Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011447.1 Kokia drynarioides strain JFW-HI SEQ_126431, 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: 482958
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 26 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--42 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 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
43 CTGACATGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2518 original size:16 final size:18
Alignment explanation
Indices: 2492--2526 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2482 ATTAGAATCA
2492 AATTGAGAAAATT-ATTT
1 AATTGAGAAAATTAATTT
2509 AATT-AGAAAATTAATTT
1 AATTGAGAAAATTAATTT
2526 A
1 A
2527 TTTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
AATTGAGAAAATTAATTT
Found at i:5964 original size:5 final size:5
Alignment explanation
Indices: 5954--6008 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
5944 AATTGAATCC
5954 TTTTA TTTTA TTTTA TTTCT- TTTTA -TTTA TTTAATA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTT--TA TTTTA TTTTA
*
6000 TGTTA TTTT
1 TTTTA TTTT
6009 CAACCTGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 5 0.12
5 32 0.74
6 1 0.02
7 5 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:9063 original size:18 final size:18
Alignment explanation
Indices: 9037--9077 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
9027 CTAGCAACCT
* *
9037 CACCACCCTCTCCCTAAC
1 CACCTCCCTCACCCTAAC
*
9055 CACCTCCCTCACCCTCAC
1 CACCTCCCTCACCCTAAC
9073 CACCT
1 CACCT
9078 TTATTACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.63, G:0.00, T:0.17
Consensus pattern (18 bp):
CACCTCCCTCACCCTAAC
Found at i:12580 original size:36 final size:36
Alignment explanation
Indices: 12533--12669 Score: 229
Period size: 36 Copynumber: 3.8 Consensus size: 36
12523 ATAATAAGTT
*
12533 ACATGGTATGAAGAACATACCCACATATTTTCTGTC
1 ACATGGCATGAAGAACATACCCACATATTTTCTGTC
* *
12569 ACATGACATGAAGAACATACCCACATATTTTCTTTC
1 ACATGGCATGAAGAACATACCCACATATTTTCTGTC
* *
12605 TCATGGCATGAAGAACATACCCACATATTTTTTGTC
1 ACATGGCATGAAGAACATACCCACATATTTTCTGTC
12641 ACATGGCATGAAGAACATACCCACATATT
1 ACATGGCATGAAGAACATACCCACATATT
12670 CACTTCACAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (36 bp):
ACATGGCATGAAGAACATACCCACATATTTTCTGTC
Found at i:12736 original size:23 final size:23
Alignment explanation
Indices: 12703--12996 Score: 372
Period size: 23 Copynumber: 12.8 Consensus size: 23
12693 CTTAATATTT
* *
12703 AATCACATTAATATTTTAGCATA
1 AATCACATTAATATTTAAGCACA
* *
12726 AACCACATTAATATTTGAGCACA
1 AATCACATTAATATTTAAGCACA
*
12749 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCACA
* *
12772 AACCACATTAATATTTGAGCACA
1 AATCACATTAATATTTAAGCACA
* *
12795 AATCATATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCACA
* * *
12818 AACCACATTTATTTTTAAGCACA
1 AATCACATTAATATTTAAGCACA
* *
12841 AATCATATTAATATTTAATCACA
1 AATCACATTAATATTTAAGCACA
*
12864 AATCACATTAATATTTGAGCACA
1 AATCACATTAATATTTAAGCACA
* *
12887 AATCATATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCACA
* **
12910 AATCACATTAATACTTAAGCATG
1 AATCACATTAATATTTAAGCACA
* *
12933 AATCACATTAATATTTAATCATA
1 AATCACATTAATATTTAAGCACA
* *
12956 AGTCATATTAATATTTAAGCACA
1 AATCACATTAATATTTAAGCACA
12979 AATCACATTAATATTTAA
1 AATCACATTAATATTTAA
12997 TCATAGATAT
Statistics
Matches: 230, Mismatches: 41, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 230 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCACA
Found at i:12871 original size:92 final size:92
Alignment explanation
Indices: 12703--13001 Score: 436
Period size: 92 Copynumber: 3.2 Consensus size: 92
12693 CTTAATATTT
* * *
12703 AATCACATTAATATTTTAGCATAAACCACATTAATATTTGAGCACAAATCACATTAATATTTAAG
1 AATCACATTAATATTTAAGCATAAACCACATTAATATTTAAGCACAAATCACATTAATATTTAAT
*
12768 CATAAACCACATTAATATTTGAGCACA
66 CATAAATCACATTAATATTTGAGCACA
* * * *
12795 AATCATATTAATATTTAAGCATAAACCACATTTATTTTTAAGCACAAATCATATTAATATTTAAT
1 AATCACATTAATATTTAAGCATAAACCACATTAATATTTAAGCACAAATCACATTAATATTTAAT
*
12860 CACAAATCACATTAATATTTGAGCACA
66 CATAAATCACATTAATATTTGAGCACA
* * * **
12887 AATCATATTAATATTTAAGCATAAATCACATTAATACTTAAGCATGAATCACATTAATATTTAAT
1 AATCACATTAATATTTAAGCATAAACCACATTAATATTTAAGCACAAATCACATTAATATTTAAT
* * *
12952 CATAAGTCATATTAATATTTAAGCACA
66 CATAAATCACATTAATATTTGAGCACA
*
12979 AATCACATTAATATTTAATCATA
1 AATCACATTAATATTTAAGCATA
13002 GATATAAGAA
Statistics
Matches: 185, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 185 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (92 bp):
AATCACATTAATATTTAAGCATAAACCACATTAATATTTAAGCACAAATCACATTAATATTTAAT
CATAAATCACATTAATATTTGAGCACA
Found at i:13785 original size:9 final size:9
Alignment explanation
Indices: 13767--13799 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
13757 AACCCATGTT
13767 TTGA-GAAG
1 TTGATGAAG
13775 TTGATGAAG
1 TTGATGAAG
13784 TTGATGAAG
1 TTGATGAAG
*
13793 GTGATGA
1 TTGATGA
13800 TAGATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (9 bp):
TTGATGAAG
Found at i:15388 original size:43 final size:43
Alignment explanation
Indices: 15255--15567 Score: 175
Period size: 43 Copynumber: 7.2 Consensus size: 43
15245 ATGCAGACAA
* * *
15255 TGCATCATCGGGTATACCAAAGTATGTATA-TTGACACGTACAG
1 TGCATCATCGGATATACCGAAGTATGTATACTTG-CACGTATAG
* ** *
15298 TGCATCATCGGATAAACCGAAG-AAATATACTTGCACATATAAG
1 TGCATCATCGGATATACCGAAGTATGTATACTTGCACGTAT-AG
* *
15341 -GCATCATTGGATATACTGAAGTATGTATACTTGCACGTATAG
1 TGCATCATCGGATATACCGAAGTATGTATACTTGCACGTATAG
* * * * ** * * *
15383 TGCATCATCGAATAAACCAAAGAAAATATACTGGCAAAACACT-TAA
1 TGCATCATCGGATATACCGAAGTATGTATACTTGC---AC-GTATAG
** * * * ** * *
15429 TGCATCATCAAATATACTGTAGTATGCATACTAACGCATATAG
1 TGCATCATCGGATATACCGAAGTATGTATACTTGCACGTATAG
* * * * * ** * * *
15472 AGCATTATCGGATAAACCAAAGAAAATATACTGGCACATACAG
1 TGCATCATCGGATATACCGAAGTATGTATACTTGCACGTATAG
* * *
15515 TGCATCATCGGATAAACCGAAGTATGTATACTGGTACGTATAG
1 TGCATCATCGGATATACCGAAGTATGTATACTTGCACGTATAG
*
15558 TGAATCATCG
1 TGCATCATCG
15568 AATAAACCAA
Statistics
Matches: 197, Mismatches: 64, Indels: 18
0.71 0.23 0.06
Matches are distributed among these distances:
42 31 0.16
43 137 0.70
46 28 0.14
47 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (43 bp):
TGCATCATCGGATATACCGAAGTATGTATACTTGCACGTATAG
Found at i:15573 original size:86 final size:86
Alignment explanation
Indices: 15255--15672 Score: 385
Period size: 86 Copynumber: 4.8 Consensus size: 86
15245 ATGCAGACAA
* * * * * * *
15255 TGCATCATCGGGTATACCAAAGTATGTATATTGACACGTACAGTGCATCATCGGATAAACCGAAG
1 TGCATCATCGGATATACCGAAGTATGTATACTGGCACGTATAGTGCATCATCGAATAAACCAAAG
* *
15320 -AAATATACTTGCACATATA-AG
66 AAAATATACTGGCA-A-ACACAG
* * *
15341 -GCATCATTGGATATACTGAAGTATGTATACTTGCACGTATAGTGCATCATCGAATAAACCAAAG
1 TGCATCATCGGATATACCGAAGTATGTATACTGGCACGTATAGTGCATCATCGAATAAACCAAAG
*
15405 AAAATATACTGGCAAAACACTTAA
66 AAAATATACTGGC-AAACAC--AG
** * * * ** * * * * *
15429 TGCATCATCAAATATACTGTAGTATGCATACTAACGCATATAGAGCATTATCGGATAAACCAAAG
1 TGCATCATCGGATATACCGAAGTATGTATACTGGCACGTATAGTGCATCATCGAATAAACCAAAG
* *
15494 AAAATATACTGGCACATACAG
66 AAAATATACTGGCAAACACAG
* * *
15515 TGCATCATCGGATAAACCGAAGTATGTATACTGGTACGTATAGTGAATCATCGAATAAACCAAAG
1 TGCATCATCGGATATACCGAAGTATGTATACTGGCACGTATAGTGCATCATCGAATAAACCAAAG
*
15580 AAAATATACTAGCAAACACAG
66 AAAATATACTGGCAAACACAG
* * * ** ** * * * *
15601 TGCATCATCGGATAAATCGAAGCAACTATAC-GGCACACACAGTGCATCATCAAATAAACCGATG
1 TGCATCATCGGATATACCGAAGTATGTATACTGGCACGTATAGTGCATCATCGAATAAACCAAAG
15665 AAAATATA
66 AAAATATA
15673 TAGACTTTTT
Statistics
Matches: 268, Mismatches: 58, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
85 89 0.33
86 108 0.40
87 1 0.00
88 5 0.02
89 65 0.24
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (86 bp):
TGCATCATCGGATATACCGAAGTATGTATACTGGCACGTATAGTGCATCATCGAATAAACCAAAG
AAAATATACTGGCAAACACAG
Found at i:15588 original size:43 final size:43
Alignment explanation
Indices: 15478--15672 Score: 176
Period size: 43 Copynumber: 4.6 Consensus size: 43
15468 ATAGAGCATT
*
15478 ATCGGATAAACCAAAGAAAATATACTGGCACATACAGTGCATC
1 ATCGGATAAACCAAAGAAAATATACTGGCACATACAGTGAATC
* * ** * * *
15521 ATCGGATAAACCGAAGTATGTATACTGGTACGTATAGTGAATC
1 ATCGGATAAACCAAAGAAAATATACTGGCACATACAGTGAATC
* * * * *
15564 ATCGAATAAACCAAAGAAAATATACTAGCAAACACAGTGCATC
1 ATCGGATAAACCAAAGAAAATATACTGGCACATACAGTGAATC
* * * * * *
15607 ATCGGATAAATCGAAGCAACTATAC-GGCACACACAGTGCATC
1 ATCGGATAAACCAAAGAAAATATACTGGCACATACAGTGAATC
** * *
15649 ATCAAATAAACCGATGAAAATATA
1 ATCGGATAAACCAAAGAAAATATA
15673 TAGACTTTTT
Statistics
Matches: 119, Mismatches: 33, Indels: 1
0.78 0.22 0.01
Matches are distributed among these distances:
42 33 0.28
43 86 0.72
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.20
Consensus pattern (43 bp):
ATCGGATAAACCAAAGAAAATATACTGGCACATACAGTGAATC
Found at i:17596 original size:43 final size:43
Alignment explanation
Indices: 17531--17634 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
17521 TATCGTTCCA
* * * *
17531 CACATACAGTGCATCATTGGATAAATC-AGAGCAACTATACTAG
