Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 9 of 106
Found at i:1406192 original size:51 final size:51
Alignment explanation
Indices: 1406122--1406233 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
1406112 AATCCCTCTG
* * *
1406122 AAACCCTAAAGTCCAAAAATCAAA-ACTATAAACCTTAAAATC-TAAAACCCCA
1 AAACCTTAAAGTCCAAAAATCAAACACTA-AAACCCT-AAATCATAAAA-CCAA
* *
1406174 AAACCTTAAA-TCCTAAAATCAAACCCTAAAACCCTAAATCATAAAACCAA
1 AAACCTTAAAGTCCAAAAATCAAACACTAAAACCCTAAATCATAAAACCAA
1406224 AAACCTTAAA
1 AAACCTTAAA
1406234 ATGAAAACCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
50 18 0.34
51 23 0.43
52 12 0.23
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.18
Consensus pattern (51 bp):
AAACCTTAAAGTCCAAAAATCAAACACTAAAACCCTAAATCATAAAACCAA
Found at i:1406206 original size:28 final size:28
Alignment explanation
Indices: 1406157--1406224 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1406147 CTATAAACCT
* *
1406157 TAAAATCTAAAACCCCAAAACCTTAAATCC
1 TAAAATC--AAACCCCAAAACCCTAAATCA
*
1406187 TAAAATCAAACCCTAAAACCCTAAATCA
1 TAAAATCAAACCCCAAAACCCTAAATCA
*
1406215 TAAAACCAAA
1 TAAAATCAAA
1406225 AACCTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 27 0.79
30 7 0.21
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (28 bp):
TAAAATCAAACCCCAAAACCCTAAATCA
Found at i:1409003 original size:19 final size:19
Alignment explanation
Indices: 1408979--1409017 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1408969 ATTAATTTCC
*
1408979 TATGTATATTT-TGTTATTT
1 TATGTAT-TTTATGGTATTT
1408998 TATGTATTTTATGGTATTT
1 TATGTATTTTATGGTATTT
1409017 T
1 T
1409018 TATTATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (19 bp):
TATGTATTTTATGGTATTT
Found at i:1409138 original size:22 final size:21
Alignment explanation
Indices: 1409112--1409158 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1409102 TGTTTTCTGA
*
1409112 TTTTTTCTGATTATCAGATATC
1 TTTTTTCTGACTATCA-ATATC
* *
1409134 TTTTTTTTTACTATCAATATC
1 TTTTTTCTGACTATCAATATC
1409155 TTTT
1 TTTT
1409159 GATTTTACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTTTCTGACTATCAATATC
Found at i:1409164 original size:22 final size:21
Alignment explanation
Indices: 1409123--1409177 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1409113 TTTTTCTGAT
*
1409123 TATCAGATATCTTTTTTTTTAC
1 TATCA-ATATCTTTTATTTTAC
1409145 TATCAATATCTTTTGATTTTAC
1 TATCAATATCTTTT-ATTTTAC
* *
1409167 TTTCTATATCT
1 TATCAATATCT
1409178 AGTTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (21 bp):
TATCAATATCTTTTATTTTAC
Found at i:1409186 original size:22 final size:20
Alignment explanation
Indices: 1409123--1409187 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 20
1409113 TTTTTCTGAT
1409123 TATCAGATATCTTTTTTTTTAC
1 TATCA-ATATC-TTTTTTTTAC
1409145 TATCAATATCTTTTGATTTTAC
1 TATCAATATCTTTT--TTTTAC
* *
1409167 TTTCTATATCTAGTTTTTTTA
1 TATCAATATCT--TTTTTTTA
1409188 TTTATTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 25 0.68
24 3 0.08
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (20 bp):
TATCAATATCTTTTTTTTAC
Found at i:1409497 original size:25 final size:25
Alignment explanation
Indices: 1409461--1409508 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1409451 TGAGGAGAAT
1409461 TTTTTCTAGAAATTT-TGGCGAAAAA
1 TTTTTCTAGAAATTTCTGG-GAAAAA
*
1409486 TTTTTCTGGAAATTTCTGGGAAA
1 TTTTTCTAGAAATTTCTGGGAAA
1409509 TTTCCAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTTTCTAGAAATTTCTGGGAAAAA
Found at i:1409552 original size:31 final size:31
Alignment explanation
Indices: 1409517--1409587 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1409507 AATTTCCAGA
* *
1409517 TTCCGGCGAAAAT-TCCGGCGAAA-CTTGAATT
1 TTCCGGC-AAAATCTCCGGC-AAACCTTAAAGT
*
1409548 TTCCGGCCAAATCTCCGGCAAACCTTAAAGT
1 TTCCGGCAAAATCTCCGGCAAACCTTAAAGT
1409579 TTCCGGCAA
1 TTCCGGCAA
1409588 CCTGCCCAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (31 bp):
TTCCGGCAAAATCTCCGGCAAACCTTAAAGT
Found at i:1409623 original size:20 final size:20
Alignment explanation
Indices: 1409600--1409643 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1409590 TGCCCAGTTT
1409600 CCGGAGAAGAATCCCAGAAA
1 CCGGAGAAGAATCCCAGAAA
* **
1409620 CCGGCGACTAATCCCAGAAA
1 CCGGAGAAGAATCCCAGAAA
1409640 CCGG
1 CCGG
1409644 CGAACTTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.32, G:0.25, T:0.07
Consensus pattern (20 bp):
CCGGAGAAGAATCCCAGAAA
Found at i:1409644 original size:20 final size:20
Alignment explanation
Indices: 1409609--1409646 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1409599 TCCGGAGAAG
1409609 AATCCCAGAAACCGGCGACT
1 AATCCCAGAAACCGGCGACT
1409629 AATCCCAGAAACCGGCGA
1 AATCCCAGAAACCGGCGA
1409647 ACTTCCGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.34, G:0.21, T:0.08
Consensus pattern (20 bp):
AATCCCAGAAACCGGCGACT
Found at i:1409682 original size:20 final size:20
Alignment explanation
Indices: 1409657--1409694 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1409647 ACTTCCGACG
*
1409657 AAATTTCCAGATTCCGGCGA
1 AAATTTCCAGAATCCGGCGA
1409677 AAATTTCCAGAATCCGGC
1 AAATTTCCAGAATCCGGC
1409695 ACCGGTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
AAATTTCCAGAATCCGGCGA
Found at i:1410048 original size:21 final size:20
Alignment explanation
Indices: 1410015--1410053 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1410005 CCGCTCCAGG
* *
1410015 TTTTTTTTTTTTTTTTTGAA
1 TTTTTTTTGTTTTATTTGAA
1410035 TTTTTATTTGTTTTATTTG
1 TTTTT-TTTGTTTTATTTG
1410054 TTTATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (20 bp):
TTTTTTTTGTTTTATTTGAA
Found at i:1410393 original size:60 final size:60
Alignment explanation
Indices: 1410185--1410584 Score: 565
Period size: 60 Copynumber: 6.7 Consensus size: 60
1410175 AAAGTTCCAA
*
1410185 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
* *
1410244 --AAAAAATACTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAATAAATTT-C
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
*
1410300 -AAAAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
*
1410357 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 -AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAATAAATTTCC
1410422 AAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCAAAATTT-C
1 AAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AAATTTCC
*
1410483 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AAATTTCC
1410544 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1410585 CTACAAAAAA
Statistics
Matches: 318, Mismatches: 9, Indels: 28
0.90 0.03 0.08
Matches are distributed among these distances:
56 45 0.14
57 61 0.19
59 50 0.16
60 87 0.27
61 11 0.03
62 6 0.02
63 2 0.01
64 8 0.03
65 48 0.15
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (60 bp):
AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
Found at i:1410446 original size:125 final size:118
Alignment explanation
Indices: 1410186--1410584 Score: 573
Period size: 125 Copynumber: 3.4 Consensus size: 118
1410176 AAGTTCCAAA
*
1410186 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC--AAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAA
* *
1410249 ATACTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAATAAATTT-C
66 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
*
1410300 AAAAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC-AAAAAA
*
1410364 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
65 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAATAAATTTCC
1410422 AAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCAAAATTT-CAA
1 -AAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCCAA
*
1410485 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTTC
61 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AAATTTCC
1410544 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1410585 CTACAAAAAA
Statistics
Matches: 260, Mismatches: 8, Indels: 29
0.88 0.03 0.10
Matches are distributed among these distances:
113 46 0.18
114 9 0.03
116 40 0.15
119 37 0.14
120 11 0.04
121 11 0.04
122 8 0.03
123 7 0.03
124 3 0.01
125 81 0.31
126 1 0.00
127 6 0.02
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (118 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAA
ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
Found at i:1415401 original size:16 final size:16
Alignment explanation
Indices: 1415377--1415447 Score: 60
Period size: 15 Copynumber: 4.7 Consensus size: 16
1415367 CCCTAAAACA
*
1415377 AAACCCTAAATCCTCT
1 AAACCCTAAAACCTCT
*
1415393 AAACTCTAAAACCTC-
1 AAACCCTAAAACCTCT
* * *
1415408 GAACCTTAAAA--TCG
1 AAACCCTAAAACCTCT
1415422 AAACCCTAAAACCTC-
1 AAACCCTAAAACCTCT
*
1415437 AAATCCTAAAA
1 AAACCCTAAAA
1415448 TTGAAACTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 9 0.20
15 18 0.41
