Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 72 of 126
Found at i:21234063 original size:52 final size:52
Alignment explanation
Indices: 21233979--21234264 Score: 368
Period size: 52 Copynumber: 5.6 Consensus size: 52
21233969 ATTTCATTTA
* * **
21233979 ATACTCACGATGACACATAATTATTAGACCTCATAATCCATGAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATGAAGGATTCAT
* * * *
21234031 ATACTCATGATGACACATAATCATCGGTCCTCATAATCCGTGAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATGAAGGATTCAT
*
21234083 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTGAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATGAAGGATTCAT
* * *
21234135 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATGAAGGATTCAT
* ** * *
21234187 ATACTCATGATGACACATAGTCATCAAACCTCATAAAT-CGTAAAGGATTC--
1 ATACTCACGATGACACATAGTCATCGGACCTCAT-AATCCATGAAGGATTCAT
21234237 ATA-T--CGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
21234265 TTTTACATTT
Statistics
Matches: 211, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
47 21 0.10
49 1 0.00
50 3 0.01
52 183 0.87
53 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATGAAGGATTCAT
Found at i:21253579 original size:41 final size:41
Alignment explanation
Indices: 21253477--21253693 Score: 281
Period size: 41 Copynumber: 5.2 Consensus size: 41
21253467 TAAAATAATA
*
21253477 TGAAATGATTCAAGCTTCGGCTTAGCAGGATTTTGAGCCGGTG
1 TGAAATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCC-G-G
** *
21253520 AATGAAATGATTCAAGCTTCGAATTAGCAGGCTTTTGAGTCGG
1 --TGAAATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCGG
* *
21253563 TGAAATGATTCAAGCTTCGGCTTAGCAAGCTTTTAAGCCGG
1 TGAAATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCGG
* * *
21253604 TGGAATGATTCAAGGTTTGGCTTAGCAGGCTTTTGAGCCGG
1 TGAAATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCGG
* * *
21253645 TGAAATGATTCAAGCTTCGGCTTAGCGGGCTTCTGAGCCAG
1 TGAAATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCGG
*
21253686 TGTAATGA
1 TGAAATGA
21253694 CGAAAGAACT
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 114 0.75
43 1 0.01
44 1 0.01
45 35 0.23
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (41 bp):
TGAAATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCGG
Found at i:21261101 original size:40 final size:41
Alignment explanation
Indices: 21261019--21261144 Score: 191
Period size: 41 Copynumber: 3.1 Consensus size: 41
21261009 ATAATATGAT
*
21261019 ATGATTCAAGCTTCGGCTTAGCAGACTTTTGAGCCAGTGAA
1 ATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCAGTGAA
*
21261060 ATGATTCAAGCTTCGGCTTGGCAGGC-TTTGAGCCAGTGAA
1 ATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCAGTGAA
* * * *
21261100 ATGATTGAAGCTTCGACTTAGCAGGCTTTTAAGCCAGTGTA
1 ATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCAGTGAA
21261141 ATGA
1 ATGA
21261145 CGAAACAACT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 37 0.48
41 40 0.52
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (41 bp):
ATGATTCAAGCTTCGGCTTAGCAGGCTTTTGAGCCAGTGAA
Found at i:21262220 original size:19 final size:21
Alignment explanation
Indices: 21262180--21262220 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
21262170 GTCCCTGTTT
*
21262180 CAATTGCTCACATGATCTTGG
1 CAATTGCTCACATGAGCTTGG
21262201 CAATTG-TCACATG-GCTTGG
1 CAATTGCTCACATGAGCTTGG
21262220 C
1 C
21262221 TACACGGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
CAATTGCTCACATGAGCTTGG
Found at i:21265498 original size:22 final size:22
Alignment explanation
Indices: 21265468--21265512 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
21265458 ATAAGTACTG
*
21265468 AATATATTATATTATTTGAAAAA
1 AATATATTAT-TGATTTGAAAAA
*
21265491 AATA-ATTATTGATTTTAAAAA
1 AATATATTATTGATTTGAAAAA
21265512 A
1 A
21265513 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 5 0.25
23 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AATATATTATTGATTTGAAAAA
Found at i:21265514 original size:17 final size:16
Alignment explanation
Indices: 21265489--21265537 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
21265479 TTATTTGAAA
21265489 AAAATAATTATTGATTTT