1 CACACACAATGCATCATCGGATAAATCGA-AACAACTATACTAG
* * *
17574 CACACACAATGCATTATCGGATAAATCGAAACAACTATATTGG
1 CACACACAATGCATCATCGGATAAATCGAAACAACTATACTAG
* *
17617 CACACATAGTGCATCATC
1 CACACACAATGCATCATC
17635 AAATGTACCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 49 0.98
44 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (43 bp):
CACACACAATGCATCATCGGATAAATCGAAACAACTATACTAG
Found at i:23982 original size:57 final size:57
Alignment explanation
Indices: 23893--24021 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 57
23883 GAATGCCACC
* *
23893 CAATGGTTGACACCACCTTTTTAACATAAAAAAAATATT-TTTCGGGTGTTTGGCAAG
1 CAATGGTCGACACCACCTTTCTAACAT-AAAAAAATATTCTTTCGGGTGTTTGGCAAG
** * * * *
23950 TTATGGTCGACACCACCTTTCCT-AGATTAAAAAATATTCTTTTGGTTGTTTGGCAAG
1 CAATGGTCGACACCACCTTT-CTAACATAAAAAAATATTCTTTCGGGTGTTTGGCAAG
*
24007 CAATGGTCTACACCA
1 CAATGGTCGACACCA
24022 TATTTTTTTG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
56 10 0.17
57 48 0.81
58 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (57 bp):
CAATGGTCGACACCACCTTTCTAACATAAAAAAATATTCTTTCGGGTGTTTGGCAAG
Found at i:25428 original size:147 final size:147
Alignment explanation
Indices: 25161--25457 Score: 594
Period size: 147 Copynumber: 2.0 Consensus size: 147
25151 AATGTCATGA
25161 CAACCTGCATAAACTAGATCTACGTGAGTGTACAGCTGGAGTAACTAACTTGTACAACTACAAGG
1 CAACCTGCATAAACTAGATCTACGTGAGTGTACAGCTGGAGTAACTAACTTGTACAACTACAAGG
25226 AAGTTAGATTTGAGAGTAGAAGGACACCTATACTTGACAATAACGATAAATACTGAGCAGAGAAG
66 AAGTTAGATTTGAGAGTAGAAGGACACCTATACTTGACAATAACGATAAATACTGAGCAGAGAAG
25291 AAGAAGAAGGGGATCAT
131 AAGAAGAAGGGGATCAT
25308 CAACCTGCATAAACTAGATCTACGTGAGTGTACAGCTGGAGTAACTAACTTGTACAACTACAAGG
1 CAACCTGCATAAACTAGATCTACGTGAGTGTACAGCTGGAGTAACTAACTTGTACAACTACAAGG
25373 AAGTTAGATTTGAGAGTAGAAGGACACCTATACTTGACAATAACGATAAATACTGAGCAGAGAAG
66 AAGTTAGATTTGAGAGTAGAAGGACACCTATACTTGACAATAACGATAAATACTGAGCAGAGAAG
25438 AAGAAGAAGGGGATCAT
131 AAGAAGAAGGGGATCAT
25455 CAA
1 CAA
25458 GCTCGTGACA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (147 bp):
CAACCTGCATAAACTAGATCTACGTGAGTGTACAGCTGGAGTAACTAACTTGTACAACTACAAGG
AAGTTAGATTTGAGAGTAGAAGGACACCTATACTTGACAATAACGATAAATACTGAGCAGAGAAG
AAGAAGAAGGGGATCAT
Found at i:27390 original size:18 final size:18
Alignment explanation
Indices: 27367--27413 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
27357 CACATCATGA
27367 TCAGATGCAGTCACATAC
1 TCAGATGCAGTCACATAC
** *
27385 TCAGATATAGTCACATGC
1 TCAGATGCAGTCACATAC
27403 TC-GTATGCAGT
1 TCAG-ATGCAGT
27414 TAGAGCAGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (18 bp):
TCAGATGCAGTCACATAC
Found at i:28477 original size:39 final size:39
Alignment explanation
Indices: 28433--28510 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
28423 GGCTACTAGG
28433 ATTATCTCTTAACCGCTCCTCTTGTATCGCATAAAGCAC
1 ATTATCTCTTAACCGCTCCTCTTGTATCGCATAAAGCAC
28472 ATTATCTCTTAACCGCTCCTCTTGTATCGCATAAAGCAC
1 ATTATCTCTTAACCGCTCCTCTTGTATCGCATAAAGCAC
28511 TCCTTGTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (39 bp):
ATTATCTCTTAACCGCTCCTCTTGTATCGCATAAAGCAC
Found at i:32455 original size:24 final size:24
Alignment explanation
Indices: 32422--32594 Score: 292
Period size: 24 Copynumber: 7.2 Consensus size: 24
32412 TCTGTCTAGA
32422 CTCGTAAGAGCTAACCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
* *
32446 TTCGTAAGAGCTAATCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
**
32470 CTCGTAAGAGCTAACCATTCTGAC
1 CTCGTAAGAGCTAACCATTCTGGG
32494 CTCGTAAGAGCTAACCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
32518 CTCGTAAGAGCTAACCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
32542 CTCGTAAGAGCTAACCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
* *
32566 CTCGTAAGAGTTAACCATTTTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
32590 CTCGT
1 CTCGT
32595 GGGGGCTAAA
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 139 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (24 bp):
CTCGTAAGAGCTAACCATTCTGGG
Found at i:50715 original size:50 final size:50
Alignment explanation
Indices: 50640--50737 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
50630 AATGAAGGTC
* * *
50640 TGGATGACCCCTGTAACACCCCTAACTCGTATCCTTTGTCGGACTAGGCT
1 TGGATGACCCCTGTAACACCCCTAACCCATATCCTTCGTCGGACTAGGCT
50690 TGGATGACCCCTGTAACACCCCTAACCCATATCCTTCGTCGGACTAGG
1 TGGATGACCCCTGTAACACCCCTAACCCATATCCTTCGTCGGACTAGG
50738 GTCAAGTAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (50 bp):
TGGATGACCCCTGTAACACCCCTAACCCATATCCTTCGTCGGACTAGGCT
Found at i:51817 original size:37 final size:37
Alignment explanation
Indices: 51750--51893 Score: 171
Period size: 37 Copynumber: 3.9 Consensus size: 37
51740 TTGATTCACC
* * * *
51750 GGTACAAAGCCTGAAAACACAGGCAGAAAGCCTACTA
1 GGTACAAAGCCCGAATACACTGGCACAAAGCCTACTA
* * *
51787 GGCACAAAGCCCGAATACACCGGAACAAAGCCTACTA
1 GGTACAAAGCCCGAATACACTGGCACAAAGCCTACTA
* * *
51824 GGTACATAGCCCGTATACACTGGCACAAAGCCTATTA
1 GGTACAAAGCCCGAATACACTGGCACAAAGCCTACTA
* * *
51861 GGTGCATAGCCCAAATACACTGGCACAAAGCCT
1 GGTACAAAGCCCGAATACACTGGCACAAAGCCT
51894 GATTATTTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 92 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.14
Consensus pattern (37 bp):
GGTACAAAGCCCGAATACACTGGCACAAAGCCTACTA
Found at i:58987 original size:37 final size:37
Alignment explanation
Indices: 58946--59078 Score: 212
Period size: 37 Copynumber: 3.6 Consensus size: 37
58936 CAAAAAGCCT
* *
58946 GAATATACCGGCACAAAGCCTACTAGGCACATAGCTC
1 GAATACACCAGCACAAAGCCTACTAGGCACATAGCTC
*
58983 GAATACACCAGCACAAAGCCTACTAGGCACATAGCCC
1 GAATACACCAGCACAAAGCCTACTAGGCACATAGCTC
* * *
59020 GAATACACCGGCACAAAGCCTTCTAGGTACATAGCTC
1 GAATACACCAGCACAAAGCCTACTAGGCACATAGCTC
59057 GAATACACCAGCACAAAGCCTA
1 GAATACACCAGCACAAAGCCTA
59079 GTAAGCATAA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 87 1.00
ACGTcount: A:0.37, C:0.32, G:0.17, T:0.14
Consensus pattern (37 bp):
GAATACACCAGCACAAAGCCTACTAGGCACATAGCTC
Found at i:59093 original size:74 final size:74
Alignment explanation
Indices: 58934--59095 Score: 243
Period size: 74 Copynumber: 2.2 Consensus size: 74
58924 CAAAAACACT
* *
58934 AGCAAAAAGCCTGAATATACCGGCACAAAGCCTACTAGGCACATAGCTCGAATACACCAGCACAA
1 AGCAAAAAGCCCGAATACACCGGCACAAAGCCTACTAGGCACATAGCTCGAATACACCAGCACAA
58999 AGCCTACTA
66 AGCCTACTA
* * * * *
59008 GGCACATAGCCCGAATACACCGGCACAAAGCCTTCTAGGTACATAGCTCGAATACACCAGCACAA
1 AGCAAAAAGCCCGAATACACCGGCACAAAGCCTACTAGGCACATAGCTCGAATACACCAGCACAA
*
59073 AGCCTAGTA
66 AGCCTACTA
*
59082 AGCATAAAGCCCGA
1 AGCAAAAAGCCCGA
59096 TTATTTAAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.14
Consensus pattern (74 bp):
AGCAAAAAGCCCGAATACACCGGCACAAAGCCTACTAGGCACATAGCTCGAATACACCAGCACAA
AGCCTACTA
Found at i:59985 original size:45 final size:45
Alignment explanation
Indices: 59921--60009 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
59911 TAATATTAGA
59921 GTTTTCCCTTATTTCATTCCTTTCTTCTTTTACCAATTTACTACC
1 GTTTTCCCTTATTTCATTCCTTTCTTCTTTTACCAATTTACTACC
*
59966 GTTTTCCCTTATTTCATTCCTTTCTTCTTTTACTAATTTACTAC
1 GTTTTCCCTTATTTCATTCCTTTCTTCTTTTACCAATTTACTAC
60010 TTTAACCTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.16, C:0.27, G:0.02, T:0.55
Consensus pattern (45 bp):
GTTTTCCCTTATTTCATTCCTTTCTTCTTTTACCAATTTACTACC
Found at i:60875 original size:19 final size:19
Alignment explanation
Indices: 60844--60881 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
60834 TAAAAATCGG
*
60844 TAAATAATATTTTGGAAAA
1 TAAATAATATTTTAGAAAA
60863 TAAA-AATATTTTTAGAAAA
1 TAAATAATA-TTTTAGAAAA
60882 ATTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TAAATAATATTTTAGAAAA
Found at i:68595 original size:25 final size:25
Alignment explanation
Indices: 68566--68639 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
68556 GACAAGATCA
68566 CGCTCTTACGAGCCAGACAGAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
* * *
68591 TGCTCTTACGAGCTAGACAGTATAT
1 CGCTCTTACGAGCCAGACAGAATAT
* *
68616 CGCTCTTATGAGCCTAGAAAGAAT
1 CGCTCTTACGAGCC-AGACAGAAT
68640 TTAACAAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 33 0.82
26 7 0.17
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (25 bp):
CGCTCTTACGAGCCAGACAGAATAT
Found at i:68840 original size:80 final size:80
Alignment explanation
Indices: 68715--68888 Score: 203
Period size: 80 Copynumber: 2.2 Consensus size: 80
68705 CATCGAAACA
* *
68715 GTCCATATTATCAACTCACGATGCTGCATACACATGCTAGTAAGAATCTGCAACATATGCAAGAT
1 GTCCATATAATCAACTCACGATGCTGCATACACATGCTAGTAAGAATCCGCAACATATGCAAGAT
68780 CTTAG-CCATCGGAGG
66 -TTAGACCATCGGAGG
* * * * *
68795 GTCCATATAATCTACTCACGATGCTGC-T-CATATAAGCTA-TCAAGAATCCGTAACATATGTAG
1 GTCCATATAATCAACTCACGATGCTGCATACACAT--GCTAGT-AAGAATCCGCAACATATGCAA
* *
68857 GATTTCGACCATTGGAGG
63 GATTTAGACCATCGGAGG
68875 GTCCATATAATCAA
1 GTCCATATAATCAA
68889 TATACAGTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 5 0.06
80 71 0.89
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (80 bp):
GTCCATATAATCAACTCACGATGCTGCATACACATGCTAGTAAGAATCCGCAACATATGCAAGAT
TTAGACCATCGGAGG