16 15 0.34
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20
Consensus pattern (16 bp):
AAACCCTAAAACCTCT
Found at i:1415425 original size:29 final size:28
Alignment explanation
Indices: 1415393--1415481 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
1415383 TAAATCCTCT
*
1415393 AAACTCTAAAACCTCGAACCTTAAAATCG
1 AAACTCTAAAACCTCAAACC-TAAAATCG
* *
1415422 AAACCCTAAAACCTCAAATCCTAAAATTG
1 AAACTCTAAAACCTCAAA-CCTAAAATCG
* *
1415451 AAACTC-CAAATCTCAAACCCTAAAATC-
1 AAACTCTAAAACCTCAAA-CCTAAAATCG
1415478 AAAC
1 AAAC
1415482 CCTCCAAACC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.08
28 17 0.33
29 28 0.55
30 2 0.04
ACGTcount: A:0.48, C:0.29, G:0.03, T:0.19
Consensus pattern (28 bp):
AAACTCTAAAACCTCAAACCTAAAATCG
Found at i:1415431 original size:14 final size:13
Alignment explanation
Indices: 1415409--1415612 Score: 69
Period size: 14 Copynumber: 14.8 Consensus size: 13
1415399 TAAAACCTCG
*
1415409 AACCTTAAAATCGA
1 AACCCTAAAATC-A
1415423 AACCCTAAAACCTCA
1 AACCCTAAAA--TCA
* *
1415438 AATCCTAAAATTGA
1 AACCCTAAAA-TCA
*
1415452 AACTCC-AAATCTCA
1 AAC-CCTAAA-ATCA
1415466 AACCCTAAAATCA
1 AACCCTAAAATCA
*
1415479 AACCCT----CCA
1 AACCCTAAAATCA
*
1415488 AACCTTAAAATTCA
1 AACCCTAAAA-TCA
*
1415502 AACCCTAAAATTA
1 AACCCTAAAATCA
* *
1415515 AAACCTTAAATCTTTTA
1 AACCCTAAAATC----A
1415532 AACCCTAAAATCAA
1 AACCCTAAAATC-A
***
1415546 AACCCTAATCCCCA
1 AACCCTAA-AATCA
1415560 AACCCT-AAATCAA
1 AACCCTAAAATC-A
* *
1415573 AACCTTAAACTTTCCA
1 AACCCTAAA--AT-CA
1415589 AACCCTAAAATTCA
1 AACCCTAAAA-TCA
*
1415603 AGCCCTAAAA
1 AACCCTAAAA
1415613 ACCTTAAAAC
Statistics
Matches: 139, Mismatches: 30, Indels: 42
0.66 0.14 0.20
Matches are distributed among these distances:
9 7 0.05
12 1 0.01
13 29 0.21
14 64 0.46
15 14 0.10
16 12 0.09
17 12 0.09
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (13 bp):
AACCCTAAAATCA
Found at i:1415489 original size:22 final size:23
Alignment explanation
Indices: 1415464--1415507 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1415454 CTCCAAATCT
1415464 CAAACCCTAAAA-TCAAACCCTC
1 CAAACCCTAAAATTCAAACCCTC
*
1415486 CAAACCTTAAAATTCAAACCCT
1 CAAACCCTAAAATTCAAACCCT
1415508 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (23 bp):
CAAACCCTAAAATTCAAACCCTC
Found at i:1416344 original size:5 final size:5
Alignment explanation
Indices: 1416336--1416388 Score: 74
Period size: 5 Copynumber: 10.6 Consensus size: 5
1416326 CTAAAAAAGA
1416336 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAAC AAAA- AACAA- AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AAAAC AAAAC AA-AAC AAAAC
1416386 AAA
1 AAA
1416389 CTTTTGAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.09
5 36 0.80
6 5 0.11
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:1417593 original size:8 final size:9
Alignment explanation
Indices: 1417568--1417592 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1417558 CTATTCAGGT
1417568 ATTTTTTTA
1 ATTTTTTTA
1417577 ATTTTTTTA
1 ATTTTTTTA
1417586 ATTTTTT
1 ATTTTTT
1417593 ATATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:1417615 original size:26 final size:26
Alignment explanation
Indices: 1417580--1417629 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1417570 TTTTTTAATT
* *
1417580 TTTTTAATTTT-TTATATATTATTTTA
1 TTTTAAATTTTATTAT-TAATATTTTA
1417606 TTTTAAATTTTATTATTAATATTT
1 TTTTAAATTTTATTATTAATATTT
1417630 ATGCATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTTAAATTTTATTATTAATATTTTA
Found at i:1417878 original size:27 final size:27
Alignment explanation
Indices: 1417848--1417905 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
1417838 TGTAAAAAGT
1417848 ATAAAAAAGAT-AATAAATAATAA-AACA
1 ATAAAAAA-ATCAAT-AATAATAATAACA
* *
1417875 ATAATAAAATCAATATTAATAATAACA
1 ATAAAAAAATCAATAATAATAATAACA
1417902 ATAA
1 ATAA
1417906 TAAATTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (27 bp):
ATAAAAAAATCAATAATAATAATAACA
Found at i:1417903 original size:15 final size:15
Alignment explanation
Indices: 1417863--1417908 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 15
1417853 AAAGATAATA
1417863 AATAATAA-AACAAT
1 AATAATAATAACAAT
1417877 AATAA-AAT--CAAT
1 AATAATAATAACAAT
*
1417889 ATTAATAATAACAAT
1 AATAATAATAACAAT
1417904 AATAA
1 AATAA
1417909 ATTTTCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 8 0.31
13 5 0.19
14 5 0.19
15 8 0.31
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:1418221 original size:20 final size:20
Alignment explanation
Indices: 1418169--1418234 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
1418159 TCAAAACCAT
*
1418169 AAACCCTAAATTCTAAAACCTC
1 AAACCCTAAATCCTAAAA--TC
*
1418191 GAAACCTTAAATCCTAAAATC
1 -AAACCCTAAATCCTAAAATC
*
1418212 AAACCCTAAATCCTAAAACC
1 AAACCCTAAATCCTAAAATC
1418232 AAA
1 AAA
1418235 AACCTCAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 21 0.54
21 2 0.05
23 16 0.41
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.20
Consensus pattern (20 bp):
AAACCCTAAATCCTAAAATC
Found at i:1420069 original size:17 final size:19
Alignment explanation
Indices: 1420042--1420080 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1420032 AAATATTAAA
1420042 TTTAATATTTTTAAA-TAT
1 TTTAATATTTTTAAAGTAT
1420060 TTTAAT-TTTTTAAAGTAT
1 TTTAATATTTTTAAAGTAT
1420078 TTT
1 TTT
1420081 TTTTGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTAATATTTTTAAAGTAT
Found at i:1421534 original size:21 final size:20
Alignment explanation
Indices: 1421506--1421550 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
1421496 TTTTTAATTT
*
1421506 TAAAAAATATAACTATTATA
1 TAAAAAATATAAATATTATA
1421526 TAAAGAAATATAAATATTATA
1 TAAA-AAATATAAATATTATA
1421547 TAAA
1 TAAA
1421551 TCCTATAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAAATATAAATATTATA
Found at i:1422920 original size:19 final size:18
Alignment explanation
Indices: 1422875--1422925 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1422865 ACAAATAAGT
*
1422875 AACAAAATAAAAAAAGCAA
1 AACAAAA-ATAAAAAGCAA
*
1422894 AACAAAAATAAAAAGGAA
1 AACAAAAATAAAAAGCAA
*
1422912 AATATAAAATAAAA
1 AACA-AAAATAAAA
1422926 CTAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (18 bp):
AACAAAAATAAAAAGCAA
Found at i:1422920 original size:25 final size:24
Alignment explanation
Indices: 1422892--1422939 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1422882 TAAAAAAAGC
1422892 AAAACAAAAATAAAAAGGAAAATAT
1 AAAACAAAAATAAAAA-GAAAATAT
* * *
1422917 AAAATAAAACTAGAAAGAAAATA
1 AAAACAAAAATAAAAAGAAAATA
1422940 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.12
Consensus pattern (24 bp):
AAAACAAAAATAAAAAGAAAATAT
Found at i:1425921 original size:4 final size:4
Alignment explanation
Indices: 1425912--1425940 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1425902 CTCTTATATC
1425912 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1425941 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1432655 original size:17 final size:17
Alignment explanation
Indices: 1432633--1432666 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1432623 TCTGATCATT
1432633 GTTTTTAACCAACCTTC
1 GTTTTTAACCAACCTTC
1432650 GTTTTTAACCAACCTTC
1 GTTTTTAACCAACCTTC
1432667 AAACTTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (17 bp):
GTTTTTAACCAACCTTC
Found at i:1433564 original size:29 final size:26
Alignment explanation
Indices: 1433506--1433576 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 26
1433496 TTTATTTTAC
1433506 ATATATATAAAATAAAAATAAAAATA
1 ATATATATAAAATAAAAATAAAAATA
1433532 ATATATATAAAAATTTAAAAATAAAAAT-
1 ATATATAT-AAAA--TAAAAATAAAAATA
*
1433560 -TATATA-AAAGTAAAAAT
1 ATATATATAAAATAAAAAT
1433577 TAAGTTTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 7 0.17
25 3 0.07
26 8 0.20
27 10 0.24
29 13 0.32
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (26 bp):
ATATATATAAAATAAAAATAAAAATA
Found at i:1433573 original size:23 final size:21
Alignment explanation
Indices: 1433517--1433576 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
1433507 TATATATAAA
*
1433517 ATAAAAATAAAAATAATATAT
1 ATAAAAATAAAAATAAAATAT
1433538 ATAAAAATTTAAAAATAAAAATTAT
1 ATAAAAA--TAAAAAT-AAAA-TAT
*
1433563 ATAAAAGTAAAAAT
1 ATAAAAATAAAAAT
1433577 TAAGTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.21
23 14 0.42
24 3 0.09
25 9 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAAAAATAAAAATAAAATAT
Found at i:1435063 original size:11 final size:10
Alignment explanation
Indices: 1435031--1435057 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1435021 GCATTTAAAG
1435031 AAAAATTCTA
1 AAAAATTCTA
1435041 AAAAATTCTA
1 AAAAATTCTA
1435051 AAAAATT
1 AAAAATT
1435058 TTTAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:1435126 original size:10 final size:10
Alignment explanation
