTGAAAAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTTTGAAGAAG
*
31478 GGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAGAAATGTGCTCACATAAGAGCT
66 GGTGCTCACATAAGAGCTAACGTATAGAGAATTCCTTTTGAAGAAATGTGCTCACATAAGAGCT
* *
31542 AGTATTCATTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTTTTTTCTGAAGAA
1 AGTATTCATTCTGAAAAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTT-TGAAGAA
* *
31607 GGGTGCTCACGTAAGAGCTAACGTATAGAGAATTCCTTTTGAAGAAGTGTGCTCACATAAGAGCT
65 GGGTGCTCACATAAGAGCTAACGTATAGAGAATTCCTTTTGAAGAAATGTGCTCACATAAGAGCT
31672 A
1 A
31673 CTGTATAGAG
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
129 52 0.43
130 70 0.57
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (129 bp):
AGTATTCATTCTGAAAAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTTTGAAGAAG
GGTGCTCACATAAGAGCTAACGTATAGAGAATTCCTTTTGAAGAAATGTGCTCACATAAGAGCT
Found at i:31957 original size:36 final size:36
Alignment explanation
Indices: 31889--31958 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
31879 GGCTTTATAG
* * *
31889 CCAATTATTGGGCGACTTAGGCTATCAGCATTATGT
1 CCAAGTATTAGGCGACTTAGGCCATCAGCATTATGT
31925 CCAAGTATTAGGCGACTTAGGCCATC-GACATTAT
1 CCAAGTATTAGGCGACTTAGGCCATCAG-CATTAT
31959 AGCCAAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (36 bp):
CCAAGTATTAGGCGACTTAGGCCATCAGCATTATGT
Found at i:32185 original size:31 final size:32
Alignment explanation
Indices: 32150--32216 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
32140 GATAGTTTGC
* *
32150 CAACACCATATGGAAGATGGTGTACTTCTT-A
1 CAACACCATATGAAAGAGGGTGTACTTCTTGA
32181 CAACACCATATGAAAGAGGGTGTACTTCTTGA
1 CAACACCATATGAAAGAGGGTGTACTTCTTGA
32213 CAAC
1 CAAC
32217 GGAAGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (32 bp):
CAACACCATATGAAAGAGGGTGTACTTCTTGA
Found at i:32355 original size:32 final size:32
Alignment explanation
Indices: 32300--32386 Score: 131
Period size: 32 Copynumber: 2.7 Consensus size: 32
32290 CAGTTTGCCG
*
32300 ACACCATGTGGAAGATGGG-GTACTTGTTGATA
1 ACACCATATGGAAGA-GGGTGTACTTGTTGATA
*
32332 ACACCATATGAAAGAGGGTGTACTTGTTGATA
1 ACACCATATGGAAGAGGGTGTACTTGTTGATA
*
32364 ACACCATATGGAAGAGGATGTAC
1 ACACCATATGGAAGAGGGTGTAC
32387 CCTCGACATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 3 0.06
32 47 0.94
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (32 bp):
ACACCATATGGAAGAGGGTGTACTTGTTGATA
Found at i:32593 original size:44 final size:44
Alignment explanation
Indices: 32543--32696 Score: 184
Period size: 44 Copynumber: 3.4 Consensus size: 44
32533 GAGGTGGTAC
32543 TTCGCGAACACCATATGTTTTTGACATTGAAAGAGGGTGATAAT
1 TTCGCGAACACCATATGTTTTTGACATTGAAAGAGGGTGATAAT
* **
32587 TTCGCGAACACCATATGTCTTTGACATTGAAAGAGGGTGATGGT
1 TTCGCGAACACCATATGTTTTTGACATTGAAAGAGGGTGATAAT
* *
32631 CTCGCGAACACCATATGCCTTTGACATTGACATTGGAAGA-GGTGATAAT
1 TTCGCGAACACCATATG--TTT----TTGACATTGAAAGAGGGTGATAAT
**
32680 TTCGTAAACACCATATG
1 TTCGCGAACACCATATG
32697 CCGTTGACGT
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
44 57 0.61
46 2 0.02
49 21 0.23
50 13 0.14
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
TTCGCGAACACCATATGTTTTTGACATTGAAAGAGGGTGATAAT
Found at i:32694 original size:49 final size:49
Alignment explanation
Indices: 32524--32704 Score: 161
Period size: 44 Copynumber: 3.9 Consensus size: 49
32514 TCGCTAACAC
* *
32524 CATTGGAAGGAGGTGGT-ACTTCGCGAACACCATATG--TTT----TTGA
1 CATTGGAA-GAGGTGATAATTTCGCGAACACCATATGCCTTTGACATTGA
* *
32567 CATTGAAAGAGGGTGATAATTTCGCGAACACCATATGTCTTTGACATTGA
1 CATTGGAAGA-GGTGATAATTTCGCGAACACCATATGCCTTTGACATTGA
* ** *
32617 -A--AG-AG-GGTGATGGTCTCGCGAACACCATATGCCTTTGACATTGA
1 CATTGGAAGAGGTGATAATTTCGCGAACACCATATGCCTTTGACATTGA
** *
32661 CATTGGAAGAGGTGATAATTTCGTAAACACCATATGCCGTTGAC
1 CATTGGAAGAGGTGATAATTTCGCGAACACCATATGCCTTTGAC
32705 GTCGCAGTTG
Statistics
Matches: 109, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 12 0.11
44 53 0.49
45 1 0.01
46 5 0.05
47 1 0.01
48 2 0.02
49 29 0.27