1 AAAA-AATT-TTGATTTT
*
21265507 AAAAAATTGTTTATTTTT
1 AAAAAATT-TTGA-TTTT
21265525 AAAAAATTTTGAT
1 AAAAAATTTTGAT
21265538 ACAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.37
18 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
AAAAAATTTTGATTTT
Found at i:21265853 original size:139 final size:136
Alignment explanation
Indices: 21265591--21265853 Score: 440
Period size: 139 Copynumber: 1.9 Consensus size: 136
21265581 TATAATGCAA
*
21265591 TTAATTATTTTAAATAACATTGTTAATTTTTTCGATTACAATGACATGAATTTTTCTTAAAACAA
1 TTAATTATTTTAAATAACATTGTTAATTTTTTCGATTACAATGACAAGAATTTTTCTTAAAACAA
21265656 TTGGTTCCATCATAAAAAATATCCATGCCAACATAATGAGGTGAAAGGACTGCTCTTAACTCTTA
66 TTGGTTCCATCATAAAAAATATCCATGCCAACATAATGAGGTGAAAGGACTGCTCTTAACTCTTA
21265721 AGGGTG
131 AGGGTG
**
21265727 TTAATTATTTTAAATAACATTGTTAACTTTTTTTTATTACAATAATGACAAGAATTTTTCTTAAA
1 TTAATTATTTTAAATAACATTGTTAA-TTTTTTCGATTAC---AATGACAAGAATTTTTCTTAAA
21265792 AGC-ATTGGTTCCATCAT-AAAAATATCCATGCCAACATAATGAGGTGAAAGGACTGCTCTTAA
62 A-CAATTGGTTCCATCATAAAAAATATCCATGCCAACATAATGAGGTGAAAGGACTGCTCTTAA
21265854 GGGTGTTAAT
Statistics
Matches: 119, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
136 26 0.22
137 11 0.09
139 45 0.38
140 36 0.30
141 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (136 bp):
TTAATTATTTTAAATAACATTGTTAATTTTTTCGATTACAATGACAAGAATTTTTCTTAAAACAA
TTGGTTCCATCATAAAAAATATCCATGCCAACATAATGAGGTGAAAGGACTGCTCTTAACTCTTA
AGGGTG
Found at i:21269299 original size:33 final size:36
Alignment explanation
Indices: 21269262--21269343 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
21269252 ATTCGAAAAA
21269262 AATTTTGAATTTCGAA-TT-A-TTCGAATCGAGTTG
1 AATTTTGAATTTCGAATTTAAGTTCGAATCGAGTTG
***
21269295 AATTTTTTTTTTCGAATTTCAAGTTCGAATCGAGTTG
1 AATTTTGAATTTCGAATTT-AAGTTCGAATCGAGTTG
21269332 AATTTTTGAATT
1 AA-TTTTGAATT
21269344 CAAATAACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
33 13 0.34
34 2 0.05
36 1 0.03
37 16 0.42
38 6 0.16
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.48
Consensus pattern (36 bp):
AATTTTGAATTTCGAATTTAAGTTCGAATCGAGTTG
Found at i:21269361 original size:18 final size:18
Alignment explanation
Indices: 21269340--21269377 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
21269330 TGAATTTTTG
21269340 AATTCAAAT-AACTCGAAT
1 AATTCAAATAAAC-CGAAT
*
21269358 AATTCGAATAAACCGAAT
1 AATTCAAATAAACCGAAT
21269376 AA
1 AA
21269378 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCAAATAAACCGAAT
Found at i:21272544 original size:26 final size:29
Alignment explanation
Indices: 21272512--21272581 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
21272502 ATATATTATT
*
21272512 TTATTTTAATATTTAAAAATTTTATAT-A
1 TTATTTTAATATTGAAAAATTTTATATAA
* *
21272540 TT-TTTTATTTATTGAAATATTTTATATAA
1 TTATTTTA-ATATTGAAAAATTTTATATAA
*
21272569 TCATTTTAATATT
1 TTATTTTAATATT
21272582 ATTTTAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 5 0.15
28 18 0.53
29 6 0.18
30 5 0.15
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
TTATTTTAATATTGAAAAATTTTATATAA
Found at i:21272584 original size:32 final size:29
Alignment explanation
Indices: 21272491--21272597 Score: 73
Period size: 28 Copynumber: 3.7 Consensus size: 29
21272481 CCGTCTATAT
* *
21272491 TATTTTTAAATATATATTAT-TTTATTTTAA
1 TATTATTAAATAT-T-TTATATATATTTTAA
* *
21272521 TA-T-TTAAAAATTTTATATAT-TTTTTA
1 TATTATTAAATATTTTATATATATTTTAA
21272547 T-TTATTGAAATATTTTATATAATCATTTTAA
1 TATTATT-AAATATTTTATAT-AT-ATTTTAA
*
21272578 TATTATTTTAATA-TTTATAT
1 TATTA-TTAAATATTTTATAT
21272598 TAAAATAGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
26 11 0.18
27 5 0.08
28 19 0.31
29 3 0.05
30 2 0.03
31 13 0.21
32 7 0.11
33 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (29 bp):
TATTATTAAATATTTTATATATATTTTAA
Found at i:21277417 original size:18 final size:16
Alignment explanation
Indices: 21277394--21277429 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
21277384 CTTAGTAAAT
21277394 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
21277412 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
21277428 AT
1 AT