Indices: 1435105--1435144 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1435095 TCTAAACCTC
1435105 TTAAAAAGTTT
1 TTAAAAA-TTT
1435116 TTAAAAATTT
1 TTAAAAATTT
1435126 TTAAAAA-TT
1 TTAAAAATTT
1435135 TT-AAAATTT
1 TTAAAAATTT
1435144 T
1 T
1435145 AAATAAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.14
9 7 0.25
10 10 0.36
11 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
TTAAAAATTT
Found at i:1435157 original size:37 final size:35
Alignment explanation
Indices: 1435116--1435208 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 35
1435106 TAAAAAGTTT
* ** *
1435116 TTAAAAATTTTTAAAAATTTTAAAATTTTAAATAAGA
1 TTAAAAATTTTAAAAAAAATCAAAATTTTAAA-AA-A
* *
1435153 TTAAAAATATTCAAAAAAATCAAAATTTTAAAAAA
1 TTAAAAATTTTAAAAAAAATCAAAATTTTAAAAAA
*
1435188 TCTAAAAAATTTAAAAAAAAT
1 T-TAAAAATTTTAAAAAAAAT
1435209 TGAAAAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
35 2 0.04
36 18 0.38
37 27 0.57
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (35 bp):
TTAAAAATTTTAAAAAAAATCAAAATTTTAAAAAA
Found at i:1435177 original size:18 final size:18
Alignment explanation
Indices: 1435156--1435225 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 18
1435146 AATAAGATTA
1435156 AAAATATTCAAAAAAATC-
1 AAAATATT-AAAAAAATCT
*
1435174 AAAAT-TTTAAAAAATCT
1 AAAATATTAAAAAAATCT
*
1435191 AAAAAATTTAAAAAAAAT-T
1 AAAATA-TT-AAAAAAATCT
1435210 GAAAA-ATTAAAAAAAT
1 -AAAATATTAAAAAAAT
1435226 GAAGATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 8 0.18
17 14 0.32
18 7 0.16
19 4 0.09
20 11 0.25
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (18 bp):
AAAATATTAAAAAAATCT
Found at i:1435205 original size:9 final size:9
Alignment explanation
Indices: 1435115--1435225 Score: 64
Period size: 9 Copynumber: 12.1 Consensus size: 9
1435105 TTAAAAAGTT
*
1435115 TTTAAAAAT
1 TTTAAAAAA
*
1435124 TTTTAAAAA
1 TTTAAAAAA
* *
1435133 TTTTAAAAT
1 TTTAAAAAA
1435142 TTTAAATAAGA
1 TTTAAA-AA-A
1435153 -TTAAAAATA
1 TTTAAAAA-A
*
1435162 TTCAAAAAA
1 TTTAAAAAA
* * *
1435171 -ATCAAAAT
1 TTTAAAAAA
1435179 TTTAAAAAA
1 TTTAAAAAA
*
1435188 TCTAAAAAA
1 TTTAAAAAA
1435197 TTTAAAAAAA
1 TTT-AAAAAA
* *
1435207 ATTGAAAAA
1 TTTAAAAAA
*
1435216 TTAAAAAAA
1 TTTAAAAAA
1435225 T
1 T
1435226 GAAGATTTAA
Statistics
Matches: 76, Mismatches: 21, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
8 4 0.05
9 51 0.67
10 21 0.28
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:1435222 original size:19 final size:20
Alignment explanation
Indices: 1435182--1435224 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1435172 TCAAAATTTT
*
1435182 AAAAAATCTAAAAAATTTAA
1 AAAAAATCTAAAAAATTAAA
*
1435202 AAAAAAT-TGAAAAATTAAA
1 AAAAAATCTAAAAAATTAAA
1435221 AAAA
1 AAAA
1435225 TGAAGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAAATCTAAAAAATTAAA
Found at i:1438598 original size:19 final size:19
Alignment explanation
Indices: 1438559--1438604 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1438549 AGGCTAACAT
1438559 AATATTTTAAAAAACTAAA
1 AATATTTTAAAAAACTAAA
* *
1438578 AA-ATTTCTAAAAAATTCAA
1 AATATTT-TAAAAAACTAAA
1438597 AATATTTT
1 AATATTTT
1438605 TTGTATTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATTTTAAAAAACTAAA
Found at i:1459504 original size:21 final size:21
Alignment explanation
Indices: 1459461--1459504 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1459451 TTAGACTTTT
* *
1459461 AATTTTAATAATTATGATTTA
1 AATTTTAATAATTATAATATA
* *
1459482 AATTTTGATAATTTTAATATA
1 AATTTTAATAATTATAATATA
1459503 AA
1 AA
1459505 AATATAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
AATTTTAATAATTATAATATA
Found at i:1459634 original size:5 final size:5
Alignment explanation
Indices: 1459624--1459649 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1459614 TTTTAAGGGA
1459624 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
1459650 CAAAGAGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1462638 original size:18 final size:18
Alignment explanation
Indices: 1462615--1462655 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1462605 CAGAAAGAAT
1462615 ACAATGAAAATTGGGAAA
1 ACAATGAAAATTGGGAAA
1462633 ACAATGAAAATTGGGAAA
1 ACAATGAAAATTGGGAAA
*
1462651 GCAAT
1 ACAAT
1462656 TGGAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (18 bp):
ACAATGAAAATTGGGAAA
Found at i:1469148 original size:11 final size:12
Alignment explanation
Indices: 1469124--1469170 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1469114 TCTAAATGCT
1469124 AAAATAATAATA
1 AAAATAATAATA
*
1469136 AAAATAA-ACTA
1 AAAATAATAATA
*
1469147 AAAATTATAATA
1 AAAATAATAATA
*
1469159 AGAATAA-AATA
1 AAAATAATAATA
1469170 A
1 A
1469171 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 14 0.48
12 15 0.52
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1469535 original size:29 final size:28
Alignment explanation
Indices: 1469473--1469547 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
1469463 TCTAAACCTT
*
1469473 AAACCCTCAAAA-CCTAAAATTTAAAATCT
1 AAACCCT-AAAATCC-AAAATTTAAAATCA
* *
1469502 TAACCCTAAAATCCAAATTTTAAAATTCA
1 AAACCCTAAAATCCAAAATTTAAAA-TCA
1469531 AAACCCTAAAATCCAAA
1 AAACCCTAAAATCCAAA
1469548 CCCCAAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 14 0.35
29 26 0.65
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACCCTAAAATCCAAAATTTAAAATCA
Found at i:1469548 original size:14 final size:14
Alignment explanation
Indices: 1469503--1469555 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1469493 TTAAAATCTT
1469503 AACCCTAAAATCCA
1 AACCCTAAAATCCA
*** *
1469517 AATTTTAAAATTCAA
1 AACCCTAAAA-TCCA
1469532 AACCCTAAAATCCA
1 AACCCTAAAATCCA
*
1469546 AACCCCAAAA
1 AACCCTAAAA
1469556 CTTTCGAAAC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCTAAAATCCA
Found at i:1469640 original size:14 final size:14
Alignment explanation
Indices: 1469607--1469669 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
1469597 CAAAACCCCA
* *
1469607 TAAAACCCAAACCC
1 TAAAATCCAAATCC
*
1469621 TTAAATCCAAATCC
1 TAAAATCCAAATCC
*
1469635 TAAAATCCAAAACC
1 TAAAATCCAAATCC
* *
1469649 TTAAAATTCTAAATTC
1 -TAAAA-TCCAAATCC
1469665 TAAAA
1 TAAAA
1469670 ACCCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 23 0.59
15 10 0.26
16 6 0.15
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATCCAAATCC
Found at i:1471650 original size:3 final size:3
Alignment explanation
Indices: 1471642--1471683 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1471632 ATAAAATTTG
1471642 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1471684 AGACTAAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1471756 original size:3 final size:3
Alignment explanation
Indices: 1471748--1471796 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1471738 TGCGTCATGC
* *
1471748 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1471796 A
1 A
1471797 CTATTATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1471804 original size:3 final size:3
Alignment explanation
Indices: 1471798--1471846 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1471788 ATAGTAATAC
*
1471798 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1471846 T
1 T
1471847 GCATGACGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1473302 original size:16 final size:16
Alignment explanation
Indices: 1473283--1473317 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1473273 ACAAATTGGG
*
1473283 TTAGTCTTAAATTATA
1 TTAGTCTTAAATTAGA
1473299 TTAGTCTTAAATTAGA
1 TTAGTCTTAAATTAGA
1473315 TTA
1 TTA
1473318 TAAGCTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (16 bp):
TTAGTCTTAAATTAGA
Found at i:1480646 original size:22 final size:22
Alignment explanation
Indices: 1480600--1480646 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1480590 AATTTAAAAT
* * *
1480600 TTTAATAAAAATTATATATAAA
1 TTTAATAAAAATAAAAAATAAA
*
1480622 TTTAATAAAAATAAAAAATATA
1 TTTAATAAAAATAAAAAATAAA
1480644 TTT
1 TTT
1480647 TAGATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATAAA
Found at i:1481209 original size:14 final size:14
Alignment explanation
Indices: 1481190--1481231 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1481180 CATTTGAATA
*
1481190 TAAATTATTTAATT
1 TAAATTATTAAATT
1481204 TAAATT-TTGAAATT
1 TAAATTATT-AAATT
1481218 T-AATTATTAAATT
1 TAAATTATTAAATT
1481231 T
1 T
1481232 TAACATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TAAATTATTAAATT
Found at i:1481893 original size:27 final size:26
Alignment explanation
Indices: 1481845--1481898 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1481835 ATTAATTAAA
**
1481845 ATTAATATATTTTTATTTAAAACATAT
1 ATTAATATATTTTTATACAAAA-ATAT
1481872 ATTAATAT-TTATTTATACAAAAATAT
1 ATTAATATATT-TTTATACAAAAATAT
1481898 A
1 A
1481899 AAATTTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTAATATATTTTTATACAAAAATAT
Found at i:1483526 original size:2 final size:2
Alignment explanation
Indices: 1483519--1483549 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1483509 ACTCATATTG
1483519 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1483550 CTTGAAGGAT
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):
AT
Found at i:1483799 original size:20 final size:20
Alignment explanation
Indices: 1483776--1483823 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1483766 TCGATATAAA
1483776 AATTATAAAATATAT-ATTTT
1 AATTA-AAAATATATAATTTT
*
1483796 AATTAAATATATATAATTTT
1 AATTAAAAATATATAATTTT
*
1483816 TATTAAAA
1 AATTAAAA
1483824 TTTTAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAAAAATATATAATTTT
Found at i:1483809 original size:19 final size:19
Alignment explanation
Indices: 1483781--1483824 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1483771 ATAAAAATTA
1483781 TAAAATATAT-ATTTTAAT
1 TAAAATATATAATTTTAAT
*
1483799 TAAATATATATAATTTTTAT
1 TAAA-ATATATAATTTTAAT
1483819 TAAAAT
1 TAAAAT
1483825 TTTAAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAATATATAATTTTAAT
Found at i:1485532 original size:2 final size:2
Alignment explanation
Indices: 1485527--1485553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1485517 TGTGTGTGTG
1485527 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 T
1485554 TCTTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1487206 original size:2 final size:2
Alignment explanation
Indices: 1487199--1487233 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1487189 ACATACATAC
1487199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1487234 AAAGATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1488667 original size:19 final size:20
Alignment explanation
Indices: 1488631--1488668 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1488621 AATCCGATCT
1488631 AAAATATTATTATATTAATA
1 AAAATATTATTATATTAATA
*
1488651 AAAATATTTTTAT-TTAAT
1 AAAATATTATTATATTAAT
1488669 TTTAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATATTATTATATTAATA
Found at i:1488828 original size:53 final size:51
Alignment explanation
Indices: 1488732--1488831 Score: 130
Period size: 53 Copynumber: 1.9 Consensus size: 51
1488722 ACATATTTCT
* * *
1488732 ATTTTAAATATTATAATGTTAATATAATATTATTTTAAGAATAATAATACA
1 ATTTTAAATATTAAAATGTTAATATAATATGATATTAAGAATAATAATACA
*
1488783 ATTTTAAATATTTTAAAATGTTAATATAA-ATAGATATTAATAATAATAA
1 ATTTTAAATA--TTAAAATGTTAATATAATAT-GATATTAAGAATAATAA
1488832 ATAGTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 10 0.24
52 2 0.05
53 30 0.71
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (51 bp):
ATTTTAAATATTAAAATGTTAATATAATATGATATTAAGAATAATAATACA
Found at i:1489165 original size:2 final size:2
Alignment explanation
Indices: 1489158--1489191 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1489148 AAGATATAAG
* *
1489158 AT AT AT AT AT AT AT AT AT AT AT GT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1489192 GCATGAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1491006 original size:23 final size:23
Alignment explanation
Indices: 1490979--1491040 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
1490969 AAATCTTTAC
1490979 GTAAAAACAAAGCAATATTTGAT
1 GTAAAAACAAAGCAATATTTGAT
1491002 GTAAAAACAAAGCAATATTTGAT
1 GTAAAAACAAAGCAATATTTGAT
1491025 GTAAAAACAAAGCAAT
1 GTAAAAACAAAGCAAT
1491041 TTGCTTATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.23
Consensus pattern (23 bp):
GTAAAAACAAAGCAATATTTGAT
Found at i:1493397 original size:190 final size:193
Alignment explanation
Indices: 1493095--1493530 Score: 519
Period size: 190 Copynumber: 2.3 Consensus size: 193
1493085 AAAATCTCAA
** ** * *
1493095 TCTCAAA-TTTTAAACACTATATTATTGCATATGTA-TATGTGTTGGTGAATTTGTGTTGAAATT
1 TCTCAAACTTTTAAACAAAATATTATTATATATGTACT-TGTGTTGGAGAATTTATGTTGAAATT
* * * *
1493158 TTGTATTCATGTTGCTTACTTTCTTTGGATTGAAATGGGTAAATTTTTTTTTATTTATTTGAACT
65 TTGTATT-ATGTTGCTTACTTTCTTTGGACTAAAATGGGCAAATTTTTTTTTATTTATTTAAACT
** * * *
1493223 AGAAATAGGAATTTTTTTATTATTGCAATAAAAGTATAAG-CACAAACTAAAATATCAAAGCATA
129 AGAAATAGGAATTTCATTATTATTGCAACAAAAGCAT-AGTCACAAACTAAAATATCAAAGCAAA
1493287 T
193 T
** * *
1493288 TCTTTAAC-TTTAAATAAAATATTATTATATATGTACTTGTATTGGAGAATTTATGTTGAAA-TT
1 TCTCAAACTTTTAAACAAAATATTATTATATATGTACTTGTGTTGGAGAATTTATGTTGAAATTT
* * *
1493351 T-TATGT-TGTTGCTTACTTTTTTTGGACTAAAATGGGCAATTTTTTTTTTGTTTATTTAAACTA
66 TGTAT-TATGTTGCTTACTTTCTTTGGACTAAAATGGGCAAATTTTTTTTTATTTATTTAAACTA
* * * * *
1493414 GAAATAGGCATTTCATTGTTATTGCAACAAAAGCATAGTCTCAAAGTAAAATCTCAAAGCAAAT
130 GAAATAGGAATTTCATTATTATTGCAACAAAAGCATAGTCACAAACTAAAATATCAAAGCAAAT
*
1493478 TCTCAAACTTTTAAACAAAATATTATTACT-TATGTACTTTTGTTGGAGAATTT
1 TCTCAAACTTTTAAACAAAATATTATTA-TATATGTACTTGTGTTGGAGAATTT
1493531 GTTGAGTAAA
Statistics
Matches: 205, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
189 2 0.01
190 107 0.52
191 42 0.20
192 5 0.02
193 48 0.23
194 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (193 bp):
TCTCAAACTTTTAAACAAAATATTATTATATATGTACTTGTGTTGGAGAATTTATGTTGAAATTT
TGTATTATGTTGCTTACTTTCTTTGGACTAAAATGGGCAAATTTTTTTTTATTTATTTAAACTAG
AAATAGGAATTTCATTATTATTGCAACAAAAGCATAGTCACAAACTAAAATATCAAAGCAAAT
Found at i:1494765 original size:3 final size:3
Alignment explanation
Indices: 1494757--1494802 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1494747 CAATAAGATA
1494757 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1494803 AGAAGAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1497474 original size:86 final size:86
Alignment explanation
Indices: 1497333--1497493 Score: 227
Period size: 86 Copynumber: 1.9 Consensus size: 86
1497323 CATTTTTGAT
* **
1497333 AGCCTTAAATGCATCTTGAAAATGGATTTTCAAAAAGCCTAAAAGGATCTTGAAAATGCATTTAC
1 AGCCTTAAATGCATCTAGAAAATGGATTGCCAAAAAGCCTAAAAGGATCTTGAAAATGCATTTAC
1497398 AAAGGGTTATCCATTTCTAAA
66 AAAGGGTTATCCATTTCTAAA
* *
1497419 AGCCTTAAATGCTTCTCAG-AAATGGATTGCCAAGAAGCCTAAAAGGAT-TTCGAAAATGCATTT
1 AGCCTTAAATGCATCT-AGAAAATGGATTGCCAAAAAGCCTAAAAGGATCTT-GAAAATGCATTT
* *
1497482 CCAAGGGGTTAT
64 ACAAAGGGTTAT
1497494 TAATTTATGA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
85 2 0.03
86 63 0.95
87 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (86 bp):
AGCCTTAAATGCATCTAGAAAATGGATTGCCAAAAAGCCTAAAAGGATCTTGAAAATGCATTTAC
AAAGGGTTATCCATTTCTAAA
Found at i:1497539 original size:86 final size:86
Alignment explanation
Indices: 1497350--1497549 Score: 226
Period size: 86 Copynumber: 2.3 Consensus size: 86
1497340 AATGCATCTT
* * *
1497350 GAAAATGGATTTTCAAAAAGCCTAAAAGGATCTTGAAAATGCATTTACAAAGGGTTATCCATTTC
1 GAAAATGGATTTTCAAGAAGCCTAAAAGGATCTTGAAAATGCATTTACAAAGGGTTATCAATTTA
* *
1497415 TAAAAGCCTTAAATGCTTCTC
66 TAAAAGCCTTAAAGGCTTATC
** * * *
1497436 -AGAAATGGATTGCCAAGAAGCCTAAAAGGAT-TTCGAAAATGCATTTCCAAGGGGTTATTAATT
1 GA-AAATGGATTTTCAAGAAGCCTAAAAGGATCTT-GAAAATGCATTTACAAAGGGTTATCAATT
* * *
1497499 TATGAGAGCTTTAAAGGCTTATC
64 TATAAAAGCCTTAAAGGCTTATC
* *
1497522 GAAAATGCATTTTCAAG-AGCCTTAAAGG
1 GAAAATGGATTTTCAAGAAGCCTAAAAGG
1497550 CTTCCTGACA
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
85 13 0.14
86 80 0.85
87 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (86 bp):
GAAAATGGATTTTCAAGAAGCCTAAAAGGATCTTGAAAATGCATTTACAAAGGGTTATCAATTTA
TAAAAGCCTTAAAGGCTTATC
Found at i:1501417 original size:200 final size:200
Alignment explanation
Indices: 1501074--1501472 Score: 647
Period size: 200 Copynumber: 2.0 Consensus size: 200
1501064 AAAACTTCAT
* * * * * * *
1501074 CAAAGAAATGTATTATAAATTTTAGGGTCTAAGATGATGTAGCTAGATATGAGACATTGTAACTT
1 CAAAGAAATGTATCATAAATTCTAGGGTCCAAGATAATGCAACTAGATATGAGACATTATAACTT
*
1501139 TTGATCACCAGAATTATGATGAAACTATAACTATATATCAACTTAATTTGTTTAATAGATATTGT
66 TTGATCACCAGAATTATGATGAAACTATAACTATATATCAACTTAATTTATTTAATAGATATTGT
*
1501204 TTTCATGCACTTAGTTGCCTAACTTTAAACCCCTATGTATTTTTTATCAAAATAATAGATGATTT
131 TTTCATGCACTTAGTTGCCTAACTTTAAACCCCTATGTATTTTTTATCAAAAGAATAGATGATTT
1501269 CATTA
196 CATTA
*
1501274 CAAAGAAATGTGTCATAAATTCTAGGGTCCAAGATAATGCAACTAGATATGAGACATTATAACTT
1 CAAAGAAATGTATCATAAATTCTAGGGTCCAAGATAATGCAACTAGATATGAGACATTATAACTT
* *
1501339 TTGATCACCAGAATTATGATGAAACTATGACTATATATCAGCTTAATTTATTTAATAGATATTG-
66 TTGATCACCAGAATTATGATGAAACTATAACTATATATCAACTTAATTTATTTAATAGATATTGT
* * *
1501403 TTTCTATGCACTTAGTTGCCTAATTTTAAATCCTTATGTATTTTTTATCAAAAGAATAGATGATT
131 TTTC-ATGCACTTAGTTGCCTAACTTTAAACCCCTATGTATTTTTTATCAAAAGAATAGATGATT
1501468 TCATT
195 TCATT
1501473 TTAGATATTA
Statistics
Matches: 183, Mismatches: 15, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
199 4 0.02
200 179 0.98
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (200 bp):
CAAAGAAATGTATCATAAATTCTAGGGTCCAAGATAATGCAACTAGATATGAGACATTATAACTT
TTGATCACCAGAATTATGATGAAACTATAACTATATATCAACTTAATTTATTTAATAGATATTGT