50 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (49 bp):
CATTGGAAGAGGTGATAATTTCGCGAACACCATATGCCTTTGACATTGA
Found at i:33049 original size:14 final size:14
Alignment explanation
Indices: 33032--33102 Score: 106
Period size: 14 Copynumber: 5.1 Consensus size: 14
33022 GGAATACTAT
*
33032 ATTGTGAATGCCAC
1 ATTGCGAATGCCAC
*
33046 ATTGCGAATACCAC
1 ATTGCGAATGCCAC
33060 ATTGCGAATGCCAC
1 ATTGCGAATGCCAC
* *
33074 ATTGCAAATACCAC
1 ATTGCGAATGCCAC
33088 ATTGCGAATGCCAC
1 ATTGCGAATGCCAC
33102 A
1 A
33103 AGCCACATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 50 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (14 bp):
ATTGCGAATGCCAC
Found at i:33055 original size:28 final size:28
Alignment explanation
Indices: 33023--33102 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 28
33013 TTGGAAGAAG
* * *
33023 GAATACTATATTGTGAATGCCACATTGC
1 GAATACCACATTGCGAATGCCACATTGC
33051 GAATACCACATTGCGAATGCCACATTGC
1 GAATACCACATTGCGAATGCCACATTGC
*
33079 AAATACCACATTGCGAATGCCACA
1 GAATACCACATTGCGAATGCCACA
33103 AGCCACATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (28 bp):
GAATACCACATTGCGAATGCCACATTGC
Found at i:33210 original size:39 final size:39
Alignment explanation
Indices: 33165--33318 Score: 209
Period size: 39 Copynumber: 3.9 Consensus size: 39
33155 AAATGTTTGA
* * * *
33165 AGCGAATGCCACATGCTTTTGACGTTGCCAATACCATAT
1 AGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
*
33204 CGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
1 AGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
*
33243 AGCGAATGCCACATGCCTTTGACGTCGCGAATACCACGT
1 AGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
* * * * *
33282 TGCAAATACCACATGCCTTTGACTTCACGAATACCAC
1 AGCGAATGCCACATGCCTTTGACGTCGCGAATACCAC
33319 GTTGCAAATA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 103 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (39 bp):
AGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
Found at i:33392 original size:52 final size:53
Alignment explanation
Indices: 33272--33437 Score: 244
Period size: 53 Copynumber: 3.2 Consensus size: 53
33262 TGACGTCGCG
* * * * * * *
33272 AATACCACGTTGCAAATACCACATGCCTTTGACTTCACGAATACCACGTTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
* *
33325 AATACCACATCGCGAATGTCACATGCCTTTGACGTGGCGAATA-CACATTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
33377 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
1 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
33430 AATACCAC
1 AATACCAC
33438 CACATGCCTT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
52 49 0.49
53 52 0.51
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (53 bp):
AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
Found at i:33988 original size:117 final size:115
Alignment explanation
Indices: 33846--34110 Score: 424
Period size: 117 Copynumber: 2.3 Consensus size: 115
33836 TTTTAAGTTG
* *
33846 CATAGGCTAGAAGT-ATCAATAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAA
1 CATAGGCCAGAA-TCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAA
* * *
33910 GGGTGCACTCGCTCCAAGTCAAAATATAGATTTTTTTGTTTTTTAATGGGCTA
65 GGGTGCACTCACTCCAAGTCAAAATATA-ATTTTTTT-TTTTTCAATAGGCTA
*
33963 CATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACTAGTGCAGCACTCCTAAG
1 CATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAAG
34028 GGTGCACTCACTCCAAGTCAAAATATAATTTTTTTTTTTTCAATAGGCTA
66 GGTGCACTCACTCCAAGTCAAAATATAATTTTTTTTTTTTCAATAGGCTA
* *
34078 CATAGGCCAAAATCATCAACAAGGAAGGACACT
1 CATAGGCCAGAATCATCAACAAGGAAGGGCACT
34111 TATGGCTACA
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
115 44 0.32
116 9 0.06
117 86 0.62
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (115 bp):
CATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAAG
GGTGCACTCACTCCAAGTCAAAATATAATTTTTTTTTTTTCAATAGGCTA
Found at i:34375 original size:41 final size:41
Alignment explanation
