Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 49 of 93
Found at i:6150480 original size:2 final size:2
Alignment explanation
Indices: 6150473--6150513 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6150463 ACCCTAATGC
6150473 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6150514 GAACGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6150644 original size:2 final size:2
Alignment explanation
Indices: 6150637--6150666 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6150627 GAAGTTTAAA
*
6150637 AT AT AT AT AC 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
6150667 TACAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6150714 original size:16 final size:17
Alignment explanation
Indices: 6150693--6150726 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
6150683 CCATGGTGAG
6150693 AAAAAATT-TTTAAAAT
1 AAAAAATTATTTAAAAT
6150709 AAAAAATTGATTTAAAAT
1 AAAAAATT-ATTTAAAAT
6150727 TATATTATTA
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:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAAAATTATTTAAAAT
Found at i:6150898 original size:11 final size:10
Alignment explanation
Indices: 6150849--6150896 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
6150839 ACCGAATCGA
6150849 TTTATAAATT
1 TTTATAAATT
*
6150859 TTTATTAATT
1 TTTATAAATT
6150869 TTTATACAATT
1 TTTATA-AATT
*
6150880 TTT-GAAATT
1 TTTATAAATT
6150889 TTTATAAA
1 TTTATAAA
6150897 ATAAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 7 0.22
10 18 0.56
11 7 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTATAAATT
Found at i:6154597 original size:47 final size:44
Alignment explanation
Indices: 6154546--6154646 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 44
6154536 TAAATTATGG
6154546 TTATATTTATTATATAAGATGATGAATATGATAATATGATAATCATT
1 TTATATTTATTAT-TAA-ATGA-GAATATGATAATATGATAATCATT
* * *
6154593 TTATA-TTA-TATTTAATTAGTATATGATAATATGATAATCATT
1 TTATATTTATTATTAAATGAGAATATGATAATATGATAATCATT
6154635 TTATATTATATT
1 TTATATT-TATT
6154647 TAATTTGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
42 28 0.58
43 4 0.08
44 4 0.08
45 4 0.08
46 3 0.06
47 5 0.10
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (44 bp):
TTATATTTATTATTAAATGAGAATATGATAATATGATAATCATT
Found at i:6154620 original size:42 final size:42
Alignment explanation
Indices: 6154571--6154656 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
6154561 AAGATGATGA
6154571 ATATGATAATATGATAATCATTTTATATTATATTTAATTAGT
1 ATATGATAATATGATAATCATTTTATATTATATTTAATTAGT
*
6154613 ATATGATAATATGATAATCATTTTATATTATATTTAATTTGT
1 ATATGATAATATGATAATCATTTTATATTATATTTAATTAGT
6154655 AT
1 AT
6154657 CTAATTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (42 bp):
ATATGATAATATGATAATCATTTTATATTATATTTAATTAGT
Found at i:6154939 original size:27 final size:27
Alignment explanation
Indices: 6154888--6154939 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
6154878 ATAAGATAAG
*
6154888 ATGATATTATTTAATATAATTTTATTT
1 ATGATATTATTTAATATAATCTTATTT
*
6154915 ATGATATTATCTTATTAT-ATCTTAT
1 ATGATATTAT-TTAATATAATCTTAT
6154940 CATAATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
ATGATATTATTTAATATAATCTTATTT
Found at i:6158162 original size:19 final size:21
Alignment explanation
Indices: 6158120--6158180 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
6158110 TTATTATTTA
6158120 TTATAAGAATTATTTAATAAT
1 TTATAAGAATTATTTAATAAT
*
6158141 TTATAATAATT-TTTAA-AAT
1 TTATAAGAATTATTTAATAAT
*
6158160 TTAT-A-AA-TATTAAATAAT
1 TTATAAGAATTATTTAATAAT
6158178 TTA
1 TTA
6158181 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
18 7 0.19
19 7 0.19
20 5 0.14
21 10 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATAAGAATTATTTAATAAT
Found at i:6158406 original size:21 final size:21
Alignment explanation
Indices: 6158376--6158433 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
6158366 AAAAATAGTG
* *
6158376 ATAACGATAAGATTAATTATT
1 ATAATGATAAAATTAATTATT
* *
6158397 GTAATGATAAAATTTATTATT
1 ATAATGATAAAATTAATTATT
*
6158418 ATAATAATAAAATTAA
1 ATAATGATAAAATTAA
6158434 AATTAGAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
ATAATGATAAAATTAATTATT
Found at i:6158945 original size:21 final size:23
Alignment explanation
Indices: 6158895--6158946 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
6158885 AATAATAAGT
*
6158895 ATTTATTTTATGATTACATAATT
1 ATTTATTTTATGATTACATAATA
*
6158918 ATCTATTTT-T-ATT-CATTAATA
1 ATTTATTTTATGATTACA-TAATA
6158939 ATTTATTT
1 ATTTATTT
6158947 GATTATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 1 0.04
23 8 0.32
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTATTTTATGATTACATAATA
Found at i:6160641 original size:15 final size:15
Alignment explanation
Indices: 6160617--6160660 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
6160607 TAGAATATTA
*
6160617 GATTTTAATTTTAAT
1 GATTTAAATTTTAAT
*
6160632 GATTTAAA-TTTAAA
1 GATTTAAATTTTAAT
*
6160646 GATTAAAATTTTAAT
1 GATTTAAATTTTAAT
6160661 TTTAATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
GATTTAAATTTTAAT
Found at i:6160658 original size:21 final size:21
Alignment explanation
Indices: 6160634--6160676 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
6160624 ATTTTAATGA
6160634 TTTAAATTTAAAGATTAAAAT
1 TTTAAATTTAAAGATTAAAAT
* *
6160655 TTTAATTTTAATGATTAAAAT
1 TTTAAATTTAAAGATTAAAAT
6160676 T
1 T
6160677 AAAATTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTAAATTTAAAGATTAAAAT
Found at i:6160682 original size:21 final size:21
Alignment explanation
Indices: 6160640--6160683 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6160630 ATGATTTAAA
**
6160640 TTTAAAGATTAAAATTTTAAT
1 TTTAAAGATTAAAATTAAAAT
*
6160661 TTTAATGATTAAAATTAAAAT
1 TTTAAAGATTAAAATTAAAAT
6160682 TT
1 TT
6160684 GATAGCCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTAAAGATTAAAATTAAAAT
Found at i:6161188 original size:27 final size:26
Alignment explanation
Indices: 6161153--6161203 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
6161143 AAAGATATAT
6161153 TTAAAAAATAAT-AAATTCTTTAATTA
1 TTAAAAAATAATAAAATT-TTTAATTA
*
6161179 TTAAATAAATTATAAAATTTTTAAT
1 TTAAA-AAATAATAAAATTTTTAAT
6161204 CTTATTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 12 0.55
28 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAAAAATAATAAAATTTTTAATTA
Found at i:6162537 original size:7 final size:7
Alignment explanation
Indices: 6162519--6162572 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
6162509 AACTCAAGCG
6162519 TTTTTAC
1 TTTTTAC
6162526 TTTTTTAC
1 -TTTTTAC
*
6162534 TTTTTAA
1 TTTTTAC
6162541 TTTTTAC
1 TTTTTAC
*
6162548 TTTTCATC
1 TTTTTA-C
6162556 TTTTT-C
1 TTTTTAC
6162562 TTTTT-C
1 TTTTTAC
6162568 TTTTT
1 TTTTT
6162573 TTAAAAAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 12 0.29
7 17 0.41
8 12 0.29
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAC
Found at i:6162566 original size:22 final size:22
Alignment explanation
Indices: 6162519--6162560 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6162509 AACTCAAGCG
*
6162519 TTTTTACTTTTTTACTTTTTAA
1 TTTTTACTTTTATACTTTTTAA
6162541 TTTTTACTTTTCAT-CTTTTT
1 TTTTTACTTTT-ATACTTTTT
6162561 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTACTTTTATACTTTTTAA
Found at i:6162574 original size:14 final size:14
Alignment explanation
Indices: 6162519--6162573 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
6162509 AACTCAAGCG
6162519 TTTTTACTTTTTTAC
1 TTTTT-CTTTTTTAC
**
6162534 TTTTTAATTTTTAC
1 TTTTTCTTTTTTAC
6162548 -TTTTCATCTTTTT-C
1 TTTTTC-T-TTTTTAC
6162562 TTTTTCTTTTTT
1 TTTTTCTTTTTT
6162574 TAAAAAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 9 0.27
14 9 0.27
15 15 0.45
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCTTTTTTAC
Found at i:6163260 original size:20 final size:18
Alignment explanation
Indices: 6163223--6163265 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
6163213 ATATATAATA
*
6163223 ATATTTTAATTATTTATT
1 ATATTTTAATTATATATT
*
6163241 CTATTTTATATTTATATATT
1 ATATTTTA-A-TTATATATT
6163261 ATATT
1 ATATT
6163266 AATAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTTAATTATATATT
Found at i:6163663 original size:21 final size:20
Alignment explanation
Indices: 6163626--6163664 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6163616 ATAGGAGACC
*
6163626 TTTTTTTTTTCTCTTTTTGT
1 TTTTTTTTTTCTATTTTTGT
*
6163646 TTTTTTTTTGTTTATTTTT
1 TTTTTTTTT-TCTATTTTT
6163665 TAGATAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (20 bp):
TTTTTTTTTTCTATTTTTGT
Found at i:6167336 original size:24 final size:22
Alignment explanation
Indices: 6167293--6167352 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
6167283 TCTTTTGCTA
6167293 ATTATTTATTTT-TTTATTTATC
1 ATTATTT-TTTTGTTTATTTATC
*
6167315 TTTGATTTTTTTGTTTGATTTATC
1 ATT-ATTTTTTTGTTT-ATTTATC
*
6167339 ATTAGTTTTTTGTT
1 ATTATTTTTTTGTT
6167353 AACATAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 6 0.19
23 17 0.53
24 9 0.28
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.72
Consensus pattern (22 bp):
ATTATTTTTTTGTTTATTTATC
Found at i:6167619 original size:22 final size:22
Alignment explanation
Indices: 6167589--6167634 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6167579 CAAAAAAGGT
6167589 AAATCATACACAGAAAAAGCAAA
1 AAATCATACA-AGAAAAAGCAAA
* *
6167612 AAAT-ATACAATAGAAAGCAAA
1 AAATCATACAAGAAAAAGCAAA
6167633 AA
1 AA
6167635 GATAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 5 0.24
23 4 0.19
ACGTcount: A:0.67, C:0.13, G:0.09, T:0.11