21277430 GCTGTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:21279068 original size:22 final size:22
Alignment explanation
Indices: 21279038--21279087 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
21279028 CCAAAATAAT
*
21279038 AATCACAATCATGTCATAATTG
1 AATCTCAATCATGTCATAATTG
21279060 AATCTCAATCATGTCATAATTG
1 AATCTCAATCATGTCATAATTG
21279082 AATCTC
1 AATCTC
21279088 CAATACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (22 bp):
AATCTCAATCATGTCATAATTG
Found at i:21286060 original size:11 final size:11
Alignment explanation
Indices: 21286027--21286060 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21286017 TTCCCAAGAG
21286027 GGGAATTGGCAA
1 GGGAATTGG-AA
21286039 GGGAA-TGGAA
1 GGGAATTGGAA
21286049 GGGAATTGGAA
1 GGGAATTGGAA
21286060 G
1 G
21286061 AGAAAACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 9 0.43
12 5 0.24
ACGTcount: A:0.35, C:0.03, G:0.47, T:0.15
Consensus pattern (11 bp):
GGGAATTGGAA
Found at i:21293512 original size:36 final size:36
Alignment explanation
Indices: 21293441--21293513 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
21293431 TTAACAACAC
*
21293441 AATCCCAAAATAATTTAATAACACAATAATCTGAAA
1 AATCCCAAAATAATTTAATAACACAATAATATGAAA
*
21293477 AATCCCAAAATAATTCATAATAA-ATAATAA-ATGAAA
1 AATCCCAAAATAATT--TAATAACACAATAATATGAAA
21293513 A
1 A
21293514 TGATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 21 0.64
37 6 0.18
38 6 0.18
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.25
Consensus pattern (36 bp):
AATCCCAAAATAATTTAATAACACAATAATATGAAA
Found at i:21294148 original size:30 final size:30
Alignment explanation
Indices: 21294077--21294141 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
21294067 TATAACCATC
*
21294077 ACACACAAC-AATATGTAGCACAAACAGAA
1 ACACACAGCAAATATGTAGCACAAACAGAA
** *
21294106 ACACACAGCAAATATGTAGCACGGACAGAG
1 ACACACAGCAAATATGTAGCACAAACAGAA
21294136 ACACAC
1 ACACAC
21294142 CTCAAATCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.49, C:0.26, G:0.15, T:0.09
Consensus pattern (30 bp):
ACACACAGCAAATATGTAGCACAAACAGAA
Found at i:21294700 original size:23 final size:23
Alignment explanation
Indices: 21294674--21294720 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
21294664 TAGAAAGATG
*
21294674 ATTGTTTACCTTTGATGGAAGAA
1 ATTGGTTACCTTTGATGGAAGAA
21294697 ATTGGTTACCTTTGATGGAAGAA
1 ATTGGTTACCTTTGATGGAAGAA
21294720 A
1 A
21294721 ATTGAGTTTT
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:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (23 bp):
ATTGGTTACCTTTGATGGAAGAA
Found at i:21296941 original size:12 final size:12
Alignment explanation
Indices: 21296924--21296949 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21296914 TGTTATCATG
21296924 ATGAATGCTATT
1 ATGAATGCTATT
21296936 ATGAATGCTATT
1 ATGAATGCTATT
21296948 AT
1 AT
21296950 TTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:21297649 original size:17 final size:16
Alignment explanation
Indices: 21297623--21297656 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
21297613 AGCATAGGAA
*
21297623 TTTAATTTAGTTTTAAT
1 TTTAACTTAG-TTTAAT
21297640 TTTAACTTAGTTTAAT
1 TTTAACTTAGTTTAAT
21297656 T
1 T
21297657 CAATTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAACTTAGTTTAAT
Found at i:21300720 original size:11 final size:11
Alignment explanation
Indices: 21300704--21300728 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21300694 CGGCAAATGA
21300704 TGACAAGGTAG
1 TGACAAGGTAG
21300715 TGACAAGGTAG
1 TGACAAGGTAG
21300726 TGA
1 TGA
21300729 ATAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.20
Consensus pattern (11 bp):
TGACAAGGTAG
Found at i:21302558 original size:9 final size:9
Alignment explanation
Indices: 21302546--21302582 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
21302536 TTTTCTAATT
21302546 TTTAATTTA
1 TTTAATTTA
21302555 TTTAATTTA
1 TTTAATTTA
*
21302564 -TTAACTT-
1 TTTAATTTA
21302571 TTTAATTTA
1 TTTAATTTA
21302580 TTT
1 TTT
21302583 TAAATTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:21302562 original size:16 final size:15
Alignment explanation