Indices: 34318--34399 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
34308 CACGCTCAGA
34318 ACGTTATTCAACGTTGATGTGGTGCTGTCAACATTGGTTGT
1 ACGTTATTCAACGTTGATGTGGTGCTGTCAACATTGGTTGT
* * *
34359 ACGTTATTCAACGTTGATGTGGTGTTGTCGACGTTGGTTGT
1 ACGTTATTCAACGTTGATGTGGTGCTGTCAACATTGGTTGT
34400 TTCAGATGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.17, C:0.13, G:0.29, T:0.40
Consensus pattern (41 bp):
ACGTTATTCAACGTTGATGTGGTGCTGTCAACATTGGTTGT
Found at i:36601 original size:31 final size:31
Alignment explanation
Indices: 36556--36664 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
36546 GGAGCTTGTT
* * *
36556 AATTGATCCCGATATACCGTCAGGACCCAAC
1 AATTGATCCTGATATTCCATCAGGACCCAAC
* * *
36587 AATTGTTCCTGATATTCCATCAGGATCTAAC
1 AATTGATCCTGATATTCCATCAGGACCCAAC
* *
36618 AATTGATCCTGATATTTCATCAGGACTCAAC
1 AATTGATCCTGATATTCCATCAGGACCCAAC
*
36649 AATTGATTCTGATATT
1 AATTGATCCTGATATT
36665 AGCTTTATCA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (31 bp):
AATTGATCCTGATATTCCATCAGGACCCAAC
Found at i:37345 original size:45 final size:45
Alignment explanation
Indices: 37253--37752 Score: 793
Period size: 45 Copynumber: 11.0 Consensus size: 45
37243 TCATCAAATC
* * *
37253 CTCCATCCTGATGGTATAAATTTCTTCCCACCATCAAAACTAATTT
1 CTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACCAATTT
* **
37299 CTCCATCCCGATGGTATAAATTTCTCACACCATCAGAATTAATTT
1 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
*
37344 CTCCATCCTTATGGTATAAATTTCTTCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACCAATTT
37390 CTCCATCCTGATGGTATAAATTTCGTCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACCAATTT
37436 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
* * *
37481 CTCTATCCTGATGGTATAAATTTCTCACACCATCAGGACTAATTT
1 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
* *
37526 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGGACTAATTT
1 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
*
37571 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGGACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
*
37616 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTT
1 CTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACCAATTT
* *
37662 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACTAATTT
1 CTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACCAATTT
* *
37708 CTCCATCCTGATGGTATAAATTTTTCACACCATCAGGACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
37753 TGCTGTGCCG
Statistics
Matches: 434, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
45 235 0.54
46 199 0.46
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (45 bp):
CTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACCAATTT
Found at i:46439 original size:31 final size:31
Alignment explanation
Indices: 46401--46541 Score: 237
Period size: 31 Copynumber: 4.5 Consensus size: 31
46391 AGGAGCTTGT
* * * *
46401 CAATTGATCCCGATATACCGTCAAGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
*
46432 CAATTGATCCTGATATTCTATCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
46463 CAATTGATCCTGATATTCCATCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
46494 CAATTGATCCTGATATTCCATCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
46525 CAATTGATCCTGATATT
1 CAATTGATCCTGATATT
46542 AACTTTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (31 bp):
CAATTGATCCTGATATTCCATCAGGACCCAA
Found at i:56982 original size:40 final size:40
Alignment explanation
Indices: 56896--56984 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
56886 CCTGAAAAAT
* * * *
56896 CGTCTTCCGATTGGCTTCTGAATATCTAAATCTGATAATC
1 CGTCTTCTGATTGACTTCTGAAAATCTAAATCTAATAATC
* **
56936 CTTCTTCTGATTGACTTCTGAAAATCTATTTCTAAATAA-C
1 CGTCTTCTGATTGACTTCTGAAAATCTAAATCT-AATAATC
56976 CGTCTTCTG
1 CGTCTTCTG
56985 GTGCATCTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.40
Consensus pattern (40 bp):
CGTCTTCTGATTGACTTCTGAAAATCTAAATCTAATAATC
Found at i:57133 original size:64 final size:64