Consensus pattern (22 bp):
AAATCATACAAGAAAAAGCAAA
Found at i:6169000 original size:16 final size:15
Alignment explanation
Indices: 6168982--6169011 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6168972 ATTTTTGATA
6168982 AAAACTAAAAAATAT
1 AAAACTAAAAAATAT
6168997 AAAACTAAAAAATAT
1 AAAACTAAAAAATAT
6169012 TTCTAACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAACTAAAAAATAT
Found at i:6171931 original size:23 final size:23
Alignment explanation
Indices: 6171893--6171939 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
6171883 TATATTTGAG
* *
6171893 ATTTTTTT-AACTTTTTATTTTTT
1 ATTTTTTTAAAATTTTT-TTATTT
6171916 ATTTTTTTAAAATTTTTTTATTT
1 ATTTTTTTAAAATTTTTTTATTT
6171939 A
1 A
6171940 AATGTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (23 bp):
ATTTTTTTAAAATTTTTTTATTT
Found at i:6174649 original size:23 final size:22
Alignment explanation
Indices: 6174602--6174644 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6174592 AATGTTTTTG
6174602 AAAGAAAATTTTATAGATATAT
1 AAAGAAAATTTTATAGATATAT
6174624 AAAG-AAATTTTAGT-GATATAT
1 AAAGAAAATTTTA-TAGATATAT
6174645 TTAAAAGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
AAAGAAAATTTTATAGATATAT
Found at i:6190143 original size:23 final size:23
Alignment explanation
Indices: 6190115--6190160 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6190105 ATTTATGGAA
6190115 TGATTTAAGTTTAAAAAGAGAAT
1 TGATTTAAGTTTAAAAAGAGAAT
* * *
6190138 TGATTTGATTTTAAAGAGAGAAT
1 TGATTTAAGTTTAAAAAGAGAAT
6190161 GAATTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (23 bp):
TGATTTAAGTTTAAAAAGAGAAT
Found at i:6190184 original size:19 final size:19
Alignment explanation
Indices: 6190146--6190184 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6190136 ATTGATTTGA
* *
6190146 TTTTAAAGAGAGAATGAAT
1 TTTTAAAGAAAGAATAAAT
*
6190165 TTTTAAAGAAAGTATAAAT
1 TTTTAAAGAAAGAATAAAT
6190184 T
1 T
6190185 CATATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (19 bp):
TTTTAAAGAAAGAATAAAT
Found at i:6190635 original size:30 final size:30
Alignment explanation
Indices: 6190601--6190672 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
6190591 ATTATTATTT
6190601 ATTAATAAAAAGAA-AAAATATATATGTAAA
1 ATTAATAAAAAGAACAAAATATATAT-TAAA
* * *
6190631 ATTAATAAAAA-AATCTATATTTATATTAAA
1 ATTAATAAAAAGAA-CAAAATATATATTAAA
6190661 ATTAATAAAAAG
1 ATTAATAAAAAG
6190673 GAATTAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 2 0.06
30 26 0.72
31 8 0.22
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (30 bp):
ATTAATAAAAAGAACAAAATATATATTAAA
Found at i:6193307 original size:2 final size:2
Alignment explanation
Indices: 6193296--6193326 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6193286 ATGGCAACTT
6193296 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6193327 AGAAAAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6195547 original size:29 final size:27
Alignment explanation
Indices: 6195492--6195550 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
6195482 TTACATATCA
6195492 AAATTATTTAAATTATAATTAAAAATT
1 AAATTATTTAAATTATAATTAAAAATT
* * *
6195519 AAATTAATTTAGATATATATTTTAAAATT
1 AAATT-ATTTAAAT-TATAATTAAAAATT
6195548 AAA
1 AAA
6195551 AATATGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 7 0.26
29 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAATTATTTAAATTATAATTAAAAATT
Found at i:6195763 original size:28 final size:29
Alignment explanation
Indices: 6195732--6195787 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
6195722 CTTTTTAAAA
6195732 AATTTTA-TAAGACATTAAAAATTCAAGC
1 AATTTTAGTAAGACATTAAAAATTCAAGC
**
6195760 AATTTTATGTAAGATTTTAAAAATTCAA
1 AATTTTA-GTAAGACATTAAAAATTCAA
6195788 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
30 17 0.71
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (29 bp):
AATTTTAGTAAGACATTAAAAATTCAAGC
Found at i:6200040 original size:13 final size:13
Alignment explanation
Indices: 6200006--6200031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6199996 AAATGTTCCA
6200006 TCACACATTAGGG
1 TCACACATTAGGG
6200019 TCACACATTAGGG
1 TCACACATTAGGG
6200032 CACCTCATTC
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:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
TCACACATTAGGG
Found at i:6204682 original size:17 final size:17
Alignment explanation
Indices: 6204660--6204694 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6204650 AAAACATGAT
6204660 CGGCGA-TCACGGGATAC
1 CGGCGATTC-CGGGATAC
6204677 CGGCGATTCCGGGATAC
1 CGGCGATTCCGGGATAC
6204694 C
1 C
6204695 ATAACCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.20, C:0.31, G:0.34, T:0.14
Consensus pattern (17 bp):
CGGCGATTCCGGGATAC
Found at i:6205001 original size:32 final size:32
Alignment explanation
Indices: 6204962--6205031 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
6204952 TTTTTGTTTT
*
6204962 ATTTTTTTATTAGTTAATTAAGCTGTATTATG
1 ATTTTTTTATTAGTTAATTAAGCTATATTATG
6204994 ATTTTTTTATTAGTTAATTAAGCTATATTATG
1 ATTTTTTTATTAGTTAATTAAGCTATATTATG
6205026 ATTTTT
1 ATTTTT
6205032 GGTGATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.59
Consensus pattern (32 bp):
ATTTTTTTATTAGTTAATTAAGCTATATTATG
Found at i:6206079 original size:58 final size:59
Alignment explanation
Indices: 6205981--6206097 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 59
6205971 GCAATGTTCT
** * *
6205981 TATGTTATGGAACAATATAAATCAATATTAATTCTATTATGAAACGATATAAATAAATA
1 TATGTTATGGAACAATATAAATCAATAAAAATTATATTATGAAACAATATAAATAAATA
* *
6206040 TATGTT-TTGAACAATATAAA-CAATAAAAATATATGTTATGAAACAATATAAATAAATA
1 TATGTTATGGAACAATATAAATCAATAAAAAT-TATATTATGAAACAATATAAATAAATA
6206098 AATGGTCTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 8 0.16
58 37 0.73
59 6 0.12
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (59 bp):
TATGTTATGGAACAATATAAATCAATAAAAATTATATTATGAAACAATATAAATAAATA
Found at i:6212295 original size:14 final size:15
Alignment explanation
Indices: 6212267--6212295 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6212257 AATCTATTTC
6212267 TCAAAATTAATATTA
1 TCAAAATTAATATTA
6212282 TCAAAATT-ATATTA
1 TCAAAATTAATATTA
6212296 AGTCCAAAAT
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
TCAAAATTAATATTA
Found at i:6212972 original size:22 final size:22
Alignment explanation
Indices: 6212925--6212973 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
6212915 TCCTTTTGTT
*
6212925 TAAGCTCTTTATACCAAATGTT
1 TAAGCTCTTTATACCAAATGTA
* *
6212947 TAAGCTC-TTATATCAATTGCTA
1 TAAGCTCTTTATACCAAATG-TA
6212969 TAAGC
1 TAAGC
6212974 ATACAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (22 bp):
TAAGCTCTTTATACCAAATGTA
Found at i:6217630 original size:16 final size:16
Alignment explanation
Indices: 6217591--6217632 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
6217581 ATATGGAAGG
6217591 TTTAGGGTTT--TGAT
1 TTTAGGGTTTGGTGAT
**
6217605 TTTAAAGTTTGGTGAT
1 TTTAGGGTTTGGTGAT
6217621 TTTAGGGTTTGG
1 TTTAGGGTTTGG
6217633 GTTTTGAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (16 bp):
TTTAGGGTTTGGTGAT
Found at i:6217643 original size:14 final size:15
Alignment explanation
Indices: 6217626--6217654 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6217616 GTGATTTTAG
6217626 GGTTTGG-GTTTTGA
1 GGTTTGGAGTTTTGA
6217640 GGTTTGGAGTTTTGA
1 GGTTTGGAGTTTTGA
6217655 TTTAAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.00, G:0.41, T:0.48
Consensus pattern (15 bp):
GGTTTGGAGTTTTGA
Found at i:6219701 original size:110 final size:109
Alignment explanation
Indices: 6219517--6219730 Score: 304
Period size: 110 Copynumber: 2.0 Consensus size: 109
6219507 GAATTGATTG
*
6219517 GGATAACACCACAAGTCAAAAATAAAAAATCGATCGGGATAACACCGTGAATCGAAATTATGCCC
1 GGATAACACCACAAGTCAAAAATAAAAAATCGATCGGGATAACACCGCGAATCGAAATTATGCCC
* * *
6219582 AGAGGTCTTAGAAATCATGCTCGGAAGTCTTACAAAATCGACTA
66 AGAGATCTTAGAAATCATGCCCAGAAGTCTTACAAAATCGACTA
* * * *
6219626 GGATAACACCACAAGTCGAAAGATAAAAAATTGATCGGGATAATACTGCGAATCGAAATTATGCC
1 GGATAACACCACAAGTC-AAAAATAAAAAATCGATCGGGATAACACCGCGAATCGAAATTATGCC
* * *
6219691 C-GAAGATCTTAGAAATTATGCCCAGAGGTCTTACAGAATC
65 CAG-AGATCTTAGAAATCATGCCCAGAAGTCTTACAAAATC
6219731 ATATCCGGAG
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
109 18 0.20
110 74 0.80
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (109 bp):
GGATAACACCACAAGTCAAAAATAAAAAATCGATCGGGATAACACCGCGAATCGAAATTATGCCC
AGAGATCTTAGAAATCATGCCCAGAAGTCTTACAAAATCGACTA
Found at i:6219781 original size:133 final size:132
Alignment explanation
Indices: 6219570--6220261 Score: 838
Period size: 133 Copynumber: 5.2 Consensus size: 132
6219560 ACCGTGAATC
* * * * * * * *
6219570 GAAATTATGCCCAGAGGTCTTAGA-AATCAT-GCTCGGAAGTCTTACAAAATCGACTAGGATAAC
1 GAAATCATGCCCGGAGGTCTTACAGAATCATATC-CGGAGGTCTTACAGAATCGATTAGAATAAC
* * * * * *
6219633 ACCACAAGTCGAAAGATAAAAAATTGATCGGGATAATACTGCGAATCGAAATTATGCCCGAAGAT
65 ACCACAAGTCAAAAGATAAAAAATTGATCGAGATAACA-TGCGAATCAAAATTATGCCCGGAGGT
6219698 CTTA
129 CTTA
* * *
6219702 GAAATTATGCCCAGAGGTCTTACAGAATCATATCCGGAGCTCTTACAGAATCGATT-GAAATAAC
1 GAAATCATGCCCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATCGATTAG-AATAAC
* * * * * *
6219766 ACCACAAGTCAAAAGATAAAAAATTAATCGAGATAATACCGTGAATCAAAATTATACCCGGAGAT
65 ACCACAAGTCAAAAGATAAAAAATTGATCGAGATAACA-TGCGAATCAAAATTATGCCCGGAGGT
6219831 CTTA
129 CTTA
* * * *
6219835 GAAATCATACCCGGAGGTCTTACAGAATCATATTCGAAGTTCTTACAGAATCGATT-GAAATAAC
1 GAAATCATGCCCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATCGATTAG-AATAAC
* * * *