TTTCATGCACTTAGTTGCCTAACTTTAAACCCCTATGTATTTTTTATCAAAAGAATAGATGATTT
CATTA
Found at i:1503075 original size:20 final size:19
Alignment explanation
Indices: 1503050--1503099 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1503040 TTTTCTTTTT
1503050 TTTTTAATATTTAATAAATA
1 TTTTTAATATTTAA-AAATA
* * *
1503070 TTTTTAAAGATTTTAAAATT
1 TTTTT-AATATTTAAAAATA
1503090 TTTTTAATAT
1 TTTTTAATAT
1503100 GGTGCCTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.16
20 14 0.56
21 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTAATATTTAAAAATA
Found at i:1504160 original size:29 final size:29
Alignment explanation
Indices: 1504128--1504187 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1504118 CATTTTATAT
*
1504128 TTATATATAT-TATTATTTTAATAAAATTA
1 TTATATA-ATGTATTATTTTAATAAAAATA
* * *
1504157 TTATTTAATGTCTTATTTTATTAAAAATA
1 TTATATAATGTATTATTTTAATAAAAATA
1504186 TT
1 TT
1504188 TTATTTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATATAATGTATTATTTTAATAAAAATA
Found at i:1505091 original size:21 final size:22
Alignment explanation
Indices: 1505058--1505098 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1505048 TGAAGTTATT
*
1505058 ATTTAATATTTTAAATTCAAAA
1 ATTTAATATTTTAAACTCAAAA
1505080 ATTTAA-ATTTTAAACTCAA
1 ATTTAATATTTTAAACTCAA
1505099 TTTGGATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTAATATTTTAAACTCAAAA
Found at i:1513912 original size:24 final size:22
Alignment explanation
Indices: 1513884--1513928 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1513874 TAAAAAATTA
*
1513884 TTTAATATACTATTAGTGAGATTT
1 TTTAA-AT-CTATAAGTGAGATTT
*
1513908 TTTAACTCTATAAGTGAGATT
1 TTTAAATCTATAAGTGAGATT
1513929 AAAATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 1 0.05
24 5 0.26
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (22 bp):
TTTAAATCTATAAGTGAGATTT
Found at i:1519394 original size:34 final size:34
Alignment explanation
Indices: 1519351--1519419 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1519341 TATGTAGGCT
*
1519351 ATTTTAAATTATTTAGTGTTATACTTATTTTCTA
1 ATTTTAAATTATTTAGAGTTATACTTATTTTCTA
*
1519385 ATTTTAAATTATTTGGAGTTATACTTATTTTCTA
1 ATTTTAAATTATTTAGAGTTATACTTATTTTCTA
1519419 A
1 A
1519420 GTATTAGGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (34 bp):
ATTTTAAATTATTTAGAGTTATACTTATTTTCTA
Found at i:1524009 original size:4 final size:4
Alignment explanation
Indices: 1524000--1524025 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1523990 CCACAACCTT
1524000 AACA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AA
1524026 AGAAGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:1524042 original size:6 final size:6
Alignment explanation
Indices: 1524031--1524060 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1524021 ACAAAAGAAG
1524031 ATGAAC ATGAAC ATGAAC ATGAAC AATGAA
1 ATGAAC ATGAAC ATGAAC ATGAAC -ATGAA
1524061 GAATAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGAAC
Found at i:1526464 original size:20 final size:20
Alignment explanation
Indices: 1526439--1526479 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1526429 TTTTGTTAAG
* *
1526439 TTAAAAAAATTTAAATTATA
1 TTAAAAAAACTAAAATTATA
*
1526459 TTAAAAATACTAAAATTATA
1 TTAAAAAAACTAAAATTATA
1526479 T
1 T
1526480 AATTCTTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAAAAACTAAAATTATA
Found at i:1526974 original size:20 final size:20
Alignment explanation
Indices: 1526951--1526992 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1526941 TTCAAATGGT
1526951 TTTGGTTTTATAGAGTTGAA
1 TTTGGTTTTATAGAGTTGAA
1526971 TTTGGTTTTATAGAGTTGAA
1 TTTGGTTTTATAGAGTTGAA
1526991 TT
1 TT
1526993 ATTGAATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (20 bp):
TTTGGTTTTATAGAGTTGAA
Found at i:1532850 original size:19 final size:19
Alignment explanation
Indices: 1532826--1532870 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
1532816 TAAGTATAAG
1532826 AAAATATAAGCAAAA-CAAC
1 AAAATATAAG-AAAATCAAC
*
1532845 -AAA-ATAAGAAAATGAAC
1 AAAATATAAGAAAATCAAC
1532862 AAAATATAA
1 AAAATATAA
1532871 AATGTGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.18
17 8 0.36
18 6 0.27
19 4 0.18
ACGTcount: A:0.71, C:0.09, G:0.07, T:0.13
Consensus pattern (19 bp):
AAAATATAAGAAAATCAAC
Found at i:1552440 original size:16 final size:18
Alignment explanation
Indices: 1552405--1552440 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1552395 TTTTGCATCT
1552405 AACATAGCTCGATGTGTA
1 AACATAGCTCGATGTGTA
1552423 AACATAGCT-GAT-TGTA
1 AACATAGCTCGATGTGTA
1552439 AA
1 AA
1552441 TTTTATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 9 0.50
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (18 bp):
AACATAGCTCGATGTGTA
Found at i:1556062 original size:157 final size:155
Alignment explanation
Indices: 1555719--1556342 Score: 555
Period size: 158 Copynumber: 4.0 Consensus size: 155
1555709 GTCTTTAGGT
* * *
1555719 CTTTGTGA--TTGGTCATGTATTGTAATTGTTGATGAACTACTTTTATAATAATTGAAAGCCTAA
1 CTTTGTGATTTTGGTTATGTATTGTAATTGTTGATGAACTACTTTTATAGTAATTCAAAGCCTAA
* * * * * * * ** * *
1555782 AATTTGTAAGAAAGTCTTTATTGAACTAGATAATACATTATGTATATTACGATACAATGACTTTG
66 AAATTATAGGAAATTCATTATTGAACTAAATAGTATTTTATGCATATTAAGATACAAT-A-TTTG
*
1555847 TGAAAGGTGAAAACTATTTTGTATTTTG
129 TGAAA-GTGAAAACTATTATGTATTTTG
* * * * * * *
1555875 CTATGTGATTATGGATGTGTATTGT-GTTGTTAATGAACTA-TCTTTATAGTAATTCAAAACCTA
1 CTTTGTGATTTTGGTTATGTATTGTAATTGTTGATGAACTACT-TTTATAGTAATTCAAAGCCT-
* * * *
1555938 AAAAATTGTAGGAAATTCAGTATTGAACTAAATAGTATTTTATGCATATTAAGATGCAATAATTG
64 AAAAATTATAGGAAATTCATTATTGAACTAAATAGTATTTTATGCATATTAAGATACAATATTTG
1556003 TGCAAAGTGATAAA-TATTATGTATTTTG
129 TG-AAAGTGA-AAACTATTATGTATTTTG
* * * * *
1556031 CTTTGTGATTTTGGTTATGTAATATAATTGTTGATGAATTACTTTTACAGTAATTGAAAGCCTAA
1 CTTTGTGATTTTGGTTATGTATTGTAATTGTTGATGAACTACTTTTATAGTAATTCAAAGCCTAA
* * * * ** *
1556096 AATTTATAGGAAATTCTTTATTGAACTAGATAGCATATTGTATG--TATTGCGATACAATGTCTT
66 AAATTATAGGAAATTCATTATTGAACTAAATAG--TATTTTATGCATATTAAGATACAA--TATT
***
1556159 TGTGAAAGATGAAAACTATTGCATATTTTG
127 TGTGAAAG-TGAAAACTATTATGTATTTTG
* ** * * *
1556189 CTTTGTGATTCTAATTGTGTATTGTGATTGTTGATGAACT-GTTATTATAGTAATTCAAAGCCTA
1 CTTTGTGATTTTGGTTATGTATTGTAATTGTTGATGAACTACTT-TTATAGTAATTCAAAGCCTA
* * * * * *
1556253 AAAA-TATAGGAAATTCAATATTGAACTAAATAGTGTTTTGTGCATATTGAGATGCAATGGCTTT
65 AAAATTATAGGAAATTCATTATTGAACTAAATAGTATTTTATGCATATTAAGATACAAT--ATTT
*
1556317 GTGAAAGGTGAAAACTATTACGTATT
128 GTGAAA-GTGAAAACTATTATGTATT
1556343 CAGGTAAAAT
Statistics
Matches: 376, Mismatches: 72, Indels: 39
0.77 0.15 0.08
Matches are distributed among these distances:
155 7 0.02
156 89 0.24
157 138 0.37
158 142 0.38
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.40
Consensus pattern (155 bp):
CTTTGTGATTTTGGTTATGTATTGTAATTGTTGATGAACTACTTTTATAGTAATTCAAAGCCTAA
AAATTATAGGAAATTCATTATTGAACTAAATAGTATTTTATGCATATTAAGATACAATATTTGTG
AAAGTGAAAACTATTATGTATTTTG
Found at i:1556219 original size:158 final size:158
Alignment explanation
Indices: 1555734--1556342 Score: 565
Period size: 157 Copynumber: 3.9 Consensus size: 158
1555724 TGATTGGTCA
* * * * * *
1555734 TGTATTGTAATTGTTGATGAACTACTTTTATAATAATTGAAAGCCTAAAATTTGTAAGAAAGTCT
1 TGTATTGTAATTGTTGATGAACTACTTTTATAGTAATTCAAAGCCTAAAATTTATAGGAAATTCA
* * * * * * *
1555799 TTATTGAACTAGATAATACATTATGTATATTACGATACAATGACTTTGTGAAAGGTGAAAACTAT
66 TTATTGAACTAAATAGTATATTGTATATATTAAGATACAATGTCTTTGTGAAAGGTGAAAACTAT
* *
1555864 TTTGTATTTTGCTATGTGATTATGGA-TG
131 TATGTATTTTGCTTTGTGATTAT-GATTG
* * * * *
1555892 TGTATTGT-GTTGTTAATGAACTA-TCTTTATAGTAATTCAAAACCTAAAAAATTGTAGGAAATT
1 TGTATTGTAATTGTTGATGAACTACT-TTTATAGTAATTCAAAGCCT-AAAATTTATAGGAAATT
* * **
1555955 CAGTATTGAACTAAATAGTAT-TT-TATGCATATTAAGATGCAA--TAATTGTGCAAA-GTGATA
64 CATTATTGAACTAAATAGTATATTGTAT--ATATTAAGATACAATGTCTTTGTG-AAAGGTGA-A
* * *
1556015 AA-TATTATGTATTTTGCTTTGTGATTTTGGTTA
125 AACTATTATGTATTTTGCTTTGTGATTATGATTG
* * * * * *
1556048 TGTAATATAATTGTTGATGAATTACTTTTACAGTAATTGAAAGCCTAAAATTTATAGGAAATTCT
1 TGTATTGTAATTGTTGATGAACTACTTTTATAGTAATTCAAAGCCTAAAATTTATAGGAAATTCA
* * * ** *
1556113 TTATTGAACTAGATAGCATATTGTATGTATTGCGATACAATGTCTTTGTGAAAGATGAAAACTAT
66 TTATTGAACTAAATAGTATATTGTATATATTAAGATACAATGTCTTTGTGAAAGGTGAAAACTAT
*** * *
1556178 TGCATATTTTGCTTTGTGATTCTAATTG
131 TATGTATTTTGCTTTGTGATTATGATTG
* * *
1556206 TGTATTGTGATTGTTGATGAACT-GTTATTATAGTAATTCAAAGCCTAAAA-ATATAGGAAATTC
1 TGTATTGTAATTGTTGATGAACTACTT-TTATAGTAATTCAAAGCCTAAAATTTATAGGAAATTC
* * * ** * * *
1556269 AATATTGAACTAAATAGTGTTTTGTGCATATTGAGATGCAATGGCTTTGTGAAAGGTGAAAACTA
65 ATTATTGAACTAAATAGTATATTGTATATATTAAGATACAATGTCTTTGTGAAAGGTGAAAACTA
*
1556334 TTACGTATT
130 TTATGTATT
1556343 CAGGTAAAAT
Statistics
Matches: 360, Mismatches: 75, Indels: 33
0.77 0.16 0.07
Matches are distributed among these distances:
155 1 0.00
156 84 0.23
157 148 0.41
158 127 0.35
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (158 bp):
TGTATTGTAATTGTTGATGAACTACTTTTATAGTAATTCAAAGCCTAAAATTTATAGGAAATTCA
TTATTGAACTAAATAGTATATTGTATATATTAAGATACAATGTCTTTGTGAAAGGTGAAAACTAT
TATGTATTTTGCTTTGTGATTATGATTG
Found at i:1558439 original size:6 final size:6
Alignment explanation
Indices: 1558411--1558446 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
1558401 AATAATAATG
1558411 TAAATA TGAAATA TAAGATA TAAATA TAAATA TAAA
1 TAAATA T-AAATA TAA-ATA TAAATA TAAATA TAAA
1558447 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (6 bp):
TAAATA
Found at i:1565911 original size:34 final size:34
Alignment explanation
Indices: 1565859--1565946 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 34
1565849 TTTGGTATAG
*** *
1565859 TGAAAAAGTTTCCCAAAATAACTTTCTAG-TACAT
1 TGAAAAAGTTTTTAAAAATAAATTT-TAGATACAT
* * * *
1565893 TGAAGAAGTTTTTGAAAATAAATTTTTGATGCAT
1 TGAAAAAGTTTTTAAAAATAAATTTTAGATACAT
1565927 TGAAAAAGTTTTTAAAAATA
1 TGAAAAAGTTTTTAAAAATA
1565947 GATATTTAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 2 0.05
34 42 0.95
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (34 bp):
TGAAAAAGTTTTTAAAAATAAATTTTAGATACAT
Found at i:1566209 original size:16 final size:18
Alignment explanation
Indices: 1566181--1566218 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1566171 GCTATATAGC
1566181 TTTTCTTTCTTATTTC-T
1 TTTTCTTTCTTATTTCAT
1566198 TTTTCTTT-TTATTTCAT
1 TTTTCTTTCTTATTTCAT
1566215 TTTT
1 TTTT
1566219 GTTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTTTCTTATTTCAT
Found at i:1567288 original size:19 final size:21
Alignment explanation
Indices: 1567250--1567293 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1567240 AGTTTATTAT
*
1567250 TTAAAATAATATTATTTAATA
1 TTAAAAAAATATTATTTAATA
1567271 TTAAAAAAATA-T-TTTAATA
1 TTAAAAAAATATTATTTAATA
1567290 TTAA
1 TTAA
1567294 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAAAAATATTATTTAATA
Found at i:1567302 original size:24 final size:25
Alignment explanation
Indices: 1567265--1567313 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1567255 ATAATATTAT
*
1567265 TTAATATTAAAAAAATATTTTAATA
1 TTAATATTAAAAAAATATTTAAATA
*
1567290 TTAATATT-TAAAAATATTTAAATA
1 TTAATATTAAAAAAATATTTAAATA
1567314 AAAAACACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAATATTAAAAAAATATTTAAATA
Found at i:1580501 original size:35 final size:35
Alignment explanation
Indices: 1580462--1580529 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
1580452 CATTTTCATT
1580462 AAATCCT-AAATCAAAGCCCTAAAACTTCAAACCTC
1 AAATCCTAAAATCAAAGCCCTAAAAC-TCAAACCTC
*
1580497 AAATCCTAAAATCAAAGCCCTAAATCTCAAACC
1 AAATCCTAAAATCAAAGCCCTAAAACTCAAACC
1580530 CTAAAATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 14 0.45
36 17 0.55
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (35 bp):
AAATCCTAAAATCAAAGCCCTAAAACTCAAACCTC
Found at i:1580521 original size:13 final size:13
Alignment explanation
Indices: 1580495--1580540 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
1580485 ACTTCAAACC
*
1580495 TCAAATCCTAAAA
1 TCAAACCCTAAAA
*
1580508 TCAAAGCCCTAAATC
1 TCAAA-CCCTAAA-A
1580523 TCAAACCCTAAAA
1 TCAAACCCTAAAA
1580536 TCAAA
1 TCAAA
1580541 AACCTAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 10 0.36
14 13 0.46
15 5 0.18
ACGTcount: A:0.50, C:0.28, G:0.02, T:0.20
Consensus pattern (13 bp):
TCAAACCCTAAAA
Found at i:1580537 original size:36 final size:35
Alignment explanation
Indices: 1580462--1580537 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 35
1580452 CATTTTCATT
*
1580462 AAATCCTAAATCAAAGCCCTAAAACTTCAAACCTC
1 AAATCCTAAATCAAAGCCCTAAAACTTCAAACCTA
*
1580497 AAATCCTAAAATCAAAGCCCTAAATC-TCAAACCCTA
1 AAATCCT-AAATCAAAGCCCTAAAACTTCAAA-CCTA
1580533 AAATC
1 AAATC
1580538 AAAAACCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 12 0.32
36 25 0.68
ACGTcount: A:0.47, C:0.30, G:0.03, T:0.20
Consensus pattern (35 bp):
AAATCCTAAATCAAAGCCCTAAAACTTCAAACCTA
Found at i:1580546 original size:14 final size:14
Alignment explanation
Indices: 1580501--1580548 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1580491 AACCTCAAAT
*
1580501 CCTAAAATCAAAGC
1 CCTAAAATCAAAAC
*
1580515 CCT-AAATCTCAAAC
1 CCTAAAATC-AAAAC
*
1580529 CCTAAAATCAAAAA
1 CCTAAAATCAAAAC
1580543 CCTAAA
1 CCTAAA
1580549 CCCCAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 5 0.18
14 18 0.64
15 5 0.18
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (14 bp):
CCTAAAATCAAAAC
Found at i:1580551 original size:21 final size:22
Alignment explanation
Indices: 1580525--1580575 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1580515 CCTAAATCTC
1580525 AAACCCTAAAATCAAAAACCT-
1 AAACCCTAAAATCAAAAACCTG
* * *
1580546 AAACCCCAAAATCCAAAACTTG
1 AAACCCTAAAATCAAAAACCTG
1580568 AAACCCTA
1 AAACCCTA
1580576 CCCCTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.53, C:0.31, G:0.02, T:0.14
Consensus pattern (22 bp):
AAACCCTAAAATCAAAAACCTG
Found at i:1580555 original size:28 final size:28
Alignment explanation
Indices: 1580490--1580555 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
1580480 CTAAAACTTC
* **
1580490 AAACCTCAAATCCTAAAATCAAAGCCCT
1 AAACCTCAAACCCTAAAATCAAAAACCT
*
1580518 AAATCTCAAACCCTAAAATCAAAAACCT
1 AAACCTCAAACCCTAAAATCAAAAACCT
*
1580546 AAACCCCAAA
1 AAACCTCAAA
1580556 ATCCAAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.15
Consensus pattern (28 bp):
AAACCTCAAACCCTAAAATCAAAAACCT
Found at i:1580563 original size:28 final size:29
Alignment explanation
Indices: 1580497--1580593 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 29
1580487 TTCAAACCTC
* * *
1580497 AAATCCTAAAATCAAAGCCCTAAATCTC-
1 AAATCCTAAAATCAAAACCCTAAACCCCA
* *
1580525 AAACCCTAAAATCAAAAACCTAAACCCCA
1 AAATCCTAAAATCAAAACCCTAAACCCCA
**
1580554 AAATCC-AAAACTTGAAACCCT--ACCCCTA
1 AAATCCTAAAA-TCAAAACCCTAAACCCC-A
1580582 AAATCC-AAAATC
1 AAATCCTAAAATC
1580594 GCAAGCCTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
27 6 0.11
28 38 0.68
29 12 0.21
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.16
Consensus pattern (29 bp):
AAATCCTAAAATCAAAACCCTAAACCCCA
Found at i:1581820 original size:26 final size:26
Alignment explanation
Indices: 1581791--1581840 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1581781 TATTAACAAT
* *
1581791 TATTGGATTTAATTGGTTTTATTTGA
1 TATTGAATTTAATTGCTTTTATTTGA
* *
1581817 TATTTAATTTAATTTCTTTTATTT
1 TATTGAATTTAATTGCTTTTATTT
1581841 TAAATTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (26 bp):
TATTGAATTTAATTGCTTTTATTTGA
Found at i:1581847 original size:26 final size:26
Alignment explanation
Indices: 1581797--1581847 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1581787 CAATTATTGG
* *
1581797 ATTTAATTGGTTTTATTTGATATTTA
1 ATTTAATTGCTTTTATTTGAAATTTA
* *
1581823 ATTTAATTTCTTTTATTTTAAATTT
1 ATTTAATTGCTTTTATTTGAAATTT
1581848 TCATAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (26 bp):
ATTTAATTGCTTTTATTTGAAATTTA
Found at i:1587281 original size:20 final size:20
Alignment explanation
Indices: 1587258--1587304 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1587248 GATGGGGCAT
*
1587258 AAAAAAATACAAAAAGCAAA
1 AAAAAAATAAAAAAAGCAAA
*
1587278 AAAAAAGTAAAAAAAGCAAA
1 AAAAAAATAAAAAAAGCAAA
1587298 AAAAAAA
1 AAAAAAA
1587305 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.04
Consensus pattern (20 bp):
AAAAAAATAAAAAAAGCAAA
Found at i:1587282 original size:11 final size:10
Alignment explanation
Indices: 1587268--1587316 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
1587258 AAAAAAATAC
1587268 AAAAAGCAAAA
1 AAAAAG-AAAA
1587279 AAAAAGTAAAA
1 AAAAAG-AAAA
1587290 AAAGCAA-AAAA
1 AAA--AAGAAAA
1587301 AAAAAGAAAA
1 AAAAAGAAAA
1587311 AAAAAG
1 AAAAAG
1587317 GGGACATCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 2 0.06
10 10 0.29
11 20 0.59
13 2 0.06
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1587302 original size:13 final size:12
Alignment explanation
Indices: 1587286--1587315 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
1587276 AAAAAAAAGT
1587286 AAAAAAAGCAAAA
1 AAAAAAAG-AAAA
1587299 AAAAAAAGAAAA
1 AAAAAAAGAAAA
1587311 AAAAA
1 AAAAA
1587316 GGGGACATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:1587310 original size:20 final size:19
Alignment explanation
Indices: 1587258--1587312 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1587248 GATGGGGCAT
* *
1587258 AAAAAAATACAAAAAGCAA
1 AAAAAAAAAAAAAAAGCAA
*
1587277 AAAAAAAGTAAAAAAAGCAA
1 AAAAAAA-AAAAAAAAGCAA
1587297 AAAAAAAAAGAAAAAA
1 AAAAAAAAA-AAAAAA
1587313 AAAGGGGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.84, C:0.05, G:0.07, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGCAA
Found at i:1587310 original size:28 final size:28