Alignment explanation
Indices: 56973--57350 Score: 458
Period size: 64 Copynumber: 5.9 Consensus size: 64
56963 ATTTCTAAAT
* * * * * *
56973 AACCGTCTTCTGGTGCA-TCTCTTAATAAGATCGTCTTCCGATCAACTTCTGAAACCTT-TTCGC
1 AACCATCTTCTGGTGTACT-TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTCTT-GA
57036 GA
63 GA
* * * *
57038 AACTATCTTCTGGTGTACTTTTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGA
* * * *
57102 AACCATCTTCTGGCGTACTTCTTGACAAGATCGTCTTCCGGTCAACTTCTAAAAACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGA
* * * * *
57166 AACCATCTTCTGGTGTACTTTTTGACAAGGTCGTCTTCCGATCATCTTCTGAAGACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGA
* *
57230 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGA
* ** *
57294 AACCATCTTCTGGTGTACTTCTTAATGAGA-CTGTCTTCCAATCAACATT-TGAAAATT
1 AACCATCTTCTGGTGTACTTCTTGACAAGATC-GTCTTCCGATCAAC-TTCTGAAAATT
57351 ACATCTTCCG
Statistics
Matches: 277, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
63 1 0.00
64 224 0.81
65 51 0.18
66 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (64 bp):
AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGA
Found at i:57364 original size:55 final size:55
Alignment explanation
Indices: 57297--57405 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
57287 GTTGAGAAAC
* *
57297 CATCTTCTGGTGTACTTCTTAATGAGACTGTCTTCCAATCAACATTTGAAAATTA
1 CATCTTCCGGTGTACTTCTAAATGAGACTGTCTTCCAATCAACATTTGAAAATTA
*
57352 CATCTTCCGGTGTACTTCTAAATGAGATTGTCTTCCAATCAACATTTGAAAATT
1 CATCTTCCGGTGTACTTCTAAATGAGACTGTCTTCCAATCAACATTTGAAAATT
57406 CTTTCTAGCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (55 bp):
CATCTTCCGGTGTACTTCTAAATGAGACTGTCTTCCAATCAACATTTGAAAATTA
Found at i:62165 original size:40 final size:40
Alignment explanation
Indices: 62107--62808 Score: 443
Period size: 41 Copynumber: 16.9 Consensus size: 40
62097 GGGAAAAAGA
* * *
62107 ACAACACCTTCCAATGAGGAAGGGCAGACTAGGAATTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAG
*
62147 ACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAAGTGAACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGG--AA-T----TTAG
* *
62194 ACAACACCTTCCGATGAGGAAGGGCGAACTGGGAATTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAG
* * * *
62234 AAAACACCTTCCGATGAGGAAGGGCAAATTGGGAAGTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAG
* * * * * *
62274 ACAACACCTACCGGTGGGGAACGGCAAACTGGTAAATTGCACAAAGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAATT-----TA-G
*
62321 CAACAACACCTCCCGATGAGGAAGGGC-AACTTGGGAA-TTACTG
1 --ACAACACCTTCCGATGAGGAAGGGCAAAC-TGGGAATTTA--G
*
62364 ACAACACCTTCCGATGAGGAAGGGCAAACT-GGACA--AAG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGA-ATTTAG
*
62402 GCAACAACACTTCCCGATGAGGAAGGGC-AACTTGGGAA-TTACTG
1 ACAAC-AC-CTT-CCGATGAGGAAGGGCAAAC-TGGGAATTTA--G
62446 ACAACACC-TCCTGATGAGGAAGGGC-AACTTGGGAATTACTA-
1 ACAACACCTTCC-GATGAGGAAGGGCAAAC-TGGGAATT--TAG
* * ***
62487 AGAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCA-
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATTTAG
* * * *
62528 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACT-G
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-TTAG
* ***
62568 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCA-
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATTTAG
* * *
62609 ACAACACCTCCCGATGGGGAAGGGCAAACTGGGAAATACTA-
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGG-AAT-TTAG
* ***
62650 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCA-
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATTTAG
* * *
62691 ACAACACC-TCCAGATGAGGAAAGGCAAA-TCGGTAATACT-G
1 ACAACACCTTCC-GATGAGGAAGGGCAAACT-GGGAAT-TTAG
* * ***
62731 ACAACACCTTCCGATGAGGAAGGGGAAACTGGACAAAGGCA-
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATTTAG
*
62772 ACAACACCTCCCGATGAGGAAGGGCAAACTGGGAATT
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT
62809 GTTAAAGGAC
Statistics