6219899 ATCACAAGTCAAAAGATAAAGAATTGATCGGGATAACAT-CGTAAATCAAAATTATGCTCGGAGG
65 ACCACAAGTCAAAAGATAAAAAATTGATCGAGATAACATGCG--AATCAAAATTATGCCCGGAGG
*
6219963 CCTTA
128 TCTTA
* * * * *
6219968 GAAATCATGTCCGGAGGTCTTACAGAATCATATCTGAAGGTCTTACAGAATCGACTAGGATAACA
1 GAAATCATGCCCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATCGATTAGAATAACA
* * * *
6220033 CCATAAGTCAAAAGATAAAAAATCGATCGAGATAACATCGCGAATCGAATTTATGCCCGGAGGTC
66 CCACAAGTCAAAAGATAAAAAATTGATCGAGATAACAT-GCGAATCAAAATTATGCCCGGAGGTC
6220098 TTA
130 TTA
* *
6220101 GAAATCATGCCCGGAGATCTTACAGAATCATACCCGGAGGTCTTACAGAATCGATTAGAATAACA
1 GAAATCATGCCCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATCGATTAGAATAACA
* * *
6220166 CCACAAGTCAAAA-ATAAAGAATCGATCGAGATAACATCGTGAATCAAAATTATGCCCGGAGGTC
66 CCACAAGTCAAAAGATAAAAAATTGATCGAGATAACAT-GCGAATCAAAATTATGCCCGGAGGTC
6220230 TTA
130 TTA
*
6220233 GAAATCATGCTCGGAGGTCTTACAGAATC
1 GAAATCATGCCCGGAGGTCTTACAGAATC
6220262 GACTGAAATA
Statistics
Matches: 490, Mismatches: 62, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
131 1 0.00
132 101 0.21
133 384 0.78
134 2 0.00
135 2 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (132 bp):
GAAATCATGCCCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATCGATTAGAATAACA
CCACAAGTCAAAAGATAAAAAATTGATCGAGATAACATGCGAATCAAAATTATGCCCGGAGGTCT
TA
Found at i:6219844 original size:22 final size:22
Alignment explanation
Indices: 6219814--6219866 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
6219804 CCGTGAATCA
* *
6219814 AAATTATACCCGGAGATCTTAG
1 AAATCATACCCGGAGATCTTAC
*
6219836 AAATCATACCCGGAGGTCTTAC
1 AAATCATACCCGGAGATCTTAC
6219858 AGAATCATA
1 A-AATCATA
6219867 TTCGAAGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
AAATCATACCCGGAGATCTTAC
Found at i:6220113 original size:22 final size:23
Alignment explanation
Indices: 6220085--6220152 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
6220075 AATCGAATTT
*
6220085 ATGCCCGGAGGTCTTAGA-AATC
1 ATGCCCGGAGGTCTTACAGAATC
*
6220107 ATGCCCGGAGATCTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
*
6220130 ATACCCGGAGGTCTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
6220153 GATTAGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (23 bp):
ATGCCCGGAGGTCTTACAGAATC
Found at i:6220242 original size:22 final size:22
Alignment explanation
Indices: 6220212--6220254 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6220202 TCGTGAATCA
*
6220212 AAATTATGCCCGGAGGTCTTAG
1 AAATCATGCCCGGAGGTCTTAG
*
6220234 AAATCATGCTCGGAGGTCTTA
1 AAATCATGCCCGGAGGTCTTA
6220255 CAGAATCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (22 bp):
AAATCATGCCCGGAGGTCTTAG
Found at i:6220326 original size:110 final size:110
Alignment explanation
Indices: 6220101--6220591 Score: 614
Period size: 110 Copynumber: 4.5 Consensus size: 110
6220091 GGAGGTCTTA
* * * * * *
6220101 GAAATCATGCCCGGAGATCTTACAGAATCATACCCGGAGGTCTTACAGAATCGA-TTAGAATAAC
1 GAAATTATGCCCGGAGGTCTTAGA-AATCATGCTCGGAGGTCTTACAGAATCGACTGA-AATAAC
* *
6220165 ACCACAAGTCAAAA-ATAAAGAATCGATCGAGATAACATCGTGAATC
64 ACCACAAGTCAAAAGATAAAGAATCGATCGGGATAACATCGCGAATC
*
6220211 AAAATTATGCCCGGAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGACTGAAATAACAC
1 GAAATTATGCCCGGAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGACTGAAATAACAC
* * *
6220276 TATAAGTCAAAAGATAAAGAATCGATCGGGATAACACCGCGAAT-
66 CACAAGTCAAAAGATAAAGAATCGATCGGGATAACATCGCGAATC
** * *
6220320 GAAAATTATATCTGGAGGTCTTAGAAATCATG-TCCGGAGGTCTTACAGAATCGATTGAAATAAC
1 G-AAATTATGCCCGGAGGTCTTAGAAATCATGCT-CGGAGGTCTTACAGAATCGACTGAAATAAC
* * *
6220384 ACCACAAGTCAAAAGATAAAGAATCGATCAGGATAACATTGTGAATC
64 ACCACAAGTCAAAAGATAAAGAATCGATCGGGATAACATCGCGAATC
* * * * * **
6220431 GAATTTATGCTCGGAGATCTTAAAAATCATAC-CTGGAGGTCTTACAGAATCGACTGGGATAACA
1 GAAATTATGCCCGGAGGTCTTAGAAATCATGCTC-GGAGGTCTTACAGAATCGACTGAAATAACA
* * *
6220495 TCACAAGTCAAAAGATAAAGAATCGATCGGGATAATATCACGAATC
65 CCACAAGTCAAAAGATAAAGAATCGATCGGGATAACATCGCGAATC
* * *
6220541 GAATTTATGCCCGGAGGTCTTAGAAATCATGCTCGAAGATCTTACAGAATC
1 GAAATTATGCCCGGAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATC
6220592 ATGTCCGAAG
Statistics
Matches: 327, Mismatches: 46, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
109 47 0.14
110 278 0.85
111 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (110 bp):
GAAATTATGCCCGGAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGACTGAAATAACAC
CACAAGTCAAAAGATAAAGAATCGATCGGGATAACATCGCGAATC
Found at i:6220594 original size:23 final size:23
Alignment explanation
Indices: 6220565--6220614 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
6220555 AGGTCTTAGA
6220565 AATCATG-CTCGAAGATCTTACAG
1 AATCATGTC-CGAAGATCTTACAG
*
6220588 AATCATGTCCGAAGGTCTTACAG
1 AATCATGTCCGAAGATCTTACAG
6220611 AATC
1 AATC
6220615 GATTGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (23 bp):
AATCATGTCCGAAGATCTTACAG
Found at i:6220641 original size:133 final size:133
Alignment explanation
Indices: 6220437--6220856 Score: 569
Period size: 133 Copynumber: 3.2 Consensus size: 133
6220427 AATCGAATTT
* * * * *
6220437 ATGCTCGGAGATCTTA-AAAATCAT-ACCTGGAGGTCTTACAGAATCGACTGGGATAACATCACA
1 ATGCTCGAAGATCTTACAGAATCATGTCC-GGAGGTCTTACAGAATCGATTGGGATAACACCACA
* *
6220500 AGTCAAAAGATAAAGAATCGATCGGGATAATATCACGAATCGAATTTATGCCCGGAGGTCTTAGA
65 AGTCAAAAGATAAAGAATCGATCGGGATAATATCGCGAATCGAATTTATGCCCGAAGGTCTTAGA
6220565 AATC
130 AATC
* ** *
6220569 ATGCTCGAAGATCTTACAGAATCATGTCCGAAGGTCTTACAGAATCGATTGAAATAACACCATAA
1 ATGCTCGAAGATCTTACAGAATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAA
* * * *
6220634 GTCAAAAGATAAAGAATCGATCGAGATAATATCGGGAATCGAATTTATGCTCGAAAGTCTTAGAA
66 GTCAAAAGATAAAGAATCGATCGGGATAATATCGCGAATCGAATTTATGCCCGAAGGTCTTAGAA
6220699 ATC
131 ATC
* * *
6220702 ATGC-CTGAAGGTCTTACAGAATCATGTCCGGAGGTCTTACAGAATAGATTGGGATAACACTACA
1 ATGCTC-GAAGATCTTACAGAATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACA
* * * *
6220766 AGTTAAAA-ATAAAAAATCGATCGGGATAACATCGTGAATCGAATTTATGCCCGAAGGTCTTAGA
65 AGTCAAAAGATAAAGAATCGATCGGGATAATATCGCGAATCGAATTTATGCCCGAAGGTCTTAGA
6220830 AATC
130 AATC
* * *
6220834 ATGCCCGGAGGTCTTACAGAATC
1 ATGCTCGAAGATCTTACAGAATC
6220857 GACTGAGATA
Statistics
Matches: 254, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
132 90 0.35
133 162 0.64
134 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (133 bp):
ATGCTCGAAGATCTTACAGAATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAA
GTCAAAAGATAAAGAATCGATCGGGATAATATCGCGAATCGAATTTATGCCCGAAGGTCTTAGAA
ATC
Found at i:6220727 original size:23 final size:23
Alignment explanation
Indices: 6220685--6220746 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
6220675 AATTTATGCT
* *
6220685 CGAAAGTCTTAGA-AATCATG-C
1 CGAAGGTCTTACAGAATCATGTC
6220706 CTGAAGGTCTTACAGAATCATGTC
1 C-GAAGGTCTTACAGAATCATGTC
*
6220730 CGGAGGTCTTACAGAAT
1 CGAAGGTCTTACAGAAT
6220747 AGATTGGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 10 0.29
23 22 0.63
24 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (23 bp):
CGAAGGTCTTACAGAATCATGTC
Found at i:6220915 original size:110 final size:109
Alignment explanation
Indices: 6220702--6221004 Score: 428
Period size: 110 Copynumber: 2.7 Consensus size: 109
6220692 CTTAGAAATC
* * * * *
6220702 ATGCCTGAAGGTCTTACAGAATCATGTCCGGAGGTCTTACAGAATAGATTGGGATAACACTACAA
1 ATGCCCGAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACAC-ACAA
* * *
6220767 GTTAAAAATAAAAAATCGATCGGGATAACATCGTGAATCGAATTT
65 GTTAAAAATAAAGAATCGATCGGGATAACATCGCGAATCAAATTT
* *
6220812 ATGCCCGAAGGTCTTAGA-AATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACATCGCAA
1 ATGCCCGAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACA-CACAA
6220876 GTTAAAAGATAAAGAATCGATCGGGATAACATCGCGAATCAAATTT
65 GTTAAAA-ATAAAGAATCGATCGGGATAACATCGCGAATCAAATTT
* * *
6220922 ATGCCCGGAGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCAACTGAGATAACACCACAA
1 ATGCCCGAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACA-CACAA
*
6220987 GTCAAAAAATAAAGAATC
65 GT-TAAAAATAAAGAATC
6221005 ACAATCGGAT
Statistics
Matches: 172, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
109 46 0.27
110 68 0.40
111 54 0.31
112 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (109 bp):
ATGCCCGAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACACAAG
TTAAAAATAAAGAATCGATCGGGATAACATCGCGAATCAAATTT
Found at i:6220953 original size:23 final size:23
Alignment explanation
Indices: 6220922--6220968 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
6220912 AATCAAATTT
6220922 ATGCCCGGAGGTCTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
*
6220945 ATGCTCGGAGGTCTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
6220968 A
1 A
6220969 ACTGAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
ATGCCCGGAGGTCTTACAGAATC
Found at i:6221383 original size:88 final size:87
Alignment explanation
Indices: 6221216--6221386 Score: 261
Period size: 87 Copynumber: 2.0 Consensus size: 87
6221206 ATCATGCTCA
*
6221216 GAGGTCTTACAGAATCAACTGAGATAACATCACAAGTCAAAAATAAAAAATCAATCGGGATAATA
1 GAGGTCTTACAAAATCAACTGAGATAACATCACAAGTCAAAAATAAAAAATCAATCGGGATAATA
* *
6221281 TCGCGAATCGAATTTATGTCCG
66 TCACGAATCAAATTTATGTCCG
* * * * *
6221303 GAGGTCTTACAAAATCGACTGGGATAACGTCACAAGTCAAAAGATAAAGAATCGATCGGGATAAT
1 GAGGTCTTACAAAATCAACTGAGATAACATCACAAGTCAAAA-ATAAAAAATCAATCGGGATAAT
6221368 ATCACGAATCAAATTTATG
65 ATCACGAATCAAATTTATG
6221387 CTTAGAGGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 38 0.51
88 37 0.49
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (87 bp):