Indices: 21302528--21302578 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
21302518 GGTGGTAAGA
*
21302528 AATTTTT-ATTTTCT
1 AATTTTTAATTTTTT
21302542 AATTTTTAATTTATTT
1 AATTTTTAATTT-TTT
*
21302558 AATTTATTAACTTTTT
1 AATTT-TTAATTTTTT
21302574 AATTT
1 AATTT
21302579 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 15 0.47
17 6 0.19
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTAATTTTTT
Found at i:21302575 original size:8 final size:7
Alignment explanation
Indices: 21302528--21302578 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 7
21302518 GGTGGTAAGA
21302528 AATTTTT
1 AATTTTT
21302535 -ATTTTCT
1 AATTTT-T
21302542 AATTTTT
1 AATTTTT
21302549 AATTTATTT
1 AA-TT-TTT
21302558 AATTTATT
1 AATTT-TT
21302566 AACTTTTT
1 AA-TTTTT
21302574 AATTT
1 AATTT
21302579 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.13
7 8 0.21
8 17 0.45
9 8 0.21
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:21302593 original size:26 final size:25
Alignment explanation
Indices: 21302544--21302593 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21302534 TATTTTCTAA
*
21302544 TTTTTAATTTATTTAATTTATTAAC
1 TTTTTAATTTATTTAAATTATTAAC
*
21302569 TTTTTAATTTATTTTAAATTGTTAA
1 TTTTTAATTTA-TTTAAATTATTAA
21302594 TATTTTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTAATTTATTTAAATTATTAAC
Found at i:21302599 original size:26 final size:24
Alignment explanation
Indices: 21302541--21302600 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
21302531 TTTTATTTTC
*
21302541 TAATTTTTAATTTATTTAATTTAT
1 TAATTTTTAATTTATTTAAATTAT
*
21302565 TAACTTTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAATTTA-TTTAAATTAT
21302591 TAATATTTTA
1 TAAT-TTTTA
21302601 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.10
25 12 0.39
26 16 0.52
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:21303497 original size:15 final size:15
Alignment explanation
Indices: 21303477--21303532 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
21303467 TAAAAAAGAG
21303477 GAAGAAGACCTTAAA
1 GAAGAAGACCTTAAA
**
21303492 GAAGAAGATCCCGAAGA
1 GAAGAAGA-CCTTAA-A
*
21303509 CGAAGAAGACCTTGAA
1 -GAAGAAGACCTTAAA
21303525 GAAGAAGA
1 GAAGAAGA
21303533 AGATTCTGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 16 0.48
16 5 0.15
17 4 0.12
18 8 0.24
ACGTcount: A:0.50, C:0.14, G:0.27, T:0.09
Consensus pattern (15 bp):
GAAGAAGACCTTAAA
Found at i:21303498 original size:18 final size:18
Alignment explanation
Indices: 21303471--21303535 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 18
21303461 GCAAGTTAAA
*
21303471 AAAGAGGAAGAAGACCTT
1 AAAGAAGAAGAAGACCTT
* *
21303489 AAAGAAGAAG-A-TCC-C
1 AAAGAAGAAGAAGACCTT
* *
21303504 GAAGACGAAGAAGACCTT
1 AAAGAAGAAGAAGACCTT
*
21303522 GAAGAAGAAGAAGA
1 AAAGAAGAAGAAGA
21303536 TTCTGAGGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
15 8 0.22
16 3 0.08
17 3 0.08
18 22 0.61
ACGTcount: A:0.52, C:0.12, G:0.28, T:0.08
Consensus pattern (18 bp):
AAAGAAGAAGAAGACCTT
Found at i:21306686 original size:9 final size:9
Alignment explanation
Indices: 21306659--21306701 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
21306649 AGCAAACATT
21306659 TTTTTTCTTC
1 TTTTTT-TTC
21306669 TTTTCTTTTC
1 TTTT-TTTTC
21306679 TTTTTTTTC
1 TTTTTTTTC
**
21306688 TCATTTTTC
1 TTTTTTTTC
21306697 TTTTT
1 TTTTT
21306702 CAAGTGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 15 0.54
10 11 0.39
11 2 0.07
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:21306694 original size:22 final size:23
Alignment explanation
Indices: 21306657--21306700 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
21306647 ATAGCAAACA
21306657 TTTTTTTTCTTC-TTTTCTTTTC
1 TTTTTTTTCTTCTTTTTCTTTTC
21306679 TTTTTTTTC-TCATTTTTCTTTT
1 TTTTTTTTCTTC-TTTTTCTTTT
21306701 TCAAGTGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.10
22 9 0.45
23 9 0.45
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTTTCTTCTTTTTCTTTTC
Found at i:21322613 original size:3 final size:3
Alignment explanation
Indices: 21322605--21322637 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21322595 AGCAAGCTGG
21322605 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
