Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 24 of 133
Found at i:5890771 original size:49 final size:49
Alignment explanation
Indices: 5890684--5890784 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
5890674 TTGGTTAGGG
* * *
5890684 TTTAGGGTTTGGTTTAGGATTTAGAACTTGATTCAGGGTTTGGGTTTGA
1 TTTAGGGTTTAGTTTAGGATTTAGAACTTAATTCAGGGTTTAGGTTTGA
* *
5890733 TTTAGGGTTTAGTTTGAGGTTTTAG-GCTTAAGTT-AGGGTTTAGGTTTGA
1 TTTAGGGTTTAGTTT-AGGATTTAGAACTTAA-TTCAGGGTTTAGGTTTGA
5890782 TTT
1 TTT
5890785 TGGGATTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
49 35 0.78
50 10 0.22
ACGTcount: A:0.18, C:0.03, G:0.32, T:0.48
Consensus pattern (49 bp):
TTTAGGGTTTAGTTTAGGATTTAGAACTTAATTCAGGGTTTAGGTTTGA
Found at i:5890874 original size:13 final size:13
Alignment explanation
Indices: 5890720--5890899 Score: 62
Period size: 12 Copynumber: 14.1 Consensus size: 13
5890710 CTTGATTCAG
5890720 GGTTT-GGGTTT-
1 GGTTTAGGGTTTA
*
5890731 GATTTAGGGTTTA
1 GGTTTAGGGTTTA
*
5890744 -GTTTGAGGTTTTA
1 GGTTT-AGGGTTTA
* *
5890757 GGCTTA-AG-TTA
1 GGTTTAGGGTTTA
5890768 GGGTTTA-GGTTT-
1 -GGTTTAGGGTTTA
* *
5890780 GATTTTGGGATTT-
1 GGTTTAGGG-TTTA
*
5890793 GGGTTAGGGTTTA
1 GGTTTAGGGTTTA
*
5890806 -GTTTAAGGTTTGA
1 GGTTTAGGGTTT-A
*
5890819 GTTAATTTAGGGTTTA
1 G---GTTTAGGGTTTA
*
5890835 GGGTTTAGGTTTTA
1 -GGTTTAGGGTTTA
* * *
5890849 TGTTAAAGGTTTA
1 GGTTTAGGGTTTA
5890862 -GTTTAGGGTTTTAA
1 GGTTTAGGG-TTT-A
5890876 GGTTTA-GGTTT-
1 GGTTTAGGGTTTA
5890887 GGTTT-GGGTTTA
1 GGTTTAGGGTTTA
5890899 G
1 G
5890900 ATTTGTTTTG
Statistics
Matches: 124, Mismatches: 25, Indels: 39
0.66 0.13 0.21
Matches are distributed among these distances:
11 21 0.17
12 36 0.29
13 35 0.28
14 16 0.13
15 5 0.04
16 1 0.01
17 10 0.08
ACGTcount: A:0.17, C:0.01, G:0.34, T:0.48
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:5890958 original size:36 final size:36
Alignment explanation
Indices: 5890861--5890967 Score: 103
Period size: 36 Copynumber: 3.0 Consensus size: 36
5890851 TTAAAGGTTT
* * *
5890861 AGTTTAGGGTTTTAAGGTTTAGGTTTGGTTTGGGTTT
1 AGTTTAGGGTTTGAGGGTTTAGGTTTGGTTTGGG-TC
* * * *
5890898 AGATTT--GTTTTG-GGATTTTGGGTTTGGGTTGGGTC
1 AG-TTTAGGGTTTGAGG-GTTTAGGTTTGGTTTGGGTC
5890933 AGTTTAGGGTTTGAGGGTTTAGGTTTGGTTTGGGT
1 AGTTTAGGGTTTGAGGGTTTAGGTTTGGTTTGGGT
5890968 TCGATAAGTG
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
34 3 0.06
35 4 0.07
36 40 0.74
37 4 0.07
38 3 0.06
ACGTcount: A:0.11, C:0.01, G:0.39, T:0.49
Consensus pattern (36 bp):
AGTTTAGGGTTTGAGGGTTTAGGTTTGGTTTGGGTC
Found at i:5892675 original size:144 final size:144
Alignment explanation
Indices: 5892467--5892740 Score: 327
Period size: 144 Copynumber: 1.9 Consensus size: 144
5892457 TCTTAGGAAG
* * * * * *
5892467 GTCAAATTATGAAAATATTCCTAAAAGGCATTTTGATAATTTCAACTTTTTCATGGTGTGATCAA
1 GTCAAATTAAGAAAATACTCCTAAAAGGCAATTTGAAAATTTCAACTTTTTCATGGTATCATCAA
* * * * *
5892532 AGTTATCAATGCATGAAAATTCATGAAATAATAACAAAATATGATCTAGAGCTTTTTGTAAAAAA
66 AGTTATCAATACATCAAAATTCATGAAATAATAACAAAACATGATATAGAGCTTTTTGCAAAAAA
5892597 CTGACCTTTAAAAT
131 CTGACCTTTAAAAT
* *
5892611 GTCAAATTAAGAAAATACTCCT-AAAGGACAATTTGAAAATTTTAATCTTTTTGA-GGTATCATC
1 GTCAAATTAAGAAAATACTCCTAAAAGG-CAATTTGAAAATTTCAA-CTTTTTCATGGTATCATC
* * * * * * * *
5892674 AAGGTTTTTAATACATCAACATTCATGAAATAATATCATAACATGATATGGAGTTTTTTGCAAAA
64 AAAGTTATCAATACATCAAAATTCATGAAATAATAACAAAACATGATATAGAGCTTTTTGCAAAA
5892739 AA
129 AA
5892741 TCAACCTTGA
Statistics
Matches: 107, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
143 5 0.05
144 95 0.89
145 7 0.07
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (144 bp):
GTCAAATTAAGAAAATACTCCTAAAAGGCAATTTGAAAATTTCAACTTTTTCATGGTATCATCAA
AGTTATCAATACATCAAAATTCATGAAATAATAACAAAACATGATATAGAGCTTTTTGCAAAAAA
CTGACCTTTAAAAT
Found at i:5892748 original size:144 final size:144
Alignment explanation
Indices: 5892467--5892856 Score: 319
Period size: 144 Copynumber: 2.7 Consensus size: 144
5892457 TCTTAGGAAG
* * * * * *
5892467 GTCAAATTATGAAAATATTCCTAAAAGGCATTTTGATAATTTCAACTTTTTCATGGTGTGATCAA
1 GTCAAATTAAGAAAATACTCCTAAAAGGCAATTTGAAAATTTCAACTTTTTCATGGTATCATCAA
* * * * *
5892532 AGTTATCAATGCATGAAAATTCATGAAATAATAACAAAATATGATCTAGAGCTTTTTGTAAAAAA
66 AGTTATCAATACATCAAAATTCATGAAATAATAACAAAACATGATATAGAGCTTTTTGCAAAAAA
*
5892597 CTGACCTTTAAAAT
131 CTAACCTTTAAAAT
* *
5892611 GTCAAATTAAGAAAATACTCCT-AAAGGACAATTTGAAAATTTTAATCTTTTTGA-GGTATCATC
1 GTCAAATTAAGAAAATACTCCTAAAAGG-CAATTTGAAAATTTCAA-CTTTTTCATGGTATCATC
* * * * * * * *
5892674 AAGGTTTTTAATACATCAACATTCATGAAATAATATCATAACATGATATGGAGTTTTTTGCAAAA
64 AAAGTTATCAATACATCAAAATTCATGAAATAATAACAAAACATGATATAGAGCTTTTTGCAAAA
*
5892739 AA-TCAACCTTGAGAAAAT
129 AACT-AACCTT--TAAAAT
* * * ** * * * * *
5892757 -T-AAATTACGAAAATAC-CCTTAAAA-GTATTTTGTTAATTTGAACCTTTTCAAGATA-CAATT
1 GTCAAATTAAGAAAATACTCC-TAAAAGGCAATTTGAAAATTTCAACTTTTTCATGGTATC-ATC
* * * * *
5892817 AATGTTTTTAATACATCAAAATTTATGAAATAATATCAAA
64 AAAGTTATCAATACATCAAAATTCATGAAATAATAACAAA
5892857 GTATGATCAA
Statistics
Matches: 200, Mismatches: 37, Indels: 19
0.78 0.14 0.07
Matches are distributed among these distances:
142 7 0.04
143 61 0.31
144 116 0.58
145 11 0.05
146 5 0.03
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (144 bp):
GTCAAATTAAGAAAATACTCCTAAAAGGCAATTTGAAAATTTCAACTTTTTCATGGTATCATCAA
AGTTATCAATACATCAAAATTCATGAAATAATAACAAAACATGATATAGAGCTTTTTGCAAAAAA
CTAACCTTTAAAAT
Found at i:5897027 original size:13 final size:12
Alignment explanation
Indices: 5897022--5897053 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
5897012 AAAAATGAGG
5897022 AAAAAAAGAAGA
1 AAAAAAAGAAGA
5897034 AAAAAGAAGAAGA
1 AAAAA-AAGAAGA
5897047 AAAAAAA
1 AAAAAAA
5897054 TACAAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAGA
Found at i:5897073 original size:33 final size:33
Alignment explanation
Indices: 5897022--5897094 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
5897012 AAAAATGAGG
5897022 AAAAAAA-GAAGAAAAAAGAAGAAGA-AA-AAAAAT
1 AAAAAAACG-AGAAAAAAG-AGAA-ATAATAAAAAT
* *
5897055 ACAAAAACGAGAAGAAAGAGAAATAATAAAAAT
1 AAAAAAACGAGAAAAAAGAGAAATAATAAAAAT
5897088 AAAAAAA
1 AAAAAAA
5897095 ATAGTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 1 0.03
32 6 0.18
33 26 0.76
34 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (33 bp):
AAAAAAACGAGAAAAAAGAGAAATAATAAAAAT
Found at i:5897409 original size:46 final size:46
Alignment explanation
Indices: 5897289--5897853 Score: 305
Period size: 49 Copynumber: 11.7 Consensus size: 46
5897279 AGTTTAAAAG
* * * * * * *
5897289 GCTCCTTTTAGCAGAGGCTTAATAACTTTAAAATTTTTTTGAAAAT
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGGAAAT
*
5897335 GGCTCCTTTAAGCAGAGGCTCAACAACTTTAAAAATCTCTTGGAAAT
1 -GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGGAAAT
* * * * * *
5897382 GCTCATATCAGTAGAGGCTTAACAACTTTAAAATCTTCTCTTGGAAAAG
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAA--ATCTCTTGG-AAAT
* * * *
5897431 GCTCCTTTCAGCAAAGGCTCAATAACTTTAAAAATCTCATATCTTGAAAAGA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAA--TC---TCTTGGAAA-T
* * * * *
5897483 GTTCCTTTCAGCAAAGGCTCAATAACTTTAAAAATCTCATATCTTGAAAAGA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAA--TC---TCTTGGAAA-T
* * * * * *
5897535 GTTCCTTTCAGCAAAGACTCAACAACTTT-AAAATTTCATCTGAAAAA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTC-T-TGGAAAT
* * * * * * *
5897582 GTTCCTCTCAGCAGAGGCTTAACAACTTTAAAATTCTTTTGAAAAA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGGAAAT
* * *
5897628 GCTCCTCT-AGCAGAGGCTCAACAACTTT-AAAATCTCATATGAAAAA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTC-T-TGGAAAT
* * * * *
5897674 GCTCCTCTT-AGTAGAGGCTTAACAACTTT-AAAATCTTATTTTAGAAAAA
1 GCTCCT-TTCAGCAGAGGCTCAACAACTTTAAAAATC---TCTT-GGAAAT
* * * * * * *
5897723 GCTCCTCTCAACAGAGGTTTAACAACTTTAAAATTTTTATCTTGGAAAA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAA---ATCTCTTGGAAAT
* * *
5897772 GCT-ATTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTCTGAAAAA
1 GCTCCTT-TCAGCAGAGGCTCAACAACTTTAAAAATCTC-T-TGGAAAT
* *
5897820 GCTCCTCTCAGCAGAGGTTCAACAACTTTAAAAA
1 GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAA
5897854 ATTTTCATCT
Statistics
Matches: 429, Mismatches: 61, Indels: 55
0.79 0.11 0.10
Matches are distributed among these distances:
44 6 0.01
45 20 0.05
46 60 0.14
47 93 0.22
48 57 0.13
49 95 0.22
50 7 0.02
51 7 0.02
52 83 0.19
53 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (46 bp):
GCTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGGAAAT
Found at i:5897494 original size:52 final size:49
Alignment explanation
Indices: 5897284--5897852 Score: 503
Period size: 47 Copynumber: 11.8 Consensus size: 49
5897274 TTGAAAGTTT
* * * * *
5897284 AAAAGGCTCCTTTTAGCAGAGGCTTAATAACTTTAAAAT-T-T-TTTTG
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
* * *
5897330 AAAATGGCTCCTTTAAGCAGAGGCTCAACAACTTTAAAA-ATC--TCTTG
1 AAAA-AGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
* * * * * * *
5897377 GAAATGCTCATATCAGTAGAGGCTTAACAACTTTAAAATCT-TCTCTTGG
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTT-G
* * *
5897426 AAAAGGCTCCTTTCAGCAAAGGCTCAATAACTTTAAAAATCTCATATCTTG
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTT-AAAATCTC-TATCTTG
* * *
5897477 AAAAGAGTTCCTTTCAGCAAAGGCTCAATAACTTTAAAAATCTCATATCTTG
1 AAAA-AGCTCCTTTCAGCAGAGGCTCAACAACTTT-AAAATCTC-TATCTTG
* * * *
5897529 AAAAGAGTTCCTTTCAGCAAAGACTCAACAACTTTAAAATTTC-ATC-TG
1 AAAA-AGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
* * *
5897577 AAAAAGTTCCTCTCAGCAGAGGCTTAACAACTTTAAAAT-TCT-T-TTG
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
* *
5897623 AAAAAGCTCCTCT-AGCAGAGGCTCAACAACTTTAAAATCTC-AT-ATG
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
* * *
5897669 AAAAAGCTCCTCTT-AGTAGAGGCTTAACAACTTTAAAATCT-TATTTTAG
1 AAAAAGCTCCT-TTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTT-G
* * * * * *
5897718 AAAAAGCTCCTCTCAACAGAGGTTTAACAACTTTAAAATTTTTATCTTG
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
* *