GAGGTCTTACAAAATCAACTGAGATAACATCACAAGTCAAAAATAAAAAATCAATCGGGATAATA
TCACGAATCAAATTTATGTCCG
Found at i:6221395 original size:88 final size:87
Alignment explanation
Indices: 6221209--6221399 Score: 267
Period size: 88 Copynumber: 2.2 Consensus size: 87
6221199 TTACAGAATC
*
6221209 ATGCTCAGAGGTCTTACAGAATCAACTGAGATAACATCACAAGTCAAAAATAAAAAATCAATCGG
1 ATGCTCAGAGGTCTTACAAAATCAACTGAGATAACATCACAAGTCAAAAATAAAAAATCAATCGG
* *
6221274 GATAATATCGCGAATCGAATTT
66 GATAATATCACGAATCAAATTT
* * * * * *
6221296 ATG-TCCGGAGGTCTTACAAAATCGACTGGGATAACGTCACAAGTCAAAAGATAAAGAATCGATC
1 ATGCT-CAGAGGTCTTACAAAATCAACTGAGATAACATCACAAGTCAAAA-ATAAAAAATCAATC
6221360 GGGATAATATCACGAATCAAATTT
64 GGGATAATATCACGAATCAAATTT
*
6221384 ATGCTTAGAGGTCTTA
1 ATGCTCAGAGGTCTTA
6221400 GAAATCATGC
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 42 0.47
88 46 0.51
89 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (87 bp):
ATGCTCAGAGGTCTTACAAAATCAACTGAGATAACATCACAAGTCAAAAATAAAAAATCAATCGG
GATAATATCACGAATCAAATTT
Found at i:6221416 original size:22 final size:22
Alignment explanation
Indices: 6221391--6221451 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
6221381 TTTATGCTTA
*
6221391 GAGGTCTTAGA-AATCATGCCCG
1 GAGGTCTTACAGAATCATG-CCG
*
6221413 GAGGTCTTACAGAATCATGTCG
1 GAGGTCTTACAGAATCATGCCG
*
6221435 GAGGTCTTATAGAATCA
1 GAGGTCTTACAGAATCA
6221452 ACTAAGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 28 0.80
23 7 0.20
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (22 bp):
GAGGTCTTACAGAATCATGCCG
Found at i:6221478 original size:132 final size:131
Alignment explanation
Indices: 6221296--6221579 Score: 320
Period size: 132 Copynumber: 2.1 Consensus size: 131
6221286 AATCGAATTT
* ** ** * *
6221296 ATGTCCGGAGGTCTTACAAAATCGACTGGGATAACGTCACAAGTCAAAAGATAAAGAATCGATCG
1 ATGT-CGGAGGTCTTACAAAATCAACTAAGATAACACCACAAGTCAAAAGATAAAAAATCGATCA
* *
6221361 GGATAATATCACGAATCAAATTTATGCTTAG-AGGTCTTAGAAA-TCATGCCCGGAGGTCTTACA
65 AGATAATATCACGAATCAAATTTATGC-CAGAAGGTCTT-GAAAGTCATGCCCGGAGGTCTTACA
6221424 GAATC
128 G-ATC
* *
6221429 ATGTCGGAGGTCTTATAGAATCAACTAAGATAACACCACAAGTCAAAAGATAAAAAATCGATCAA
1 ATGTCGGAGGTCTTACAAAATCAACTAAGATAACACCACAAGTCAAAAGATAAAAAATCGATCAA
** ** * * * *
6221494 GATAATATTGCGAATTGAATTTATGCCCGAAGGTCTTGAAAGTTATGTCCGGAGGTCTTAGAGAT
66 GATAATATCACGAATCAAATTTATGCCAGAAGGTCTTGAAAGTCATGCCCGGAGGTCTTACAGAT
*
6221559 T
131 C
*
6221560 ATGCCCGGAGGTCTTACAAA
1 ATG-TCGGAGGTCTTACAAA
6221580 TCTTAAAATC
Statistics
Matches: 125, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
131 10 0.08
132 111 0.89
133 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (131 bp):
ATGTCGGAGGTCTTACAAAATCAACTAAGATAACACCACAAGTCAAAAGATAAAAAATCGATCAA
GATAATATCACGAATCAAATTTATGCCAGAAGGTCTTGAAAGTCATGCCCGGAGGTCTTACAGAT
C
Found at i:6221540 original size:22 final size:22
Alignment explanation
Indices: 6221514--6221575 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
6221504 CGAATTGAAT
*
6221514 TTATGCCCGAAGGTCTTGAAAG-
1 TTATGCCCGGAGGTCTT-AAAGA
* *
6221536 TTATGTCCGGAGGTCTTAGAGA
1 TTATGCCCGGAGGTCTTAAAGA
6221558 TTATGCCCGGAGGTCTTA
1 TTATGCCCGGAGGTCTTA
6221576 CAAATCTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 3 0.09
22 32 0.91
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (22 bp):
TTATGCCCGGAGGTCTTAAAGA
Found at i:6221765 original size:121 final size:120
Alignment explanation
Indices: 6221551--6221888 Score: 498
Period size: 121 Copynumber: 2.8 Consensus size: 120
6221541 TCCGGAGGTC
*
6221551 TTAGAGATTATGCCCGGAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTCATAATCAGAGGC
1 TTAGAGATTATGCCCGGAGGTCTTACAAATATTAAAATCTTTGAATGCT-CTCATAATCAGAGGC
* *
6221616 AATGAAACTTTAAAATTTGAAAATCTTTTAATTTTGAAAGTCATACGCAGAGGCTT
65 AATGAAACTTTAAAATTTGAAAATCTTTTAATCTTGAAAGTCATACACAGAGGCTT
** * *
6221672 TTAGAGATTATGCTTGGAGGTCTTACAAATTTTAAAATCTTTGAATGCTCATCATAATCAAAGGC
1 TTAGAGATTATGCCCGGAGGTCTTACAAATATTAAAATCTTTGAATGCTC-TCATAATCAGAGGC
* * *
6221737 AATGAAACTTTAAATTTTGAAAATCTTTTAATCTTGAAAGTCGTGCACAGAGGCTT
65 AATGAAACTTTAAAATTTGAAAATCTTTTAATCTTGAAAGTCATACACAGAGGCTT
* * * *
6221793 TTAGAGATTATGCCCGAAGGTCTTACAAA-ATCAAAATCTTTAAATGCTTCTCATAATTAGAGGC
1 TTAGAGATTATGCCCGGAGGTCTTACAAATATTAAAATCTTTGAATGC-TCTCATAATCAGAGGC
*
6221857 AATGAAACTTTAGAAATTTAAAAATCTTTTAA
65 AATGAAACTTTA-AAATTTGAAAATCTTTTAA
6221889 AACATGGCTT
Statistics
Matches: 195, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
120 40 0.21
121 155 0.79
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (120 bp):
TTAGAGATTATGCCCGGAGGTCTTACAAATATTAAAATCTTTGAATGCTCTCATAATCAGAGGCA
ATGAAACTTTAAAATTTGAAAATCTTTTAATCTTGAAAGTCATACACAGAGGCTT
Found at i:6222002 original size:41 final size:41
Alignment explanation
Indices: 6221945--6222023 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
6221935 TTTCTGAGGA
*
6221945 TGGTTCCCTCTAAACAGATGTTTTGAAATCTTGATTGAAAT
1 TGGTTCCCTCTAAACAGAGGTTTTGAAATCTTGATTGAAAT
6221986 TGGTT-CCTCTTAAACAGAGGTTTTGAAATCTTGATTGA
1 TGGTTCCCTC-TAAACAGAGGTTTTGAAATCTTGATTGA
6222024 GAACAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 4 0.11
41 32 0.89
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (41 bp):
TGGTTCCCTCTAAACAGAGGTTTTGAAATCTTGATTGAAAT
Found at i:6222038 original size:41 final size:41
Alignment explanation
Indices: 6221951--6222042 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
6221941 AGGATGGTTC
* ***
6221951 CCTC-TAAACAGATGTTTTGAAATCTTGATTGAAATTGGTT
1 CCTCTTAAACAGAGGTTTTGAAATCTTGATTGAAATCAATT
6221991 CCTCTTAAACAGAGGTTTTGAAATCTTGATTGAGAA-CAATT
1 CCTCTTAAACAGAGGTTTTGAAATCTTGATTGA-AATCAATT
**
6222032 TTTCTTAAACA
1 CCTCTTAAACA
6222043 AAGACTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.09
41 38 0.86
42 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (41 bp):
CCTCTTAAACAGAGGTTTTGAAATCTTGATTGAAATCAATT
Found at i:6223741 original size:9 final size:9
Alignment explanation
Indices: 6223727--6223771 Score: 81
Period size: 9 Copynumber: 4.9 Consensus size: 9
6223717 GTCCTTTTTA
6223727 TTTTTTATT
1 TTTTTTATT
6223736 TTTTTTACTT
1 TTTTTTA-TT
6223746 TTTTTTATT
1 TTTTTTATT
6223755 TTTTTTATT
1 TTTTTTATT
6223764 TTTTTTAT
1 TTTTTTAT
6223772 GCCTCATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 26 0.74
10 9 0.26
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTATT
Found at i:6223751 original size:19 final size:18
Alignment explanation
Indices: 6223727--6223771 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 18
6223717 GTCCTTTTTA
6223727 TTTTTTATTTTTTTTACTT
1 TTTTTTATTTTTTTTA-TT
6223746 TTTTTTATTTTTTTTATT
1 TTTTTTATTTTTTTTATT
6223764 TTTTTTAT
1 TTTTTTAT
6223772 GCCTCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (18 bp):
TTTTTTATTTTTTTTATT
Found at i:6226017 original size:14 final size:15
Alignment explanation
Indices: 6226000--6226028 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6225990 AAGATTTTAG
6226000 GGTTTGG-GTTTTGA
1 GGTTTGGAGTTTTGA
6226014 GGTTTGGAGTTTTGA
1 GGTTTGGAGTTTTGA
6226029 TTTAAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.00, G:0.41, T:0.48
Consensus pattern (15 bp):
GGTTTGGAGTTTTGA
Found at i:6226039 original size:14 final size:14
Alignment explanation
Indices: 6226022--6226066 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
6226012 GAGGTTTGGA
6226022 GTTTTGATTTAAGG
1 GTTTTGATTTAAGG
* *
6226036 GTTTGGATTTTAGG
1 GTTTTGATTTAAGG
6226050 GATTTTGGATTTAAGG
1 G-TTTT-GATTTAAGG
6226066 G
1 G
6226067 GCTTAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 3 0.12
16 9 0.36
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
GTTTTGATTTAAGG
Found at i:6226047 original size:15 final size:15
Alignment explanation
Indices: 6226027--6226066 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
6226017 TTGGAGTTTT
6226027 GATTTAAGGG-TTTG
1 GATTTAAGGGATTTG
*
6226041 GATTTTAGGGATTTTG
1 GATTTAAGGGA-TTTG
6226057 GATTTAAGGG
1 GATTTAAGGG
6226067 GCTTAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (15 bp):
GATTTAAGGGATTTG
Found at i:6227453 original size:11 final size:11
Alignment explanation
Indices: 6227421--6227456 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
6227411 AACTCCAAGG
*
6227421 TGGCTGTAGGG
1 TGGCTGTAGGC
6227432 TGGCTGTAGGC
1 TGGCTGTAGGC
6227443 TGGCTGTAGGC
1 TGGCTGTAGGC
6227454 TGG
1 TGG
6227457 TGAGCATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.08, C:0.14, G:0.50, T:0.28
Consensus pattern (11 bp):
TGGCTGTAGGC
Found at i:6227561 original size:13 final size:12
Alignment explanation
Indices: 6227539--6227576 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
6227529 ACCCTCAGCC
6227539 TTTTTTTTGTTT
1 TTTTTTTTGTTT
6227551 TTTTTTCTTGTTT
1 TTTTTT-TTGTTT
6227564 TTATTTTTT-TTT
1 TT-TTTTTTGTTT
6227576 T
1 T
6227577 ACGTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.03, C:0.03, G:0.05, T:0.89
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:6234522 original size:14 final size:14
Alignment explanation
Indices: 6234503--6234534 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6234493 ATATTTTTAT
*
6234503 TAAAAATATATATC
1 TAAAAATATATATA
6234517 TAAAAATATATATA
1 TAAAAATATATATA
6234531 TAAA
1 TAAA
6234535 TTTATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAAATATATATA
Found at i:6234622 original size:14 final size:14
Alignment explanation
Indices: 6234585--6234622 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
6234575 TAATAAAATC
*
6234585 TTTTAATTTATCAA
1 TTTTAATTTTTCAA
6234599 TTTTAATTTTT-AA
1 TTTTAATTTTTCAA
6234612 TTTTAATTTTT
1 TTTTAATTTTT