Matches: 529, Mismatches: 79, Indels: 109
0.74 0.11 0.15
Matches are distributed among these distances:
38 5 0.01
39 8 0.02
40 166 0.31
41 244 0.46
42 24 0.05
43 6 0.01
44 8 0.02
45 2 0.00
46 1 0.00
47 36 0.07
48 5 0.01
49 24 0.05
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (40 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAG
Found at i:62380 original size:41 final size:41
Alignment explanation
Indices: 62322--62803 Score: 470
Period size: 41 Copynumber: 11.8 Consensus size: 41
62312 GCACAAAGGC
* * *
62322 AACAACACCTCCCGATGAGGAAGGGC-AACTTGGGAATTACT
1 AACAACACCTTCCGATGAGGAAGGGCAAAC-TGGCAAATACT
* **
62363 GACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAATACT
* *
62404 AACAACA-CTTCCCGATGAGGAAGGGC-AACTTGGGAATTACT
1 AACAACACCTT-CCGATGAGGAAGGGCAAAC-TGGCAAATACT
* * *
62445 GACAACACC-TCCTGATGAGGAAGGGC-AACTTGGGAATTACT
1 AACAACACCTTCC-GATGAGGAAGGGCAAAC-TGGCAAATACT
* **
62486 AAGAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAATACT
* * *
62527 AACAACACCTCCCGATGAGGAAGGGCAAATTGG-TAATACT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAATACT
* **
62567 GACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAATACT
* * *
62608 AACAACACCTCCCGATGGGGAAGGGCAAACTGGGAAATACT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAATACT
**
62649 AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAATACT
* *
62690 AACAACACC-TCCAGATGAGGAAAGGCAAA-TCGG-TAATACT
1 AACAACACCTTCC-GATGAGGAAGGGCAAACT-GGCAAATACT
* * **
62730 GACAACACCTTCCGATGAGGAAGGGGAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAATACT
*
62771 AACAACACCTCCCGATGAGGAAGGGCAAACTGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG
62804 GAATTGTTAA
Statistics
Matches: 365, Mismatches: 54, Indels: 44
0.79 0.12 0.10
Matches are distributed among these distances:
39 6 0.02
40 73 0.20
41 260 0.71
42 26 0.07
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.13
Consensus pattern (41 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAATACT
Found at i:62595 original size:81 final size:81
Alignment explanation
Indices: 62364--62799 Score: 576
Period size: 82 Copynumber: 5.3 Consensus size: 81
62354 GGAATTACTG
* * *
62364 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-ACAAAGGC-AACAACA-CTTCCCGATGAGGAA
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTA-ATA--CTAACAACACCTT-CCGATGAGGAA
* *** *
62426 GGGC-AACTTGG-GAATTACTG
62 GGGCAAAC-TGGACAAAGGC-A
* * * *
62446 ACAACACCTCCTGATGAGGAAGGGCAACTTGGGAATTACTAAGAACACCTTCCGATGAGGAAGGG
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAA-TACTAACAACACCTTCCGATGAGGAAGGG
62511 CAAACTGGACAAAGGCA
65 CAAACTGGACAAAGGCA
*
62528 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTCCGATGAGGAAGGGC
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTAACAACACCTTCCGATGAGGAAGGGC
62593 AAACTGGACAAAGGCA
66 AAACTGGACAAAGGCA
* * *
62609 ACAACACCTCCCGATGGGGAAGGGCAAACTGGGAAATACTAACAACACCTTCCGATGAGGAAGGG
1 ACAACACCTCCCGATGAGGAAGGGCAAA-TTGGTAATACTAACAACACCTTCCGATGAGGAAGGG
62674 CAAACTGGACAAAGGCA
65 CAAACTGGACAAAGGCA
* * * * *
62691 ACAACACCTCCAGATGAGGAAAGGCAAATCGGTAATACTGACAACACCTTCCGATGAGGAAGGGG
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTAACAACACCTTCCGATGAGGAAGGGC
62756 AAACTGGACAAAGGCA
66 AAACTGGACAAAGGCA
62772 ACAACACCTCCCGATGAGGAAGGGCAAA
1 ACAACACCTCCCGATGAGGAAGGGCAAA
62800 CTGGGAATTG
Statistics
Matches: 318, Mismatches: 29, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
81 147 0.46
82 160 0.50
83 11 0.03
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.13
Consensus pattern (81 bp):
ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTAACAACACCTTCCGATGAGGAAGGGC
AAACTGGACAAAGGCA
Found at i:62658 original size:163 final size:163
Alignment explanation
Indices: 62106--62806 Score: 649
Period size: 163 Copynumber: 4.2 Consensus size: 163
62096 AGGGAAAAAG
* * * * * *
62106 AACAACACCTTCCAATGAGGAAGGGCAGACTAGG-AAT-TTAGACAACACCTTCCGGTGAGGAAG