21322638 TCCTGTGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21326810 original size:14 final size:15
Alignment explanation
Indices: 21326786--21326816 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
21326776 GAGTGTTTTG
21326786 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
21326801 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
21326815 AA
1 AA
21326817 TAAAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:21327392 original size:13 final size:13
Alignment explanation
Indices: 21327369--21327402 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
21327359 CTCATTTCAC
21327369 AACTGAAAATTAAA
1 AACT-AAAATTAAA
*
21327383 AACTAAAATTGAA
1 AACTAAAATTAAA
21327396 AACTAAA
1 AACTAAA
21327403 GTCTAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (13 bp):
AACTAAAATTAAA
Found at i:21328669 original size:21 final size:22
Alignment explanation
Indices: 21328639--21328680 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
21328629 ATTCACATGT
21328639 TTTCTTACTCATGTTTCTTTTG
1 TTTCTTACTCATGTTTCTTTTG
* *
21328661 TTTC-TACTCTTTTTTCTTTT
1 TTTCTTACTCATGTTTCTTTT
21328681 TTCTTTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTCTTACTCATGTTTCTTTTG
Found at i:21335158 original size:17 final size:18
Alignment explanation
Indices: 21335136--21335170 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21335126 TCTCCTATAG
21335136 TTTCACA-ATCTATAGTT
1 TTTCACAGATCTATAGTT
*
21335153 TTTCACAGTTCTATAGTT
1 TTTCACAGATCTATAGTT
21335171 GTCACATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTCACAGATCTATAGTT
Found at i:21335175 original size:17 final size:15
Alignment explanation
Indices: 21335130--21335180 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
21335120 TTACAGTCTC
21335130 CTATAGTTTCACAAT
1 CTATAGTTTCACAAT
*
21335145 CTATAGTTTTTCACAGTT
1 CTATAG--TTTCACA-AT
21335163 CTATAGTTGTCAC-AT
1 CTATAGTT-TCACAAT
21335178 CTA
1 CTA
21335181 AAGATCACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.33
16 2 0.07
17 11 0.37
18 7 0.23
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (15 bp):
CTATAGTTTCACAAT
Found at i:21336210 original size:50 final size:50
Alignment explanation
Indices: 21336090--21336220 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 50
21336080 AAACATTGTT
* * *
21336090 TGTGGACATGCCACCACTGATTTGCAGATAAACTGCCATTGATAACACTTA
1 TGTGGACAAGCCACCATTGATTTGCAGATAAACCGCCATTGATAACAC-TA
**
21336141 TGTGGACAAGCCACCATTGATTTGCAGATTTACCGCCATTGATTTAA-A-TA
1 TGTGGACAAGCCACCATTGATTTGCAGATAAACCGCCATTGA--TAACACTA
*
21336191 TGTGAACAAGCCACCATTGATTTGCAGATA
1 TGTGGACAAGCCACCATTGATTTGCAGATA
21336221 TATTGCCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
50 30 0.42
51 37 0.52
52 1 0.01
53 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (50 bp):
TGTGGACAAGCCACCATTGATTTGCAGATAAACCGCCATTGATAACACTA
Found at i:21336229 original size:50 final size:50
Alignment explanation
Indices: 21336090--21336231 Score: 180
Period size: 50 Copynumber: 2.8 Consensus size: 50
21336080 AAACATTGTT
* * *
21336090 TGTGGACATGCCACCACTGATTTGCAGATAAACTGCCATTGATAACACTTA
1 TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTGATAACAC-TA
* *
21336141 TGTGGACAAGCCACCATTGATTTGCAGATTTACCGCCATTGATTTAA-A-TA
1 TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTGA--TAACACTA
* *
21336191 TGTGAACAAGCCACCATTGATTTGCAGATATATTGCCATTG
1 TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTG
21336232 CTTCCACTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
50 39 0.49
51 37 0.46
52 1 0.01
53 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTGATAACACTA
Found at i:21339323 original size:28 final size:28
Alignment explanation
Indices: 21339292--21339412 Score: 113
Period size: 28 Copynumber: 4.3 Consensus size: 28
21339282 GTTACTCTGA
*
21339292 ATCTTGCT-TGGTAAGAGCATTATTCTAC
1 ATCTGGCTCTGGT-AGAGCATTATTCTAC
*
21339320 ATCTGGCTCCGGTAGAGCATTATTCTAC
1 ATCTGGCTCTGGTAGAGCATTATTCTAC
* * *
21339348 ATCTGGCTCGGGTAGAGCGTTACTCTGA-
1 ATCTGGCTCTGGTAGAGCATTATTCT-AC
* *
21339376 ATCTTGCT-TGGGTTGAGCATTATTCTAC
1 ATCTGGCTCT-GGTAGAGCATTATTCTAC