6234623 ATATAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAATTTTTCAA
Found at i:6236508 original size:7 final size:7
Alignment explanation
Indices: 6236496--6236521 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6236486 TTAATTATGC
6236496 ATTTAAA
1 ATTTAAA
6236503 ATTTAAA
1 ATTTAAA
6236510 ATTTAAA
1 ATTTAAA
6236517 ATTTA
1 ATTTA
6236522 TTAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAA
Found at i:6237147 original size:36 final size:36
Alignment explanation
Indices: 6237047--6237148 Score: 86
Period size: 40 Copynumber: 2.7 Consensus size: 36
6237037 TAGATTTATC
6237047 TTATT-TTATTTTATTTATTTATTTTTTAATTATCTGTCAA
1 TTATTATTATTTT-TTT-TTT-TTTTTTAATTATC--TCAA
*
6237087 TT-TTATTCATTTATCTCTTTTTTTTTT-ATTATC-CAA
1 TTATTATT-ATTT-T-TTTTTTTTTTTTAATTATCTCAA
6237123 TTATTATTATTTTTTTTTTCTTTTTT
1 TTATTATTATTTTTTTTTT-TTTTTT
6237149 GGAAGGTTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
34 5 0.09
35 7 0.13
36 9 0.17
37 5 0.09
39 8 0.15
40 10 0.19
41 7 0.13
42 3 0.06
ACGTcount: A:0.20, C:0.08, G:0.01, T:0.72
Consensus pattern (36 bp):
TTATTATTATTTTTTTTTTTTTTTTAATTATCTCAA
Found at i:6237470 original size:27 final size:26
Alignment explanation
Indices: 6237423--6237473 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
6237413 TCATCAGAAA
**
6237423 TTTTTTGGGAATTTTTCAAAATTTTT
1 TTTTTTGGGAATTTTGAAAAATTTTT
6237449 TTTTTTGGGAATTTCTGAAAAATTT
1 TTTTTTGGGAATTT-TGAAAAATTT
6237474 CAGATTCCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.57
Consensus pattern (26 bp):
TTTTTTGGGAATTTTGAAAAATTTTT
Found at i:6237619 original size:19 final size:20
Alignment explanation
Indices: 6237595--6237637 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6237585 CCGGTGAACC
*
6237595 TCCGGTGA-AATTTTCAGAT
1 TCCGGTGACAATTTTCAGAA
*
6237614 TCCGGTGACATTTTTCAGAA
1 TCCGGTGACAATTTTCAGAA
6237634 TCCG
1 TCCG
6237638 ACGAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
TCCGGTGACAATTTTCAGAA
Found at i:6237969 original size:12 final size:12
Alignment explanation
Indices: 6237954--6237984 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6237944 ATTTTTTTTC
6237954 ATTTATTTGTTT
1 ATTTATTTGTTT
*
6237966 ATTTATTTTTTT
1 ATTTATTTGTTT
6237978 ATTTATT
1 ATTTATT
6237985 AGATTAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (12 bp):
ATTTATTTGTTT
Found at i:6238024 original size:11 final size:10
Alignment explanation
Indices: 6238008--6238083 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 10
6237998 TTAATATTCT
6238008 TTTTATCTTTA
1 TTTT-TCTTTA
*
6238019 TTTTATTTTTA
1 TTTT-TCTTTA
*
6238030 TTTTTGTTTTA
1 TTTTT-CTTTA
*
6238041 CTTTTCTTTA
1 TTTTTCTTTA
6238051 --TTT-TTTA
1 TTTTTCTTTA
*
6238058 TTTTTATTTA
1 TTTTTCTTTA
6238068 TTTTT-TTTA
1 TTTTTCTTTA
*
6238077 TTATTCT
1 TTTTTCT
6238084 ATTTTCTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 11 0.20
10 15 0.27
11 23 0.41
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTA
Found at i:6238028 original size:6 final size:6
Alignment explanation
Indices: 6238007--6238088 Score: 62
Period size: 6 Copynumber: 13.7 Consensus size: 6
6237997 TTTAATATTC
* * * * *
6238007 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTC TTTAT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
6238052 TTTTTA TTTTTA TTTATTT TTTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA TTT-TTA TTTTTA TT-TT-TA TTTT
6238089 CTTTAAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.20
6 35 0.58
7 9 0.15
8 4 0.07
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:6238029 original size:17 final size:17
Alignment explanation
Indices: 6238007--6238075 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
6237997 TTTAATATTC
6238007 TTTTTATCTTTATTTTA
1 TTTTTATCTTTATTTTA
* *
6238024 TTTTTATTTTTGTTTTA
1 TTTTTATCTTTATTTTA
*
6238041 -CTTT-TCTTTATTTTTTA
1 TTTTTATCTTTA--TTTTA
6238058 TTTTTA--TTTATTTT-
1 TTTTTATCTTTATTTTA
6238072 TTTT
1 TTTT
6238076 ATTATTCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.10
15 8 0.19
16 3 0.07
17 24 0.57
18 3 0.07
ACGTcount: A:0.13, C:0.04, G:0.01, T:0.81
Consensus pattern (17 bp):
TTTTTATCTTTATTTTA
Found at i:6238044 original size:27 final size:25
Alignment explanation
Indices: 6238007--6238088 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 25
6237997 TTTAATATTC
6238007 TTTTTATCTTTATTTTATTTTTATTTT
1 TTTTTA-CTTT-TTTTATTTTTATTTT
6238034 TGTTTTACTTTTCTTTATTTTTTATTTT
1 T-TTTTACTTTT-TTTA-TTTTTATTTT
* *
6238062 TATTTATTTTTTTTATTATTCTATTTT
1 TTTTTACTTTTTTTATT-TT-TATTTT
6238089 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
25 2 0.04
26 7 0.15
27 23 0.48
28 16 0.33
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (25 bp):
TTTTTACTTTTTTTATTTTTATTTT
Found at i:6238086 original size:17 final size:16
Alignment explanation
Indices: 6238047--6238093 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
6238037 TTTACTTTTC
*
6238047 TTTATTTTTTATTTTTA
1 TTTATTTTTT-TTATTA
6238064 TTTATTTTTTTTATTA
1 TTTATTTTTTTTATTA
*
6238080 TTCTATTTTCTTTA
1 TT-TATTTTTTTTA
6238094 AATAAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTTTTTATTA
Found at i:6238265 original size:58 final size:58
Alignment explanation
Indices: 6238115--6238338 Score: 295
Period size: 58 Copynumber: 3.7 Consensus size: 58
6238105 AAATTTCCAA
* * * *
6238115 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATCAAAATTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTC
6238175 AAAAAAATATTTTTAGGGAAAAGTTGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
1 AAAAAAATATTTTT--GG----G--GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
6238240 C
58 C
* *
6238241 AAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
6238299 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
6238339 TCCTGCACAA
Statistics
Matches: 148, Mismatches: 8, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
58 78 0.53
60 15 0.10
62 1 0.01
64 2 0.01
66 21 0.14
68 31 0.21
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:6242260 original size:11 final size:11
Alignment explanation
Indices: 6242246--6242294 Score: 71
Period size: 11 Copynumber: 4.3 Consensus size: 11
6242236 AAAGATGATG
6242246 AAAAAAGAAAA
1 AAAAAAGAAAA
6242257 AAAAAAGAGAAA
1 AAAAAAGA-AAA
6242269 AAAAGAAGAAAA
1 AAAA-AAGAAAA
*
6242281 AAAAATGAAAA
1 AAAAAAGAAAA
6242292 AAA
1 AAA
6242295 GAGATTTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
11 17 0.49
12 14 0.40
13 4 0.11
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:6242283 original size:22 final size:21
Alignment explanation
Indices: 6242217--6242296 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
6242207 ACAATGGATG
*
6242217 AAAAATGAGCAAAAAGAAAAAA
1 AAAAATGA-AAAAAAGAAAAAA
* **
6242239 GATGATG-AAAAAAGAAAAAA
1 AAAAATGAAAAAAAGAAAAAA
6242259 AAAAGA-GAAAAAAAGAAGAAAA
1 AAAA-ATGAAAAAAAGAA-AAAA
6242281 AAAAATGAAAAAAAGA
1 AAAAATGAAAAAAAGA
6242297 GATTTTGGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 14 0.30
21 11 0.23
22 22 0.47
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAATGAAAAAAAGAAAAAA
Found at i:6243583 original size:42 final size:41
Alignment explanation
Indices: 6243506--6243969 Score: 668
Period size: 41 Copynumber: 11.1 Consensus size: 41
6243496 ATGATTGTCA
*
6243506 AGGAGCAATTTACTTTTCAAAGTTTCGT--TGCCTCTGTATAG
1 AGGAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAG
**
6243547 AGGAGCAATTTACTTTTCAAAAGTTATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
6243589 AGGAGCAATTTA-TTTTCTAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
6243630 AGGAGCAATTTACTTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-C-AAAGTCGTGGTGCCTCTGTTTAG
*
6243673 AGGAGCAATTTACTTTTCCAAAGTCGTGCTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
6243715 AGGAGCAATTTA-TTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-C-AAAGTCGTGGTGCCTCTGTTTAG
* *
6243757 AGGAACAATTTACTTTTTCAAAGTCGTGCTGCCTCTGTTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAG
6243799 AGGAGCAATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
6243839 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
6243880 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
6243921 AGGAGCAATTTATGTTTTTCAAAGTCGTTGAGCTTTTGTTTAG
1 AGGAGCAATTTA--CTTTTCAAAGTCGTGGTGCCTCTGTTTAG
6243964 AGGAGC
1 AGGAGC
6243970 TTTGGTAAAA
Statistics
Matches: 392, Mismatches: 20, Indels: 20
0.91 0.05 0.05
Matches are distributed among these distances:
40 41 0.10
41 140 0.36
42 133 0.34
43 74 0.19
44 4 0.01
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:6243683 original size:84 final size:84
Alignment explanation
Indices: 6243506--6243932 Score: 658
Period size: 84 Copynumber: 5.1 Consensus size: 84
6243496 ATGATTGTCA
*
6243506 AGGAGCAATTTACTTTTC-AAAGTTTCGT--TGCCTCTGTATAGAGGAGCAATTTACTTTTCAAA
1 AGGAGCAATTTACTTTTCTAAAG--TCGTGCTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAA
**
6243568 AGTTATGGTGCCTCTGTTTAG
64 AGTCGTGGTGCCTCTGTTTAG
* *
6243589 AGGAGCAATTTA-TTTTCTAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAA
1 AGGAGCAATTTACTTTTCTAAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAA
6243653 GTCGTGGTGCCTCTGTTTAG
65 GTCGTGGTGCCTCTGTTTAG
*
6243673 AGGAGCAATTTACTTTTCCAAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAAA
1 AGGAGCAATTTACTTTTCTAAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAA
6243737 GTCGTGGTGCCTCTGTTTAG
65 GTCGTGGTGCCTCTGTTTAG
*
6243757 AGGAACAATTTACTTTT-TCAAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTAC-TTTC-AAA