Found at i:73069 original size:80 final size:80
Alignment explanation
Indices: 72983--73131 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 80
72973 CCTCATGACA
*
72983 CTGCTCACACAAGCTGTCAAGAATCCACAACACATGCAGGATCTCAGCCACCGGAGGGTCCATAT
1 CTGCTCACACAAGCTGTCAAGAATCCACAACACATGCAGGATCTCAGCCACCGAAGGGTCCATAT
73048 AATCTACTAACTATG
66 AATCTACTAACTATG
* ** * * * * *
73063 CTGCTCACATAATTTGTCAAGAATCCGCAACATATGTAGGATCTTAGCCATCGAAGGGTCCATAT
1 CTGCTCACACAAGCTGTCAAGAATCCACAACACATGCAGGATCTCAGCCACCGAAGGGTCCATAT
73128 AATC
66 AATC
73132 AATCTCTGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (80 bp):
CTGCTCACACAAGCTGTCAAGAATCCACAACACATGCAGGATCTCAGCCACCGAAGGGTCCATAT
AATCTACTAACTATG
Found at i:76732 original size:20 final size:20
Alignment explanation
Indices: 76707--76744 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
76697 AGTTAGACAA
76707 GATCAATCAATATCACACCG
1 GATCAATCAATATCACACCG
76727 GATCAATCAATATCACAC
1 GATCAATCAATATCACAC
76745 TATCACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (20 bp):
GATCAATCAATATCACACCG
Found at i:78413 original size:21 final size:21
Alignment explanation
Indices: 78389--78439 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
78379 CCTATGCTAG
78389 TTCTACCGATACAAG-TATAAC
1 TTCTACCGATACAAGTTAT-AC
* *
78410 TTCTACCAATACAAGTTATGC
1 TTCTACCGATACAAGTTATAC
78431 TTCTACCGA
1 TTCTACCGA
78440 AACTAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTTATAC
Found at i:92670 original size:17 final size:18
Alignment explanation
Indices: 92648--92681 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
92638 TAAATGAGTT
92648 AATTAGGAT-TAAATTGA
1 AATTAGGATATAAATTGA
*
92665 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
92682 GATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGA
Found at i:93003 original size:18 final size:18
Alignment explanation
Indices: 92980--93014 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
92970 TTTGTGATCA
92980 AAATTGAAATTGAAAGTC
1 AAATTGAAATTGAAAGTC
*
92998 AAATTGGAATTGAAAGT
1 AAATTGAAATTGAAAGT
93015 GATATGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (18 bp):
AAATTGAAATTGAAAGTC
Found at i:97918 original size:12 final size:13
Alignment explanation
Indices: 97878--97919 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
97868 AAAAATCACA
97878 AAAAGA-AAGAA-
1 AAAAGAGAAGAAG
*
97889 AAAACAGAAGAAG
1 AAAAGAGAAGAAG
97902 AAAAGAGAA-AAG
1 AAAAGAGAAGAAG
97914 AAAAGA
1 AAAAGA
97920 AGTATATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 5 0.19
12 14 0.52
13 8 0.30
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAGAAG
Found at i:101421 original size:18 final size:18
Alignment explanation
Indices: 101395--101429 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
101385 CGCCATCGAA
* *
101395 GAAAGAGAAAGGCAAGGC
1 GAAAAAGAAAGACAAGGC
101413 GAAAAAGAAAGACAAGG
1 GAAAAAGAAAGACAAGG
101430 AATCCCATGT
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:0.57, C:0.09, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAAAAGAAAGACAAGGC
Found at i:106245 original size:37 final size:37
Alignment explanation
Indices: 106190--106410 Score: 248
Period size: 37 Copynumber: 6.0 Consensus size: 37
106180 TTTAATTCGA
* * * *
106190 GCTATGTGTCTAGTAGGCTTCGTGTCGGTGTATTCGG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* * *
106227 GCTGTGTGCCTAGCAGGCTTTGTGCCGGTGTAATCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* * * *
106264 TCTATGTACCTAGTAGGCTTCGTGCCGGTGTATTTAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* *
106301 GCTATGTGCCTAGCAGGCTTCGTGTCAGTGTATTCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* **
106338 GCTATGTGCCTAGCAGGCTTAGTGCCAATGTATTC-G
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* *
106374 GACTATGTGTCTAGCAGGCCTTTGTGCCGGTG-ATTCA
1 G-CTATGTGCCTAGCAGG-CTTCGTGCCGGTGTATTCA
106411 AGAATGCTTG
Statistics
Matches: 154, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
36 2 0.01
37 142 0.92
38 10 0.06
ACGTcount: A:0.15, C:0.20, G:0.31, T:0.33
Consensus pattern (37 bp):
GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
Found at i:107485 original size:49 final size:50
Alignment explanation
Indices: 107427--107530 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 50
107417 TGAATATACA
107427 TAAGTGTATGCAAATTGATATTGTGAATGATGTTATGGTGTGATTGTAAG
1 TAAGTGTATGCAAATTGATATTGTGAATGATGTTATGGTGTGATTGTAAG
*
107477 TAAG-GTATGCAAATTGATATTGTGAATGATGTTGTGGTGTGATTGTAAG
1 TAAGTGTATGCAAATTGATATTGTGAATGATGTTATGGTGTGATTGTAAG
107526 TAAGT
1 TAAGT
107531 TAGTTTTAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 48 0.92
50 4 0.08
ACGTcount: A:0.30, C:0.02, G:0.29, T:0.39
Consensus pattern (50 bp):
TAAGTGTATGCAAATTGATATTGTGAATGATGTTATGGTGTGATTGTAAG
Found at i:109102 original size:13 final size:13
Alignment explanation
Indices: 109084--109108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109074 TGTTCTCGAG
109084 TATACATACAAAT
1 TATACATACAAAT
109097 TATACATACAAA
1 TATACATACAAA
109109 AACGTTGTAA
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:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (13 bp):
TATACATACAAAT
Found at i:109205 original size:22 final size:22
Alignment explanation
Indices: 109162--109208 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
109152 TTCAAAATTA
* *
109162 TAATACAAGTTCAAATTGAAAT
1 TAATACAAATTCAAATTAAAAT
* *
109184 TAATACAAATTGAATTTAAAAT
1 TAATACAAATTCAAATTAAAAT
109206 TAA
1 TAA
109209 ATTTAAGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (22 bp):
TAATACAAATTCAAATTAAAAT
Found at i:109341 original size:12 final size:12
Alignment explanation
Indices: 109324--109357 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
109314 GAAACTTTAA
109324 TTTAAATTTAGG
1 TTTAAATTTAGG
*
109336 TTTAAATTAAGG
1 TTTAAATTTAGG
109348 TTTAAATTTA
1 TTTAAATTTA
109358 AAATTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TTTAAATTTAGG
Found at i:109430 original size:6 final size:6
Alignment explanation
Indices: 109405--109549 Score: 100
Period size: 6 Copynumber: 24.7 Consensus size: 6
109395 TTTAATTTCG
* * * *
109405 AAATTA AAATTGA AAA-TA AAATTA AAATTG AAATTG AATTTA AAATAA
1 AAATTA AAATT-A AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
* * * * * * *
109453 AAATTA CAGTTA AAATGA AAATT- AAATGA AAA-TG AAATTT AAATGA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
* * * * * *
109499 AATTTA AAATT- AAATTA AATTTC AAATTA AAATTG AAATTT GAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
109546 AAAT
1 AAAT
109550 GAAATGAAAT
Statistics
Matches: 104, Mismatches: 30, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
5 16 0.15
6 84 0.81
7 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:109797 original size:22 final size:23
Alignment explanation
Indices: 109763--109819 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
109753 TATAAAAAAA
109763 ATAAAAAAAAATAAA-AAATTAT
1 ATAAAAAAAAATAAATAAATTAT
* *
109785 ATAACAAATAATAAATAAATT-T
1 ATAAAAAAAAATAAATAAATTAT
*
109807 -TAAAAAAATATAA
1 ATAAAAAAAAATAA
109820 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 10 0.34
22 14 0.48
23 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAAAAAAAATAAATAAATTAT
Found at i:109798 original size:10 final size:10
Alignment explanation
Indices: 109754--109804 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
109744 CCTAACGGGT
109754 ATAAAAAA-A
1 ATAAAAAATA
*
109763 ATAAAAAAAA
1 ATAAAAAATA
109773 ATAAAAAATTA
1 ATAAAAAA-TA
*
109784 TATAACAAATA
1 -ATAAAAAATA
109795 ATAAATAAAT
1 ATAAA-AAAT
109805 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 8 0.23
10 13 0.37
11 7 0.20
12 7 0.20
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:109816 original size:19 final size:20
Alignment explanation
Indices: 109754--109816 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 20
109744 CCTAACGGGT
* *
109754 ATAAAAAA-AATAAAAAAAA
1 ATAAAAAATTATATAAAAAA
109773 ATAAAAAATTATATAACAAATA
1 ATAAAAAATTATATAA-AAA-A
109795 ATAAATAAATT-T-TAAAAAA
1 ATAAA-AAATTATATAAAAAA
109814 ATA
1 ATA
109817 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 12 0.32
20 8 0.21
21 6 0.16
22 7 0.18
23 5 0.13
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAAAAATTATATAAAAAA
Found at i:112053 original size:116 final size:117
Alignment explanation
Indices: 111829--112062 Score: 321
Period size: 116 Copynumber: 2.0 Consensus size: 117
111819 TTCAAATACT
*
111829 CAAAAAAATATTTTATTATTCATATTTTTTTTAGTGTCGACCATTGCTTGCCAAACACCTAAAAA
1 CAAAAAAATATTTTATTATTCATATTTTTTTGAGTGTCGACCATTGCTTGCCAAACACCTAAAAA
* * *
111894 AATATTTTTTTTAATGTTAAAAAGGTGATGTCGGCTATTGGGTGCCATCCACC
66 AATA-TTTTTTTAATGTGAAAAAGGTGATGTCGACCATTGGGTGCCATCCACC
* * * * *
111947 CAAAAATAATAATTTT-TTATTCGTATTTTTTTGGGTGTTGGCCATTGCTTGCCAAACACC-CAA
1 CAAAAA-AAT-ATTTTATTATTCATATTTTTTTGAGTGTCGACCATTGCTTGCCAAACACCTAAA
* *
112010 AAAATA-TTTTTTAATGTGAAAAAGGTGGTGTCGACCATTGGGTGTCATCCACC
64 AAAATATTTTTTTAATGTGAAAAAGGTGATGTCGACCATTGGGTGCCATCCACC
112063 GATACTTTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
116 42 0.41
118 14 0.14