* *
21339404 TTCTAGCTC
1 ATCTGGCTC
21339413 GAAAAGAGCG
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
27 1 0.01
28 71 0.93
29 4 0.05
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (28 bp):
ATCTGGCTCTGGTAGAGCATTATTCTAC
Found at i:21339437 original size:28 final size:27
Alignment explanation
Indices: 21339396--21339567 Score: 164
Period size: 28 Copynumber: 6.1 Consensus size: 27
21339386 GGTTGAGCAT
* *
21339396 TATTCTACTTCTAGCTCGAAAAGAGCGA
1 TATTCTAATTCTGGCTC-AAAAGAGCGA
* * * *
21339424 TATTCTGATCCTAGCTCAGAAATAGCGA
1 TATTCTAATTCTGGCTCA-AAAGAGCGA
* * *
21339452 TATTTTGATTTTGGCTCGAAAAGAGCGA
1 TATTCTAATTCTGGCTC-AAAAGAGCGA
21339480 TATTCTAATTCTGGCTCAAAAAGAGCGA
1 TATTCTAATTCTGGCTC-AAAAGAGCGA
*
21339508 TATTCTAATTCTGGCTCAGAAAGAGAGA
1 TATTCTAATTCTGGCTCA-AAAGAGCGA
* * * *
21339536 TATTCCAGTACTGGCTCAGAAAGAGCAA
1 TATTCTAATTCTGGCTCA-AAAGAGCGA
21339564 TATT
1 TATT
21339568 TTGTTCTAGG
Statistics
Matches: 122, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.02
28 119 0.98
29 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (27 bp):
TATTCTAATTCTGGCTCAAAAGAGCGA
Found at i:21339470 original size:56 final size:56
Alignment explanation
Indices: 21339409--21339583 Score: 192
Period size: 56 Copynumber: 3.1 Consensus size: 56
21339399 TCTACTTCTA
* * * *
21339409 GCTCGAAAAGAGCGATATTCTGATCCTAGCTCAGAAATAGCGATATTTTGATTTTG
1 GCTCGAAAAGAGCGATATTCTAATACTGGCTCAGAAAGAGCGATATTTTGATTTTG
* * * * *
21339465 GCTCGAAAAGAGCGATATTCTAATTCTGGCTCAAAAAGAGCGATATTCTAATTCTG
1 GCTCGAAAAGAGCGATATTCTAATACTGGCTCAGAAAGAGCGATATTTTGATTTTG
* * * * *
21339521 GCTC-AGAAAGAGAGATATTCCAGTACTGGCTCAGAAAGAGCAATATTTTG-TTCTAG
1 GCTCGA-AAAGAGCGATATTCTAATACTGGCTCAGAAAGAGCGATATTTTGATT-TTG
21339577 GCTCGAA
1 GCTCGAA
21339584 TGGATAATGA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
55 3 0.03
56 94 0.96
57 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (56 bp):
GCTCGAAAAGAGCGATATTCTAATACTGGCTCAGAAAGAGCGATATTTTGATTTTG
Found at i:21339551 original size:84 final size:84
Alignment explanation
Indices: 21339390--21339567 Score: 198
Period size: 84 Copynumber: 2.1 Consensus size: 84
21339380 TGCTTGGGTT
* * * * * *
21339390 GAGCATTATTCTACTTCTAGCTCGAAAAGAGCGATATTCTGATCCTAGCTCAGAAATAGCGATAT
1 GAGCAATATTCTAATTCTAGCTCAAAAAGAGCGATATTCTAATCCTAGCTCAGAAAGAGAGATAT
** **
21339455 TTTGATTTTGGCTC-GAAAA
66 TCAGATACTGGCTCAG-AAA
* * * *
21339474 GAGCGATATTCTAATTCTGGCTCAAAAAGAGCGATATTCTAATTCTGGCTCAGAAAGAGAGATAT
1 GAGCAATATTCTAATTCTAGCTCAAAAAGAGCGATATTCTAATCCTAGCTCAGAAAGAGAGATAT
21339539 TCCAG-TACTGGCTCAGAAA
66 T-CAGATACTGGCTCAGAAA
21339558 GAGCAATATT
1 GAGCAATATT
21339568 TTGTTCTAGG
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 75 0.97
85 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (84 bp):
GAGCAATATTCTAATTCTAGCTCAAAAAGAGCGATATTCTAATCCTAGCTCAGAAAGAGAGATAT
TCAGATACTGGCTCAGAAA
Found at i:21340332 original size:54 final size:54
Alignment explanation
Indices: 21340245--21340359 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 54
21340235 GTGCAGATTT
*
21340245 CACACGGGCAACACACGGGCTGGGACACAACCGTTTGGCCCTATTTAGCATGGA
1 CACATGGGCAACACACGGGCTGGGACACAACCGTTTGGCCCTATTTAGCATGGA
* * *
21340299 CACATGGGCAACACACGGGCTGGGACACGACCGTTTGGCCTTATTTTGCATGGA
1 CACATGGGCAACACACGGGCTGGGACACAACCGTTTGGCCCTATTTAGCATGGA
21340353 CACATGG
1 CACATGG
21340360 CCTAGCACAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.24, C:0.28, G:0.29, T:0.19
Consensus pattern (54 bp):
CACATGGGCAACACACGGGCTGGGACACAACCGTTTGGCCCTATTTAGCATGGA
Found at i:21343319 original size:31 final size:31
Alignment explanation
Indices: 21343281--21343354 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
21343271 GTTAAAGTGA
**
21343281 ACGGGAAAAGGAAAGATGAAATTGGGGTTAT
1 ACGGGAAAAGGAAAGATGAAATCAGGGTTAT
*
21343312 ACGGGAAAAGGAAAGATGAGATCAGGGTTAT
1 ACGGGAAAAGGAAAGATGAAATCAGGGTTAT
*
21343343 ACGAGAAAAGGA
1 ACGGGAAAAGGA
21343355 TTCATTGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.45, C:0.05, G:0.35, T:0.15
Consensus pattern (31 bp):
ACGGGAAAAGGAAAGATGAAATCAGGGTTAT
Found at i:21344406 original size:18 final size:18
Alignment explanation