1 AGGAGCAATTTACTTTTCT-AAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAA
6243819 GTCGTGGTGCCTCTGTTTAG
65 GTCGTGGTGCCTCTGTTTAG
* *
6243839 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTC-AAAG
1 AGGAGCAATTTACTTTTCTAAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAG
6243902 TCGTGGTGCCTCTGTTTAG
66 TCGTGGTGCCTCTGTTTAG
6243921 AGGAGCAATTTA
1 AGGAGCAATTTA
6243933 TGTTTTTCAA
Statistics
Matches: 323, Mismatches: 12, Indels: 19
0.91 0.03 0.05
Matches are distributed among these distances:
81 38 0.12
82 83 0.26
83 45 0.14
84 119 0.37
85 38 0.12
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (84 bp):
AGGAGCAATTTACTTTTCTAAAGTCGTGCTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAG
TCGTGGTGCCTCTGTTTAG
Found at i:6243997 original size:10 final size:9
Alignment explanation
Indices: 6243976--6244039 Score: 67
Period size: 10 Copynumber: 6.7 Consensus size: 9
6243966 GAGCTTTGGT
*
6243976 AAAAAATAA
1 AAAAAACAA
6243985 AAAAAACATA
1 AAAAAACA-A
6243995 AAAAATA-AA
1 AAAAA-ACAA
6244004 AAAAACACAA
1 AAAAA-ACAA
6244014 AAAAACACAA
1 AAAAA-ACAA
6244024 AAAAAACAA
1 AAAAAACAA
6244033 AGAAAAA
1 A-AAAAA
6244040 ATAAAAAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
9 19 0.39
10 29 0.59
11 1 0.02
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (9 bp):
AAAAAACAA
Found at i:6244015 original size:8 final size:9
Alignment explanation
Indices: 6243985--6244033 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
6243975 TAAAAAATAA
*
6243985 AAAAAACAT
1 AAAAAACAC
* *
6243994 AAAAAATAA
1 AAAAAACAC
6244003 AAAAAACAC
1 AAAAAACAC
6244012 AAAAAAACAC
1 -AAAAAACAC
*
6244022 AAAAAAAAC
1 AAAAAACAC
6244031 AAA
1 AAA
6244034 GAAAAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 25 0.74
10 9 0.26
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.04
Consensus pattern (9 bp):
AAAAAACAC
Found at i:6244045 original size:18 final size:18
Alignment explanation
Indices: 6243976--6244047 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 18
6243966 GAGCTTTGGT
*
6243976 AAAAAATAA-AAAAAACA
1 AAAAAAAAATAAAAAACA
6243993 TAAAAAATAAA-AAAAACACA
1 -AAAAAA-AAATAAAAA-ACA
6244013 AAAAAACACAA-AAAAAACA
1 AAAAAA-A-AATAAAAAACA
*
6244032 AAGAAAAAATAAAAAA
1 AAAAAAAAATAAAAAA
6244048 TGACAATGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.04
18 13 0.28
19 22 0.47
20 10 0.21
ACGTcount: A:0.85, C:0.08, G:0.01, T:0.06
Consensus pattern (18 bp):
AAAAAAAAATAAAAAACA
Found at i:6244053 original size:21 final size:19
Alignment explanation
Indices: 6243976--6244047 Score: 92
Period size: 18 Copynumber: 3.7 Consensus size: 19
6243966 GAGCTTTGGT
*
6243976 AAAAAATAAAAAAAAC-AT
1 AAAAAATAAAAAAAACAAA
6243994 AAAAAATAAAAAAAACACAA
1 AAAAAATAAAAAAAACA-AA
*
6244014 AAAAACACAAAAAAAACAAA
1 AAAAA-ATAAAAAAAACAAA
6244034 GAAAAAATAAAAAA
1 -AAAAAATAAAAAA
6244048 TGACAATGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.34
20 15 0.32
21 16 0.34
ACGTcount: A:0.85, C:0.08, G:0.01, T:0.06
Consensus pattern (19 bp):
AAAAAATAAAAAAAACAAA
Found at i:6244351 original size:30 final size:27
Alignment explanation
Indices: 6244298--6244353 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
6244288 GTATATCTGT
*
6244298 ATTTATTTATTTTTTTATTTAGAATAG
1 ATTTATTTATTTTTTTATATAGAATAG
6244325 ATTTATATGTATTTTATTTATATAGAATA
1 ATTTAT-T-TATTTT-TTTATATAGAATA
6244354 TTTATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 1 0.04
29 6 0.24
30 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (27 bp):
ATTTATTTATTTTTTTATATAGAATAG
Found at i:6245436 original size:17 final size:17
Alignment explanation
Indices: 6245416--6245470 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
6245406 TTTATCTTTA
6245416 TTTTATTTTCATTT-TT
1 TTTTATTTTCATTTATT
6245432 GTTTTACTTTTC-TTTATT
1 -TTTTA-TTTTCATTTATT
*
6245450 TTTTATTTTTATTTATT
1 TTTTATTTTCATTTATT
6245467 TTTT
1 TTTT
6245471 TTATTATTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
16 4 0.12
17 23 0.68
18 7 0.21
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTATTTTCATTTATT
Found at i:6245441 original size:27 final size:25
Alignment explanation
Indices: 6245404--6245485 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 25
6245394 TTTAATATTC
6245404 TTTTTATCTTTATTTTATTTTCATTTT
1 TTTTTA-CTTT-TTTTATTTTCATTTT
*
6245431 TGTTTTACTTTTCTTTATTTTTTATTTT
1 T-TTTTACTTTT-TTTA-TTTTCATTTT
* *
6245459 TATTTATTTTTTTTATTATTCTATTTT
1 TTTTTACTTTTTTTATT-TTC-ATTTT
6245486 CTTTAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
25 2 0.04
26 7 0.15
27 22 0.48
28 15 0.33
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (25 bp):
TTTTTACTTTTTTTATTTTCATTTT
Found at i:6245462 original size:13 final size:13
Alignment explanation
Indices: 6245444--6245485 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6245434 TTTACTTTTC
6245444 TTTATTTTTTATT
1 TTTATTTTTTATT
6245457 TTTATTTATTT-TT
1 TTTATTT-TTTATT
*
6245470 TTTATTATTCTATT
1 TTTATT-TTTTATT
6245484 TT
1 TT
6245486 CTTTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:6245483 original size:17 final size:16
Alignment explanation
Indices: 6245444--6245490 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
6245434 TTTACTTTTC
*
6245444 TTTATTTTTTATTTTTA
1 TTTATTTTTT-TTATTA
6245461 TTTATTTTTTTTATTA
1 TTTATTTTTTTTATTA
*
6245477 TTCTATTTTCTTTA
1 TT-TATTTTTTTTA
6245491 AATAAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTTTTTATTA
Found at i:6245590 original size:58 final size:58
Alignment explanation
Indices: 6245506--6245784 Score: 418
Period size: 58 Copynumber: 4.8 Consensus size: 58
6245496 AAATCAAAAT
* * * *
6245506 TTTCAAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATAAA
1 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT--AAAAATAAA
* * *
6245566 TTT-CAAAAAAGT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAA
1 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAA
6245624 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
1 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
* * *
6245682 TTTTCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA
1 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
6245740 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
6245785 TCCTGCACAA
Statistics
Matches: 200, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
56 5 0.03
58 139 0.69
59 14 0.07
60 42 0.21
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (58 bp):
TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA
Found at i:6245651 original size:118 final size:118
Alignment explanation
Indices: 6245495--6245786 Score: 484
Period size: 118 Copynumber: 2.5 Consensus size: 118
6245485 TCTTTAAATA
* * *
6245495 AAAATCAAAATTTTCAAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
1 AAAATCAAAA-TTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTT--AAA
6245560 AATAAA-TTTCAAAAAAGT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
63 AATAAATTTTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
*
6245614 AAAATCAAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAAATCAAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
*
6245679 AAATTTTCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTG
66 AAATTTTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
6245732 AAAAT--AAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC
1 AAAATCAAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC
6245787 CTGCACAAGA
Statistics
Matches: 165, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
116 58 0.35
117 12 0.07
118 85 0.52
119 10 0.06
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (118 bp):
AAAATCAAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
AAATTTTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:6251059 original size:14 final size:14
Alignment explanation
Indices: 6251035--6251071 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6251025 TATTAATATT
6251035 TTTAT-TAAAAATA
1 TTTATCTAAAAATA
6251048 TTTATCTAAAAATA
1 TTTATCTAAAAATA
*
6251062 TATATC-AAAA
1 TTTATCTAAAA
6251072 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTATCTAAAAATA
Found at i:6256092 original size:22 final size:22
Alignment explanation
Indices: 6256054--6256095 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6256044 TATAATCATG
6256054 AAAATAATTAATATATTTTTAT
1 AAAATAATTAATATATTTTTAT
*
6256076 AAAACTAATTTAT-TATTTTT
1 AAAA-TAATTAATATATTTTT
6256096 TTACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAATAATTAATATATTTTTAT
Found at i:6256740 original size:21 final size:21
Alignment explanation
Indices: 6256714--6256759 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
6256704 ATTACTTTAT
* *
6256714 TTAAATAAATTTCACCTATCC
1 TTAAATAAATATCACCTAACC
* *
6256735 TTAAATTAGTATCACCTAACC
1 TTAAATAAATATCACCTAACC
6256756 TTAA
1 TTAA
6256760 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAATAAATATCACCTAACC
Found at i:6257305 original size:22 final size:23
Alignment explanation
Indices: 6257261--6257307 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6257251 TTTTTATAAA
*
6257261 ATAAAAATAATTAATATATTTTT
1 ATAAAAATAATTAATATAATTTT
*
6257284 ATAAAAATAATTTAT-TAATTTT
1 ATAAAAATAATTAATATAATTTT
6257306 AT
1 AT
6257308 TACTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAAAATAATTAATATAATTTT
Found at i:6257308 original size:28 final size:29
Alignment explanation
Indices: 6257245--6257308 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
6257235 GTAAGTTTGG
6257245 ATTTTATTTTTATAAAATAAAAATAATTA
1 ATTTTATTTTTATAAAATAAAAATAATTA