119 42 0.41
120 5 0.05
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (117 bp):
CAAAAAAATATTTTATTATTCATATTTTTTTGAGTGTCGACCATTGCTTGCCAAACACCTAAAAA
AATATTTTTTTAATGTGAAAAAGGTGATGTCGACCATTGGGTGCCATCCACC
Found at i:112291 original size:16 final size:17
Alignment explanation
Indices: 112266--112298 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
112256 GTTTTAGGTC
112266 ATTTAGGTAAA-TAATT
1 ATTTAGGTAAATTAATT
*
112282 ATTTATGTAAATTAATT
1 ATTTAGGTAAATTAATT
112299 TTTTTGCCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
ATTTAGGTAAATTAATT
Found at i:116880 original size:30 final size:30
Alignment explanation
Indices: 116828--116894 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
116818 AACAAAGGGG
* *
116828 AGATAGGAATGGCCTTTGGAGTTGTCAGGA
1 AGATAGGAATGGCCTTTCGAGTTCTCAGGA
*
116858 AGATATGG-ATGGGCTTTCGAGTTCTCAGGA
1 AGATA-GGAATGGCCTTTCGAGTTCTCAGGA
*
116888 ACATAGG
1 AGATAGG
116895 GGATATAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 28 0.88
31 2 0.06
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (30 bp):
AGATAGGAATGGCCTTTCGAGTTCTCAGGA
Found at i:118046 original size:20 final size:21
Alignment explanation
Indices: 118023--118074 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
118013 TAAGTCTAAA
118023 AATATATTTATATTATTT-TT
1 AATATATTTATATTATTTATT
* *
118043 AATATA-ATATTTTATTTATT
1 AATATATTTATATTATTTATT
*
118063 AAAAT-TTTATAT
1 AATATATTTATAT
118075 ATAATGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATATTTATATTATTTATT
Found at i:118084 original size:15 final size:13
Alignment explanation
Indices: 118039--118090 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
118029 TTTATATTAT
118039 TTTTAATATAATA
1 TTTTAATATAATA
* *
118052 TTTTATTTATTAAAA
1 TTTTA-ATA-TAATA
118067 TTTTATATATAATGA
1 TTTTA-ATATAAT-A
118082 TTTTAATAT
1 TTTTAATAT
118091 TTTTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 9 0.28
15 18 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TTTTAATATAATA
Found at i:120521 original size:26 final size:26
Alignment explanation
Indices: 120476--120542 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
120466 ATATAAATTT
120476 GAAA-TAAAAG-TTTTGGGGTTT-GG
1 GAAAGTAAAAGTTTTTGGGGTTTGGG
120499 GAGAAGTAAAAGTTTTTGGGGTTTGGG
1 GA-AAGTAAAAGTTTTTGGGGTTTGGG
120526 GAAAGTAAAA-TTTTTGG
1 GAAAGTAAAAGTTTTTGG
120543 AGGAAAGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 13 0.32
26 19 0.47
27 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (26 bp):
GAAAGTAAAAGTTTTTGGGGTTTGGG
Found at i:122805 original size:62 final size:59
Alignment explanation
Indices: 122694--122810 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 59
122684 ATCACTTTAA
* * * *
122694 TATTAAATTAACATAATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAACAAAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
122753 TATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAA
1 TATTAAAATAACAAAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATTAA
122811 GATAATTACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 20 0.41
60 1 0.02
62 28 0.57
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (59 bp):
TATTAAAATAACAAAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:122861 original size:12 final size:11
Alignment explanation
Indices: 122836--122896 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
122826 ATTAAATTAA
*
122836 TAAAATACTAT
1 TAAAATAATAT
122847 TAAAATAAGTAT
1 TAAAATAA-TAT
*
122859 TAAATTAA-AT
1 TAAAATAATAT
122869 TAAATATTAAACTAT
1 TAAA-A-T-AA-TAT
122884 TAAAATAATAT
1 TAAAATAATAT
122895 TA
1 TA
122897 TTTTTTGAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
10 6 0.15
11 12 0.29
12 13 0.32
13 3 0.07
14 1 0.02
15 6 0.15
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:122867 original size:17 final size:17
Alignment explanation
Indices: 122823--122879 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
122813 TAATTACTTT
*
122823 AATATTAAATTAATA-A
1 AATATTAAATTAAAATA
*
122839 AATACT--ATTAAAATA
1 AATATTAAATTAAAATA
* *
122854 AGTATTAAATTAAATTA
1 AATATTAAATTAAAATA
122871 AATATTAAA
1 AATATTAAA
122880 CTATTAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 5 0.16
17 16 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATATTAAATTAAAATA
Found at i:122888 original size:37 final size:36
Alignment explanation
Indices: 122821--122896 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
122811 GATAATTACT
122821 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
122858 TTAA-ATTAAATTAAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAATT-AATA-AAATACTATTAAAATAATA
122894 TTA
1 TTA
122897 TTTTTTGAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:125967 original size:282 final size:282
Alignment explanation
Indices: 125463--126030 Score: 1082
Period size: 282 Copynumber: 2.0 Consensus size: 282
125453 TAGCTTTGGA
125463 GTCAAACTTCATCCTAACCTTTAAATGGCCAAAATTTGTTCACGAAGTCGCATGCCTTGGTCTTC
1 GTCAAACTTCATCCTAACCTTTAAATGGCCAAAATTTGTTCACGAAGTCGCATGCCTTGGTCTTC
125528 TATAAGGGAGGCTTGGGAATTCTAAACCTCTTTCAACAGCAAGATCGAGAGTTCACATGTGAGGT
66 TATAAGGGAGGCTTGGGAATTCTAAACCTCTTTCAACAGCAAGATCGAGAGTTCACATGTGAGGT
* *
125593 GAGGGTTCGTACACCATGAAACTTAGGTCATCCCATTGAGTAGTGTCGGAAGCTTCACCGTCAGA
131 GAGGGTTCGTACACCATGAAACTTAGGTCATCCCATCGAGTAGTGTCGAAAGCTTCACCGTCAGA
125658 TCCATCATCTTCTGGTTTAGTAAGAATGGGATTCGATTATGAAATAACTATAATTTTCACACCAT
196 TCCATCATCTTCTGGTTTAGTAAGAATGGGATTCGATTATGAAATAACTATAATTTTCACACCAT
125723 CGAGGCTTGCCTCATCTATTAG
261 CGAGGCTTGCCTCATCTATTAG
*
125745 GTCAAACTTCATCCTAACCTTTAAATGGCCAAAATTTGTTCACGAAGTCGCATGCCTTGGTTTTC
1 GTCAAACTTCATCCTAACCTTTAAATGGCCAAAATTTGTTCACGAAGTCGCATGCCTTGGTCTTC
*
125810 TATAAGGGAGGCTTGGGAATTCTAAACCTCTTTCAACAGCAAGATCGAGAGTTCGCATGTGAGGT
66 TATAAGGGAGGCTTGGGAATTCTAAACCTCTTTCAACAGCAAGATCGAGAGTTCACATGTGAGGT
125875 GAGGGTTCGTACACCATGAAACTTAGGTCATCCCATCGAGTAGTGTCGAAAGCTTCACCGTCAGA
131 GAGGGTTCGTACACCATGAAACTTAGGTCATCCCATCGAGTAGTGTCGAAAGCTTCACCGTCAGA
* *
125940 TCCATCATCTTCTGGTTTAGTAAGAATGGGATTCGGTTATGAAATAACTATAATTTTTACACCAT
196 TCCATCATCTTCTGGTTTAGTAAGAATGGGATTCGATTATGAAATAACTATAATTTTCACACCAT
126005 CGAGGCTTGCCTCATCTATTAG
261 CGAGGCTTGCCTCATCTATTAG
126027 GTCA
1 GTCA
126031 TTATCTATTT
Statistics
Matches: 280, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
282 280 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (282 bp):
GTCAAACTTCATCCTAACCTTTAAATGGCCAAAATTTGTTCACGAAGTCGCATGCCTTGGTCTTC
TATAAGGGAGGCTTGGGAATTCTAAACCTCTTTCAACAGCAAGATCGAGAGTTCACATGTGAGGT
GAGGGTTCGTACACCATGAAACTTAGGTCATCCCATCGAGTAGTGTCGAAAGCTTCACCGTCAGA
TCCATCATCTTCTGGTTTAGTAAGAATGGGATTCGATTATGAAATAACTATAATTTTCACACCAT
CGAGGCTTGCCTCATCTATTAG
Found at i:140570 original size:23 final size:23
Alignment explanation
Indices: 140519--140570 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
140509 TTTTGCTTTT
*
140519 TTTTTTTAAAAAGAAAAAATTTA
1 TTTTTTTAAAAAGAAAAAATATA
**
140542 GATTTTTAAAAA-ATAAAAATATA
1 TTTTTTTAAAAAGA-AAAAATATA
140565 TTTTTT
1 TTTTTT
140571 AGTCATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTTTTTAAAAAGAAAAAATATA
Found at i:140716 original size:23 final size:23
Alignment explanation
Indices: 140664--140719 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
140654 GAAAAGTTTT
* * *
140664 TATTTTTTTAAAAAGAGAAAGTT
1 TATTTTTTTAAAAAGAAAAAATC
*
140687 TAGTTTTTTAAAAA-ATAAAAATC
1 TATTTTTTTAAAAAGA-AAAAATC
140710 TATTTTTTTA
1 TATTTTTTTA
140720 GTTATGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (23 bp):
TATTTTTTTAAAAAGAAAAAATC
Found at i:140809 original size:152 final size:147
Alignment explanation
Indices: 140515--140965 Score: 561
Period size: 154 Copynumber: 3.0 Consensus size: 147
140505 AAAGTTTTGC
* *
140515 TTTTTTTTTTTAAAAAGAAAAAATTTAGATTTTTAAAAAATAAAAA-TATATTTTTTAGTCATTT
1 TTTTTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAAATTAT-TTTTTTAGTCATTT
* * * *
140579 TAAA-AAAAGTTTAAATTTTTAAAAATAAAGTTTTGATTTTTTAAACTATTTTGAAATAAATGCT
65 TAAAGAAAAGTTTAAATTTTTAAAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGCT
140643 TTGATCTTTAAGAAAAGT
130 TTGATCTTTAAGAAAAGT
* * *
140661 TTTTATTTTTTTAAAAAGAGAAAGTTTAGTTTTTTAAAAAATAAAAATCTATTTTTTTAGTTATG
1 TTTT-TTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAAAT-TATTTTTTTAGTCATT
* *
140726 TTAAAGGAAAATTTTTAAATTTTTAAAAACAAAATTTTGAGTTTTTTTAACTATTTCGAAATAAA
64 TTAAA-GAAAA-GTTTAAATTTTTAAAAACAAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAA
* *
140791 AACTTTGATCTTTAAGAAAAATT
126 AGCTTTGATCTTTAAG-AAAAGT
* * *
140814 TTGATTTTTTTTTTAAAAGAGAAAGTTTAGATTTTAAAAAAATAAAAA-TATTATTTTGTAGTGA
1 TT--TTTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAAATTATT-TTTT-TAGTCA
* *
140878 TTTTAAAGAAAAAAAGTTTAAAATTTTAAAAAC-AAGTTCTTGATTTTTTTAACTATTACGAAAT
62 TTTTAAAG---AAAAGTTTAAATTTTTAAAAACAAAGTT-TTGATTTTTTTAACTATTTCGAAAT
*
140942 -AAAGCTTTGATATTTAAGAAAAGT
123 AAAAGCTTTGATCTTTAAGAAAAGT
140966 AGTGATTTTA
Statistics
Matches: 264, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
146 4 0.02
147 39 0.15
148 16 0.06
149 3 0.01
150 4 0.02
151 25 0.09