1 AACAACACCTCCCGATGAGGAAGGGCAAACTGGGAAATACTA-ACAACACCTTCCGATGAGGAAG
* * * *
62169 GGCAAACTGGGA-AAAGTGAACTTAGACAACACCTTCCGATGAGGAAGGGCGAACTGGGAAT-TT
65 GGCAAACT-GGACAAAG-G--C-TA-ACAACACCTCCCGATGAGGAAGGGCAAACTGGTAATACT
* * * * **
62232 AAAAAACACCTTCCGATGAGGAAGGGCAAATTGG-GAAGTTA
124 -GACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAAG-GC
* * * * * * *
62273 AACAACACCTACCGGTGGGGAACGGCAAACTGGTAAATTGCACAAAGGCAACAACACCTCCCGAT
1 AACAACACCTCCCGATGAGGAAGGGCAAACTGGGAAA-T--AC-----TAACAACACCTTCCGAT
* *** * *
62338 GAGGAAGGGC-AACTTGG-GAATTACTGACAACACCTTCCGATGAGGAAGGGCAAACTGG-ACA-
58 GAGGAAGGGCAAAC-TGGACAAAGGCTAACAACACCTCCCGATGAGGAAGGGCAAACTGGTA-AT
* * * ***
62399 A-AGGCAACAACACTTCCCGATGAGGAAGGGC-AACTTGGGAATTAC
121 ACTGACAAC-AC-CTT-CCGATGAGGAAGGGCAAAC-TGGCAAAGGC
* * * *
62444 TGACAACACCTCCTGATGAGGAAGGGC-AACTTGGGAATTACTAAGAACACCTTCCGATGAGGAA
1 -AACAACACCTCCCGATGAGGAAGGGCAAAC-TGGGAAATACTAACAACACCTTCCGATGAGGAA
*
62508 GGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAA
64 GGGCAAACTGGACAAAGGCTAACAACACCTCCCGATGAGGAAGGGCAAACTGGTAATACTGACAA
62572 CACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC
129 CACCTTCCGATGAGGAAGGGCAAACTGG-CAAAGGC
*
62608 AACAACACCTCCCGATGGGGAAGGGCAAACTGGGAAATACTAACAACACCTTCCGATGAGGAAGG
1 AACAACACCTCCCGATGAGGAAGGGCAAACTGGGAAATACTAACAACACCTTCCGATGAGGAAGG
* *
62673 GCAAACTGGACAAAGGC-AACAACACCTCCAGATGAGGAAAGGCAAA-TCGGTAATACTGACAAC
66 GCAAACTGGACAAAGGCTAACAACACCTCCCGATGAGGAAGGGCAAACT-GGTAATACTGACAAC
*
62736 ACCTTCCGATGAGGAAGGGGAAACTGGACAAAGGC
130 ACCTTCCGATGAGGAAGGGCAAACTGG-CAAAGGC
62771 AACAACACCTCCCGATGAGGAAGGGCAAACTGGGAA
1 AACAACACCTCCCGATGAGGAAGGGCAAACTGGGAA
62807 TTGTTAAAGG
Statistics
Matches: 444, Mismatches: 60, Indels: 64
0.78 0.11 0.11
Matches are distributed among these distances:
162 1 0.00
163 202 0.45
164 70 0.16
165 10 0.02
166 5 0.01
167 26 0.06
168 5 0.01
169 6 0.01
170 37 0.08
171 23 0.05
172 27 0.06
175 7 0.02
176 24 0.05
177 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (163 bp):
AACAACACCTCCCGATGAGGAAGGGCAAACTGGGAAATACTAACAACACCTTCCGATGAGGAAGG
GCAAACTGGACAAAGGCTAACAACACCTCCCGATGAGGAAGGGCAAACTGGTAATACTGACAACA
CCTTCCGATGAGGAAGGGCAAACTGGCAAAGGC
Found at i:64419 original size:28 final size:28
Alignment explanation
Indices: 64385--64442 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
64375 CTCTCCTTCA
64385 AACCCTAACAGTTGCAGCGCCGCTCCTC
1 AACCCTAACAGTTGCAGCGCCGCTCCTC
**
64413 AACCCTATTAGTTGCAGCGCCGCTCCTC
1 AACCCTAACAGTTGCAGCGCCGCTCCTC
64441 AA
1 AA
64443 TCTTCACCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (28 bp):
AACCCTAACAGTTGCAGCGCCGCTCCTC
Found at i:69067 original size:15 final size:15
Alignment explanation
Indices: 69033--69083 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
69023 CCAAAACCTT
69033 TTGAAAA-CTTATTT-
1 TTGAAAACCTT-TTTC
69047 TTGAAAACCTTTTTC
1 TTGAAAACCTTTTTC
**
69062 TTGAAAACAATTTTC
1 TTGAAAACCTTTTTC
69077 TTGAAAA
1 TTGAAAA
69084 ACGTCTCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 10 0.30
15 23 0.70
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (15 bp):
TTGAAAACCTTTTTC
Found at i:72023 original size:38 final size:38
Alignment explanation
Indices: 71981--72082 Score: 195
Period size: 38 Copynumber: 2.7 Consensus size: 38
71971 TTTGGATTTC
*
71981 TTTATTTTCCAAAATTTTCTTTTGGAATTACCTAAACT
1 TTTATTTTCCAAAATCTTCTTTTGGAATTACCTAAACT
72019 TTTATTTTCCAAAATCTTCTTTTGGAATTACCTAAACT
1 TTTATTTTCCAAAATCTTCTTTTGGAATTACCTAAACT
72057 TTTATTTTCCAAAATCTTCTTTTGGA
1 TTTATTTTCCAAAATCTTCTTTTGGA
72083 GTTGCTTAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (38 bp):
TTTATTTTCCAAAATCTTCTTTTGGAATTACCTAAACT
Found at i:72761 original size:13 final size:13
Alignment explanation
Indices: 72743--72770 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
72733 GAATAATTTC
72743 ATTCAGTTTCATT
1 ATTCAGTTTCATT
72756 ATTCAGTTTCATT
1 ATTCAGTTTCATT
72769 AT
1 AT
72771 ATAGTACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTCAGTTTCATT
Found at i:73007 original size:14 final size:14
Alignment explanation
Indices: 72984--73019 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
72974 TTGGCGACCA
*
72984 AGAATATGCATTTC
1 AGAATTTGCATTTC
72998 AGAATTTGCATTTC
1 AGAATTTGCATTTC
73012 AGAATTTG
1 AGAATTTG
73020 TCACCAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (14 bp):
AGAATTTGCATTTC
Found at i:76035 original size:20 final size:20
Alignment explanation
Indices: 76010--76061 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
76000 GTAAATGTAG
* *
76010 GTTTGGGTTTTTAATTTTCT
1 GTTTGGGTTTTTAAGTTTAT
**
76030 GTTTGGGCCTTTAAGTTTAT
1 GTTTGGGTTTTTAAGTTTAT
76050 GTTTGGGCTTTT
1 GTTTGGG-TTTT
76062 GGTGTTAGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.10, C:0.08, G:0.25, T:0.58
Consensus pattern (20 bp):
GTTTGGGTTTTTAAGTTTAT
Found at i:76910 original size:34 final size:35
Alignment explanation
Indices: 76871--76970 Score: 134
Period size: 37 Copynumber: 2.9 Consensus size: 35
76861 CAGCTTAATT
*
76871 TTTCAAATTGGGAAAGTTCCCATCAAG-TT-AAAG
1 TTTCAAATTGGGAAAGTTCCCATCAAGTTTCAAAA
*
76904 TCTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
1 T-TTCAAATTGGGAAAGTTCCCATCAAG-TTTCAAAA
76941 TTGTCAAATTGGGAAAGTTCCCATC-AGTTT
1 TT-TCAAATTGGGAAAGTTCCCATCAAGTTT
76971 TCAACGCATT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
33 1 0.02
34 25 0.42
35 3 0.05
36 5 0.08
37 26 0.43
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (35 bp):
TTTCAAATTGGGAAAGTTCCCATCAAGTTTCAAAA
Found at i:76957 original size:37 final size:37
Alignment explanation
Indices: 76872--76974 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 37
76862 AGCTTAATTT
* *
76872 TTCAAATTGGGAAAGTTCCCATCAAG--TT-AAAGTC
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAATC
76906 TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAAT-
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAATC
76942 TGTCAAATTGGGAAAGTTCCCAT-CAGTTTTCAA
1 T-TCAAATTGGGAAAGTTCCCATCCAGTTTTCAA
76975 CGCATTCAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
34 25 0.40
36 13 0.21
37 25 0.40
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (37 bp):
TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAATC
Found at i:77031 original size:34 final size:36
Alignment explanation
Indices: 76992--77092 Score: 100
Period size: 40 Copynumber: 2.8 Consensus size: 36
76982 AATTTAGCTG
*
76992 GTTTTCAAATTGGGAAAGTTCCCATCA-T-GTTTTA
1 GTTTTCAAATTGGGAAAGTTCCCATCATTCGTTTCA
* *
77026 GTTTTCAATTTAGCGGAAA-TTCCTATCAGTTTCGGTTTCA
1 GTTTTCAAATT-G-GGAAAGTTCCCATCA--TTC-GTTTCA
*
77066 GTTTTCAAAGTGGGAAAGTTCCCATCA
1 GTTTTCAAATTGGGAAAGTTCCCATCA
77093 AAAGCATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
34 10 0.19
35 9 0.17
36 5 0.09
38 6 0.11
39 9 0.17
40 14 0.26
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (36 bp):
GTTTTCAAATTGGGAAAGTTCCCATCATTCGTTTCA
Found at i:83196 original size:16 final size:16
Alignment explanation
Indices: 83170--83240 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 16
83160 TGAAGGTTCA
*
83170 ACCCG-AACCCGATTG
1 ACCCGAAACCCGAATG
*
83185 ACCCGAAACCCGAATA
1 ACCCGAAACCCGAATG
** * *
83201 ATTCGAGATCCGAATG
1 ACCCGAAACCCGAATG
* *
83217 ACCCAAAACCCGATTG
1 ACCCGAAACCCGAATG
*
83233 ATCCGAAA
1 ACCCGAAA
83241 AAAACTGACG
Statistics
Matches: 40, Mismatches: 15, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
15 5 0.12
16 35 0.88
ACGTcount: A:0.37, C:0.32, G:0.17, T:0.14
Consensus pattern (16 bp):
ACCCGAAACCCGAATG
Found at i:87348 original size:23 final size:22
Alignment explanation
Indices: 87307--87349 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
87297 GTGGGATTTT
87307 TAATAATAATTATTCAATAAAA
1 TAATAATAATTATTCAATAAAA
* *
87329 TAATAATTATTTATTTAATAA
1 TAATAA-TAATTATTCAATAA
87350 TTAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAATAATTATTCAATAAAA
Found at i:87354 original size:19 final size:19
Alignment explanation