* * * *
6257274 A-TATATTTTTATAAAA-ATAATTTATTA
1 ATTTTATTTTTATAAAATAAAAATAATTA
6257301 ATTTTATT
1 ATTTTATT
6257309 ACTTTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 9 0.31
28 19 0.66
29 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTATTTTTATAAAATAAAAATAATTA
Found at i:6257341 original size:21 final size:21
Alignment explanation
Indices: 6257316--6257361 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
6257306 ATTACTTTAT
* *
6257316 TTAAATAAATTTCACCTATCC
1 TTAAATAAATATCACCTAACC
* *
6257337 TTAAATTAGTATCACCTAACC
1 TTAAATAAATATCACCTAACC
6257358 TTAA
1 TTAA
6257362 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAATAAATATCACCTAACC
Found at i:6257818 original size:608 final size:608
Alignment explanation
Indices: 6256054--6257870 Score: 2641
Period size: 597 Copynumber: 3.0 Consensus size: 608
6256044 TATAATCATG
* * *
6256054 AAAATAATTAATATATTTTTATAAAACTAATTTATT-ATTTTTTTACTTTATTAAAATAAATTTC
1 AAAATAATTAATATATTTTTATAAAAATAATTTATTAATTTTATTACTTTATTTAAATAAATTTC
* * * * * *
6256118 ACTTATCGTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATATGATGCAACCTTTTATATC
66 ACCTATCCTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATATTAT-CAGCTTTTTATATT
* ** *
6256183 TATAATTTAGCA-TAAATATAATCTAAAAAAAACTAGCAACTACGTAGACTATCGGTAAAATGCT
130 TATAATTTAGCATTAAATATAATCTAAAAATAACTAGCAACT-CGTAGACTATTAGTAAAATGTT
** * * *
6256247 GAACTCTTAATTTCAATGATTAATATTCGAATTCTAATAATCTCAAATACTAAAAAAAAATAATA
194 GAACTCTTAATTTCAATGATTAGGATTCGAATTATGATAATCTCAAATA-T-TAAAAAAATAATA
*
6256312 TAAAAATATTCTATTAAAATACATGTATATAAAAATAGGAAAATATAGTTAATGAACAAATA-GA
257 TAAAAATA-TCTATTAAAATACATGTACATAAAAATAGGAAAATATAGTTAATGAACAAATATG-
*
6256376 AGCTTTCTAATAATATTTTTTAAATTGATTATTTAATTATTATTTGACATAAATAAATATGCCAA
320 AGCTTTCTAATAAAATTTTTTAAATTGA-TATTTAATTATTATTTGA-ATAAATAAATATGCCAA
* *
6256441 TTGCAATCAAATTATTAAGTTTTTAATATATAAAAATAAATTTTAAACTTAATTTTAACATATAT
383 TTGCAATCAAATTATTAAGTTTTTAATATATAAAAATAAAATTTAAAATTAATTTTAACATATAT
*
6256506 TTCTCATATTATAAATTTTTTAATGCCTTTTGTTTGATAAATTCATAAAAAATTAAAATAACTTA
448 TTCTCATATTATAAATTTTTTAATGTCTTTTGTTTGATAAATTCATAAAAAATTAAAATAACTTA
* *
6256571 TTTTAAAATAAATGGTTGTCCAATCAAGAAACAATATTTTTACATTTGAAAATGAGAAATTAAGA
513 TTTTAAAATAAATGGTTGTCCAATCAAGAAACAATATTTTTACATTTGAAAATGTGAATTTAAGA
*
6256636 AAGTGAGTTTGGATTTTAATTTTATAAAATA
578 AAGTGAGTTTGGATTTTATTTTTATAAAATA
*
6256667 AAAATAATTAATAGATTTTTAT-AAAA-AA---ATTAATTTTATTACTTTATTTAAATAAATTTC
1 AAAATAATTAATATATTTTTATAAAAATAATTTATTAATTTTATTACTTTATTTAAATAAATTTC
6256727 ACCTATCCTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATA-T-T-AGTCTTTTTATATT
66 ACCTATCCTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATATTATCAG-CTTTTTATATT
6256789 TATAATTTAGCATTAAATATAATCTAAAAATAACTAGC-A-----AGACTATTAGTAAAATGTTG
130 TATAATTTAGCATTAAATATAATCTAAAAATAACTAGCAACTCGTAGACTATTAGTAAAATGTTG
* * * * * * * * * *
6256848 AACTTTTAGTTTCAGTGATTAGGTTTTGAATTTTGATAATCTCAAATACTAAAAAAAAAAAAAAA
195 AACTCTTAATTTCAATGATTAGGATTCGAATTATGATAATCTCAAATATTAAAAAAATAATATAA
* *
6256913 AAATATCTATTAAAATACATATACATAGAAATAGGAAAATATAGTTAATGAACAAATATGAGCTT
260 AAATATCTATTAAAATACATGTACATAAAAATAGGAAAATATAGTTAATGAACAAATATGAGCTT
* *
6256978 TGTAATAAAATTTTTTAAATTGATCATTTAATTATTATTTGACATAAATAAATATGCCAATTTCA
325 TCTAATAAAATTTTTTAAATTGAT-ATTTAATTATTATTTGA-ATAAATAAATATGCCAATTGCA
* *
6257043 ATC-AATATATTAGGTTTTTAATATATAAAAATAAAATTTAAAATTATTTTTAACATATATTTCT
388 ATCAAAT-TATTAAGTTTTTAATATATAAAAATAAAATTTAAAATTAATTTTAACATATATTTCT
* **
6257107 AATATTATAAAAATTTTAATGTCTTTTGTTTGATAAATTCATAAAAAATTAAAATAACTTATTTT
452 CATATTATAAATTTTTTAATGTCTTTTGTTTGATAAATTCATAAAAAATTAAAATAACTTATTTT
*
6257172 AAAATAAATGATTGTCCAATCAAGAAACAATATTTTTACATTTGAAAATGTGAATTTAAGAAAGT
517 AAAATAAATGGTTGTCCAATCAAGAAACAATATTTTTACATTTGAAAATGTGAATTTAAGAAAGT
*
6257237 AAGTTTGGATTTTATTTTTATAAAATA
582 GAGTTTGGATTTTATTTTTATAAAATA
6257264 AAAATAATTAATATATTTTTATAAAAATAATTTATTAATTTTATTACTTTATTTAAATAAATTTC
1 AAAATAATTAATATATTTTTATAAAAATAATTTATTAATTTTATTACTTTATTTAAATAAATTTC
*
6257329 ACCTATCCTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATATTATACAGCTTTTTATGTT
66 ACCTATCCTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATATTAT-CAGCTTTTTATATT
* * *
6257394 TATAATTTAGCATTAAATATAATCTAAAAATAATTAGCAACTGCGTAGACTATTTGTAAAATATT
130 TATAATTTAGCATTAAATATAATCTAAAAATAACTAGCAACT-CGTAGACTATTAGTAAAATGTT
* * *
6257459 AAACTCTTAATTTCAATAATTAGGATTCGAATTATGATAATCTTAAATATTAAAAAAATAATATA
194 GAACTCTTAATTTCAATGATTAGGATTCGAATTATGATAATCTCAAATATTAAAAAAATAATATA
**
6257524 AAAATATCTGCTAAAATACATGTACATAAAAATAGGAAAATATAGTTAATGAACAAATATGAGCT
259 AAAATATCTATTAAAATACATGTACATAAAAATAGGAAAATATAGTTAATGAACAAATATGAGCT
* **
6257589 TTCTAATAAAATTTTTTAAATTGACTATTTAATTGTTATTTG-AT-AA-AAATATTTCAATTGCA
324 TTCTAATAAAATTTTTTAAATTGA-TATTTAATTATTATTTGAATAAATAAATATGCCAATTGCA
* * * * * *
6257651 ATCAAATTGTTATGTTTTTAATATATAAAAATAAAAATAAAAAATAATTTTAACATATATTTTTC
388 ATCAAATTATTAAGTTTTTAATATATAAAAATAAAATTTAAAATTAATTTTAACATATATTTCTC
* * ** *
6257716 AGATTATAAATTTTTTAATATCTTTTGTTTGATAAATTTTTAAAAAATTAAAATAACTTATATTA
453 ATATTATAAATTTTTTAATGTCTTTTGTTTGATAAATTCATAAAAAATTAAAATAACTTATTTTA
* * * * * *
6257781 AAATAAATGGTTGTCTAATAAAAAAATAGTATTTTTACATTTGAAATTGTGAATTTAAGAAAGTG
518 AAATAAATGGTTGTCCAATCAAGAAACAATATTTTTACATTTGAAAATGTGAATTTAAGAAAGTG
*
6257846 ATTTTGGATTTTATTTGTTATAAAA
583 AGTTTGGATTTTATTT-TTATAAAA
6257871 ATTGTAAATA
Statistics
Matches: 1081, Mismatches: 98, Indels: 54
0.88 0.08 0.04
Matches are distributed among these distances:
596 4 0.00
597 340 0.31
598 22 0.02
599 2 0.00
600 56 0.05
602 78 0.07
603 1 0.00
604 1 0.00
605 48 0.04
606 25 0.02
607 25 0.02
608 199 0.18
609 83 0.08
610 2 0.00
611 2 0.00
612 171 0.16
613 22 0.02
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (608 bp):
AAAATAATTAATATATTTTTATAAAAATAATTTATTAATTTTATTACTTTATTTAAATAAATTTC
ACCTATCCTTAAATTAGTATCACCTAACCTTAATTTTATTTTTATATTATCAGCTTTTTATATTT
ATAATTTAGCATTAAATATAATCTAAAAATAACTAGCAACTCGTAGACTATTAGTAAAATGTTGA
ACTCTTAATTTCAATGATTAGGATTCGAATTATGATAATCTCAAATATTAAAAAAATAATATAAA
AATATCTATTAAAATACATGTACATAAAAATAGGAAAATATAGTTAATGAACAAATATGAGCTTT
CTAATAAAATTTTTTAAATTGATATTTAATTATTATTTGAATAAATAAATATGCCAATTGCAATC
AAATTATTAAGTTTTTAATATATAAAAATAAAATTTAAAATTAATTTTAACATATATTTCTCATA
TTATAAATTTTTTAATGTCTTTTGTTTGATAAATTCATAAAAAATTAAAATAACTTATTTTAAAA
TAAATGGTTGTCCAATCAAGAAACAATATTTTTACATTTGAAAATGTGAATTTAAGAAAGTGAGT
TTGGATTTTATTTTTATAAAATA
Found at i:6258647 original size:6 final size:6
Alignment explanation
Indices: 6258636--6258667 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6258626 GGCCGTGATT
*
6258636 ATGGTG ATGGTG ATGGTG ATGGTG ATGATG AT
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG AT
6258668 AGAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (6 bp):
ATGGTG
Found at i:6259724 original size:6 final size:6
Alignment explanation
Indices: 6259715--6259754 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
6259705 ATATTGATAT
* *
6259715 ATATAA ATATAA ATATGA ATATAA ATATAA ATATAT ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
6259755 GTTAATATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:6259754 original size:18 final size:18
Alignment explanation
Indices: 6259711--6259754 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
6259701 AACCATATTG
6259711 ATATATATAAATATAAAT
1 ATATATATAAATATAAAT
6259729 ATGA-ATATAAATATAAAT
1 AT-ATATATAAATATAAAT
6259747 ATATATAT
1 ATATATAT
6259755 GTTAATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATATATAAATATAAAT
Found at i:6268835 original size:18 final size:18
Alignment explanation
Indices: 6268786--6268827 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
6268776 ACAAGGTGGA
6268786 ATGCATAAAGGGCATTTC
1 ATGCATAAAGGGCATTTC
6268804 ATGCATAAAGGGCATTTC
1 ATGCATAAAGGGCATTTC
6268822 ATGCAT
1 ATGCAT
6268828 GTCAGGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (18 bp):
ATGCATAAAGGGCATTTC
Found at i:6271594 original size:399 final size:394
Alignment explanation
Indices: 6270821--6271595 Score: 1158
Period size: 399 Copynumber: 2.0 Consensus size: 394
6270811 ATCTGATTAG
**
6270821 TAAATAAATAAATAAAATTGAAAGTTTGAGATTAGGCGTGATAATTGTTATTAGAAGATTAGGAG
1 TAAATAAATAAATAAAATTGAAAGTTTGAGATTAGGCGTGATAATCATTATTAGAAGATTAGGAG
* * * *
6270886 CTAATTTTTAGCTTTGCGAATTGAGTTGAAACTCTATCAATTTTGTCTTGCAAATCCTTGCAATT
66 CTAATCTTTAGCTTTGCGAATTAAGTTGAAACTCTATCAATTTTATCTTACAAATCCTTGCAATT
* * *
6270951 CATCAACAAAGAGGGACAGAATGAAGAAGCAACAATTCAAAAATACATTTTTGGATCATACATGC
131 CATCAACAAAGAGGGACAGAATAAAGAAGCAACAATTCAAAAATACATTTTTGGATCACACAAGC
*
6271016 CTACAATTGCCTCTATTTTCATTTGCCAAATTCCAAACTAATCCATTCACCATACACATAGAGAC
196 CTACAATTGCCTCTATTTTCATTTGCCAAATTCCAAACTAATCCATTCACCATACACACAGAGAC
* * * * * * *
6271081 AACATTATATAGTGATCAAACAGAAAACTATTGAAAAACAACAAAGAAATAAGCTATTAGTAGTT
261 AACAATATACAGTGATCAAACAAAAAACTACTAAAAAACAACAAAGAAATAAACTATTAGCAGTT
* *
6271146 TTCGATCACCATCTTTACCTCACATAATTTTAGCAATAACCTCATCATCTCTTCTGATTAGTAAA
326 TTCGATCACCATCTTTACCCCACATAATTCTAGCAATAACCTCATCATCTCTTCTGATTAGTAAA
6271211 TAAA
391 TAAA
* * *
6271215 TAAATAAATAAATAAAGTTGAAAGTTT-ATTATTAAGCTCGGTGATAATCATTATTAGAAGATTA
1 TAAATAAATAAATAAAATTGAAAGTTTGA-GATT-AG-GC-GTGATAATCATTATTAGAAGATTA
* ** *
6271279 GGTGCTAATCTTTAGCTTTTTGAATTAAGTTGAAACTCTATCAATTTTATCTTATAAATCCTTGC
62 GGAGCTAATCTTTAGCTTTGCGAATTAAGTTGAAACTCTATCAATTTTATCTTACAAATCCTTGC
* * *
6271344 AATTCATTAACAAAGAGGGGATAGGAATAAAGAAGCAACAATTCAGAAATACATTTTTGGATCAC
127 AATTCATCAACAAAGA-GGGACA-GAATAAAGAAGCAACAATTCAAAAATACATTTTTGGATCAC
* * * *