5897767 GAAAAGCT-ATTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCT-TC-TG
1 AAAAAGCTCCTT-TCAGCAGAGGCTCAACAACTTT-AAAATCTCTATCTTG
* *
5897815 AAAAAGCTCCTCTCAGCAGAGGTTCAACAACTTTAAAA
1 AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAA
5897853 AATTTTCATC
Statistics
Matches: 444, Mismatches: 55, Indels: 47
0.81 0.10 0.09
Matches are distributed among these distances:
45 24 0.05
46 65 0.15
47 103 0.23
48 43 0.10
49 95 0.21
50 19 0.04
51 12 0.03
52 83 0.19
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (49 bp):
AAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCTATCTTG
Found at i:5917412 original size:9 final size:9
Alignment explanation
Indices: 5917395--5917442 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
5917385 AGAAAAAATT
5917395 AAATAAATAA
1 AAAT-AATAA
*
5917405 TAATAATAA
1 AAATAATAA
5917414 AAATAATAA
1 AAATAATAA
5917423 AAAT-A-AA
1 AAATAATAA
*
5917430 AAATAAAAA
1 AAATAATAA
5917439 AAAT
1 AAAT
5917443 GGTGTTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 6 0.18
8 2 0.06
9 23 0.68
10 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAATAA
Found at i:5917419 original size:15 final size:15
Alignment explanation
Indices: 5917399--5917442 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
5917389 AAAATTAAAT
*
5917399 AAATAATAATAATAA
1 AAATAATAAAAATAA
5917414 AAATAATAAAAATAAA
1 AAATAATAAAAAT-AA
*
5917430 AAATAAAAAAAAT
1 AAATAATAAAAAT
5917443 GGTGTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:5919480 original size:22 final size:22
Alignment explanation
Indices: 5919439--5919480 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5919429 CTCAATGGGG
*
5919439 TGAACTTATGTCGAGCCCAAGC
1 TGAACTTATGTCAAGCCCAAGC
* *
5919461 TGAAGTTATGTCAAGTCCAA
1 TGAACTTATGTCAAGCCCAA
5919481 CCCATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TGAACTTATGTCAAGCCCAAGC
Found at i:5922287 original size:27 final size:25
Alignment explanation
Indices: 5922256--5922338 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 25
5922246 GATCAGATCA
5922256 TATTTTTTTGAATTTTGATTTCTGTTT
1 TATTTTTTTGAATTTT-ATTTCT-TTT
* *
5922283 TATTTTTTCTTTAATTTTTTTTCTTTT
1 TA-TTTTT-TTGAATTTTATTTCTTTT
* *
5922310 TTTTTATTTTGGATTTTTATTTCTTTT
1 TATTT-TTTT-GAATTTTATTTCTTTT
5922337 TA
1 TA
5922339 GTAAAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
26 5 0.11
27 22 0.49
28 10 0.22
29 8 0.18
ACGTcount: A:0.13, C:0.05, G:0.06, T:0.76
Consensus pattern (25 bp):
TATTTTTTTGAATTTTATTTCTTTT
Found at i:5922310 original size:10 final size:10
Alignment explanation
Indices: 5922280--5922338 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
5922270 TTGATTTCTG
5922280 TTTTATTTTT
1 TTTTATTTTT
*
5922290 TCTTTAATTTT
1 T-TTTATTTTT
*
5922301 TTTTCTTTTT
1 TTTTATTTTT
5922311 TTTTATTTTGGAT
1 TTTTATTTT---T
*
5922324 TTTTATTTCT
1 TTTTATTTTT
5922334 TTTTA
1 TTTTA
5922339 GTAAAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 22 0.55
11 9 0.22
13 9 0.22
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:5922607 original size:29 final size:29
Alignment explanation
Indices: 5922575--5922636 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
5922565 AATTTCATAT
*
5922575 TAAATAAGATGTCTACAAAAAATATTTAA
1 TAAATAAGATGTCTACAAAAAATATCTAA
* *
5922604 TAAATAGGATGTCTACAAAGAATATCTAA
1 TAAATAAGATGTCTACAAAAAATATCTAA
5922633 TAAA
1 TAAA
5922637 CGACGAAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (29 bp):
TAAATAAGATGTCTACAAAAAATATCTAA
Found at i:5925389 original size:16 final size:16
Alignment explanation
Indices: 5925342--5925390 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5925332 TATGTGGTAC
* *
5925342 AAATACAGTCAGATAT
1 AAATAAAGTCAAATAT
5925358 AAAT-AA-T-AACATAT
1 AAATAAAGTCAA-ATAT
5925372 AAATAAAGTCAAATAT
1 AAATAAAGTCAAATAT
5925388 AAA
1 AAA
5925391 GTATGCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 3 0.11
16 12 0.44
17 2 0.07
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.24
Consensus pattern (16 bp):
AAATAAAGTCAAATAT
Found at i:5928743 original size:52 final size:52
Alignment explanation
Indices: 5928681--5928784 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
5928671 ATCTCTATAT
5928681 TTGTAGGGATTCTTCTTTGGATAAAAGATATTTCATACGTTAAACATTAGAG
1 TTGTAGGGATTCTTCTTTGGATAAAAGATATTTCATACGTTAAACATTAGAG
*
5928733 TTGTAGGGATTCTTCTTTGGATTAAAGATATTTCATACGTTAAACATTAGAG
1 TTGTAGGGATTCTTCTTTGGATAAAAGATATTTCATACGTTAAACATTAGAG
5928785 AGTATGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (52 bp):
TTGTAGGGATTCTTCTTTGGATAAAAGATATTTCATACGTTAAACATTAGAG
Found at i:5932481 original size:20 final size:23
Alignment explanation
Indices: 5932451--5932498 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
5932441 TACAAAAATA
*
5932451 TAAA-ATATATATTA-TTTTTAT
1 TAAATATATATATAATTTTTTAT
*
5932472 TAAATTTATATATAATTTTTTAT
1 TAAATATATATATAATTTTTTAT
5932495 TAAA
1 TAAA
5932499 ATTTTAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 8 0.35
23 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAAATATATATATAATTTTTTAT
Found at i:5938096 original size:2 final size:2
Alignment explanation
Indices: 5938089--5938114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5938079 CTAAATAAGG
5938089 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
5938115 GGCAATCTCC
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:5939020 original size:52 final size:51
Alignment explanation
Indices: 5938928--5939073 Score: 188
Period size: 52 Copynumber: 2.8 Consensus size: 51
5938918 AACTTGTAAA
* * * *
5938928 AGAAGAATTCTAAGAGAAAGAAAATTC-AAATAGGTAAGTTTGACTTGCAAG
1 AGAAGAATTCTAAGAGAAAG-AGATTCTTAATAGGCAAGTTTGACTTACAAG
5938979 AGAAGAATTCTACATGA-AAAGAGATTCTTAATAGGCAAGTTTGACTTACAAG
1 AGAAGAATTCTA-A-GAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAG
* *
5939031 AGAAGAATTCTAAGAGGAGAGAGATTCTTAATGGGCAAGTTTG
1 AGAAGAATTCTAAGA-GAAAGAGATTCTTAATAGGCAAGTTTG
5939074 TATGATTATA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
50 2 0.02
51 18 0.21
52 62 0.74
53 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (51 bp):
AGAAGAATTCTAAGAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAG
Found at i:5939614 original size:31 final size:31
Alignment explanation
Indices: 5939558--5939642 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
5939548 AGGCTTTTAG
* * *
5939558 CCCAACAAATGGTATCAGAGCTGTGGTGATC
1 CCCAACAAATGATATTAAAGCTGTGGTGATC
* * *
5939589 CCTAACAAATGATATTAAAGTTGTGGTGTTC
1 CCCAACAAATGATATTAAAGCTGTGGTGATC
* * *
5939620 CCCAATAAGTGATATTAGAGCTG
1 CCCAACAAATGATATTAAAGCTG
5939643 AATGTTTGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (31 bp):
CCCAACAAATGATATTAAAGCTGTGGTGATC
Found at i:5939994 original size:11 final size:11
Alignment explanation
Indices: 5939978--5940019 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5939968 AATCTCATAA
5939978 GAGATTTGTTT
1 GAGATTTGTTT
*
5939989 GAGATTTGTTA
1 GAGATTTGTTT
*
5940000 GAGATGTGTTT
1 GAGATTTGTTT
5940011 GAGATTTGT
1 GAGATTTGT
5940020 CAGATATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5940009 original size:22 final size:22
Alignment explanation
Indices: 5939977--5940019 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5939967 AAATCTCATA
*
5939977 AGAGATTTGTTTGAGATTTGTT
1 AGAGATGTGTTTGAGATTTGTT
5939999 AGAGATGTGTTTGAGATTTGT
1 AGAGATGTGTTTGAGATTTGT
5940020 CAGATATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (22 bp):
AGAGATGTGTTTGAGATTTGTT
Found at i:5940197 original size:52 final size:53
Alignment explanation
Indices: 5940044--5940200 Score: 189
Period size: 52 Copynumber: 3.0 Consensus size: 53
5940034 TGGACAAGAA
*
5940044 GACTTACAAAAGAAGAATTCTAAGAGAAAAGAGATTCTTAATAGGTA-AA-TTT
1 GACTTACAAGAGAAGAATTCTAAGAGAAAAGAGATTCTTAATAGG-ACAAGTTT
* * * * *
5940096 GACTTGCAAGAGAAGAATTTTAA-ATGAAAAAAGATTTTTAATATG-CAAGTTT
1 GACTTACAAGAGAAGAATTCTAAGA-GAAAAGAGATTCTTAATAGGACAAGTTT
* *
5940148 GACTTACAAGAGAAGAATTCTAAGAGGAGAGAGATTCTTAAT-GGACAAGTTT
1 GACTTACAAGAGAAGAATTCTAAGAGAAAAGAGATTCTTAATAGGACAAGTTT
5940200 G
1 G
5940201 TATGGTTATA
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
51 4 0.05
52 82 0.94
53 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (53 bp):
GACTTACAAGAGAAGAATTCTAAGAGAAAAGAGATTCTTAATAGGACAAGTTT
Found at i:5940850 original size:107 final size:108
Alignment explanation
Indices: 5940652--5940853 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 108
5940642 GCATAATGTT
* * **** *
5940652 AAGGCCTTCTAAATAATCTCTGTTTTTATTCCAAAGCTATGCTTCTTGTAAAGCATATGCATAGA
1 AAGGCCTTCTAAATAATCTCTATTTCTATTCCAAAGCTACAAATCTTCTAAAGCATATGCATAGA
* ** **
5940717 CAATAGCTACTTTTACATGATGAAAGAATAAATGCATGACGTC
66 CAATAGATACTCATACATGACAAAAGAATAAATGCATGACGTC
* *
5940760 AAGGTCTTCTAAATAATCTTTATTTCTATTCC-AAGCTACAAATCTTCTAAAGCATATGCATAGA
1 AAGGCCTTCTAAATAATCTCTATTTCTATTCCAAAGCTACAAATCTTCTAAAGCATATGCATAGA
5940824 CAAT-GTATACTCATACATGACAAAAGAATA
66 CAATAG-ATACTCATACATGACAAAAGAATA
5940854 GAAGTCAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
106 1 0.01
107 50 0.63
108 28 0.35
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (108 bp):
AAGGCCTTCTAAATAATCTCTATTTCTATTCCAAAGCTACAAATCTTCTAAAGCATATGCATAGA
CAATAGATACTCATACATGACAAAAGAATAAATGCATGACGTC
Found at i:5942973 original size:20 final size:20
Alignment explanation
Indices: 5942935--5942999 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
5942925 GGTTTGGGTA
5942935 GATTTAGGATTT-GGAGTTTT
1 GATTTAGGATTTAGG-GTTTT
*
5942955 GATTTAGGATTTAGGGTTTAAG
1 GATTTAGGATTTAGGGTTT--T
*
5942977 GCTTTA-G-TTTAGGGTTTT
1 GATTTAGGATTTAGGGTTTT
5942995 GATTT
1 GATTT
5943000 TAGGGTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.11
20 26 0.68
21 3 0.08
22 5 0.13
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (20 bp):
GATTTAGGATTTAGGGTTTT
Found at i:5944115 original size:62 final size:60
Alignment explanation
Indices: 5943985--5944132 Score: 190
Period size: 61 Copynumber: 2.4 Consensus size: 60
5943975 GCTTTTATAC
* * **