152 45 0.17
153 28 0.11
154 74 0.28
155 22 0.08
156 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (147 bp):
TTTTTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAAATAAAAATTATTTTTTTAGTCATTTT
AAAGAAAAGTTTAAATTTTTAAAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGCTT
TGATCTTTAAGAAAAGT
Found at i:141475 original size:21 final size:21
Alignment explanation
Indices: 141451--141492 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
141441 TTTACTCACA
*
141451 CTTATATAATTTTTATTTATT
1 CTTATATAATCTTTATTTATT
* *
141472 CTTATTTCATCTTTATTTATT
1 CTTATATAATCTTTATTTATT
141493 TTCATATCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTATATAATCTTTATTTATT
Found at i:146010 original size:16 final size:16
Alignment explanation
Indices: 145989--146019 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
145979 ATAATGTGAA
*
145989 AATAATGATGAAATGC
1 AATAATAATGAAATGC
146005 AATAATAATGAAATG
1 AATAATAATGAAATG
146020 AGGTCCCCAA
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:0.55, C:0.03, G:0.16, T:0.26
Consensus pattern (16 bp):
AATAATAATGAAATGC
Found at i:146565 original size:160 final size:160
Alignment explanation
Indices: 146301--146610 Score: 530
Period size: 160 Copynumber: 1.9 Consensus size: 160
146291 TGACTGCAAC
*
146301 AACACTTTCGTGGTTAAAACATTCAAACCCAAAGATTAAACAGTAAAAGCAAGCTTGGATAAAAT
1 AACACTTTCGTGGTCAAAACATTCAAACCCAAAGATTAAACAGTAAAAGCAAGCTTGGATAAAAT
* * * * * * *
146366 ATCATTTAGTCTAGAAATCAAGTATACTTTCTTACAATCTTGAAATAAACATGAATCGCTAGTGT
66 ATCATTTAGTCTAAAAATCAAGTATACTTCCATACAATCTTGAAATAAACATGAATCACCAGCGA
146431 TTAAGAAAGAAATATAAAAGAAACTGTAAT
131 TTAAGAAAGAAATATAAAAGAAACTGTAAT
146461 AACACTTTCGTGGTCAAAACATTCAAACCCAAAGATTAAACAGTAAAAGCAAGCTTGGATAAAAT
1 AACACTTTCGTGGTCAAAACATTCAAACCCAAAGATTAAACAGTAAAAGCAAGCTTGGATAAAAT
* *
146526 ATCATTTAGTCTAAAAATCAAGTGTACTTCCATACAATCTTGAAATAAAGATGAATCACCAGCGA
66 ATCATTTAGTCTAAAAATCAAGTATACTTCCATACAATCTTGAAATAAACATGAATCACCAGCGA
146591 TTAAGAAAGAAATATAAAAG
131 TTAAGAAAGAAATATAAAAG
146611 GACAAATGGA
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
160 140 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (160 bp):
AACACTTTCGTGGTCAAAACATTCAAACCCAAAGATTAAACAGTAAAAGCAAGCTTGGATAAAAT
ATCATTTAGTCTAAAAATCAAGTATACTTCCATACAATCTTGAAATAAACATGAATCACCAGCGA
TTAAGAAAGAAATATAAAAGAAACTGTAAT
Found at i:150921 original size:55 final size:55
Alignment explanation
Indices: 150833--150939 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
150823 CTAATTTCGT
* * *
150833 TGCATGACCATATCCCGAATTACACCCAGAATTGTCATCACATCTGACAGCTTGC
1 TGCATGACCATATCCAGAATTACACCCAAAATTGTCACCACATCTGACAGCTTGC
* * * * *
150888 TGCATGAGCATATCTAGAATTGCACCCAAAATTGTCGCCACATCTGATAGCT
1 TGCATGACCATATCCAGAATTACACCCAAAATTGTCACCACATCTGACAGCT
150940 GTCTGGATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (55 bp):
TGCATGACCATATCCAGAATTACACCCAAAATTGTCACCACATCTGACAGCTTGC
Found at i:152690 original size:36 final size:36
Alignment explanation
Indices: 152650--152732 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
152640 TTCTTGCTGT
* **
152650 GACAGTTTTGGTGCAATTTGGAAGTGCTCATGCAAC
1 GACAGTTTTGGTGCAATCTAAAAGTGCTCATGCAAC
**
152686 GACAGTTTTGGTGCAATCTAAAAGTGCTCATGCGGC
1 GACAGTTTTGGTGCAATCTAAAAGTGCTCATGCAAC
152722 GACAGTTTTGG
1 GACAGTTTTGG
152733 GCACAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (36 bp):
GACAGTTTTGGTGCAATCTAAAAGTGCTCATGCAAC
Found at i:153895 original size:18 final size:17
Alignment explanation
Indices: 153829--153887 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
153819 ATATATATGG
* **
153829 AAATGCAATGACAATGT
1 AAATGCAGTGACAATAA
* *
153846 AGATGCAGCGACAATAA
1 AAATGCAGTGACAATAA
153863 AAATGCAGTGACAATACA
1 AAATGCAGTGACAATA-A
153881 AAATGCA
1 AAATGCA
153888 TGGACAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 26 0.76
18 8 0.24
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:157068 original size:36 final size:36
Alignment explanation
Indices: 157028--157119 Score: 130
Period size: 36 Copynumber: 2.5 Consensus size: 36
157018 ATATTCCTGT
* * *
157028 GGCGACAGTTTTGGTGCAATCTGGAAGTGCTCATGC
1 GGCGATAGTTTTGGTGCAATCTGAAAGTGCTAATGC
157064 GGCGATAGTTTTGGTGCAATCTGAAAGTGCTAATGC
1 GGCGATAGTTTTGGTGCAATCTGAAAGTGCTAATGC
**
157100 GATGATAGTTTTGGGTGCAA
1 GGCGATAGTTTT-GGTGCAA
157120 ATTTGGATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 43 0.86
37 7 0.14
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (36 bp):
GGCGATAGTTTTGGTGCAATCTGAAAGTGCTAATGC
Found at i:164798 original size:17 final size:18
Alignment explanation
Indices: 164776--164811 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
164766 TAAATGAGTT
164776 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
164793 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
164811 A
1 A
164812 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:170578 original size:13 final size:13
Alignment explanation
Indices: 170562--170586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
170552 TGAGTTCGTA
170562 AATAATTATTAGG
1 AATAATTATTAGG
170575 AATAATTATTAG
1 AATAATTATTAG
170587 TCTAGTAGTG
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AATAATTATTAGG
Found at i:171461 original size:18 final size:18
Alignment explanation
Indices: 171438--171483 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
171428 ATTAGATAGT
*
171438 TAATTAGAATGTGGAAGG
1 TAATTAGAATATGGAAGG
171456 TAATTAGAATATGGAAGG
1 TAATTAGAATATGGAAGG
*
171474 AAATT-GAATA
1 TAATTAGAATA
171484 AAAATAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (18 bp):
TAATTAGAATATGGAAGG
Found at i:171545 original size:17 final size:18
Alignment explanation
Indices: 171523--171556 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
171513 TAAATGAGTT
171523 AATTAGGAT-TAAATTGA
1 AATTAGGATATAAATTGA
*
171540 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
171557 GATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGA
Found at i:171873 original size:18 final size:18
Alignment explanation
Indices: 171850--171886 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
171840 TTTGTGATCA
171850 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
171868 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
171886 A
1 A
171887 TATGAAGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:171881 original size:12 final size:12
Alignment explanation
Indices: 171850--171905 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
171840 TTTGTGATCA
171850 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
171862 AAAGTGAAATTG
1 AAATTGAAAGTG
*
171874 GAATTGAAAGTG
1 AAATTGAAAGTG
*
171886 ATA-TG-AAGTG
1 AAATTGAAAGTG
171896 TAAATTGAAA
1 -AAATTGAAA
171906 ATCCCTATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
12 22 0.67
13 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:172998 original size:43 final size:43
Alignment explanation
Indices: 172930--173024 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
172920 AAATGAACTG
* * *
172930 TATAA-TTAATAACATGTCAAGATATTAATAAGAGTAAAGTTA
1 TATAATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAA
* * *
172972 TATAATTTAGTAACATG-CAACCATATTAACATGAGTCAAGTAA
1 TATAATTTAATAACATGTCAA-CATATTAACAAGAGTAAAGTAA
173015 TATAATTTAA
1 TATAATTTAA
173025 CATGTTAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 8 0.18
43 36 0.82
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (43 bp):
TATAATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAA
Found at i:180948 original size:18 final size:18
Alignment explanation
Indices: 180925--180959 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
180915 AATTAAATTT
180925 AAAATTAACCAAACTTAA
1 AAAATTAACCAAACTTAA
*
180943 AAAATTAATCAAACTTA
1 AAAATTAACCAAACTTA
180960 CCTTTCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAACCAAACTTAA
Found at i:181115 original size:6 final size:6
Alignment explanation
Indices: 181104--181152 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
181094 CATTACATTT
* *
181104 TTCTCC TTCTCC TCCTCCTCC TTCTCC TCCTCC TTTTCC TTCTCC TTCT
1 TTCTCC TTCTCC T--T-CTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCT
181153 TCCGTCTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 29 0.81
7 1 0.03
8 1 0.03
9 5 0.14
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
TTCTCC
Found at i:181149 original size:15 final size:15
Alignment explanation
Indices: 181106--181137 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
181096 TTACATTTTT
181106 CTCCTTCTCCTCCTC
1 CTCCTTCTCCTCCTC
181121 CTCCTTCTCCTCCTC
1 CTCCTTCTCCTCCTC
181136 CT
1 CT
181138 TTTCCTTCTC
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:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (15 bp):
CTCCTTCTCCTCCTC
Found at i:182455 original size:15 final size:15
Alignment explanation
Indices: 182435--182466 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
182425 TTATCTTCAA
182435 TGAGGTACACCGCTG
1 TGAGGTACACCGCTG
182450 TGAGGTACACCGCTG
1 TGAGGTACACCGCTG
182465 TG
1 TG
182467 CGCAAAAGAA