Alignment explanation
Indices: 1587257--1587311 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1587247 AGATGGGGCA
**
1587257 TAAAAAAATACAAAAAGCAAAAAAAAAG
1 TAAAAAAATACAAAAAAAAAAAAAAAAG
*
1587285 TAAAAAAA-GCAAAAAAAAAAAGAAAAA
1 TAAAAAAATACAAAAAAAAAAA-AAAAA
1587312 AAAAGGGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.82, C:0.05, G:0.07, T:0.05
Consensus pattern (28 bp):
TAAAAAAATACAAAAAAAAAAAAAAAAG
Found at i:1588715 original size:47 final size:47
Alignment explanation
Indices: 1588662--1588769 Score: 198
Period size: 47 Copynumber: 2.3 Consensus size: 47
1588652 AAGAAGAGTC
*
1588662 TTTGCATTTGCATCGTTTGCATCTACATCATAAGAAAGACATTTGCA
1 TTTGCATTTGCATCGTTTGCATCTACATCATAAGAAAGACATTTACA
*
1588709 TTTGCATTTGCATTGTTTGCATCTACATCATAAGAAAGACATTTACA
1 TTTGCATTTGCATCGTTTGCATCTACATCATAAGAAAGACATTTACA
1588756 TTTGCATTTGCATC
1 TTTGCATTTGCATC
1588770 TGTATAAGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (47 bp):
TTTGCATTTGCATCGTTTGCATCTACATCATAAGAAAGACATTTACA
Found at i:1589516 original size:22 final size:22
Alignment explanation
Indices: 1589490--1589548 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1589480 TTGAAATTTA
*
1589490 TAAGACCTTTGGGCATAATCTT-
1 TAAGACCTTTGGGCACAA-CTTC
* *
1589512 TAAGACCTCTGGACACAACTTC
1 TAAGACCTTTGGGCACAACTTC
*
1589534 TAAGACCTTCGGGCA
1 TAAGACCTTTGGGCA
1589549 AAAGATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (22 bp):
TAAGACCTTTGGGCACAACTTC
Found at i:1589532 original size:127 final size:126
Alignment explanation
Indices: 1589293--1589635 Score: 413
Period size: 127 Copynumber: 2.7 Consensus size: 126
1589283 ACATTCAAGC
* * * * **
1589293 AAAAGATTTTTAAATTTTTAAAATTTCATTACCTCTAATTAAGAAGAGCATTCACGGATTTTGAG
1 AAAAGATTTTTAAATTTTTAAAGTTTCATTGCCTCTGATT-AG-AGAACATTCAAAGATTTTGAG
* * * * *
1589358 ATTTGTAAGA-CTTTCGGACGTAATCTTTAAAGCTTTTGGGCATAACTT-TCAAGACCTCCAGGA
64 ATTTGTAAGACCTTT-GGACATAATCTTTAAAGCCTCTGGACACAACTTCT-AAGACCTCCAGGA
* *
1589421 AAAAGATTTTTAAATTTTTAAAGTTTCATTGCCTTTGATTAGAGGAACATTCAAAGATTTTGAAA
1 AAAAGATTTTTAAATTTTTAAAGTTTCATTGCCTCTGATTAGA-GAACATTCAAAGATTTTGAGA
* * * * *
1589486 TTTATAAGACCTTTGGGCATAATCTTT-AAGACCTCTGGACACAACTTCTAAGACCTTCGGGC
65 TTTGTAAGACCTTTGGACATAATCTTTAAAG-CCTCTGGACACAACTTCTAAGACCTCCAGGA
* *
1589548 AAAAGATTTTTAAATTTTCAAAGTTTCATTGTCTCTGATTAGAGAAGCATTCAAAGATTTTGAGA
1 AAAAGATTTTTAAATTTTTAAAGTTTCATTGCCTCTGATTAGAGAA-CATTCAAAGATTTTGAGA
*
1589613 TTTGTAAGACCTTTGGATATAAT
65 TTTGTAAGACCTTTGGACATAAT
1589636 TTCCATTCAT
Statistics
Matches: 185, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
126 7 0.04
127 137 0.74
128 41 0.22
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (126 bp):
AAAAGATTTTTAAATTTTTAAAGTTTCATTGCCTCTGATTAGAGAACATTCAAAGATTTTGAGAT
TTGTAAGACCTTTGGACATAATCTTTAAAGCCTCTGGACACAACTTCTAAGACCTCCAGGA
Found at i:1589972 original size:22 final size:22
Alignment explanation
Indices: 1589940--1589995 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1589930 ATCCCAGTCG
*
1589940 ATTTTGTAAGACCTTCAAGCATA
1 ATTTT-TAAGACCTCCAAGCATA
**
1589963 ATTTTTAAGACCTCCGGGCATA
1 ATTTTTAAGACCTCCAAGCATA
*
1589985 ATTTCTAAGAC
1 ATTTTTAAGAC
1589996 TTTTGGGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (22 bp):
ATTTTTAAGACCTCCAAGCATA
Found at i:1589982 original size:109 final size:110
Alignment explanation
Indices: 1589747--1589988 Score: 306
Period size: 109 Copynumber: 2.2 Consensus size: 110
1589737 TGGCATGATC
* * *
1589747 TTTAAGACCTCTGGGTATAATTTTGATTCGCGATATTGTCCTGATCGATTCTTTATTTTTTAACT
1 TTTAAGACCTCTGGGCATAATTTTGATTCGCAATATTATCCTGATCGATTCTTTATTTTTTAACT
* ** * * *
1589812 TGCGGTGTGATCTTAGTCGATTCTGTAAGATCTCCAGGCATGATT
66 TACGGTGTGATCCCAGTCGATTCTGTAAGACCTCCAAGCATAATT
* * * * * *
1589857 TCTAAGACTTATGGGCATAATTTTGATTTGCAATGTTATCCTGATCGATTC-TTATTTTTTGACT
1 TTTAAGACCTCTGGGCATAATTTTGATTCGCAATATTATCCTGATCGATTCTTTATTTTTTAACT
* * *
1589921 TACGGTGTTATCCCAGTCGATTTTGTAAGACCTTCAAGCATAATT
66 TACGGTGTGATCCCAGTCGATTCTGTAAGACCTCCAAGCATAATT
*
1589966 TTTAAGACCTCCGGGCATAATTT
1 TTTAAGACCTCTGGGCATAATTT
1589989 CTAAGACTTT
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
109 67 0.61
110 43 0.39
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (110 bp):
TTTAAGACCTCTGGGCATAATTTTGATTCGCAATATTATCCTGATCGATTCTTTATTTTTTAACT
TACGGTGTGATCCCAGTCGATTCTGTAAGACCTCCAAGCATAATT
Found at i:1590003 original size:22 final size:22
Alignment explanation
Indices: 1589958--1590032 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
1589948 AGACCTTCAA
* *
1589958 GCATAATTTTTAAGACCTCCGG
1 GCATAATTTCTAAGACTTCCGG
**
1589980 GCATAATTTCTAAGACTTTTGG
1 GCATAATTTCTAAGACTTCCGG
* *
1590002 GCATAGTCTCTAAGACTTCCGG
1 GCATAATTTCTAAGACTTCCGG
1590024 GCATAATTT
1 GCATAATTT
1590033 TGATTCGTGG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (22 bp):
GCATAATTTCTAAGACTTCCGG
Found at i:1590120 original size:153 final size:153
Alignment explanation
Indices: 1589857--1590147 Score: 424
Period size: 153 Copynumber: 1.9 Consensus size: 153
1589847 AGGCATGATT
* * *
1589857 TCTAAGACTTATGGGCATAATTTTGATTTGCAATGTTATCCTGATCGATTCTTATTTTTTGACTT
1 TCTAAGACTTACGGGCATAATTTTGATTCGCAATGTTATCCCGATCGATTCTTATTTTTTGACTT
*
1589922 ACGGTGTTATCCCAGTCGATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAAT
66 ACAGTGTTATCCCAGTCGATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAAT
1589987 TTCTAAGACTTTTGGGCATAGTC
131 TTCTAAGACTTTTGGGCATAGTC
* *** *
1590010 TCTAAGACTTCCGGGCATAATTTTGATTCGTGGTGTTGTCCCGATCGATTTCTTATTTTTTGA-T
1 TCTAAGACTTACGGGCATAATTTTGATTCGCAATGTTATCCCGATCGA-TTCTTATTTTTTGACT
* * * * *
1590074 TACAGTGTTGTCTCAGTCGATTTTGTAAGACC-TCTAGGCATGATTTTTAAGACCTTCGGGCATA
65 TACAGTGTTATCCCAGTCGATTTTGTAAGACCTTC-AAGCATAATTTTTAAGACCTCCGGGCATA
1590138 ATTTCTAAGA
129 ATTTCTAAGA
1590148 TCTCCGAGCA
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
152 2 0.02
153 106 0.87
154 14 0.11
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (153 bp):
TCTAAGACTTACGGGCATAATTTTGATTCGCAATGTTATCCCGATCGATTCTTATTTTTTGACTT
ACAGTGTTATCCCAGTCGATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAAT
TTCTAAGACTTTTGGGCATAGTC
Found at i:1590135 original size:22 final size:22
Alignment explanation
Indices: 1590092--1590202 Score: 64
Period size: 22 Copynumber: 5.0 Consensus size: 22
1590082 TGTCTCAGTC
*
1590092 GATTTTGTAAGACC-TCTAGGCAT
1 GATTTT-TAAGACCTTC-GGGCAT
1590115 GATTTTTAAGACCTTCGGGCAT
1 GATTTTTAAGACCTTCGGGCAT
* * * * *
1590137 AATTTCTAAGATCTCCGAGCAT
1 GATTTTTAAGACCTTCGGGCAT
* *** * *
1590159 AATCGCTAA-AACTTCTAGGCAT
1 GATTTTTAAGACCTTC-GGGCAT
*
1590181 GATCTTTAAGACCTTCGGGCAT
1 GATTTTTAAGACCTTCGGGCAT
1590203 AATCTCGATT
Statistics
Matches: 68, Mismatches: 17, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
21 4 0.06
22 51 0.75
23 13 0.19
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (22 bp):
GATTTTTAAGACCTTCGGGCAT
Found at i:1590180 original size:153 final size:153
Alignment explanation
Indices: 1589870--1590180 Score: 394
Period size: 153 Copynumber: 2.0 Consensus size: 153
1589860 AAGACTTATG
* * *
1589870 GGCATAATTTTGATTTGCAATGTTATCCTGATCGATTCTTATTTTTTGACTTACGGTGTTATCCC
1 GGCATAATTTTGATTCGCAATGTTATCCCGATCGATTCTTATTTTTTGACTTACAGTGTTATCCC
**
1589935 AGTCGATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAATTTCTAAGACTTTT
66 AGTCGATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAATTTCTAAGACTTCC
* * * * *
1590000 GGGCATAGTCTCTAAGACTTCCG
131 GAGCATAATCGCTAAAACTTCCA
*** * * *
1590023 GGCATAATTTTGATTCGTGGTGTTGTCCCGATCGATTTCTTATTTTTTGA-TTACAGTGTTGTCT
1 GGCATAATTTTGATTCGCAATGTTATCCCGATCGA-TTCTTATTTTTTGACTTACAGTGTTATCC
* * *
1590087 CAGTCGATTTTGTAAGACC-TCTAGGCATGATTTTTAAGACCTTCGGGCATAATTTCTAAGA-TC
65 CAGTCGATTTTGTAAGACCTTC-AAGCATAATTTTTAAGACCTCCGGGCATAATTTCTAAGACT-
*
1590150 TCCGAGCATAATCGCTAAAACTTCTA
128 TCCGAGCATAATCGCTAAAACTTCCA
1590176 GGCAT
1 GGCAT
1590181 GATCTTTAAG
Statistics
Matches: 135, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
152 3 0.02
153 118 0.87
154 14 0.10
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (153 bp):
GGCATAATTTTGATTCGCAATGTTATCCCGATCGATTCTTATTTTTTGACTTACAGTGTTATCCC
AGTCGATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAATTTCTAAGACTTCC
GAGCATAATCGCTAAAACTTCCA
Found at i:1590207 original size:22 final size:22
Alignment explanation
Indices: 1590110--1590207 Score: 74
Period size: 22 Copynumber: 4.5 Consensus size: 22
1590100 AAGACCTCTA
* *
1590110 GGCATGATTTTTAAGACCTTCG
1 GGCATAATCTTTAAGACCTTCG
* *
1590132 GGCATAAT-TTCTAAGATCTCCG
1 GGCATAATCTT-TAAGACCTTCG
* ** * *
1590154 AGCATAATCGCTAA-AACTTCTA
1 GGCATAATCTTTAAGACCTTC-G
*
1590176 GGCATGATCTTTAAGACCTTCG
1 GGCATAATCTTTAAGACCTTCG
1590198 GGCATAATCT
1 GGCATAATCT
1590208 CGATTCACGG
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
21 6 0.11
22 45 0.80
23 5 0.09