5943985 AAGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTCTTGATAATTTTTATTTTT
1 AAGAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTCTTGATAATTTTAATTTCA
* * *
5944045 AAGAAAAATTGATACTTCCAACTTTTCCTAAAAAAAAATTTTTTTTTTGA-AATTTTAATTTCA
1 AAG-AAAATTGATACTTTCAACTTTTCCT---AAAAAATATTTTTCTTGATAATTTTAATTTCA
5944108 AAGAAAATTGATACTTTCAACTTTT
1 AAGAAAATTGATACTTTCAACTTTT
5944133 TCTCAAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
60 3 0.04
61 24 0.32
62 21 0.28
63 13 0.17
64 15 0.20
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (60 bp):
AAGAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTCTTGATAATTTTAATTTCA
Found at i:5944212 original size:58 final size:58
Alignment explanation
Indices: 5944142--5944470 Score: 294
Period size: 58 Copynumber: 5.5 Consensus size: 58
5944132 TTCTCAAAAT
*
5944142 ACTTTT-TGAAAAATTTTATTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCA
1 ACTTTTCTCAAAAATTTTATTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCA
* * * * * * * *
5944199 ACTTTTCTTAAAAAATATTTTTTTATAAAAAATCTTTATTTTTAAGGAAATTTGGTACTTCCA
1 ACTTTTC-TCAAAAAT-TTTATTT-T-AGAAAT-TTTATTTTCAAGAAAAATTGATACTTTCA
*
5944262 ACTTTTCCTAAAAAATGTATATATTTTTTA-AAACTTTTATTTTCAAGAAAAATTGATACTTTCA
1 ACTTTT-CTCAAAAAT-T-T-TA--TTTTAGAAA-TTTTATTTTCAAGAAAAATTGATACTTTCA
* * * *
5944326 ACTTTTCCTTAAAAA-TATATTTTTA-AAATTTTATTTTTAAGAAAAATTGATACTTTTA
1 ACTTTT-CTCAAAAATTTTA-TTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCA
* * *
5944384 ACTTTTTCTCAAAAATATT-TTTTAGAAAATTTA-TTT-AAGGAAAATTGATACTTTCA
1 AC-TTTTCTCAAAAATTTTATTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCA
* *
5944440 ACTTTTTCCCAAAAATTTTTTTTTAGAAATT
1 AC-TTTTCTCAAAAATTTTATTTTAGAAATT
5944471 GAAAATTTTA
Statistics
Matches: 228, Mismatches: 28, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
56 35 0.15
57 24 0.11
58 44 0.19
59 21 0.09
60 8 0.04
61 1 0.00
62 6 0.03
63 39 0.17
64 43 0.19
65 3 0.01
66 1 0.00
67 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.47
Consensus pattern (58 bp):
ACTTTTCTCAAAAATTTTATTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCA
Found at i:5944220 original size:72 final size:72
Alignment explanation
Indices: 5944078--5944221 Score: 202
Period size: 72 Copynumber: 2.0 Consensus size: 72
5944068 TTTCCTAAAA
* * *
5944078 AAAAATTTTTTTTTTGAAATTTTAATTTCAAAGAAAATTGATACTTTCAACTTTTTCTCAAAATA
1 AAAAATTTTATTTTAGAAATTTTAATTTCAAAGAAAATTGATACTTTCAACTTTTTCTAAAAATA
5944143 CTTTTTG
66 CTTTTTG
*
5944150 AAAAATTTTATTTTAGAAATTTTATTTTC-AAGAAAAATTGATACTTTCAAC-TTTTCTTAAAAA
1 AAAAATTTTATTTTAGAAATTTTAATTTCAAAG-AAAATTGATACTTTCAACTTTTTC-T-AAAA
*
5944213 ATATTTTTT
63 ATACTTTTT
5944222 TATAAAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
71 8 0.12
72 45 0.70
73 11 0.17
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (72 bp):
AAAAATTTTATTTTAGAAATTTTAATTTCAAAGAAAATTGATACTTTCAACTTTTTCTAAAAATA
CTTTTTG
Found at i:5944601 original size:3 final size:3
Alignment explanation
Indices: 5944593--5944630 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5944583 AATAAGCATA
5944593 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5944631 AAACAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5945287 original size:14 final size:15
Alignment explanation
Indices: 5945257--5945291 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
5945247 TTTTTACTTA
5945257 TGTTTTCTTTCTATG
1 TGTTTTCTTTCTATG
5945272 TGTTTTCTTT-TATG
1 TGTTTTCTTTCTATG
5945286 TGTTTT
1 TGTTTT
5945292 GCCTTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.06, C:0.09, G:0.14, T:0.71
Consensus pattern (15 bp):
TGTTTTCTTTCTATG
Found at i:5945588 original size:13 final size:12
Alignment explanation
Indices: 5945541--5945589 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
5945531 GATAAAGTCA
5945541 AAATAATAATAAT
1 AAATAATAAT-AT
*
5945554 AAAAAATAAATAT
1 AAATAAT-AATAT
5945567 AAATAAATAATAT
1 AAAT-AATAATAT
5945580 AATATAATAA
1 AA-ATAATAA
5945590 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 23 0.74
14 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:5945591 original size:17 final size:17
Alignment explanation
Indices: 5945543--5945591 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
5945533 TAAAGTCAAA
*
5945543 ATAATAATAATAAAAAAT
1 ATAAT-ATAATAAATAAT
5945561 A-AATATAAATAAATAAT
1 ATAATAT-AATAAATAAT
5945578 ATAATATAATAAAT
1 ATAATATAATAAAT
5945592 TAATTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 20 0.71
18 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAATATAATAAATAAT
Found at i:5945599 original size:17 final size:16
Alignment explanation
Indices: 5945544--5945599 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
5945534 AAAGTCAAAA
*
5945544 TAATAATAATAAAAAAT
1 TAAT-ATAATAAATAAT
*
5945561 AAATATAAATAAATAAT
1 TAATAT-AATAAATAAT
5945578 ATAATATAATAAATTAAT
1 -TAATATAATAAA-TAAT
5945596 TAAT
1 TAAT
5945600 TAACCCAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 22 0.67
18 9 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATATAATAAATAAT
Found at i:5947059 original size:16 final size:17
Alignment explanation
Indices: 5947038--5947076 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
5947028 AAATTTATCA
*
5947038 TATATTGAC-GTTTAAT
1 TATATTGACAGTTAAAT
5947054 TATATTGACAGTTAAAT
1 TATATTGACAGTTAAAT
5947071 TATATT
1 TATATT
5947077 AGTAAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (17 bp):
TATATTGACAGTTAAAT
Found at i:5947328 original size:17 final size:17
Alignment explanation
Indices: 5947303--5947337 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5947293 CTAATAAAAA
* *
5947303 TTCTCAAAAGCTATAAT
1 TTCTAAAAAACTATAAT
5947320 TTCTAAAAAACTATAAT
1 TTCTAAAAAACTATAAT
5947337 T
1 T
5947338 ATTAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (17 bp):
TTCTAAAAAACTATAAT
Found at i:5947476 original size:12 final size:12
Alignment explanation
Indices: 5947459--5947483 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5947449 ATTTTTAAAT
5947459 TTAAATATTTTA
1 TTAAATATTTTA
5947471 TTAAATATTTTA
1 TTAAATATTTTA
5947483 T
1 T
5947484 AATATTATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAAATATTTTA
Found at i:5949115 original size:14 final size:15
Alignment explanation
Indices: 5949087--5949115 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5949077 GACATAACTA
5949087 TTGTTTTATTTAATT
1 TTGTTTTATTTAATT
5949102 TTGTTTTA-TTAATT
1 TTGTTTTATTTAATT
5949116 CTAAACTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (15 bp):
TTGTTTTATTTAATT
Found at i:5949701 original size:20 final size:20
Alignment explanation
Indices: 5949676--5949716 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5949666 TTGTTTGATT
5949676 AATTTAATGATAGGGCTTTA
1 AATTTAATGATAGGGCTTTA
*
5949696 AATTTAATGGTAGGGCTTTA
1 AATTTAATGATAGGGCTTTA
5949716 A
1 A
5949717 GCCTCTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (20 bp):
AATTTAATGATAGGGCTTTA
Found at i:5952504 original size:14 final size:14
Alignment explanation
Indices: 5952487--5952516 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5952477 CAAGAATTTA
5952487 TTTTCAAGTTATAG
1 TTTTCAAGTTATAG
5952501 TTTTCAAGTTATAG
1 TTTTCAAGTTATAG
5952515 TT
1 TT
5952517 AAGTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTTTCAAGTTATAG
Found at i:5953097 original size:3 final size:3
Alignment explanation
Indices: 5953084--5953195 Score: 62
Period size: 3 Copynumber: 33.7 Consensus size: 3
5953074 TCTTAGTTAC
** * *
5953084 TTA TTA TTTA TTA TTA TTA TCTA TTA AGA TATA TATA TTA TTT TTA TTT
1 TTA TTA -TTA TTA TTA TTA T-TA TTA TTA T-TA T-TA TTA TTA TTA TTA
* * *
5953133 TTA TTA TTTA TCTG TTGA TATA CATA TTG TTA TTTA TCTA TTA TTA TTA
1 TTA TTA -TTA T-TA TT-A T-TA -TTA TTA TTA -TTA T-TA TTA TTA TTA
5953182 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
5953196 TATCTATTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
3 57 0.67
4 27 0.32
5 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5953144 original size:40 final size:39
Alignment explanation
Indices: 5953087--5953187 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 39
5953077 TAGTTACTTA
*
5953087 TTATTTATTATTATTATCTATTAAGATATATATATTATT-T
1 TTATTT-TTATTATTATCTATT-AGATATACATATTATTAT
* *
5953127 TTATTTTTATTATTTATCTGTT-GATATACATATTGTTAT
1 TTATTTTTATTA-TTATCTATTAGATATACATATTATTAT
*
5953166 TTATCTATTATTATTAT-TATTA
1 TTAT-TTTTATTATTATCTATTA
5953188 TTATTATTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
38 16 0.31
39 15 0.29
40 21 0.40
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (39 bp):
TTATTTTTATTATTATCTATTAGATATACATATTATTAT
Found at i:5953185 original size:20 final size:19
Alignment explanation
Indices: 5953176--5953254 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 19
5953166 TTATCTATTA
5953176 TTAT-TATTATTATTATTAT
1 TTATCTATTATTATT-TTAT
*
5953195 TTATCTATTAATAGTTTTAT
1 TTATCTATTATTA-TTTTAT
*
5953215 TTATCTAATTATT-TTTTTT
1 TTATCT-ATTATTATTTTAT
*
5953234 GTTATCTATTAATATATTTAT
1 -TTATCTATTATTAT-TTTAT
5953255 CTTTTTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
19 14 0.29
20 24 0.49
21 11 0.22
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.65
Consensus pattern (19 bp):
TTATCTATTATTATTTTAT
Found at i:5953214 original size:29 final size:29
Alignment explanation
Indices: 5953122--5953215 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
5953112 ATATATATAT
* * * *
5953122 TATTTTTATTTTTATTATTTATCTGTTGA
1 TATTATTATTATTATTATTTATCTATTAA
* * *
5953151 TA-TA-CA-TATTGTTATTTATCTATTAT
1 TATTATTATTATTATTATTTATCTATTAA
5953177 TATTATTATTATTATTATTTATCTATTAA
1 TATTATTATTATTATTATTTATCTATTAA
5953206 TAGTT-TTATT
1 TA-TTATTATT
5953216 TATCTAATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
26 17 0.33
27 3 0.06
28 2 0.04
29 27 0.53
30 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (29 bp):
TATTATTATTATTATTATTTATCTATTAA
Found at i:5953608 original size:6 final size:6
Alignment explanation