Indices: 21344370--21344407 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
21344360 GTAATAAAGT
*
21344370 ATATATAATAAAATTAAA
1 ATATATAATAAAATCAAA
21344388 ATATATAA-AAATATCAAA
1 ATATATAATAAA-ATCAAA
21344406 AT
1 AT
21344408 GAAGCTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATATAATAAAATCAAA
Found at i:21345156 original size:6 final size:6
Alignment explanation
Indices: 21345145--21345191 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
21345135 TCTTCCTCTG
*
21345145 CTCTTT CTCTTT CTCTTT CTCTTT CTCTTT CTCTTC CTCTTT CTCTT
1 CTCTTT CTCTTT CTCTTT CTCTTT CTCTTT CTCTTT CTCTTT CTCTT
21345192 CCTTTCCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
CTCTTT
Found at i:21345192 original size:12 final size:12
Alignment explanation
Indices: 21345145--21345209 Score: 84
Period size: 12 Copynumber: 5.8 Consensus size: 12
21345135 TCTTCCTCTG
*
21345145 CTCTTTCTCTTT
1 CTCTTTCTCTTC
*
21345157 CTCTTTCTCTTT
1 CTCTTTCTCTTC
21345169 CTCTTTCTCTTC
1 CTCTTTCTCTTC
21345181 CTCTTTCTCTT-
1 CTCTTTCTCTTC
21345192 C-CTTTC-CTTC
1 CTCTTTCTCTTC
21345202 C-CTTTCTC
1 CTCTTTCTC
21345210 GTTGGAGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
9 3 0.06
10 11 0.22
11 2 0.04
12 34 0.68
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
CTCTTTCTCTTC
Found at i:21349033 original size:16 final size:16
Alignment explanation
Indices: 21348997--21349031 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21348987 ATTCAACCCG
21348997 TTTTAAATTTATAATA
1 TTTTAAATTTATAATA
*
21349013 TTTTAAATTT-TATTA
1 TTTTAAATTTATAATA
21349028 TTTT
1 TTTT
21349032 TATATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTAAATTTATAATA
Found at i:21363756 original size:25 final size:23
Alignment explanation
Indices: 21363728--21363773 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
21363718 GTTTGATCCA
21363728 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
21363753 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
21363774 CCTTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:21367891 original size:52 final size:52
Alignment explanation
Indices: 21367821--21368071 Score: 286
Period size: 52 Copynumber: 4.8 Consensus size: 52
21367811 TAAGCCATAA
* * * *
21367821 ATTAAGAGGTCCGATGACTTTGTATCATCATGAGTATATGCATCCTTTATGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* * * *
21367873 ATTAAGAGGTCTGATGACTCCGTGTCATCGTGAGTATATGAATCCTTTACGA
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* * * *
21367925 ATTAAGAGATCTGATGACTCTATGTCATCATGAGTAAATGAATCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* ** * *
21367977 ATTAGGAGGTCCGATGACTCTGTGTCATTGTGAGTATATAAATCCCTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* * * ** * *
21368029 ATTATGAGGTTCGGTGGTTATGTGTCATCGTGAGTATATGAAT
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAAT
21368072 GAAGTGAAAT
Statistics
Matches: 168, Mismatches: 31, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 168 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
Found at i:21372034 original size:23 final size:23
Alignment explanation
Indices: 21372006--21372056 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
21371996 ATCAAGTGTT
21372006 TGTGGCGTATTTGGTAAAACCTA
1 TGTGGCGTATTTGGTAAAACCTA
* * * *
21372029 TGTGGCTTATTTTGTAAAGCCTT
1 TGTGGCGTATTTGGTAAAACCTA
21372052 TGTGG
1 TGTGG
21372057 TATATTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (23 bp):
TGTGGCGTATTTGGTAAAACCTA
Found at i:21372062 original size:23 final size:22
Alignment explanation
Indices: 21372004--21372062 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
21371994 CTATCAAGTG
*
21372004 TTTGTGGCGTATTTGGTAAAACC
1 TTTGTGG-TTATTTGGTAAAACC
* * *
21372027 TATGTGGCTTATTTTGTAAAGCC
1 TTTGTGG-TTATTTGGTAAAACC
21372050 TTTGTGGTATATT
1 TTTGTGGT-TATT
21372063 CTATGATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (22 bp):
TTTGTGGTTATTTGGTAAAACC
Found at i:21383691 original size:24 final size:23
Alignment explanation
Indices: 21383646--21383691 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
21383636 AGATTCAGAC
*
21383646 TTTTCTTGTTCTCTGTTTCTTTA