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:0.19, C:0.25, G:0.34, T:0.22
Consensus pattern (15 bp):
TGAGGTACACCGCTG
Found at i:190037 original size:81 final size:81
Alignment explanation
Indices: 189901--190159 Score: 326
Period size: 81 Copynumber: 3.2 Consensus size: 81
189891 GTGTACAGTT
* * * * * * *
189901 CTACTCACACAAGCTGACGAGGA-CTCGCAACATATGC-AGGAGCTCAGCCACCGCTACAGTTTA
1 CTACTCACACAAGCTGATGAGAATC-CACAACATATGCGA-AACCTCAACCATCGCTACAGTTTA
189964 TGTCACCTGCTCACAATG
64 TGTCACCTGCTCACAATG
* *
189982 CTACTCACACAAGCTTATGAGAATCCACAACATATGCGAAACCTCAACCATCGCTACGGTTTATG
1 CTACTCACACAAGCTGATGAGAATCCACAACATATGCGAAACCTCAACCATCGCTACAGTTTATG
*
190047 TCACCCGCTCACAATG
66 TCACCTGCTCACAATG
* * *
190063 ATACTCACACAAGCTGATGAGAATCCACAACATATGCGAAACCTCAACTATCGCTACAGTCTATG
1 CTACTCACACAAGCTGATGAGAATCCACAACATATGCGAAACCTCAACCATCGCTACAGTTTATG
* *
190128 TCA-CTCACTCACGATG
66 TCACCT-GCTCACAATG
*
190144 CTGCTCACACAAGCTG
1 CTACTCACACAAGCTG
190160 TCAAGAATCT
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.01
81 152 0.98
82 2 0.01
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.21
Consensus pattern (81 bp):
CTACTCACACAAGCTGATGAGAATCCACAACATATGCGAAACCTCAACCATCGCTACAGTTTATG
TCACCTGCTCACAATG
Found at i:192687 original size:35 final size:35
Alignment explanation
Indices: 192641--192812 Score: 245
Period size: 35 Copynumber: 4.9 Consensus size: 35
192631 AGCTTTGATC
* *
192641 TGCTTATGTCTCGTTTAGAGCATAAGGTTATGGAT
1 TGCTTATGTCTCGGTTAGAGCGTAAGGTTATGGAT
* *
192676 TGCTTACGTCTCGGTTAGAGCATAAGGTTATGGAT
1 TGCTTATGTCTCGGTTAGAGCGTAAGGTTATGGAT
* *
192711 TGCTTATGTCTCGATTAGAGCGTAAGGTTATGAATT
1 TGCTTATGTCTCGGTTAGAGCGTAAGGTTATGGA-T
*
192747 TGCTTATGTCTCGGTTAGAGCGTAAGGTTATGGGT
1 TGCTTATGTCTCGGTTAGAGCGTAAGGTTATGGAT
* * *
192782 TGGTTACGTCTCGGTTAGAGCGTAATGTTAT
1 TGCTTATGTCTCGGTTAGAGCGTAAGGTTAT
192813 CATAGCTCGA
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
35 92 0.74
36 32 0.26
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (35 bp):
TGCTTATGTCTCGGTTAGAGCGTAAGGTTATGGAT
Found at i:192777 original size:71 final size:70
Alignment explanation
Indices: 192641--192812 Score: 245
Period size: 71 Copynumber: 2.4 Consensus size: 70
192631 AGCTTTGATC
* * *
192641 TGCTTATGTCTCGTTTAGAGCATAAGGTTATGGATTGCTTACGTCTCGGTTAGAGCATAAGGTTA
1 TGCTTATGTCTCGATTAGAGCGTAAGGTTATGAATTGCTTACGTCTCGGTTAGAGCATAAGGTTA
192706 TGGAT
66 TGGAT
* *
192711 TGCTTATGTCTCGATTAGAGCGTAAGGTTATGAATTTGCTTATGTCTCGGTTAGAGCGTAAGGTT
1 TGCTTATGTCTCGATTAGAGCGTAAGGTTATGAA-TTGCTTACGTCTCGGTTAGAGCATAAGGTT
*
192776 ATGGGT
65 ATGGAT
* * * *
192782 TGGTTACGTCTCGGTTAGAGCGTAATGTTAT
1 TGCTTATGTCTCGATTAGAGCGTAAGGTTAT
192813 CATAGCTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
70 31 0.34
71 60 0.66
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (70 bp):
TGCTTATGTCTCGATTAGAGCGTAAGGTTATGAATTGCTTACGTCTCGGTTAGAGCATAAGGTTA
TGGAT
Found at i:194734 original size:19 final size:20
Alignment explanation
Indices: 194710--194747 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
194700 TAGTCCTTAA
*
194710 ACTTTA-AAATCATCAAATT
1 ACTTTACAAATAATCAAATT
194729 ACTTTACAAATAATCAAAT
1 ACTTTACAAATAATCAAAT
194748 CTAACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (20 bp):
ACTTTACAAATAATCAAATT
Found at i:207402 original size:23 final size:23
Alignment explanation
Indices: 207372--207419 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
207362 TTCTTATTAT
207372 GTTAATTTATATTTTCCGTGATG
1 GTTAATTTATATTTTCCGTGATG
207395 GTTAATTTATATTTTCCGTGATG
1 GTTAATTTATATTTTCCGTGATG
207418 GT
1 GT
207420 ATCTTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (23 bp):
GTTAATTTATATTTTCCGTGATG
Found at i:215021 original size:24 final size:23
Alignment explanation
Indices: 214981--215037 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
214971 CATTAGAGCT
*
214981 TCTGTCGCTAGAGGTGTGTCTCTG
1 TCTGT-GCTACAGGTGTGTCTCTG
215005 TCTGTGCTACAGTGTGTGTCTCTG
1 TCTGTGCTACAG-GTGTGTCTCTG
215029 TCTGTGCTA
1 TCTGTGCTA
215038 TATATTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.09, C:0.21, G:0.30, T:0.40
Consensus pattern (23 bp):
TCTGTGCTACAGGTGTGTCTCTG
Found at i:215880 original size:5 final size:5
Alignment explanation
Indices: 215870--215902 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
215860 TAAACTCGAT
*
215870 CCCGA CCCGA CCCGA CCCGA CCTGA CCCGA CCC
1 CCCGA CCCGA CCCGA CCCGA CCCGA CCCGA CCC
215903 ATATTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.61, G:0.18, T:0.03
Consensus pattern (5 bp):
CCCGA
Found at i:216016 original size:49 final size:48
Alignment explanation
Indices: 215935--216030 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 48
215925 TATTACATAC
* * *
215935 AACAAATTTAAAAAATATATAATATATCAAATACACTTAAAAACATTAA
1 AACAAATTTAAAAAATAAATAATATATAAAATAC-CTTAAAAAAATTAA
*
215984 AACAAATATTAAAAAATAAATAA-ATTTAAAATACCTTAAAAAAATTA
1 AACAAAT-TTAAAAAATAAATAATATATAAAATACCTTAAAAAAATTA
216031 TATTAAGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 12 0.29
49 16 0.38
50 14 0.33
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (48 bp):
AACAAATTTAAAAAATAAATAATATATAAAATACCTTAAAAAAATTAA
Found at i:216163 original size:20 final size:21
Alignment explanation
Indices: 216140--216181 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
216130 AAAACGCATA
*
216140 AAAAATAACATCCA-AACAAC
1 AAAAATAACAACCACAACAAC
216160 AAAAATAACAACCACAACAAC
1 AAAAATAACAACCACAACAAC
216181 A
1 A
216182 GTAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAAATAACAACCACAACAAC
Found at i:216238 original size:47 final size:46
Alignment explanation
Indices: 216187--216285 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 46
216177 CAACAGTAAA
** *
216187 AATAACAGTAAAACAACATTAAAAATAACA-AAAATAGCGA-CAAAAAC
1 AATAACA--AAAACAACACAAAAAATAACACAAAATAGCAATC-AAAAC
*
216234 AATAACAAAAATAACACAAAAAATAACACGAAAATAGCAATCAAAAC
1 AATAACAAAAACAACACAAAAAATAACAC-AAAATAGCAATCAAAAC
216281 AATAA
1 AATAA
216286 AAATCAACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 18 0.40
47 26 0.58
48 1 0.02
ACGTcount: A:0.68, C:0.15, G:0.05, T:0.12
Consensus pattern (46 bp):
AATAACAAAAACAACACAAAAAATAACACAAAATAGCAATCAAAAC
Found at i:216241 original size:24 final size:22
Alignment explanation
Indices: 216210--216285 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 22
216200 CAACATTAAA
216210 AATAACAAAAATAGCGACAAAAAC
1 AATAACAAAAATAGC-AC-AAAAC
*
216234 AATAACAAAAATAACACAAAA-
1 AATAACAAAAATAGCACAAAAC
216255 AATAACACGAAAATAGCAATCAAAAC
1 AATAACA--AAAATAGC-A-CAAAAC
216281 AATAA
1 AATAA
216286 AAATCAACTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
21 7 0.16
22 4 0.09
23 9 0.20
24 15 0.33
25 5 0.11
26 5 0.11
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (22 bp):
AATAACAAAAATAGCACAAAAC
Found at i:216269 original size:23 final size:21
Alignment explanation
Indices: 216184--216261 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 21
216174 CAACAACAGT
* **
216184 AAAAATAACAGTAAAACAACATT
1 AAAAATAACA--AAAATAACACA
*
216207 AAAAATAACAAAAATAGCGACAA
1 AAAAATAACAAAAATAAC-AC-A
216230 AAACAATAACAAAAATAACACA
1 AAA-AATAACAAAAATAACACA
216252 AAAAATAACA
1 AAAAATAACA
216262 CGAAAATAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
21 13 0.28
22 5 0.11
23 15 0.32
24 14 0.30
ACGTcount: A:0.71, C:0.14, G:0.04, T:0.12
Consensus pattern (21 bp):
AAAAATAACAAAAATAACACA
Found at i:216287 original size:20 final size:20
Alignment explanation
Indices: 216264--216329 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
216254 AAATAACACG
216264 AAAATAGCAA-TCAAAACAAT
1 AAAA-AGCAACTCAAAACAAT
* *
216284 AAAAATCAACTCAAAACAGCAA
1 AAAAAGCAACTCAAAACA--AT
* *
216306 AAAAATCAAC-CAAAACAGT
1 AAAAAGCAACTCAAAACAAT
216325 AAAAA
1 AAAAA
216330 AAGCATCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.23
20 12 0.31
21 7 0.18
22 11 0.28
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAAAGCAACTCAAAACAAT
Found at i:216312 original size:22 final size:21
Alignment explanation
Indices: 216284--216331 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
216274 TCAAAACAAT
216284 AAAAATCAACTCAAAACAGCAA
1 AAAAATCAAC-CAAAACAGCAA
*
216306 AAAAATCAACCAAAACAGTAA
1 AAAAATCAACCAAAACAGCAA
216327 AAAAA
1 AAAAA
216332 GCATCAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (21 bp):
AAAAATCAACCAAAACAGCAA
Found at i:216330 original size:20 final size:21
Alignment explanation
Indices: 216274--216330 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
216264 AAAATAGCAA
*
216274 TCAAAACAAT-AAAAATCAAC
1 TCAAAACAGTAAAAAATCAAC
*
216294 TCAAAACAGCAAAAAAATCAAC
1 TCAAAACAG-TAAAAAATCAAC
216316 -CAAAACAGTAAAAAA
1 TCAAAACAGTAAAAAA
216331 AGCATCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
21 8 0.25
22 10 0.31
ACGTcount: A:0.67, C:0.19, G:0.04, T:0.11
Consensus pattern (21 bp):
TCAAAACAGTAAAAAATCAAC
Found at i:216339 original size:20 final size:19
Alignment explanation
Indices: 216273--216342 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
216263 GAAAATAGCA
*
216273 ATCAAAACAATAAAAATCAAC
1 ATCAAAACAGTAAAAA--AAC
*