Indices: 5953586--5953746 Score: 77
Period size: 6 Copynumber: 26.7 Consensus size: 6
5953576 CGTTCCCAGG
* * *
5953586 TTTTT- TTTTTCA TTTTTA TTTTT- TATTTA TTTATTA TTATTA TTATTA
1 TTTTTA TTTTT-A TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA
* ** * * *
5953634 TTAGATTA GATTTG TTTAATA TTCTTTTA TTTTTA TCTTTA -TTTTA TTTTTA
1 TT--TTTA TTTTTA TTT-TTA TT-TT-TA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
5953686 TTTTTA -TTTTA -CTTT- TTTTTA TTTTTA TTTTCA CTTTTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5953730 -TTTTA TTATTTTA TTTT
1 TTTTTA -T-TTTTA TTTT
5953747 CTTTAAATAA
Statistics
Matches: 122, Mismatches: 19, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
5 34 0.28
6 58 0.48
7 16 0.13
8 14 0.11
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:5953678 original size:17 final size:16
Alignment explanation
Indices: 5953658--5953746 Score: 99
Period size: 17 Copynumber: 5.2 Consensus size: 16
5953648 TTTAATATTC
5953658 TTTTATTTTTATCTTTA
1 TTTTATTTTTAT-TTTA
5953675 TTTTATTTTTATTTTTA
1 TTTTATTTTTA-TTTTA
*
5953692 TTTTACTTTT-TTTTA
1 TTTTATTTTTATTTTA
*
5953707 TTTTTATTTTCACTTTTA
1 -TTTTATTTTTA-TTTTA
5953725 TTTTATTTTATTATTTTA
1 TTTTA-TTT-TTATTTTA
5953743 TTTT
1 TTTT
5953747 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.08
16 8 0.13
17 29 0.47
18 18 0.29
19 2 0.03
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:5953679 original size:5 final size:5
Alignment explanation
Indices: 5953658--5953746 Score: 85
Period size: 6 Copynumber: 16.8 Consensus size: 5
5953648 TTTAATATTC
5953658 TTTTA TTTTTA TCTTTA TTTTA TTTTTA TTTTTA TTTTA CTTTT- TTTTA
1 TTTTA -TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA
5953707 TTTTTA TTTTCA CTTTTA TTTTA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5953747 CTTTAAATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 19
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 31 0.42
6 32 0.43
7 4 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5953827 original size:57 final size:57
Alignment explanation
Indices: 5953765--5954091 Score: 338
Period size: 56 Copynumber: 5.7 Consensus size: 57
5953755 AAAATCCAAA
* *
5953765 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTTTC
* * *
5953823 AAAAAATATTTTTAGGGAAAAGTTGAAAGCATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
* ** * *
5953880 AAAAAAGGTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAA----TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
* * * ** * *
5953941 AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
* * * * * *
5953998 CAAAAATA-TTTTGGGGAAAAATTAAAAGTATCGATTTT-TTTCAAAATTAAAG-TTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAAT-AAGTTTTC
* *
5954054 TAAAAATA-TTTTGGAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
5954092 TCCTGCACAA
Statistics
Matches: 229, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
55 1 0.00
56 68 0.30
57 60 0.26
58 48 0.21
61 52 0.23
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
Found at i:5958034 original size:21 final size:20
Alignment explanation
Indices: 5957999--5958075 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
5957989 ACAATGGATG
* *
5957999 AAAAATGAGAAAAAAGATA-A
1 AAAAATGA-AAAAAAAAAAGA
* *
5958019 AAAGATGATAAAAAAAAAGA
1 AAAAATGAAAAAAAAAAAGA
*
5958039 AAAAATAGAGAAAAAAAAAGA
1 AAAAAT-GAAAAAAAAAAAGA
5958060 AAAAATGAAAAAAAAA
1 AAAAATGAAAAAAAAA
5958076 TTCAAATTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 7 0.15
20 22 0.46
21 19 0.40
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAAATGAAAAAAAAAAAGA
Found at i:5958041 original size:20 final size:19
Alignment explanation
Indices: 5957999--5958075 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 19
5957989 ACAATGGATG
* * *
5957999 AAAAATGAGAAAAAAGATA
1 AAAAATGAAAAAAAAAAGA
5958018 AAAAGATGATAAAAAAAAAGA
1 AAAA-ATGA-AAAAAAAAAGA
5958039 AAAAATAGAGAAAAAAAAAGA
1 AAAAAT-GA-AAAAAAAAAGA
5958060 AAAAATGAAAAAAAAA
1 AAAAATGAAAAAAAAA
5958076 TTCAAATTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
19 12 0.24
20 8 0.16
21 31 0.61
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAATGAAAAAAAAAAGA
Found at i:5959946 original size:41 final size:40
Alignment explanation
Indices: 5959888--5960191 Score: 350
Period size: 41 Copynumber: 7.4 Consensus size: 40
5959878 ATGATTGTCA
* *
5959888 AGGAGCAATTTATTTTTCAAAGTTTCATTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAG
*
5959929 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
* *
5959970 AGGAGCAATTTATTTTTCAAAGTTTCGTTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAG
* * *
5960011 AGGAGAAATTTACTTTTCAAAG-TCGTGGTGCCTCTATTTAA
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
5960052 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
* *
5960093 AGGAGCAATTTA-TTTTCTAAAGTCGTGGTTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTC-AAAGT--TCGTTGCCTCTGTTTAG
5960135 AGGAGCAATTTACTTTTCAAAGTT-GTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
5960176 AGGAGC-ATTTATCTTT
1 AGGAGCAATTTA-CTTT
5960192 AAAGTCATGG
Statistics
Matches: 232, Mismatches: 17, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
39 9 0.04
40 11 0.05
41 171 0.74
42 29 0.12
43 9 0.04
44 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (40 bp):
AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
Found at i:5960024 original size:82 final size:82
Alignment explanation
Indices: 5959887--5960203 Score: 450
Period size: 82 Copynumber: 3.9 Consensus size: 82
5959877 CATGATTGTC
* *
5959887 AAGGAGCAATTTATTTTTCAAAGTTTCATTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
1 AAGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
*
5959952 CGTGGTGCCTCTGTTTA
66 CGTGGTGCCTCTATTTA
* * *
5959969 AAGGAGCAATTTATTTTTCAAAGTTTCGTTACCTCTGTTTAGAGGAGAAATTTACTTTTCAAAGT
1 AAGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
5960034 CGTGGTGCCTCTATTTA
66 CGTGGTGCCTCTATTTA
5960051 AAGGAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCTAA
1 AAGGAGCAATTTACTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AA
5960113 AGTCGTGGTTGCCTCTATTTA
63 AGTCGTGG-TGCCTCTATTTA
* *
5960134 GAGGAGCAATTTACTTTTCAAAGTTGT-GGTGCCTCTGTTTAGAGGAGC-ATTTA-TCTTT-AAA
1 AAGGAGCAATTTACTTTTCAAAGTT-TCGTTGCCTCTGTTTAGAGGAGCAATTTACT-TTTCAAA
*
5960195 GTCATGGTG
64 GTCGTGGTG
5960204 TTTCTGGTTA
Statistics
Matches: 217, Mismatches: 10, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
80 6 0.03
81 14 0.06
82 139 0.64
83 56 0.26
85 1 0.00
86 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (82 bp):
AAGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
CGTGGTGCCTCTATTTA
Found at i:5960107 original size:123 final size:124
Alignment explanation
Indices: 5959916--5960203 Score: 433
Period size: 123 Copynumber: 2.3 Consensus size: 124
5959906 AAAGTTTCAT
5959916 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAAAGGAGCAATTT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAAAGGAGCAATTT
* *
5959981 ATTTT-TCAAAGT-TTCGTTACCTCTGTTTAGAGGAGAAATTTACTTTTCAAAGTCGTGG
66 ATTTTCT-AAAGTCGTCGTTACCTCTATTTAGAGGAGAAATTTACTTTTCAAAGTCGTGG
* * *
5960039 TGCCTCTATTTAAAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAAAGGAGCAATTT
* * * *
5960104 ATTTTCTAAAGTCGTGGTTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTTGTGG
66 ATTTTCTAAAGTCGTCGTTACCTCTATTTAGAGGAGAAATTTACTTTTCAAAGTCGTGG
*
5960163 TGCCTCTGTTTAGAGGAGC-ATTTA-TCTTT-AAAGTCATGGTG
1 TGCCTCTGTTTAGAGGAGCAATTTACT-TTTCAAAGTCGTGGTG
5960204 TTTCTGGTTA
Statistics
Matches: 150, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
122 12 0.08
123 80 0.53
124 58 0.39
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (124 bp):
TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAAAGGAGCAATTT
ATTTTCTAAAGTCGTCGTTACCTCTATTTAGAGGAGAAATTTACTTTTCAAAGTCGTGG
Found at i:5960290 original size:12 final size:12
Alignment explanation
Indices: 5960275--5960308 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5960265 GATCAAATTT
5960275 AAAAAAAAATAA
1 AAAAAAAAATAA
*
5960287 AAAAAAACATAA
1 AAAAAAAAATAA
5960299 AAAATAAAAA
1 AAAA-AAAAA
5960309 AATTTACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:5960457 original size:45 final size:44
Alignment explanation
Indices: 5960315--5960466 Score: 166
Period size: 44 Copynumber: 3.5 Consensus size: 44
5960305 AAAAAATTTA
***
5960315 CCTCTGATTAGAGGAACCTT-T-TATTTTTCAAAAGTCGTTGAG
1 CCTCTGATTAGAGGAGTTTTGTCTATTTTTCAAAAGTCGTTGAG
* **
5960357 CCTCTGATTAGAGGAGTTTTATCTATTTTTCAAAAGTATTTGAG
1 CCTCTGATTAGAGGAGTTTTGTCTATTTTTCAAAAGTCGTTGAG
** * *
5960401 CCTCTGATTAGAAAAGTTTTGTTTATGTTCTTC-AAAGTCGTTAAG
1 CCTCTGATTAGAGGAGTTTTGTCTAT-TT-TTCAAAAGTCGTTGAG
*
5960446 CCTCTGCTTAGAGGAGTTTTG
1 CCTCTGATTAGAGGAGTTTTG
5960467 ATTAAATTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
42 17 0.19
43 1 0.01
44 41 0.45
45 29 0.32
46 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (44 bp):
CCTCTGATTAGAGGAGTTTTGTCTATTTTTCAAAAGTCGTTGAG
Found at i:5961271 original size:13 final size:12
Alignment explanation
Indices: 5961253--5961328 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 12
5961243 TGTTTAATAT
5961253 TCTTTTATTTTTA
1 TCTTTT-TTTTTA
5961266 TCTTTTTTTTTA
1 TCTTTTTTTTTA
*
5961278 TTTTACTTTTCTTTA
1 TCTT--TTTT-TTTA
*
5961293 T-TTTTTTTTCA
1 TCTTTTTTTTTA
*
5961304 -CTTTTATTTTA
1 TCTTTTTTTTTA
5961315 T-TTTATTATTTTA
1 TCTTT-TT-TTTTA
5961328 T
1 T
5961329 TTTCTTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
11 14 0.27
12 14 0.27
13 12 0.24
14 6 0.12
15 5 0.10
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTTTTTTTTTA
Found at i:5961276 original size:5 final size:5
Alignment explanation
Indices: 5961268--5961331 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
5961258 TATTTTTATC
* * *
5961268 TTTTT TTTTA TTTTA CTTTT- CTTTA TTTTT TTTTCA CTTTTA TTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTT-A -TTTTA TTTTA
5961315 TTTTA --TTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