6271409 ACAAGCCTACAATTGCCTCTGTTTTCATTTGCCAAATTTCAAACTAATCCCTTCATCATACACAC
190 ACAAGCCTACAATTGCCTCTATTTTCATTTGCCAAATTCCAAACTAATCCATTCACCATACACAC
6271474 AGAGACAACAATATACAGTGATCAAACAAAAAACTACTAAAAAACAACAAAGAAA-ACAACTATT
255 AGAGACAACAATATACAGTGATCAAACAAAAAACTACTAAAAAACAACAAAGAAATA-AACTATT
* *
6271538 AGCAGTTTTTGATCACTATCTTTACCCCACATAATTCTAGCAATAACCTCATCATCTC
319 AGCAGTTTTCGATCACCATCTTTACCCCACATAATTCTAGCAATAACCTCATCATCTC
6271596 CTCTACCAGA
Statistics
Matches: 339, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
393 1 0.00
394 29 0.09
395 2 0.01
396 1 0.00
397 94 0.28
398 6 0.02
399 206 0.61
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (394 bp):
TAAATAAATAAATAAAATTGAAAGTTTGAGATTAGGCGTGATAATCATTATTAGAAGATTAGGAG
CTAATCTTTAGCTTTGCGAATTAAGTTGAAACTCTATCAATTTTATCTTACAAATCCTTGCAATT
CATCAACAAAGAGGGACAGAATAAAGAAGCAACAATTCAAAAATACATTTTTGGATCACACAAGC
CTACAATTGCCTCTATTTTCATTTGCCAAATTCCAAACTAATCCATTCACCATACACACAGAGAC
AACAATATACAGTGATCAAACAAAAAACTACTAAAAAACAACAAAGAAATAAACTATTAGCAGTT
TTCGATCACCATCTTTACCCCACATAATTCTAGCAATAACCTCATCATCTCTTCTGATTAGTAAA
TAAA
Found at i:6272950 original size:6 final size:6
Alignment explanation
Indices: 6272935--6272974 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
6272925 AAAAATTTAG
*
6272935 AAAATAA AAAATA AAAGTAA AAAATA AAAATA AAAATA AA
1 AAAAT-A AAAATA AAAAT-A AAAATA AAAATA AAAATA AA
6272975 TTATGATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 20 0.67
7 10 0.33
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:6272957 original size:19 final size:19
Alignment explanation
Indices: 6272935--6272974 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6272925 AAAAATTTAG
*
6272935 AAAATAAAAAATAAAAGTAA
1 AAAAT-AAAAATAAAAATAA
6272955 AAAATAAAAATAAAAATAA
1 AAAATAAAAATAAAAATAA
6272974 A
1 A
6272975 TTATGATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATAAAAATAA
Found at i:6273944 original size:11 final size:11
Alignment explanation
Indices: 6273928--6273960 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
6273918 GACAATGATG
6273928 TGAGAACACTT
1 TGAGAACACTT
6273939 TGAGAACACTT
1 TGAGAACACTT
6273950 TGAGAAC-CTT
1 TGAGAACACTT
6273960 T
1 T
6273961 AGATTTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (11 bp):
TGAGAACACTT
Found at i:6276897 original size:9 final size:9
Alignment explanation
Indices: 6276885--6276924 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
6276875 AAAAAGAATG
6276885 AAAAATAAA
1 AAAAATAAA
6276894 AAAAATAAA
1 AAAAATAAA
*
6276903 AAAATTAAA
1 AAAAATAAA
*
6276912 AAAAGTAAA
1 AAAAATAAA
6276921 AAAA
1 AAAA
6276925 GAATGAGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:6276956 original size:17 final size:17
Alignment explanation
Indices: 6276936--6276968 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6276926 AATGAGGAAT
6276936 GTGAAAAAATGAAAAAG
1 GTGAAAAAATGAAAAAG
6276953 GTGAAAAAATGAAAAA
1 GTGAAAAAATGAAAAA
6276969 AATAAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (17 bp):
GTGAAAAAATGAAAAAG
Found at i:6277690 original size:79 final size:78
Alignment explanation
Indices: 6277553--6277847 Score: 301
Period size: 79 Copynumber: 3.7 Consensus size: 78
6277543 CATAATCTAT
* * * * * *
6277553 GAGTTGTGATTAAATGATGGAAATAATGTGGTTCAGTGGACAAAATTTGTTTTAAAATTGTTAGT
1 GAGTTGTGATCAAATGATGGAAATAATGTGGATCAGTGGATAAAATTTATTCTAAAATTGCTAGT
*
6277618 ACTGTGAAGTCTGA
66 GCTGTGAAG-CTGA
* * * *
6277632 GAGTTATGATCAAATGATAGAAATAATGTAGATCGGTGGATAAAATTTATTC-ATAAATTGCTAG
1 GAGTTGTGATCAAATGATGGAAATAATGTGGATCAGTGGATAAAATTTATTCTA-AAATTGCTAG
*
6277696 TGCTGTGAAGCTTGT
65 TGCTGTGAAGC-TGA
* * * *
6277711 GACTTGTAATCAAATGATGGAAACAATGTGGA-CTAGTGGATGAAATTTATTCTAAAATTGCTAG
1 GAGTTGTGATCAAATGATGGAAATAATGTGGATC-AGTGGATAAAATTTATTCTAAAATTGCTAG
*
6277775 TGTTGTGAAGCCT-A
65 TGCTGTGAAG-CTGA
* * * * *
6277789 GGAGTTGTGATCAAATGATGAAAATATTATGGATTAGTGGATGAAAA-TTGTTCTAAAAT
1 -GAGTTGTGATCAAATGATGGAAATAATGTGGATCAGTGGAT-AAAATTTATTCTAAAAT
6277848 AGTTAGTATC
Statistics
Matches: 177, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
78 3 0.02
79 169 0.95
80 5 0.03
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (78 bp):
GAGTTGTGATCAAATGATGGAAATAATGTGGATCAGTGGATAAAATTTATTCTAAAATTGCTAGT
GCTGTGAAGCTGA
Found at i:6285208 original size:20 final size:20
Alignment explanation
Indices: 6285171--6285209 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6285161 GCCTCCAAAG
*
6285171 GAGGCTTTTAGTTCATCAAT
1 GAGGCTTTCAGTTCATCAAT
6285191 GAGGCTTTCA-TTCAATCAA
1 GAGGCTTTCAGTTC-ATCAA
6285210 AATTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
GAGGCTTTCAGTTCATCAAT
Found at i:6286469 original size:15 final size:15
Alignment explanation
Indices: 6286433--6286471 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
6286423 GCTATATCAC
*
6286433 TTTGAAATT-TGGGT
1 TTTGAAATTGTGGCT
*
6286447 TGTGAAATTGTGGCT
1 TTTGAAATTGTGGCT
6286462 TTTGAAATTG
1 TTTGAAATTG
6286472 GTATATTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46
Consensus pattern (15 bp):
TTTGAAATTGTGGCT
Found at i:6288262 original size:24 final size:24
Alignment explanation
Indices: 6288225--6288283 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
6288215 AGTTAAAAAT
* *
6288225 AATGAGAATCTTTAAGGAGTTTTA
1 AATGAGAATTTTTAAGAAGTTTTA
*
6288249 AATGAAAATTTTTAAGAAGTTTTA
1 AATGAGAATTTTTAAGAAGTTTTA
6288273 AATGAGAATTT
1 AATGAGAATTT
6288284 GTGAATGGGA
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:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (24 bp):
AATGAGAATTTTTAAGAAGTTTTA
Found at i:6288280 original size:14 final size:13
Alignment explanation
Indices: 6288244--6288327 Score: 59
Period size: 14 Copynumber: 6.6 Consensus size: 13
6288234 CTTTAAGGAG
*
6288244 TTTTAAATGAAAA
1 TTTTAAATGAGAA
* *
6288257 TTTTTAA-GA-AG
1 TTTTAAATGAGAA
6288268 TTTTAAATGAGAA
1 TTTTAAATGAGAA
* *
6288281 TTTGTGAATGGGAA
1 TTT-TAAATGAGAA
* *
6288295 TTTTTAA-G-GAG
1 TTTTAAATGAGAA
6288306 TTTTAAATGAGAA
1 TTTTAAATGAGAA
6288319 TCTTTAAAT
1 T-TTTAAAT
6288328 TTTTTGAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
11 15 0.27
12 6 0.11
13 16 0.29
14 18 0.33
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (13 bp):
TTTTAAATGAGAA
Found at i:6288367 original size:49 final size:51
Alignment explanation
Indices: 6288307--6288402 Score: 144
Period size: 49 Copynumber: 1.9 Consensus size: 51
6288297 TTTAAGGAGT
* *
6288307 TTTAAATGAGAATCTTTAAATTTTTTGAA-TAA-AATCTTTGT-TTTTGATC
1 TTTAAATGAGAATCGTTAAA-TTTTTAAAGTAAGAATCTTTGTGTTTTGATC
6288356 TTTAAATGAGAATCGTTAAATTTTTAAAGTAAGAATCTTTGTGTTTT
1 TTTAAATGAGAATCGTTAAATTTTTAAAGTAAGAATCTTTGTGTTTT
6288403 AAATGAGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 7 0.17
49 22 0.52
50 9 0.21
51 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (51 bp):
TTTAAATGAGAATCGTTAAATTTTTAAAGTAAGAATCTTTGTGTTTTGATC
Found at i:6288855 original size:16 final size:16
Alignment explanation
Indices: 6288831--6288877 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
6288821 ATGTAAATCC
6288831 TGAAATCTTGTGAATT
1 TGAAATCTTGTGAATT
* * *
6288847 TGAATTCTTGCGAAAT
1 TGAAATCTTGTGAATT
*
6288863 TGAAATCTTATGAAT
1 TGAAATCTTGTGAAT
6288878 CTAAATTCTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (16 bp):
TGAAATCTTGTGAATT
Found at i:6288980 original size:23 final size:23
Alignment explanation
Indices: 6288950--6289016 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
6288940 TGAATCTTTG
*
6288950 AATTGTGAACCTTTAAATTTTAA
1 AATTGTGAATCTTTAAATTTTAA
* *
6288973 AATTGTGATTCTTTAAA--TTCA
1 AATTGTGAATCTTTAAATTTTAA
* *
6288994 AATTGTGAATCTTTGATTTTTAA
1 AATTGTGAATCTTTAAATTTTAA
6289017 TTGCAAATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 17 0.49
23 18 0.51
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (23 bp):
AATTGTGAATCTTTAAATTTTAA
Found at i:6292018 original size:2 final size:2
Alignment explanation
Indices: 6292011--6292035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6292001 GTGTACAATC
6292011 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6292036 GAAATATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6292294 original size:90 final size:90
Alignment explanation
Indices: 6292130--6292303 Score: 192
Period size: 90 Copynumber: 1.9 Consensus size: 90
6292120 ATATAATTAT
* *
6292130 TTTTTTCTTCACATTTATTAATTAAAACAATAGTAGGTTCTCTATATTCTTATAAGATGTATATA
1 TTTTTTCTTCACATTTATCAATTAAAACAATAGTAGGTTCTCTATATTCTTATAAGAAGTATATA
6292195 TGTACATACAT-GCTATACATATACA
66 TGTACATACATAG-TATACATATACA
* * * * * * * *
6292220 TTTTTTCTTCATATTTATCAATTGAAATAATAGT-GGATTTTGTATATTTTTATAATTAAG-ATG
1 TTTTTTCTTCACATTTATCAATTAAAACAATAGTAGG-TTCTCTATATTCTTATAA-GAAGTATA
* *
6292283 TATTTATATACATAGTATACA
64 TATGTACATACATAGTATACA
6292304 CATTGCCATT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
89 2 0.03
90 64 0.93
91 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.47
Consensus pattern (90 bp):
TTTTTTCTTCACATTTATCAATTAAAACAATAGTAGGTTCTCTATATTCTTATAAGAAGTATATA
TGTACATACATAGTATACATATACA
Found at i:6298060 original size:40 final size:40
Alignment explanation
Indices: 6298010--6298093 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
6298000 AAGAAAATTT
*
6298010 TGACTCTAATATCATATTAAACTTCTAACTTAAAATCAAG
1 TGACTCTAATATCATATTAAACATCTAACTTAAAATCAAG
* *
6298050 TGACTTTAATATCATATTAAGCATCTAACTTAAAATCAAG
1 TGACTCTAATATCATATTAAACATCTAACTTAAAATCAAG
6298090 TGAC
1 TGAC
6298094 GATAATTAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (40 bp):
TGACTCTAATATCATATTAAACATCTAACTTAAAATCAAG
Done.