216294 -TCAAAACAGCAAAAAAATC
1 ATCAAAACAGTAAAAAAA-C
*
216313 AACCAAAACAGTAAAAAAAGC
1 -ATCAAAACAGTAAAAAAA-C
216334 ATCAAAACA
1 ATCAAAACA
216343 ACAATATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 21 0.52
21 16 0.40
ACGTcount: A:0.66, C:0.20, G:0.04, T:0.10
Consensus pattern (19 bp):
ATCAAAACAGTAAAAAAAC
Found at i:216918 original size:22 final size:23
Alignment explanation
Indices: 216893--216953 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 23
216883 TCAAAATAAT
216893 AATATTTAAAATTAAA-TTATTA
1 AATATTTAAAATTAAATTTATTA
* *
216915 AATATTCATAATTTAAATTCTTATTA
1 AATATTTA-AAATTAAA-T-TTATTA
216941 AATATTATAAAAT
1 AATATT-TAAAAT
216954 AATTCATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
26 15 0.50
27 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATTTAAAATTAAATTTATTA
Found at i:236768 original size:15 final size:16
Alignment explanation
Indices: 236748--236786 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
236738 ATGAGTACTT
* *
236748 AAAGAAAAAATTGTA-
1 AAAGAAAAAAATATAG
236763 AAAGAAAAAAATATAG
1 AAAGAAAAAAATATAG
236779 AAAGAAAA
1 AAAGAAAA
236787 TTTTTTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAGAAAAAAATATAG
Found at i:238841 original size:17 final size:17
Alignment explanation
Indices: 238815--238848 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
238805 CACTATTATT
238815 ACTTGAACATTATGTAC
1 ACTTGAACATTATGTAC
*
238832 ACTTGCACATTATGTAC
1 ACTTGAACATTATGTAC
238849 CAATCTTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (17 bp):
ACTTGAACATTATGTAC
Found at i:241557 original size:55 final size:55
Alignment explanation
Indices: 241479--241583 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
241469 TTATCCTGAT
* * *
241479 AGCTATCAGATGCGACGATAATTCTAGGCATAATTTTGGATATGCTCATGCAACG
1 AGCTATCAGATGCGACGACAATTCTACGCATAATTCTGGATATGCTCATGCAACG
* ** *
241534 AGCTGTCAGATGCGGTGACAATTCTACGCGTAATTCTGGATATGCTCATG
1 AGCTATCAGATGCGACGACAATTCTACGCATAATTCTGGATATGCTCATG
241584 AAGTGACATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (55 bp):
AGCTATCAGATGCGACGACAATTCTACGCATAATTCTGGATATGCTCATGCAACG
Found at i:244375 original size:21 final size:21
Alignment explanation
Indices: 244351--244396 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
244341 TTCTCTTTCG
*
244351 CCTCTTCAACA-CAGACTTCCT
1 CCTCTCCAACATCA-ACTTCCT
244372 CCTCTCCAACATCAACTTCCT
1 CCTCTCCAACATCAACTTCCT
244393 CCTC
1 CCTC
244397 AACAACAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.22, C:0.48, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCTCCAACATCAACTTCCT
Found at i:244402 original size:21 final size:21
Alignment explanation
Indices: 244357--244403 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
244347 TTCGCCTCTT
**
244357 CAACACAGACTTCCTCCTCTC
1 CAACACAGACTTCCTCCTCAA
244378 CAACATCA-ACTTCCTCCTCAA
1 CAACA-CAGACTTCCTCCTCAA
244399 CAACA
1 CAACA
244404 GGTTCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.32, C:0.45, G:0.02, T:0.21
Consensus pattern (21 bp):
CAACACAGACTTCCTCCTCAA
Found at i:244876 original size:130 final size:129
Alignment explanation
Indices: 244657--244917 Score: 450
Period size: 130 Copynumber: 2.0 Consensus size: 129
244647 CTACAATAGA
*
244657 GCTATTCTAGACCTTGGTATAAGCATAGAACAAATTTTTTTTGATCTGCCATATCCTCTATTGCA
1 GCTATTCTAGACCTTGGTATAAGCATAGAACAAATTTTTTTTGATCTGCCATATCCTCTACTGCA
* * *
244722 GTGACAAGCCTGATCTTCCTATTGCTGATGGAATTGGCCAACTTCTCAACAGCCTTCATTTTGT
66 GTGACAAGCCTGATCTTCCTATTGCTGAAGGAAATAGCCAACTTCTCAACAGCCTTCATTTTGT
* *
244786 GCTATTCTAGACCTTGGTATAAGCATAGAACAATTTTTTTTTGATCTGCCCATATCCTCTACTGT
1 GCTATTCTAGACCTTGGTATAAGCATAGAACAAATTTTTTTTGATCTG-CCATATCCTCTACTGC
*
244851 AGTGACAAGCCTGATCTTTCTATTGCTGAAGGAAATAGCCAACTTCTCAACAGCCTTCATTTTGT
65 AGTGACAAGCCTGATCTTCCTATTGCTGAAGGAAATAGCCAACTTCTCAACAGCCTTCATTTTGT
244916 GC
1 GC
244918 AGCAAGGTTG
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 47 0.38
130 77 0.62
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (129 bp):
GCTATTCTAGACCTTGGTATAAGCATAGAACAAATTTTTTTTGATCTGCCATATCCTCTACTGCA
GTGACAAGCCTGATCTTCCTATTGCTGAAGGAAATAGCCAACTTCTCAACAGCCTTCATTTTGT
Found at i:245512 original size:5 final size:6
Alignment explanation
Indices: 245500--245524 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
245490 AATAAACTTG
245500 AACAAA AACAAA AACAAA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA A
245525 TAAAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:261648 original size:24 final size:24
Alignment explanation
Indices: 261616--261675 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
261606 TAACTTGTAT
*
261616 TGTATCGGTAGTTCATAGTACTGA
1 TGTATCGGTAGTTCATAGCACTGA
261640 TGTATCGGTAGTTCATAGCACTGA
1 TGTATCGGTAGTTCATAGCACTGA
261664 TGTATCGGTAGT
1 TGTATCGGTAGT
261676 AGGTAAGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (24 bp):
TGTATCGGTAGTTCATAGCACTGA
Found at i:266929 original size:16 final size:17
Alignment explanation
Indices: 266898--266931 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
266888 CAAAATGAAT
266898 GCAGTGACAAAATAAAAA
1 GCAGTGAC-AAATAAAAA
266916 GCAGTGAC-AATAAAAA
1 GCAGTGACAAATAAAAA
266932 TGCATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (17 bp):
GCAGTGACAAATAAAAA
Found at i:275631 original size:217 final size:218
Alignment explanation
Indices: 275256--275689 Score: 791
Period size: 217 Copynumber: 2.0 Consensus size: 218
275246 CTAGACTTAG
*
275256 ATATACATTTTAGAAAATAAAAATGAAATAAAAAAGAGGTTTTTTTGCCTACCACCGTGCACGGC
1 ATATACATTTTAGAAAATAAAAATGAAATAAAAAAGAGATTTTTTTGCCTACCACCGTGCACGGC
* *
275321 ATCTCGTCGCATTTTCGGGTAACGGCAGAGCAGCGGAGAACGATAGATCGGCAATGGACCAACGA
66 ATCTCGACGCATTTTCGGGTAACGGCAGAGCAGCAGAGAACGATAGATCGGCAATGGACCAACGA
275386 GACCTCCATGGTCGAACATGGGAGATTTTTCGAGAGAGAGCACAGAGAGTAGAGTTTGAGAGA-A
131 GACCTCCATGGTCGAACATGGGAGATTTTTCGAGAGAGAGCACAGAGAGTAGAGTTTGAGAGAGA
275450 AAAAAAAAGAAAGACAAAAGATT
196 AAAAAAAAGAAAGACAAAAGATT
275473 ATATACATTTTAGAAAATAAAAATGAAATAAAAAAGAGATTTTTTTGCCTACCACCGTGCACGGC
1 ATATACATTTTAGAAAATAAAAATGAAATAAAAAAGAGATTTTTTTGCCTACCACCGTGCACGGC
* * *
275538 ATCTC-ACGGCGTTTTCGGGTAATGGCAGAGCAGCATAGAACGATAGATCGGCAATGGACCAACG
66 ATCTCGAC-GCATTTTCGGGTAACGGCAGAGCAGCAGAGAACGATAGATCGGCAATGGACCAACG
275602 AGACCTCCATGGTCGAACATGGGAGATTTTTCGAGAGAGAGCACAGAGAGTAGAGTTTGAGAGAG
130 AGACCTCCATGGTCGAACATGGGAGATTTTTCGAGAGAGAGCACAGAGAGTAGAGTTTGAGAGAG
275667 AAAAAAAAAGAAAGACAAAAGAT
195 AAAAAAAAAGAAAGACAAAAGAT
275690 GTTTTGGAAA
Statistics
Matches: 209, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
216 1 0.00
217 185 0.89
218 23 0.11
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (218 bp):
ATATACATTTTAGAAAATAAAAATGAAATAAAAAAGAGATTTTTTTGCCTACCACCGTGCACGGC
ATCTCGACGCATTTTCGGGTAACGGCAGAGCAGCAGAGAACGATAGATCGGCAATGGACCAACGA
GACCTCCATGGTCGAACATGGGAGATTTTTCGAGAGAGAGCACAGAGAGTAGAGTTTGAGAGAGA
AAAAAAAAGAAAGACAAAAGATT
Found at i:276416 original size:2 final size:2
Alignment explanation
Indices: 276409--276440 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
276399 TTCTCTTTAA
276409 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
276441 GCATAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287591 original size:20 final size:21
Alignment explanation
Indices: 287566--287604 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
287556 TGCATTTTTA
*
287566 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
287586 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
287605 TGCTCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:295739 original size:17 final size:18
Alignment explanation
Indices: 295709--295742 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
295699 GCTTTAGGGA
*
295709 ATATGCCAAGATCTTCAC
1 ATATGCCAAAATCTTCAC
295727 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
295743 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:300351 original size:359 final size:359
Alignment explanation
Indices: 299692--300409 Score: 1355
Period size: 359 Copynumber: 2.0 Consensus size: 359
299682 TTATACAGGA
*
299692 TACAATTTAGTACTTCATTTATGCTGTTTAGGATAGAACTACAAAGAACAAGATTAATAGAGAGC
1 TACAATTTAGTACTTCATTTATGCTGTTTAGGATAGAACAACAAAGAACAAGATTAATAGAGAGC
299757 TCAAAAATACTATTATTTGAACAAATAGGACAAAAGAAACTGTGTACTTGCCTCTAGATTGCCAG
66 TCAAAAATACTATTATTTGAACAAATAGGACAAAAGAAACTGTGTACTTGCCTCTAGATTGCCAG
299822 CTGTAGTAGTTTGCATGATGAGGGGCCATTACCACTACCGTGACCAGGAATTCAGGGATGTGTGA
131 CTGTAGTAGTTTGCATGATGAGGGGCCATTACCACTACCGTGACCAGGAATTCAGGGATGTGTGA
299887 ACTTCTCACTGAAAAATTGCAGTTCCAGCCTCGTAGAAATGCTTCAATTTAAACAAGTTCCCCAG
196 ACTTCTCACTGAAAAATTGCAGTTCCAGCCTCGTAGAAATGCTTCAATTTAAACAAGTTCCCCAG
* *
299952 GTTTTATGTATCGAGACTGCCTGTGGAAAGGAATGCAGTTTTCAATATGTACATCACTAGCACCC
261 GTTTTATGAATCGAGACTGCATGTGGAAAGGAATGCAGTTTTCAATATGTACATCACTAGCACCC
300017 ATATAGGAGGAAGAGCAATGCAATGGCCCCCTTT
326 ATATAGGAGGAAGAGCAATGCAATGGCCCCCTTT
*
300051 TACAATTTAGTACTTCATTTATGCTGTTTAGGATAGAACAACAAAGAACAAGATTAATATAGAGC
1 TACAATTTAGTACTTCATTTATGCTGTTTAGGATAGAACAACAAAGAACAAGATTAATAGAGAGC
300116 TCAAAAATACTATTATTTGAACAAATAGGACAAAAGAAACTGTGTACTTGCCTCTAGATTGCCAG