5961332 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 33 0.69
6 5 0.10
7 4 0.08
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:5961287 original size:15 final size:17
Alignment explanation
Indices: 5961255--5961331 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 17
5961245 TTTAATATTC
5961255 TTTTATTTTTATCTTTTT
1 TTTTA-TTTTATCTTTTT
5961273 TTTTATTTTA-C-TTTT
1 TTTTATTTTATCTTTTT
* *
5961288 CTTTATTTT-T-TTTTCAC
1 TTTTATTTTATCTTTT--T
5961305 TTTTATTTTAT-TTTATT
1 TTTTATTTTATCTTT-TT
5961322 ATTTTATTTT
1 -TTTTATTTT
5961332 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
15 15 0.31
16 1 0.02
17 13 0.27
18 18 0.38
19 1 0.02
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTATCTTTTT
Found at i:5961308 original size:27 final size:26
Alignment explanation
Indices: 5961262--5961313 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5961252 TTCTTTTATT
*
5961262 TTTATCTTTTTTTTTATTTTACTTTTC
1 TTTATCTTTTTTTTCATTTTA-TTTTC
5961289 TTTAT-TTTTTTTTCACTTTTATTTT
1 TTTATCTTTTTTTTCA-TTTTATTTT
5961314 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTATCTTTTTTTTCATTTTATTTTC
Found at i:5961314 original size:32 final size:30
Alignment explanation
Indices: 5961273--5961332 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
5961263 TTATCTTTTT
* *
5961273 TTTTATTTTACTTTTCTTTATTTTTTTTTCAC
1 TTTTATTTTA-TTTT-ATTATTTTATTTTCAC
5961305 TTTTATTTTATTTTATTATTTTATTTTC
1 TTTTATTTTATTTTATTATTTTATTTTC
5961333 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 12 0.46
31 4 0.15
32 10 0.38
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTATTTTATTTTATTATTTTATTTTCAC
Found at i:5961319 original size:27 final size:27
Alignment explanation
Indices: 5961254--5961326 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
5961244 GTTTAATATT
*
5961254 CTTTTATTTTTATCTTTTTTTTTATTTTA
1 CTTTTA-TTTTAT-TTTTTTTTCATTTTA
*
5961283 CTTTT-CTTTATTTTTTTTTCACTTTTA
1 CTTTTATTTTATTTTTTTTTCA-TTTTA
*
5961310 -TTTTATTTTATTATTTT
1 CTTTTATTTTATTTTTTT
5961327 ATTTTCTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 13 0.34
27 20 0.53
29 5 0.13
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (27 bp):
CTTTTATTTTATTTTTTTTTCATTTTA
Found at i:5961329 original size:13 final size:13
Alignment explanation
Indices: 5961307--5961331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5961297 TTTTTCACTT
5961307 TTATTTTATTTTA
1 TTATTTTATTTTA
5961320 TTATTTTATTTT
1 TTATTTTATTTT
5961332 CTTTAAATAA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:5961415 original size:58 final size:57
Alignment explanation
Indices: 5961349--5961502 Score: 220
Period size: 58 Copynumber: 2.7 Consensus size: 57
5961339 TAAAATCCAA
* *
5961349 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA-ATTTCC
* * *
5961407 AAAAAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
* *
5961464 AAAACAA-GTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAA-AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
5961503 TTCTGCACAA
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
57 36 0.42
58 50 0.58
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
Found at i:5963869 original size:24 final size:24
Alignment explanation
Indices: 5963837--5963882 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5963827 GGAGTAATAT
5963837 TAATATTATTAAT-ATTAATAAAAA
1 TAATATTA-TAATAATTAATAAAAA
* *
5963861 TAATTTTATAATAATTATTAAA
1 TAATATTATAATAATTAATAAA
5963883 TGAGTATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATATTATAATAATTAATAAAAA
Found at i:5964625 original size:2 final size:2
Alignment explanation
Indices: 5964618--5964646 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5964608 TAATTCCCTG
5964618 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5964647 GTTTTCTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5964638 original size:13 final size:13
Alignment explanation
Indices: 5964620--5964645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5964610 ATTCCCTGTA
5964620 TATATATATATAT
1 TATATATATATAT
5964633 TATATATATATAT
1 TATATATATATAT
5964646 AGTTTTCTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:5964638 original size:15 final size:15
Alignment explanation
Indices: 5964618--5964646 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5964608 TAATTCCCTG
5964618 TATATATATATATAT
1 TATATATATATATAT
5964633 TATATATATATATA
1 TATATATATATATA
5964647 GTTTTCTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:5965101 original size:10 final size:12
Alignment explanation
Indices: 5965064--5965132 Score: 72
Period size: 12 Copynumber: 5.7 Consensus size: 12
5965054 ATATTATTTT
5965064 TAATATAAATATGA
1 TAAT-TAAATAT-A
5965078 -AATTAAATATA
1 TAATTAAATATA
5965089 T-ATATAAATATA
1 TAAT-TAAATATA
5965101 TAATTAAATATA
1 TAATTAAATATA
*
5965113 AAATTAAATA-A
1 TAATTAAATATA
5965124 TTAATTAAA
1 -TAATTAAA
5965133 AAATAAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
11 4 0.08
12 40 0.82
13 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
TAATTAAATATA
Found at i:5965123 original size:20 final size:20
Alignment explanation
Indices: 5965064--5965140 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
5965054 ATATTATTTT
*
5965064 TAATATAAATATGAAATTAAA
1 TAAT-TAAATATAAAATTAAA
* *
5965085 T-A-TATATAT-AAA-TATA
1 TAATTAAATATAAAATTAAA
5965101 TAATTAAATATAAAATTAAA
1 TAATTAAATATAAAATTAAA
* *
5965121 TAATTAATTA-AAAAATAAA
1 TAATTAAATATAAAATTAAA
5965140 T
1 T
5965141 TTTTTATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.09
17 4 0.09
18 12 0.26
19 12 0.26
20 13 0.28
21 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
TAATTAAATATAAAATTAAA
Found at i:5965349 original size:15 final size:14
Alignment explanation
Indices: 5965329--5965358 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5965319 TATCGATAGA
5965329 ATATATAAATTAAAT
1 ATATATAAA-TAAAT
5965344 ATATATAAATAAAT
1 ATATATAAATAAAT
5965358 A
1 A
5965359 GTGTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATATAAATAAAT
Found at i:5967847 original size:60 final size:61
Alignment explanation
Indices: 5967783--5967914 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 61
5967773 AAAGAAAAGG
*
5967783 TCGTAATTGAT-TTCATTTAAAAGTTTAAAATAT-TCAATTATAACGTTTAATTAAAA-AAA-A
1 TCGTAATTGATCAT-ATTTAAAAG-TTAAAAT-TCTCAATTATAACGTTTAATTAAAAGAAACA
* * * * * *
5967843 TCGTAATAGCTCATATTTAAATGTTAACATTGCTCAATTATGATGTTTAATTAAAAGAAACA
1 TCGTAATTGATCATATTTAAAAGTTAAAATT-CTCAATTATAACGTTTAATTAAAAGAAACA
5967905 TCGTAATTGA
1 TCGTAATTGA
5967915 GTCTTTTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
58 1 0.02
59 6 0.10
60 38 0.66
61 4 0.07
62 9 0.16
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (61 bp):
TCGTAATTGATCATATTTAAAAGTTAAAATTCTCAATTATAACGTTTAATTAAAAGAAACA
Found at i:5969706 original size:29 final size:29
Alignment explanation
Indices: 5969674--5969732 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5969664 GTGGATTTCA
*
5969674 TAAATTTATTTGAAAAGGTTTTTTTTCTT
1 TAAATTTATTTGAAAAGATTTTTTTTCTT
5969703 TAAATTTATTTGAAAAGATTTTTTTTCTT
1 TAAATTTATTTGAAAAGATTTTTTTTCTT
5969732 T
1 T
5969733 TTCTCTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.59
Consensus pattern (29 bp):
TAAATTTATTTGAAAAGATTTTTTTTCTT
Found at i:5969870 original size:33 final size:34
Alignment explanation
Indices: 5969806--5969869 Score: 98
Period size: 32 Copynumber: 1.9 Consensus size: 34
5969796 ATAAAGTCAA
5969806 TAAAATAATAAAATAAAACTAAAATAAAAAAACT
1 TAAAATAATAAAATAAAACTAAAATAAAAAAACT
5969840 TAAAA-AATAAAAT-AAA-TAAAATGAAAAAAA
1 TAAAATAATAAAATAAAACTAAAAT-AAAAAAA
5969870 AAACCTACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.21
32 10 0.34
33 8 0.28
34 5 0.17
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.19
Consensus pattern (34 bp):
TAAAATAATAAAATAAAACTAAAATAAAAAAACT
Found at i:5970657 original size:3 final size:3
Alignment explanation
Indices: 5970641--5970733 Score: 95
Period size: 3 Copynumber: 32.3 Consensus size: 3
5970631 AATGAATGAA
5970641 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
5970687 AAT AAC AAC AAC AAC AAC AAC AAT AAT -AT AGT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5970733 A
1 A
5970734 CAATATTCTA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
2 8 0.10
3 74 0.90
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:5970761 original size:17 final size:17
Alignment explanation
Indices: 5970736--5970770 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5970726 ATATAATACA
* *
5970736 ATATTCTATACTACTAT
1 ATATACTATACTAATAT
5970753 ATATACTATACTAATAT
1 ATATACTATACTAATAT
5970770 A
1 A
5970771 CCATATTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATACTATACTAATAT
Found at i:5970816 original size:3 final size:3
Alignment explanation
Indices: 5970808--5970848 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
5970798 TAACAACGAC
* *
5970808 AAT AAT AAT AAT AAT AAT AACA AAT AAT AAT ACT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
5970849 CAAAAAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5971288 original size:14 final size:14
Alignment explanation
Indices: 5971269--5971306 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
5971259 TGATCTAGAT
5971269 TGACCAAGATTTAA
1 TGACCAAGATTTAA
5971283 TGACCAAGATTTAA
1 TGACCAAGATTTAA
5971297 TGACCAAGAT
1 TGACCAAGAT
5971307 GAAATTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (14 bp):
TGACCAAGATTTAA
Found at i:5972520 original size:8 final size:8
Alignment explanation
Indices: 5972507--5972551 Score: 56
Period size: 8 Copynumber: 5.4 Consensus size: 8
5972497 TCAATTTGGC
5972507 TTTCATTT
1 TTTCATTT
5972515 TTTCATTTT
1 TTTCA-TTT
5972524 TTTCATTT
1 TTTCATTT
5972532 TTTC-TTT
1 TTTCATTT
5972539 TTCATCATTT
1 TT--TCATTT
5972549 TTT
1 TTT
5972552 TTCGAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 5 0.15
8 13 0.39
9 10 0.30
10 5 0.15
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTCATTT
Found at i:5972529 original size:17 final size:16
Alignment explanation
Indices: 5972507--5972551 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
5972497 TCAATTTGGC
5972507 TTTCATTTTTTCATTTT
1 TTTCATTTTTTC-TTTT
5972524 TTTCATTTTTTCTTTT
1 TTTCATTTTTTCTTTT
*
5972540 TCATCATTTTTT
1 T-TTCATTTTTT
5972552 TTCGAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCATTTTTTCTTTT
Found at i:5977024 original size:19 final size:19
Alignment explanation
Indices: 5977000--5977076 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 19
5976990 TGAAGTCAAT
5977000 AAAATAATAAAAAAACTAA
1 AAAATAATAAAAAAACTAA
5977019 AAAATAAAATAAAATAAACTTAA
1 AAAAT--AATAAAA-AAAC-TAA
5977042 AAAATAA-AATCAAAAACTAA
1 AAAATAATAA--AAAAACTAA
*
5977062 AAATAAAATAAAAAA
1 AAA-ATAATAAAAAA
5977077 GGGAGAACCT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
19 5 0.10
20 12 0.24
21 16 0.33
22 8 0.16
23 8 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAATAATAAAAAAACTAA
Found at i:5977024 original size:24 final size:23
Alignment explanation
Indices: 5976997--5977076 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
5976987 AAATGAAGTC
5976997 AATAAAATAATAAAAAAAC-TAAAA
1 AATAAAAT-A-AAAAAAACTTAAAA
*
5977021 AATAAAATAAAATAAACTTAAAA
1 AATAAAATAAAAAAAACTTAAAA
*
5977044 AATAAAAT--CAAAAAC-T-AAA
1 AATAAAATAAAAAAAACTTAAAA
5977063 AATAAAATAAAAAA
1 AATAAAATAAAAAA
5977077 GGGAGAACCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.22
20 1 0.02
21 8 0.16
22 7 0.14
23 14 0.29
24 8 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (23 bp):
AATAAAATAAAAAAAACTTAAAA
Found at i:5977056 original size:13 final size:12
Alignment explanation
Indices: 5976997--5977074 Score: 65
Period size: 13 Copynumber: 6.6 Consensus size: 12
5976987 AAATGAAGTC
5976997 AATAAAATAATAA
1 AATAAAATAA-AA
*
5977010 AA-AAACTAAAA
1 AATAAAATAAAA
5977021 AATAAAAT--AA
1 AATAAAATAAAA
*
5977031 AATAAACTTAAAA
1 AATAAA-ATAAAA
5977044 AATAAAATCAAAA
1 AATAAAAT-AAAA
* *
5977057 ACTAAAA-ATAA
1 AATAAAATAAAA
5977068 AATAAAA
1 AATAAAA
5977075 AAGGGAGAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
10 8 0.15
11 14 0.26
12 11 0.21
13 20 0.38
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:5977835 original size:3 final size:3
Alignment explanation
Indices: 5977829--5977883 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
5977819 GGAATGAAAT
*
5977829 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5977874 TAA T-A TAA TA
1 TAA TAA TAA TA
5977884 TTTTGTACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 38 0.83
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5984500 original size:714 final size:711
Alignment explanation
Indices: 5983043--5985139 Score: 2424
Period size: 714 Copynumber: 2.9 Consensus size: 711
5983033 ATGGAACTAT
** * * ** * *
5983043 ATTAATACACGAAAAATGTGTTCCATTATAAACTAAACCAAAATATTAAAGTTAATATCTTGTGA
1 ATTAATACATAAAAAATGTGTTCTATTATAAACTAAACAAAAATATTAAAACTAATACCTTATGA
* * * *** * * * *
5983108 GATTCTTAATCCATTCATGCATGTAATGGTATTCTTTAGCACTCTACCATCTATTGCAAAACCTT
66 GATCCTCAACCCATTCCCACGTGTAATGGTATACCTTAGCACTTTACCATCTATTGCAAAACCTT
* * *
5983173 TCCATCCTGGTAGAACATATATGAATTGCATATATATGGTGCAAACACCAAAGACATTAGTAGCA
131 TCCATCCTGATAGAACATATATGAATTGCATATATAGGGTGCAAACACCAAAGACATTGGTAGCA
* * * * *
5983238 ATTTAATTTTTCCTAGTTCTGTAT-TCAGGCCTGTCAACTACGTTTATATTGACCTTGATGTATG
196 ATTTCATTTTT-CTAGTCCTGTATCT-AGGCCTGTCAACTGCATCTATATTGACCTTGATGTATG
** * * *
5983302 TTTTATCTAAGGCACCTAAACAACCTTTGAACCATTTTTATCTATTATTTATTGAATTCTCCACT
259 TCCTATCTAAGGCACCTAAACAACCTTTGAACCATTTTTATCTATTATCTATTGAATTTTTCACT
* ** *
5983367 ATTAGTTTGGGTTTTTTTAAACTATAAGGTATGCAGTCTTAAAACAGAATTTAACATAGAATGAA
324 ATCAGTTTAAG-TTTTTTAAACAAT-AGGTATGCAGTCTTAAAACAGAATTTAACATAGAATGAA
* * * *
5983432 ATTGCCTATTAATTATCTCTTCAAATCTAGTTACTTGACACTTCATAACCTTATTTTTTGTGTGA
387 ATTG-CTACTAATTATCTCTTCAGATCTAGCTACTTGACACTTCATAACCTTATTTTTTGTATGA
* * * ***
5983497 TAGG-CAATGATGTGGAGGAAGCTAATAACCAATTCTTTTATTGACATATATCTAGATGCCTACG
451 T-GGACAATGATGTGGAGGAAGCTAATAACCAGTTCTTCTATTAACATATATCTAGATGCCTGTA
* * ** * * *
5983561 ATC-CTCCTTATGTTTGAAGCAGATGACATAATTTTGTAAAAG-CTCTCATATCTATTCTAGTAT
515 ATCTC-CCTTCTGTTTGAAGCAAATGACATAATTTTACAAAAGTTTATC-TATCCATTCTAGTAT
* ** * *
5983624 TATTTATATACTGTCTA-TCATTT-AAAAGCCATTGCATTTAAGTTTAACTCTCTAATATGTAGC
578 TATTTATAAACTGTCTATTC-TTTAAAAAATCATTACATTTAAGTTTAACTTTCTAATATGTAGC
* * ** *
5983687 CTATCATAAGAGATTTTACCATAATACATAAAAAAAAGGTAATAGTAATTACCTATTATAGTGAA
642 CTATCATAAGAGGTTCTACCATAATACATAAAAAAAAGGTAATAAAAATTACCTATTATAGAGAA
5983752 ACAAC
707 ACAAC
* *
5983757 ATTAATACATAAAACATGTGTTCTATTATAAACTTAATC-AAAATATTAAAACTAATACCTTATG
1 ATTAATACATAAAAAATGTGTTCTATTATAAAC-TAAACAAAAATATTAAAACTAATACCTTATG
* **** * ** *
5983821 GGATCCTCAATTTGTTCCCACGTGTAATGGTATACCTTAACACTTTACCATCTGCTGCAAAACTT
65 AGATCCTCAACCCATTCCCACGTGTAATGGTATACCTTAGCACTTTACCATCTATTGCAAAACCT
* * * * *
5983886 TTCCATCTTAATAAAACATATATAAATTGCATATAT-GGAGTGCAAACACCAAGGACATTGGTAG
130 TTCCATCCTGATAGAACATATATGAATTGCATATATAGG-GTGCAAACACCAAAGACATTGGTAG
* * * * * *
5983950 TAATTTCATTATTTCTTGTCCTGTATCTAGGCTTATCAATTGCATCTATATTGACATTGATGTAT
194 CAATTTCATT-TTTCTAGTCCTGTATCTAGGCCTGTCAACTGCATCTATATTGACCTTGATGTAT
* * * *
5984015 GTCCCATCTAAGGCACCCAAACAACATTTGAACCATTTTTATCTATTATCTGTTGAATTTTTCAC
258 GTCCTATCTAAGGCACCTAAACAACCTTTGAACCATTTTTATCTATTATCTATTGAATTTTTCAC
*
5984080 TATCAGTTTAAGTTTTTTAAACAATAGGATATGCAGTCTTAAAACAGAATTTAACACAGAATGAA
323 TATCAGTTTAAGTTTTTTAAACAATAGG-TATGCAGTCTTAAAACAGAATTTAACATAGAATGAA
*** *
5984145 ATTGTCTACTAATTATCT-TTCTAGATCTAGCTACTTGATGTTTCATAATCTTATTTTTTGTATG
387 ATTG-CTACTAATTATCTCTTC-AGATCTAGCTACTTGACACTTCATAACCTTATTTTTTGTATG
* * * * * *
5984209 ATGGACAATGATGTGAAAGAAGCTAATAACTAGTTCTTCTATTAACATATGTTTAGATGCTTGTA
450 ATGGACAATGATGTGGAGGAAGCTAATAACCAGTTCTTCTATTAACATATATCTAGATGCCTGTA
* *
5984274 ATCTCCCTTCTGTTTGAAGTAAATGACATAATTTTACAAAAGTTTTTCTATCCATTCTAGTATTA
515 ATCTCCCTTCTGTTTGAAGCAAATGACATAATTTTACAAAAGTTTATCTATCCATTCTAGTATTA
* * * *
5984339 TTTGTACACTGTCTATTGCTTTAAAAAATGATTACATTTAAGTTTAACTTTCTAATATGTAGTCT
580 TTTATAAACTGTCTATT-CTTTAAAAAATCATTACATTTAAGTTTAACTTTCTAATATGTAGCCT
*
5984404 ATCATAAGAGGTTCTACCATAATACATAAAAGAAAGGTAATAAAAATTACCTATTATAGAGAAAC
644 ATCATAAGAGGTTCTACCATAATACATAAAAAAAAGGTAATAAAAATTACCTATTATAGAGAAAC
5984469 AAC
709 AAC
* * *
5984472 ATTAATACATAAAAAATGTGTT-TATTATATACTAAACAAAAATATTAAAGCTAATACCTTGTGA
1 ATTAATACATAAAAAATGTGTTCTATTATAAACTAAACAAAAATATTAAAACTAATACCTTATGA
* * * * * * * *
5984536 TATCTTTAACCCATTCCTATGTGTAATGGCATCCCTTAGCACTTTACCATCTATTGCAGAACCTT
66 GATCCTCAACCCATTCCCACGTGTAATGGTATACCTTAGCACTTTACCATCTATTGCAAAACCTT
* * * * * *
5984601 TCTATCCTGATAGAACATATATGAATTGTATATCTAGGGTGCAAAGACCAAAGATATTGGTACCA
131 TCCATCCTGATAGAACATATATGAATTGCATATATAGGGTGCAAACACCAAAGACATTGGTAGCA
** * * * *
5984666 ATTTCATTTTTTCTAGTCCTGTATCTAAACCCGTCAACTGCATCTACATTGACCTTAATGTATAT
196 ATTTCA-TTTTTCTAGTCCTGTATCTAGGCCTGTCAACTGCATCTATATTGACCTTGATGTATGT
* *
5984731 CCTATCTAAGGCACCTAAATAACCTTTAAACCATTTTTATCTATTATCTATTGAATTCTTTGC-C
260 CCTATCTAAGGCACCTAAACAACCTTTGAACCATTTTTATCTATTATCTATTGAATT-TTT-CAC
* * * * * * * * * *
5984795 -ATC-GATTCACGTTTTTTAAACAACAGGGTGTGTAGTCTCAAAATAGAGTTCAACATAAAATGA
323 TATCAG-TTTAAGTTTTTTAAACAATA-GGTATGCAGTCTTAAAACAGAATTTAACATAGAATGA
* * *
5984858 AATTGCTTACTAATTATCTCTTCAGATCTATCTACTTCACACTTCATAACCCTATTTTTTGTATG
386 AATTGC-TACTAATTATCTCTTCAGATCTAGCTACTTGACACTTCATAACCTTATTTTTTGTATG
* * * * * *
5984923 ATGGACAATAACGTGGAGGAAGTTAATAACCAGTTCTTCTGTTAACATATATCTAAATTCCTGTA
450 ATGGACAATGATGTGGAGGAAGCTAATAACCAGTTCTTCTATTAACATATATCTAGATGCCTGTA
* * * *
5984988 ATCTCCCTTCTATTTGAAGCAAATGATATAATTTTACAAAAATTGTAGC-ATCCATTCTAGTATT
515 ATCTCCCTTCTGTTTGAAGCAAATGACATAATTTTACAAAAGTT-TATCTATCCATTCTAGTATT
* * *
5985052 ATCTATAAATTGTCTATTATTCTAAAAAATCATTACATTTAAGTTTAACTCTT-TAATATGTAGC
579 ATTTATAAACTGTCTATTCTT-TAAAAAATCATTACATTTAAGTTTAACT-TTCTAATATGTAGC
* * *
5985116 CTCTCATAAAAGGTTCCACCATAA
642 CTATCATAAGAGGTTCTACCATAA
5985140 GGTACTCTAT
Statistics
Matches: 1160, Mismatches: 199, Indels: 48
0.82 0.14 0.03
Matches are distributed among these distances:
712 8 0.01
713 221 0.19
714 785 0.68
715 145 0.12
716 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (711 bp):
ATTAATACATAAAAAATGTGTTCTATTATAAACTAAACAAAAATATTAAAACTAATACCTTATGA
GATCCTCAACCCATTCCCACGTGTAATGGTATACCTTAGCACTTTACCATCTATTGCAAAACCTT
TCCATCCTGATAGAACATATATGAATTGCATATATAGGGTGCAAACACCAAAGACATTGGTAGCA
ATTTCATTTTTCTAGTCCTGTATCTAGGCCTGTCAACTGCATCTATATTGACCTTGATGTATGTC
CTATCTAAGGCACCTAAACAACCTTTGAACCATTTTTATCTATTATCTATTGAATTTTTCACTAT
CAGTTTAAGTTTTTTAAACAATAGGTATGCAGTCTTAAAACAGAATTTAACATAGAATGAAATTG
CTACTAATTATCTCTTCAGATCTAGCTACTTGACACTTCATAACCTTATTTTTTGTATGATGGAC
AATGATGTGGAGGAAGCTAATAACCAGTTCTTCTATTAACATATATCTAGATGCCTGTAATCTCC
CTTCTGTTTGAAGCAAATGACATAATTTTACAAAAGTTTATCTATCCATTCTAGTATTATTTATA
AACTGTCTATTCTTTAAAAAATCATTACATTTAAGTTTAACTTTCTAATATGTAGCCTATCATAA
GAGGTTCTACCATAATACATAAAAAAAAGGTAATAAAAATTACCTATTATAGAGAAACAAC
Found at i:5996049 original size:16 final size:16
Alignment explanation
Indices: 5996030--5996066 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5996020 AAGTGCCAAG
5996030 AAAATATAAA-AAAAAT
1 AAAATA-AAATAAAAAT
5996046 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
5996062 AAAAT
1 AAAAT
5996067 TAGGAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:6012923 original size:30 final size:29
Alignment explanation
Indices: 6012887--6012948 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6012877 TAATGTTCAG
6012887 ATTATAAAT-AAATACAACATTTAATATTTT
1 ATTAT-AATCAAATA-AACATTTAATATTTT
* * *
6012917 ATTATAATCAATTAAACTTTTAATTTTTT
1 ATTATAATCAAATAAACATTTAATATTTT
6012946 ATT
1 ATT
6012949 TTCATTCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTATAATCAAATAAACATTTAATATTTT
Found at i:6012966 original size:29 final size:29
Alignment explanation
Indices: 6012906--6012969 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
6012896 AAATACAACA
*