Indices: 87305--87356 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
87295 ATGTGGGATT
87305 TTTAATAATAATTATTCAA
1 TTTAATAATAATTATTCAA
** *
87324 TAAAATAATAATTATT-TA
1 TTTAATAATAATTATTCAA
87342 TTTAATAATTAATTA
1 TTTAATAA-TAATTA
87357 ATTTCAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATAATAATTATTCAA
Found at i:91270 original size:27 final size:28
Alignment explanation
Indices: 91237--91301 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
91227 TAATGTTTAA
91237 TGTTTTTTGCTACCATAAAGAAGTTCAC
1 TGTTTTTTGCTACCATAAAGAAGTTCAC
* *
91265 TGTTTTTTGCTACCATAAATAAGTTTAC
1 TGTTTTTTGCTACCATAAAGAAGTTCAC
91293 TGTTTTTTG
1 TGTTTTTTG
91302 GTAGTTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48
Consensus pattern (28 bp):
TGTTTTTTGCTACCATAAAGAAGTTCAC
Found at i:94021 original size:16 final size:16
Alignment explanation
Indices: 94000--94030 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
93990 TGATAACTAA
94000 ATTACATTTATAAAAT
1 ATTACATTTATAAAAT
*
94016 ATTACATTTGTAAAA
1 ATTACATTTATAAAA
94031 AGCTGTAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACATTTATAAAAT
Found at i:95724 original size:22 final size:22
Alignment explanation
Indices: 95689--95836 Score: 119
Period size: 22 Copynumber: 6.8 Consensus size: 22
95679 TGAATATTTT
95689 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTATCC
* * * *
95711 TATTAACTTTTGATAACCATTC
1 TATGAAATTTTGATAACTATCC
*
95733 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAACTATCC
*
95754 TATGAAATTGTGATAA--ACTCC
1 TATGAAATTTTGATAACTA-TCC
* * *
95775 ATATGAAACTTTGATAGCCTA-AC
1 -TATGAAATTTTGATA-ACTATCC
*
95798 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTATCC
95821 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
95837 CTTCTTATGA
Statistics
Matches: 98, Mismatches: 19, Indels: 20
0.72 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 20 0.20
22 59 0.60
23 16 0.16
25 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATCC
Found at i:95846 original size:44 final size:45
Alignment explanation
Indices: 95689--95836 Score: 148
Period size: 44 Copynumber: 3.4 Consensus size: 45
95679 TGAATATTTT
* *
95689 TATGAAATTTTGATAACTATCCTATTAACTTTTGAT-AACCATT-C
1 TATGAAATTTTGATAACTATCCTATGAAATTTTGATAAACC-TTCC
* *
95733 TATGAAATTTTGATAATTA-CCTATGAAATTGTGATAAA-C-TCC
1 TATGAAATTTTGATAACTATCCTATGAAATTTTGATAAACCTTCC
* * * *
95775 ATATGAAACTTTGATAGCCTA-ACTATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATA-ACTATCCTATGAAATTTTGATAAACCTTCC
95821 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
95837 CTTCTTATGA
Statistics
Matches: 86, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 29 0.34
44 40 0.47
45 12 0.14
46 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.39
Consensus pattern (45 bp):
TATGAAATTTTGATAACTATCCTATGAAATTTTGATAAACCTTCC
Found at i:96724 original size:2 final size:2
Alignment explanation
Indices: 96719--96745 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
96709 ATATATATAT
96719 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
96746 ACTACTCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:98282 original size:27 final size:26
Alignment explanation
Indices: 98227--98287 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
98217 ATAAATTTCC
*
98227 ATTATTTTAATAATGGAATAATTACAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
98255 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
98282 A-TATTT
1 ATTATTT
98288 GAAAAAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 8 0.27
27 15 0.50
28 7 0.23
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:98359 original size:15 final size:15
Alignment explanation
Indices: 98339--98369 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
98329 TTCGTACTTT
*
98339 TATATATAGTATATA
1 TATATATACTATATA
98354 TATATATACTATATA
1 TATATATACTATATA
98369 T
1 T
98370 TATTTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (15 bp):
TATATATACTATATA
Done.