66 TCAAAAATACTATTATTTGAACAAATAGGACAAAAGAAACTGTGTACTTGCCTCTAGATTGCCAG
* *
300181 CTGTAGTAGTTTGCATGATGAGGGGCCATTACCACTACGGTGACCAGGAATTCAGGGCTGTGTGA
131 CTGTAGTAGTTTGCATGATGAGGGGCCATTACCACTACCGTGACCAGGAATTCAGGGATGTGTGA
* *
300246 ACTTCTCACTGAAAAATTGCAGTTCCAGCCTTGTAGAAATGCTTCAATTTAAACAAGTTTCCCAG
196 ACTTCTCACTGAAAAATTGCAGTTCCAGCCTCGTAGAAATGCTTCAATTTAAACAAGTTCCCCAG
*
300311 GTTTTATGAATTGAGACTGCATGTGGAAAGGAATGCAGTTTTCAATATGTACATCACTAGCACCC
261 GTTTTATGAATCGAGACTGCATGTGGAAAGGAATGCAGTTTTCAATATGTACATCACTAGCACCC
300376 ATATAGGAGGAAGAGCAATGCAATGGCCCCCTTT
326 ATATAGGAGGAAGAGCAATGCAATGGCCCCCTTT
300410 ACAGTAACAA
Statistics
Matches: 350, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
359 350 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (359 bp):
TACAATTTAGTACTTCATTTATGCTGTTTAGGATAGAACAACAAAGAACAAGATTAATAGAGAGC
TCAAAAATACTATTATTTGAACAAATAGGACAAAAGAAACTGTGTACTTGCCTCTAGATTGCCAG
CTGTAGTAGTTTGCATGATGAGGGGCCATTACCACTACCGTGACCAGGAATTCAGGGATGTGTGA
ACTTCTCACTGAAAAATTGCAGTTCCAGCCTCGTAGAAATGCTTCAATTTAAACAAGTTCCCCAG
GTTTTATGAATCGAGACTGCATGTGGAAAGGAATGCAGTTTTCAATATGTACATCACTAGCACCC
ATATAGGAGGAAGAGCAATGCAATGGCCCCCTTT
Found at i:304615 original size:2 final size:2
Alignment explanation
Indices: 304608--304633 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
304598 ATCAACACTC
304608 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
304634 TTGAAATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304962 original size:38 final size:39
Alignment explanation
Indices: 304889--304998 Score: 145
Period size: 38 Copynumber: 2.9 Consensus size: 39
304879 TGAAGGCGGC
* *
304889 TAGGGCAAATGGAGAAATGAAGAAGATG-AGTAAAGAGGT
1 TAGGGCAAATGGAG-AAGGAAGAAGAGGAAGTAAAGAGGT
*
304928 TAGGGCAAATGGAGAAGGAAGAATAGGAAG-AAAGAGGT
1 TAGGGCAAATGGAGAAGGAAGAAGAGGAAGTAAAGAGGT
* *
304966 TAGGGAAAATGGGGAAGGAAGAAGAGGAA-TAAA
1 TAGGGCAAATGGAGAAGGAAGAAGAGGAAGTAAA
304999 TAGTGAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 47 0.75
39 16 0.25
ACGTcount: A:0.48, C:0.02, G:0.38, T:0.12
Consensus pattern (39 bp):
TAGGGCAAATGGAGAAGGAAGAAGAGGAAGTAAAGAGGT
Found at i:305407 original size:24 final size:24
Alignment explanation
Indices: 305375--305433 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
305365 ATAATCTTTT
305375 AATTAAACTCTGTTTATTTGTTTC
1 AATTAAACTCTGTTTATTTGTTTC
*
305399 AATTAAACTTTGTTTATTTGTTTC
1 AATTAAACTCTGTTTATTTGTTTC
* *
305423 AGTCAAACTCT
1 AATTAAACTCT
305434 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
AATTAAACTCTGTTTATTTGTTTC
Found at i:307376 original size:28 final size:24
Alignment explanation
Indices: 307322--307369 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
307312 AATAATCTTC
307322 CAATTAAACTCTATTTATTTGTTT
1 CAATTAAACTCTATTTATTTGTTT
* *
307346 CAATTAAACTTTGTTTATTTGTTT
1 CAATTAAACTCTATTTATTTGTTT
307370 TAGTCAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (24 bp):
CAATTAAACTCTATTTATTTGTTT
Found at i:308195 original size:56 final size:56
Alignment explanation
Indices: 308129--308240 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
308119 AAATACATAT
*
308129 GGGTGCCGACCATTACAGTTCCAGCACCAAAAACATTAGTTTTTTTAATCCCCGAC
1 GGGTACCGACCATTACAGTTCCAGCACCAAAAACATTAGTTTTTTTAATCCCCGAC
*
308185 GGGTACCGACCATTACAGTTCCAGCACTAAAAACATTAGTTTTTTTAATCCCCGAC
1 GGGTACCGACCATTACAGTTCCAGCACCAAAAACATTAGTTTTTTTAATCCCCGAC
308241 TCAATCACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (56 bp):
GGGTACCGACCATTACAGTTCCAGCACCAAAAACATTAGTTTTTTTAATCCCCGAC
Found at i:325306 original size:85 final size:85
Alignment explanation
Indices: 325156--325326 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
325146 CTTCCAAACC
* * * * *
325156 CCATCTTCTTGATGAGATATAGAGAAGTGGGTCGAAGCAATAAAATGGTCATCTTCCTAGCGAGA
1 CCATCTTCCTGATGAGATATAGAGAAGTGGATCGAAACAATAAAACGGTCATCTTCCTAACGAGA
* * *
325221 TGCAGAGAAGTGAACCAAAT
66 TACAAAGAAGTAAACCAAAT
* * ** * *
325241 CCATCTTCCTGATGAGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTAATGAGA
1 CCATCTTCCTGATGAGATATAGAGAAGTGGATCGAAACAATAAAACGGTCATCTTCCTAACGAGA
*
325306 TACAAAGAAGTAAATCAAAT
66 TACAAAGAAGTAAACCAAAT
325326 C
1 C
325327 AATTAAGCGA
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (85 bp):
CCATCTTCCTGATGAGATATAGAGAAGTGGATCGAAACAATAAAACGGTCATCTTCCTAACGAGA
TACAAAGAAGTAAACCAAAT
Found at i:325997 original size:17 final size:17
Alignment explanation
Indices: 325965--325998 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
325955 ACAAACCCTA
*
325965 ACCCAACAGGCCCAAAT
1 ACCCAACAAGCCCAAAT
*
325982 ACCCAACAAGCTCAAAT
1 ACCCAACAAGCCCAAAT
325999 TCATTCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.38, G:0.09, T:0.09
Consensus pattern (17 bp):
ACCCAACAAGCCCAAAT
Found at i:326330 original size:16 final size:15
Alignment explanation
Indices: 326304--326333 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
326294 TCATTCAAGG
326304 TATATTATATACTCA
1 TATATTATATACTCA
326319 TATATATATATACTC
1 TATAT-TATATACTC
326334 TATTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATTATATACTCA
Found at i:327581 original size:18 final size:19
Alignment explanation
Indices: 327545--327581 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
327535 ATCACGTGTT
327545 TGTCATTATATTTTTATCA
1 TGTCATTATATTTTTATCA
327564 TGTCA-TAT-TTTATTATCA
1 TGTCATTATATTT-TTATCA
327582 CATGTGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 9 0.53
19 5 0.29
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (19 bp):
TGTCATTATATTTTTATCA
Found at i:330496 original size:47 final size:47
Alignment explanation
Indices: 330442--330536 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
330432 TATAATAAAA
330442 TTATTCAAAAAAATCACCTCAAAATGCATAGAATAATTAAGATCGGT
1 TTATTCAAAAAAATCACCTCAAAATGCATAGAATAATTAAGATCGGT
330489 TTATTCAAAAAAATCACCTCAAAATGCATAGAATAATTAAGATCGGT
1 TTATTCAAAAAAATCACCTCAAAATGCATAGAATAATTAAGATCGGT
330536 T
1 T
330537 AATTTTGCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (47 bp):
TTATTCAAAAAAATCACCTCAAAATGCATAGAATAATTAAGATCGGT
Found at i:330620 original size:18 final size:16
Alignment explanation
Indices: 330592--330633 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 16
330582 AATTAATAAT
330592 TTTTTAAAATTTTTTA
1 TTTTTAAAATTTTTTA
330608 CTTTTTAATAATTTTTTA
1 -TTTTTAA-AATTTTTTA
330626 TTTTTAAA
1 TTTTTAAA
330634 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.58
18 9 0.38
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAAAATTTTTTA
Found at i:330767 original size:16 final size:16
Alignment explanation
Indices: 330746--330776 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
330736 AATGTAAATT
330746 CAAAAATTAAAATAAG
1 CAAAAATTAAAATAAG
*
330762 CAAAAATTTAAATAA
1 CAAAAATTAAAATAA
330777 AGGATTAAAG
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:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (16 bp):
CAAAAATTAAAATAAG
Found at i:332017 original size:32 final size:31
Alignment explanation
Indices: 331968--332040 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
331958 TTTAACAAAT
* * *
331968 TTAATTAATCAGTATGAATTATTAAATTAAA
1 TTAATTAATTAATATGAATCATTAAATTAAA
331999 TTAATTAATTAATCATGAATCATTAAATTAAA
1 TTAATTAATTAAT-ATGAATCATTAAATTAAA
* *
332031 ATAATAAATT
1 TTAATTAATT
332041 TATAAACTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 11 0.31
32 25 0.69
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (31 bp):
TTAATTAATTAATATGAATCATTAAATTAAA
Found at i:333505 original size:9 final size:9
Alignment explanation
Indices: 333493--333527 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
333483 ACTCAAATCA
333493 CTCTCAACT
1 CTCTCAACT
333502 CTCTCAACT
1 CTCTCAACT
*
333511 CTATCGAACT
1 CTCTC-AACT
333521 CTCTCAA
1 CTCTCAA
333528 ATACACGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.26, C:0.40, G:0.03, T:0.31
Consensus pattern (9 bp):
CTCTCAACT
Found at i:335483 original size:21 final size:20
Alignment explanation
Indices: 335427--335476 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
335417 ATTAGAATGA
*
335427 GTTATATTAAG-TATAAATAGG
1 GTTA-ATTAAGAT-TAAAAAGG
*
335448 TTTAATTAAGATTAAAAAGG
1 GTTAATTAAGATTAAAAAGG
335468 GTTAATTAA
1 GTTAATTAA
335477 AGCTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (20 bp):
GTTAATTAAGATTAAAAAGG
Found at i:336978 original size:30 final size:30
Alignment explanation
Indices: 336954--337097 Score: 179
Period size: 29 Copynumber: 4.9 Consensus size: 30
336944 AAAATTGTTT
*
336954 TTTGACCCTTAAATTTTCCAAAAATTCCAA
1 TTTGACCCTTAAATTTTCCAAAAATTCAAA
* *
336984 TTTGACCCCTAAACTTTT-CTAAAATTCAAA
1 TTTGACCCTTAAA-TTTTCCAAAAATTCAAA
*
337014 TTTGACCC-TAAATTTTCCAAAAAATCAAA
1 TTTGACCCTTAAATTTTCCAAAAATTCAAA
*
337043 TTTAACCCTTAAA-TTTCCAAAAATTCAAA
1 TTTGACCCTTAAATTTTCCAAAAATTCAAA
* *
337072 TTTAACCCCTAAA-TTTCCTAAAAATT
1 TTTGACCCTTAAATTTTCC-AAAAATT
337098 AACCTCTAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.04
29 53 0.52
30 41 0.40
31 4 0.04
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.35
Consensus pattern (30 bp):
TTTGACCCTTAAATTTTCCAAAAATTCAAA
Done.