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (22 bp):
GGCATAATCTTTAAGACCTTCG
Found at i:1590265 original size:175 final size:174
Alignment explanation
Indices: 1589939--1590322 Score: 450
Period size: 175 Copynumber: 2.2 Consensus size: 174
1589929 TATCCCAGTC
* * ** * * *
1589939 GATTTTGTAAGACCTTCAAGCATAATTTTTAAGACCTCCGGGCATAATTTCTAAGACTTTTGGGC
1 GATTTT-TAAGACCTTCAAGCATAATTTCTAAGACCTCCGAGCATAATCGCTAAAACTTCTAGGC
* * ** * *
1590004 ATAGTCTCTAAGACTTCCGGGCATAATTTTGATTCGTGGTGTTGTCCCGATCGATTTCTTATTTT
65 ATAGTCTCTAAGACTTCCGGGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCCTTATTTT
* * *
1590069 TTGATTACAGTGTTGTCTCAGTCGATTTTGTAAGACCTCTAGGCAT
130 TTAATTACAGTGTTATCTCAGTCGATTTTGTAAGACCTCT-GACAT
** *
1590115 GATTTTTAAGACCTTCGGGCATAATTTCTAAGATCTCCGAGCATAATCGCTAAAACTTCTAGGCA
1 GATTTTTAAGACCTTCAAGCATAATTTCTAAGACCTCCGAGCATAATCGCTAAAACTTCTAGGCA
* * *
1590180 T-GATCTTTAAGACCTT-CGGGCATAATCTCGATTCACGGTGTTAT-CTGATTGATTCCTTATTT
66 TAG-TCTCTAAGA-CTTCCGGGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCCTTATTT
* *
1590242 TTTAACTTACGGTGTTATCTCAGTTGATTTTGTAAGACCTCTGACAT
129 TTTAA-TTACAGTGTTATCTCAGTCGATTTTGTAAGACCTCTGACAT
* * * *
1590289 AATCTTTAAGACCTTCAAGCATGATTTTTAAGAC
1 GATTTTTAAGACCTTCAAGCATAATTTCTAAGAC
1590323 TTGCGGGCAT
Statistics
Matches: 174, Mismatches: 31, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
174 51 0.29
175 114 0.66
176 9 0.05
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (174 bp):
GATTTTTAAGACCTTCAAGCATAATTTCTAAGACCTCCGAGCATAATCGCTAAAACTTCTAGGCA
TAGTCTCTAAGACTTCCGGGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCCTTATTTTT
TAATTACAGTGTTATCTCAGTCGATTTTGTAAGACCTCTGACAT
Found at i:1590429 original size:22 final size:22
Alignment explanation
Indices: 1590404--1590490 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 22
1590394 GTCGATTCTG
* * *
1590404 TAAGATCTCCAGGTATAATTTC
1 TAAGACCTCCGGGCATAATTTC
**
1590426 TAAGACCTCCGGGCATAATCAC
1 TAAGACCTCCGGGCATAATTTC
* * *
1590448 TAAGACCTCCCGGCATGATTTT
1 TAAGACCTCCGGGCATAATTTC
* * *
1590470 TAAAATCTCCGGGTATAATTT
1 TAAGACCTCCGGGCATAATTT
1590491 TGATTCACGG
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (22 bp):
TAAGACCTCCGGGCATAATTTC
Found at i:1590463 original size:131 final size:130
Alignment explanation
Indices: 1590187--1590469 Score: 291
Period size: 131 Copynumber: 2.2 Consensus size: 130
1590177 GCATGATCTT
* * * * *
1590187 TAAGACCTTCGGGCATAATCTCGATTCACGGTGTTATCTGATTGATTCCTTATTTTTTAACTTAC
1 TAAGACCTCCGGGCATAATTTTGATTCACAGTGTTATCTGATCGATTCCTTATTTTTTAACTTAC
* * * * * * ***
1590252 GGTGTTATCTCAGTTGATTTTGTAAGACCTCTGACATAATCTTTAAGACCTTCAAGCATGATTTT
66 GGTGTTATCCCAGTCGATTCTGTAAGACCTCAGACATAATCTTTAAGACCTCCAAGCATAATCAC
* * * *
1590317 TAAGACTTGCGGGCATAATTTTGATTCGCAGTGTTATCCTGATCGATTTCTTATTTTTTAACTT-
1 TAAGACCTCCGGGCATAATTTTGATTCACAGTGTTAT-CTGATCGATTCCTTATTTTTTAACTTA
* * ** **
1590381 TGGTGTTATCCCAGTCGATTCTGTAAGATCTCCAGGTATAAT-TTCTAAGACCTCCGGGCATAAT
65 CGGTGTTATCCCAGTCGATTCTGTAAGACCT-CAGACATAATCTT-TAAGACCTCCAAGCATAAT
1590445 CAC
128 CAC
* *
1590448 TAAGACCTCCCGGCATGATTTT
1 TAAGACCTCCGGGCATAATTTT
1590470 TAAAATCTCC
Statistics
Matches: 123, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
130 59 0.48
131 64 0.52
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (130 bp):
TAAGACCTCCGGGCATAATTTTGATTCACAGTGTTATCTGATCGATTCCTTATTTTTTAACTTAC
GGTGTTATCCCAGTCGATTCTGTAAGACCTCAGACATAATCTTTAAGACCTCCAAGCATAATCAC
Found at i:1590618 original size:22 final size:22
Alignment explanation
Indices: 1590558--1590620 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
1590548 ATCAATTTTG
* * *
1590558 TAAGACCTTTAGGCATGATTTT
1 TAAGACCTTTGGGCATAATTTC
* **
1590580 TAAGACCTTCGAACATAATTTC
1 TAAGACCTTTGGGCATAATTTC
1590602 TAAGACCTTTGGGCATAAT
1 TAAGACCTTTGGGCATAAT
1590621 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (22 bp):
TAAGACCTTTGGGCATAATTTC
Found at i:1590727 original size:110 final size:109
Alignment explanation
Indices: 1590574--1590840 Score: 282
Period size: 110 Copynumber: 2.4 Consensus size: 109
1590564 CTTTAGGCAT
* ** * *
1590574 GATTTTTAAGACCTTCGAACATAATTTCTAAGACCTTTGGGCATAATCTCGATTCACGGTGTTGT
1 GATTTTTAAGACCTTCGAACATGATTTCTAAGACCTTCAGGCATAATCTCGATTCACAGTGTTAT
* * ** * **
1590639 CCCAATCGATTCCTTATTTTTGAACTTTTGGTGTTGTCTTAGTC
66 CCCAATCGATTCCTTATTTTTCAAATTACGGTGTTATCCCAGTC
* * * * *
1590683 GATTTTATAAGATCTTCGAACATGATTTCTAAGACCTCCAGGCATAATTTTGATTCGCAGTGTTA
1 GATTTT-TAAGACCTTCGAACATGATTTCTAAGACCTTCAGGCATAATCTCGATTCACAGTGTTA
** **
1590748 TCCTGATCGATTTTTTATTTTTCAAATTACGGTGTTATCCCAGTC
65 TCCCAATCGATTCCTTATTTTTCAAATTACGGTGTTATCCCAGTC
* * * * *
1590793 GATTCTGTAAGACCTCCGAACATGATTTTTAAAACCTTCAAGCATAAT
1 GATT-TTTAAGACCTTCGAACATGATTTCTAAGACCTTCAGGCATAAT
1590841 TTCTAAGACC
Statistics
Matches: 128, Mismatches: 28, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
109 6 0.05
110 121 0.95
111 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (109 bp):
GATTTTTAAGACCTTCGAACATGATTTCTAAGACCTTCAGGCATAATCTCGATTCACAGTGTTAT
CCCAATCGATTCCTTATTTTTCAAATTACGGTGTTATCCCAGTC
Found at i:1590729 original size:132 final size:131
Alignment explanation
Indices: 1590447--1590732 Score: 295
Period size: 132 Copynumber: 2.2 Consensus size: 131
1590437 GGCATAATCA
* * * * * *
1590447 CTAAGACCTCCCGGCATGATTTTTAAAATCTCCGGGTATAATTTTGATTCACGGTGTTGTCCCAA
1 CTAAGACCT-CCGGCATAATTTCTAAAACCTCCGGGCATAATCTCGATTCACGGTGTTGTCCCAA
** * * *
1590512 TCGATTTTTTATTTTTCAACTTATAATGTTATCTCAATCAATTTTGTAAGACCTTTAGGCATGAT
65 TCGATTCCTTATTTTTCAACTTATAATGTTATCTCAATCAATTTTATAAGACCTTGAGACATGAT
1590577 TT
130 TT
* * * * **
1590579 TTAAGACCTTCGAACATAATTTCTAAGACCTTTGGGCATAATCTCGATTCACGGTGTTGTCCCAA
1 CTAAGACCTCCG-GCATAATTTCTAAAACCTCCGGGCATAATCTCGATTCACGGTGTTGTCCCAA
* * ** * * * * *
1590644 TCGATTCCTTATTTTTGAACTTTTGGTGTTGTCTTAGTCGATTTTATAAGATCTTCGA-ACATGA
65 TCGATTCCTTATTTTTCAACTTATAATGTTATCTCAATCAATTTTATAAGACCTT-GAGACATGA
1590708 TTT
129 TTT
1590711 CTAAGACCTCCAGGCATAATTT
1 CTAAGACCTCC-GGCATAATTT
1590733 TGATTCGCAG
Statistics
Matches: 122, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
131 2 0.02
132 118 0.97
133 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (131 bp):
CTAAGACCTCCGGCATAATTTCTAAAACCTCCGGGCATAATCTCGATTCACGGTGTTGTCCCAAT
CGATTCCTTATTTTTCAACTTATAATGTTATCTCAATCAATTTTATAAGACCTTGAGACATGATT
T
Found at i:1590858 original size:22 final size:22
Alignment explanation
Indices: 1590833--1590909 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
1590823 AAAACCTTCA
1590833 AGCATAATTTCTAAGACCTCTG
1 AGCATAATTTCTAAGACCTCTG
* * *
1590855 AGCATAATCTCTAAGATCTCCG
1 AGCATAATTTCTAAGACCTCTG
* * *
1590877 GGCATGATTTCCT-GGACCTCT-
1 AGCATAATTT-CTAAGACCTCTG
1590898 AGGCATAATTTC
1 A-GCATAATTTC
1590910 GATTCACAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 1 0.02
22 39 0.93
23 2 0.05
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (22 bp):
AGCATAATTTCTAAGACCTCTG
Found at i:1591013 original size:22 final size:22
Alignment explanation
Indices: 1590976--1591018 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1590966 GTTGATTCTA
* *
1590976 TAAGACCTCTGAGCATGATTTT
1 TAAGACCTCCGAGCATAATTTT
*
1590998 TAAGACCTCCGTGCATAATTT
1 TAAGACCTCCGAGCATAATTT
1591019 CGATTCGCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (22 bp):
TAAGACCTCCGAGCATAATTTT
Found at i:1592784 original size:22 final size:22
Alignment explanation
Indices: 1592736--1592783 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1592726 ATTATTATAT
1592736 AAAAATTAATTAAAAAAGGGTA
1 AAAAATTAATTAAAAAAGGGTA
1592758 AAAAATTAATTAAAAAA-GGTA
1 AAAAATTAATTAAAAAAGGGTA
1592779 AAAAA
1 AAAAA
1592784 AGAATAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (22 bp):
AAAAATTAATTAAAAAAGGGTA
Found at i:1592815 original size:3 final size:3
Alignment explanation
Indices: 1592809--1592878 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
1592799 TAAAAAAAGC
*
1592809 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1592857 A-A ATTA ATA ATA TTA TTA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA A
1592879 ATTTTCATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.93
4 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1593058 original size:28 final size:28
Alignment explanation
Indices: 1593014--1593100 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
1593004 TCCTAAATAA
* *
1593014 AAACCCTAAAA-CTAAAACTTTAAACCTC
1 AAACCCTAAAATC-AAAACCTCAAACCTC
*
1593042 AAACCCTAAAATCAAAACCTCAAATCTC
1 AAACCCTAAAATCAAAACCTCAAACCTC
* * *
1593070 AAACTCTAGAATCAAAAACCT-AAACCCC
1 AAACCCTAAAATC-AAAACCTCAAACCTC
1593098 AAA
1 AAA
1593101 ATCTGAAACT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 42 0.84
29 8 0.16
ACGTcount: A:0.52, C:0.30, G:0.01, T:0.17
Consensus pattern (28 bp):
AAACCCTAAAATCAAAACCTCAAACCTC
Done.