6012906 TTTAATATTTTATTATAATCAATTAAACT
1 TTTAATATTTTATTATAATCAACTAAACT
* * * *
6012935 TTTAATTTTTTATTTTCATTCAACTAAATT
1 TTTAATATTTTATTAT-AATCAACTAAACT
6012965 TTTAA
1 TTTAA
6012970 ATACACAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTAATATTTTATTATAATCAACTAAACT
Found at i:6015800 original size:18 final size:19
Alignment explanation
Indices: 6015751--6015805 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
6015741 AAAAAAAAGA
* *
6015751 AAAAGGAAAAAGTA-A-AA
1 AAAAGGAAAAAATATATAT
*
6015768 AAAAGGAAAATATATATAT
1 AAAAGGAAAAAATATATAT
6015787 AAAA-GAAAAAATATATAT
1 AAAAGGAAAAAATATATAT
6015805 A
1 A
6015806 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 12 0.38
18 15 0.47
19 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (19 bp):
AAAAGGAAAAAATATATAT
Found at i:6031975 original size:91 final size:91
Alignment explanation
Indices: 6031875--6032054 Score: 333
Period size: 91 Copynumber: 2.0 Consensus size: 91
6031865 CCAACTTGGC
*
6031875 CCTAGTGCCTCTTAGCCTCTACTCCTTAGCTAACTCATCCCTGCCATTGCGTTCTGTGGATAAAC
1 CCTAGTGCCTCTTAGCCTCTACTCCTTAGCTAACTCATCCCTGCCATTGCGTTCTGTGGATAAAA
6031940 GACCTTTGCAACTGATTTAATGCAGT
66 GACCTTTGCAACTGATTTAATGCAGT
* *
6031966 CCTAGTGCCTCTTAGCCTCTAGTCGTTAGCTAACTCATCCCTGCCATTGCGTTCTGTGGATAAAA
1 CCTAGTGCCTCTTAGCCTCTACTCCTTAGCTAACTCATCCCTGCCATTGCGTTCTGTGGATAAAA
6032031 GACCTTTGCAACTGATTTAATGCA
66 GACCTTTGCAACTGATTTAATGCA
6032055 ACTAAACCAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (91 bp):
CCTAGTGCCTCTTAGCCTCTACTCCTTAGCTAACTCATCCCTGCCATTGCGTTCTGTGGATAAAA
GACCTTTGCAACTGATTTAATGCAGT
Found at i:6036202 original size:26 final size:27
Alignment explanation
Indices: 6036150--6036206 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
6036140 CCCCAATGGG
*
6036150 TTTTTATTTTCATTATTTAATATATAT
1 TTTTTATTTTCATTATCTAATATATAT
** *
6036177 TTTTTATTTTTTTTATCTATTA-ATAT
1 TTTTTATTTTCATTATCTAATATATAT
6036203 TTTT
1 TTTT
6036207 ATTATTTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTATTTTCATTATCTAATATATAT
Found at i:6036245 original size:41 final size:42
Alignment explanation
Indices: 6036178--6036284 Score: 123
Period size: 41 Copynumber: 2.6 Consensus size: 42
6036168 AATATATATT
6036178 TTTTATTTTTTTTATCTATTAATATTT-TTATTATTTATCTGC
1 TTTTATTTTTTTTATCTATTAATATTTCTT-TTATTTATCTGC
* * **
6036220 TTTTATTTTTTATTATTTA-T-CTATTTCTTTTATTTATCTAA
1 TTTTATTTTTT-TTATCTATTAATATTTCTTTTATTTATCTGC
*
6036261 TTTT-TTTTTGTTATCTATTAATAT
1 TTTTATTTTTTTTATCTATTAATAT
6036285 ATTTATCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
39 6 0.11
40 6 0.11
41 22 0.41
42 14 0.26
43 6 0.11
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (42 bp):
TTTTATTTTTTTTATCTATTAATATTTCTTTTATTTATCTGC
Found at i:6036254 original size:17 final size:16
Alignment explanation
Indices: 6036226--6036279 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 16
6036216 CTGCTTTTAT
6036226 TTTTTATTATTTATCTA
1 TTTTT-TTATTTATCTA
6036243 TTTCTTTTATTTATCTAA
1 TTT-TTTTATTTATCT-A
*
6036261 TTTTTTTTTGTTATCTA
1 TTTTTTTAT-TTATCTA
6036278 TT
1 TT
6036280 AATATATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTTATTTATCTA
Found at i:6036255 original size:24 final size:23
Alignment explanation
Indices: 6036150--6036256 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 23
6036140 CCCCAATGGG
*
6036150 TTTTTATTTTCATTATTTAATATATAT
1 TTTTTA-TTT-ATTATTT-ATCTAT-T
6036177 TTTTTATTT-TT-TTTATCTATT
1 TTTTTATTTATTATTTATCTATT
* * *
6036198 AATATT-TTTATTATTTATCTGCTT
1 -TTTTTATTTATTATTTATCT-ATT
6036222 TTATTT-TTTATTATTTATCTATT
1 TT-TTTATTTATTATTTATCTATT
6036245 TCTTTTATTTAT
1 T-TTTTATTTAT
6036257 CTAATTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
21 4 0.06
22 10 0.15
23 17 0.26
24 26 0.39
26 3 0.05
27 6 0.09
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (23 bp):
TTTTTATTTATTATTTATCTATT
Found at i:6036505 original size:18 final size:17
Alignment explanation
Indices: 6036478--6036513 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6036468 ACAAAAGAAA
*
6036478 ACACACAGAAAAACACAG
1 ACACAAAGAAAAA-ACAG
6036496 ACACAAAGAAAAAACAG
1 ACACAAAGAAAAAACAG
6036513 A
1 A
6036514 AGCTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (17 bp):
ACACAAAGAAAAAACAG
Found at i:6036697 original size:6 final size:6
Alignment explanation
Indices: 6036686--6036752 Score: 55
Period size: 6 Copynumber: 10.5 Consensus size: 6
6036676 TTTAATATTC
* * *
6036686 TTTTAT TTTTAT CTTTAT TTTACTTT TCTTTAT TTTTAT TTTCAT TTTTA-
1 TTTTAT TTTTAT TTTTAT TTT--TAT T-TTTAT TTTTAT TTTTAT TTTTAT
6036736 TTTTATT ATTTTAT TTT
1 TTTTA-T -TTTTAT TTT
6036753 CTTTAAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 5 0.10
6 30 0.61
7 4 0.08
8 8 0.16
9 2 0.04
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:6036707 original size:5 final size:5
Alignment explanation
Indices: 6036686--6036752 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 5
6036676 TTTAATATTC
*
6036686 TTTTA TTTTTA TCTTTA TTTTA CTTTT- CTTTA TTTTTA TTTTCA TTTTTA
1 TTTTA -TTTTA T-TTTA TTTTA -TTTTA TTTTA -TTTTA TTTT-A -TTTTA
6036736 TTTTA --TTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
6036753 CTTTAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 21 0.41
6 20 0.39
7 4 0.08
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:6036717 original size:15 final size:14
Alignment explanation
Indices: 6036697--6036757 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 14
6036687 TTTATTTTTA
6036697 TCTTTATTTTACTTT
1 TCTTTATTTTA-TTT
6036712 TCTTTATTTTTATTT
1 TCTTTA-TTTTATTT
*
6036727 TC-AT-TTTTATTT
1 TCTTTATTTTATTT
*
6036739 T-ATTATTTTATTT
1 TCTTTATTTTATTT
6036752 TCTTTA
1 TCTTTA
6036758 AATAAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.26
13 9 0.23
14 4 0.10
15 11 0.28
16 5 0.13
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTATTTTATTT
Found at i:6036723 original size:21 final size:21
Alignment explanation
Indices: 6036693--6036757 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
6036683 TTCTTTTATT
*
6036693 TTTATCTTTATTTTACTTTTC
1 TTTATTTTTATTTTACTTTTC
6036714 TTTATTTTTATTTT-CATTTT-
1 TTTATTTTTATTTTAC-TTTTC
*
6036734 TATT-TTATTATTTTA-TTTTC
1 T-TTATTTTTATTTTACTTTTC
6036754 TTTA
1 TTTA
6036758 AATAAAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 6 0.16
20 12 0.32
21 19 0.51
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTTATTTTACTTTTC
Found at i:6036732 original size:27 final size:26
Alignment explanation
Indices: 6036681--6036753 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
6036671 AATTGTTTAA
*
6036681 TATTCTTTTATTTTTATCTTT-A-TTT
1 TATTTTTTTATTTTTAT-TTTCATTTT
6036706 TACTTTTCTTTATTTTTATTTTCATTTT
1 TA-TTTT-TTTATTTTTATTTTCATTTT
*
6036734 TATTTTATTA-TTTTATTTTC
1 TATTTTTTTATTTTTATTTTC
6036754 TTTAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 12 0.29
26 9 0.21
27 16 0.38
28 5 0.12
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTTTTTTATTTTTATTTTCATTTT
Found at i:6036847 original size:58 final size:57
Alignment explanation
Indices: 6036769--6037163 Score: 377
Period size: 58 Copynumber: 6.7 Consensus size: 57
6036759 ATAAAATTCA
6036769 AAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAAT-TTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* *
6036827 AAAAAAAGTTTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAA-TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* * * * * *
6036885 AAAAAAGGTTTTTTTTTAGGAAAAGTTGAAAGTATTAATTTTT-TTCGAAACTAAAGTTTC
1 AAAAAA---ATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAAATAAATTTTC
* * ** *
6036945 CAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
1 AAAAAAAT-TTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTC
* *
6037004 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT-TTAAGAATAAATTTTC
1 AAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* ** * *
6037061 AAAAAAAAAAGTTTTTTTTGAGGAAAAGTTGAAAGTGTCAATTTTTCTCGAAATTAAAGTTTC
1 ---AAAAAAA---TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* * * *
6037124 TAAAAAATATTTT-AGGGAGAAGTTGAAAATATCAATTTTT
1 AAAAAAATTTTTTGA-GGAAAAGTTGAAAGTATCAATTTTT
6037164 TCTGTACAAA
Statistics
Matches: 283, Mismatches: 35, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
56 1 0.00
57 35 0.12
58 98 0.35
59 45 0.16
60 62 0.22
62 30 0.11
63 12 0.04
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (57 bp):
AAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
Found at i:6036909 original size:118 final size:116
Alignment explanation
Indices: 6036769--6037164 Score: 444
Period size: 118 Copynumber: 3.4 Consensus size: 116
6036759 ATAAAATTCA
6036769 AAAAAAATA-TTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
1 AAAAAAATATTTTTTAGG-AAAAGTTGAAAGTATCAATTTTT-TTAAAAATAAATTTTCAAAAAA
* *
6036833 AGTTTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAA-TTTTC
64 AGTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTC
* * * * * * *
6036885 AAAAAAGGTTTTTTTTTAGGAAAAGTTGAAAGTATTAATTTTTTTCGAAACTAAAGTTTCCAAAA
1 AAAAAA--ATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTTT-AAAAATAAATTTTCAAAAA
* * * *
6036950 AA-TATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
63 AAGT-TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTC
* *
6037004 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTTTAAGAATAAATTTTCAAAAAAAA
1 AAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTTTAAAAATAAATTTTC---AAAAA
* * * *
6037069 AAGTTTTTTTTGAGGAAAAGTTGAAAGTGTCAATTTTTCTCGAAATTAAAG-TTTC
63 AAG--TTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTC
* * *
6037124 TAAAAAATA--TTTTAGGGAGAAGTTGAAAATATCAATTTTTT
1 AAAAAAATATTTTTTA-GGAAAAGTTGAAAGTATCAATTTTTT
6037165 CTGTACAAAA
Statistics
Matches: 237, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
116 16 0.07
117 36 0.15
118 82 0.35
119 49 0.21
120 12 0.05
121 41 0.17
122 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (116 bp):
AAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTTTTAAAAATAAATTTTCAAAAAAAG
TTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTC
Found at i:6038993 original size:22 final size:21
Alignment explanation
Indices: 6038967--6039041 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
6038957 AAATAATAAT
*
6038967 TAAATCAATTCATATAATCAGC
1 TAAATCAATTCTTATAATC-GC
* *
6038989 TAAATCAATAT-TTAATATTCTC
1 TAAATCAAT-TCTT-ATAATCGC
*
6039011 TAAATCAATTCTTATAATCTGT
1 TAAATCAATTCTTATAATC-GC
6039033 TAAATCAAT
1 TAAATCAAT
6039042 ATTTAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.14
22 31 0.72
23 6 0.14
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAATCAATTCTTATAATCGC
Found at i:6039020 original size:44 final size:44
Alignment explanation
Indices: 6038967--6039059 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
6038957 AAATAATAAT
6038967 TAAATCAATTCATATAATCAGCTAAATCAATATTTAATATTCTC
1 TAAATCAATTCATATAATCAGCTAAATCAATATTTAATATTCTC
* * * *
6039011 TAAATCAATTCTTATAATCTGTTAAATCAATATTTAATATTCTT
1 TAAATCAATTCATATAATCAGCTAAATCAATATTTAATATTCTC
6039055 TAAAT
1 TAAAT
6039060 TAATATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.43
Consensus pattern (44 bp):
TAAATCAATTCATATAATCAGCTAAATCAATATTTAATATTCTC
Found at i:6039057 original size:22 final size:22
Alignment explanation
Indices: 6038989--6039065 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
6038979 TATAATCAGC
*
6038989 TAAATCAATATTTAATATTCTC
1 TAAATCAATATTTAATATTCTT
*
6039011 TAAATCAAT-TCTT-ATAATCTGT
1 TAAATCAATAT-TTAATATTCT-T
6039033 TAAATCAATATTTAATATTCTT
1 TAAATCAATATTTAATATTCTT
*
6039055 TAAATTAATAT
1 TAAATCAATAT
6039066 CAAATCAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
21 7 0.15
22 33 0.70
23 7 0.15
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (22 bp):
TAAATCAATATTTAATATTCTT
Found at i:6039072 original size:33 final size:32
Alignment explanation
Indices: 6039034--6039099 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
6039024 ATAATCTGTT
** * *
6039034 AAATCAATATTTAATATTCTTTAAATTAATATC
1 AAATCAATATAAAATATT-ATTAAAATAATATC
6039067 AAATCAATATAAAATATTATTAAAATAATATC
1 AAATCAATATAAAATATTATTAAAATAATATC
6039099 A
1 A
6039100 TTGATAGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATCAATATAAAATATTATTAAAATAATATC
Found at i:6044906 original size:16 final size:19
Alignment explanation
Indices: 6044872--6044908 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
6044862 AAAACACGAT
6044872 ATGATAACACAATATAAAA
1 ATGATAACACAATATAAAA
6044891 ATGAT-ACA-AATA-AAAA
1 ATGATAACACAATATAAAA
6044907 AT
1 AT
6044909 AAAAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 3 0.17
19 5 0.28
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (19 bp):
ATGATAACACAATATAAAA
Found at i:6047460 original size:13 final size:13
Alignment explanation
Indices: 6047442--6047467 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6047432 CTTTGATCAG
6047442 TTCTTCAATTGCT
1 TTCTTCAATTGCT
6047455 TTCTTCAATTGCT
1 TTCTTCAATTGCT
6047468 GAGCAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (13 bp):
TTCTTCAATTGCT
Found at i:6048169 original size:112 final size:112
Alignment explanation
Indices: 6047972--6048195 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
6047962 GACAGAAGGT
*
6047972 TTTAGATCAATATAAAAGTCTGTCATTATTATGTGTTGTGTTTTCTCTTAAACTTGATGATCTGA
1 TTTAGATCAATATAAAAGTCTGTCATTATTATGTGTTGTGTTTTCTCTTAAACGTGATGATCTGA
*
6048037 AGTCATTTTATGCTATCTTATTCTGATATTGTTTGGTCATAACAACC
66 AGTCATTTTATGCTATCTTATTCTGATATTGTTCGGTCATAACAACC
*
6048084 TTTAGATCAATATAAAAGTCTGTCATTATTATGTGTTGTTTTTTCTCTTAAACGTGATGATCTGA
1 TTTAGATCAATATAAAAGTCTGTCATTATTATGTGTTGTGTTTTCTCTTAAACGTGATGATCTGA
6048149 AGTCATTTTATGCTATCTTATTCTGATATTGTTCGGTCATAACAACC
66 AGTCATTTTATGCTATCTTATTCTGATATTGTTCGGTCATAACAACC
6048196 CTCCCTATTA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (112 bp):
TTTAGATCAATATAAAAGTCTGTCATTATTATGTGTTGTGTTTTCTCTTAAACGTGATGATCTGA
AGTCATTTTATGCTATCTTATTCTGATATTGTTCGGTCATAACAACC
Found at i:6052494 original size:38 final size:39
Alignment explanation
Indices: 6052442--6052516 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
6052432 AAAATTATAT
* *
6052442 AAATAAAAATATAAAAATAATATAATTTAAAATTTTAAA
1 AAATAAAAATATAAAAATAATAAAATTAAAAATTTTAAA
* **
6052481 AAATTAAAA-ATAAATTTAATAAAATTAAAAATTTTA
1 AAATAAAAATATAAAAATAATAAAATTAAAAATTTTA
6052517 TTTTATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 23 0.74
39 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (39 bp):
AAATAAAAATATAAAAATAATAAAATTAAAAATTTTAAA
Found at i:6052576 original size:30 final size:30
Alignment explanation
Indices: 6052525--6052581 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
6052515 TATTTTATAT
* *
6052525 TTTTATATAACATAAATTATAATACATAAA
1 TTTTATATAAAATAAATTATAAAACATAAA
*
6052555 TTTTATATAAAATATCA-TATAAAACAT
1 TTTTATATAAAATA-AATTATAAAACAT
6052582 TTTATATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 22 0.96
31 1 0.04
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (30 bp):
TTTTATATAAAATAAATTATAAAACATAAA
Found at i:6062181 original size:22 final size:23
Alignment explanation
Indices: 6062154--6062215 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 23
6062144 ATTTTTTTAA
6062154 TTTTATTTATAAAATTAAA-AAT
1 TTTTATTTATAAAATTAAATAAT
*
6062176 TTTTATTGATAATATATTAAATAAT
1 TTTTATTTATAA-A-ATTAAATAAT
* *
6062201 TTTTATATAAAAAAT
1 TTTTATTTATAAAAT
6062216 ATGATTTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 11 0.33
23 3 0.09
24 7 0.21
25 12 0.36
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTATTTATAAAATTAAATAAT
Found at i:6062203 original size:24 final size:22
Alignment explanation
Indices: 6062151--6062203 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
6062141 TGAATTTTTT
*
6062151 TAATTTTATTTATAAAATTAAA
1 TAATTTTATTGATAAAATTAAA
6062173 -AATTTTTATTGATAATATATTAAA
1 TAA-TTTTATTGATAA-A-ATTAAA
6062197 TAATTTT
1 TAATTTT
6062204 TATATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.08
22 11 0.42
23 1 0.04
24 10 0.38
25 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATTTTATTGATAAAATTAAA
Found at i:6062555 original size:21 final size:21
Alignment explanation
Indices: 6062507--6062560 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
6062497 AATAACAGTG
* *
6062507 ATAATAAGATTAGTTATTATA
1 ATAATAAGATTAGTTATCAAA
*
6062528 ATGATAAGATTGAG-TATCAAA
1 ATAATAAGATT-AGTTATCAAA
*
6062549 ATAATAAAATTA
1 ATAATAAGATTA
6062561 AATCAATTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (21 bp):
ATAATAAGATTAGTTATCAAA
Found at i:6064841 original size:7 final size:7
Alignment explanation
Indices: 6064829--6064858 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
6064819 TGATAAATCA
6064829 TTTATTT
1 TTTATTT
6064836 TTTATTT
1 TTTATTT
6064843 TTTATTT
1 TTTATTT
6064850 TTTATTT
1 TTTATTT
6064857 TT
1 TT
6064859 CAATTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTATTT
Found at i:6068102 original size:33 final size:33
Alignment explanation
Indices: 6068056--6068119 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
6068046 CAAGCAGATC
* **
6068056 TGATAATTTGTATATTTGTGTCATATAAAATAT
1 TGATAATTCGTATATTTGTACCATATAAAATAT
6068089 TGATAATTCGTATATTTGTACCATATAAAAT
1 TGATAATTCGTATATTTGTACCATATAAAAT
6068120 TATGTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (33 bp):
TGATAATTCGTATATTTGTACCATATAAAATAT
Found at i:6068878 original size:33 final size:33
Alignment explanation
Indices: 6068836--6068903 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
6068826 TTCTTTATAG
6068836 TAGCATTTACTAAAAGTGAAAATCTTAGTTACA
1 TAGCATTTACTAAAAGTGAAAATCTTAGTTACA
6068869 TAGCATTTACTAAAAGTGAAAATCTTAGTTACA
1 TAGCATTTACTAAAAGTGAAAATCTTAGTTACA
6068902 TA
1 TA
6068904 AATTAAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (33 bp):
TAGCATTTACTAAAAGTGAAAATCTTAGTTACA
Found at i:6072695 original size:38 final size:39
Alignment explanation
Indices: 6072643--6072722 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 39
6072633 ATGAGCAGAC
* *
6072643 ATATTGTAAGCCATTACTTAGAGATAATTTTTAAA-AAA
1 ATATTGTAAGCCATTAATTAAAGATAATTTTTAAAGAAA
6072681 ATATTGT-AGACCATTAATTAAAGATAATTTTTAAAGAAA
1 ATATTGTAAG-CCATTAATTAAAGATAATTTTTAAAGAAA
6072720 ATA
1 ATA
6072723 AGTAAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 2 0.05
38 30 0.79
39 6 0.16
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.36
Consensus pattern (39 bp):
ATATTGTAAGCCATTAATTAAAGATAATTTTTAAAGAAA
Found at i:6074526 original size:29 final size:29
Alignment explanation
Indices: 6074490--6074582 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
6074480 ATATTGATTT
6074490 AAATTTTATTTTAATTTTTAATTTTTATA
1 AAATTTTATTTTAATTTTTAATTTTTATA
* *
6074519 AAATTTTAATTAAATTTTTAATTGTTTA-A
1 AAATTTTATTTTAATTTTTAATT-TTTATA
*
6074548 AATTATTTTATTTTAAATTTTT--TATTTATA
1 AA--ATTTTATTTT-AATTTTTAATTTTTATA
6074578 AAATT
1 AAATT
6074583 ATCTAAATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.06
29 28 0.52
30 8 0.15
31 8 0.15
32 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
AAATTTTATTTTAATTTTTAATTTTTATA
Found at i:6074562 original size:16 final size:16
Alignment explanation
Indices: 6074543--6074584 Score: 61
Period size: 14 Copynumber: 2.7 Consensus size: 16
6074533 TTTTTAATTG
6074543 TTTAAAATTATTTTAT
1 TTTAAAATTATTTTAT
6074559 TTT-AAATT-TTTTAT
1 TTTAAAATTATTTTAT
6074573 TTATAAAATTAT
1 TT-TAAAATTAT
6074585 CTAAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 8 0.35
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAAAATTATTTTAT
Found at i:6074579 original size:15 final size:16
Alignment explanation
Indices: 6074543--6074584 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
6074533 TTTTTAATTG
6074543 TTTA-AAATTATTTTA
1 TTTATAAATTATTTTA
6074558 TTT-TAAATT-TTTTA
1 TTTATAAATTATTTTA
6074572 TTTATAAAATTAT
1 TTTAT-AAATTAT
6074585 CTAAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.35
15 9 0.39
16 5 0.22
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAAATTATTTTA
Done.