1 TTTTCTTGTTCTCTGATTCTTTA
21383669 TTTTC-TGTTCATCTTGATTCTTT
1 TTTTCTTGTTC-TC-TGATTCTTT
21383692 TCAATTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.07, C:0.17, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTCTTGTTCTCTGATTCTTTA
Found at i:21386587 original size:20 final size:20
Alignment explanation
Indices: 21386555--21386597 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
21386545 ATTATCACTG
21386555 TTCATGATATGA-CTCTACTA
1 TTCATGATATGACCT-TACTA
21386575 TTCATGACT-TGACCTTACTA
1 TTCATGA-TATGACCTTACTA
21386595 TTC
1 TTC
21386598 CTAGGACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (20 bp):
TTCATGATATGACCTTACTA
Found at i:21387341 original size:23 final size:25
Alignment explanation
Indices: 21387315--21387360 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21387305 CCAATTAGGG
21387315 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
21387338 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
21387361 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:21390311 original size:11 final size:11
Alignment explanation
Indices: 21390295--21390340 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
21390285 TCATGTTTTT
21390295 AAAAAAATTGA
1 AAAAAAATTGA
*
21390306 AAAAAAATTTA
1 AAAAAAATTGA
**
21390317 AAAAATTTTG-
1 AAAAAAATTGA
21390327 AAAAAAATTGA
1 AAAAAAATTGA
21390338 AAA
1 AAA
21390341 GTTCAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:21390316 original size:21 final size:22
Alignment explanation
Indices: 21390292--21390333 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21390282 CTTTCATGTT
21390292 TTTAAAAAA-ATTGAAAAAAAA
1 TTTAAAAAATATTGAAAAAAAA
*
21390313 TTTAAAAAATTTTGAAAAAAA
1 TTTAAAAAATATTGAAAAAAA
21390334 TTGAAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
TTTAAAAAATATTGAAAAAAAA
Found at i:21390396 original size:5 final size:5
Alignment explanation
Indices: 21390359--21390422 Score: 58
Period size: 5 Copynumber: 11.8 Consensus size: 5
21390349 AAAAAATTAG
*
21390359 TTTA- TTTAT TTTCATT TTTAGT TTTAGT TTTAT TTTAT TCTAT TTTATT
1 TTTAT TTTAT TTT-A-T TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTA-T
21390408 TTTAAT TTTAT TTTA
1 TTT-AT TTTAT TTTA
21390423 ATTATGCACT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.08
5 22 0.42
6 21 0.40
7 5 0.10
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:21391363 original size:12 final size:12
Alignment explanation
Indices: 21391346--21391375 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21391336 TAAAAAAAGT
21391346 AAAAAATCGAAA
1 AAAAAATCGAAA
*
21391358 AAAAAATTGAAA
1 AAAAAATCGAAA
21391370 AAAAAA
1 AAAAAA
21391376 AGAATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAAAATCGAAA
Found at i:21391403 original size:16 final size:16
Alignment explanation
Indices: 21391355--21391389 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
21391345 TAAAAAATCG
21391355 AAAAAAA-AATTGAAA
1 AAAAAAAGAATTGAAA
21391370 AAAAAAAGAATTGAAA
1 AAAAAAAGAATTGAAA
21391386 AAAA
1 AAAA
21391390 TTGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAAAAGAATTGAAA
Found at i:21392457 original size:23 final size:25
Alignment explanation
Indices: 21392431--21392476 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21392421 CCAATTAGGG
21392431 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
21392454 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
21392477 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:21392887 original size:15 final size:15
Alignment explanation
Indices: 21392850--21392887 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
21392840 TTATGTGTGC
*
21392850 TTAATTCTTGATATA
1 TTAATTCTTGAGATA
*
21392865 GT-ATTCTTGAGATA
1 TTAATTCTTGAGATA
21392879 TTAATTCTT
1 TTAATTCTT
21392888 ATTTGATGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (15 bp):
TTAATTCTTGAGATA
Found at i:21401252 original size:18 final size:18
Alignment explanation
Indices: 21401229--21401267 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
21401219 GTATAATATT
21401229 CAAAAATTTAAAAATCAC
1 CAAAAATTTAAAAATCAC
21401247 CAAAAATTTAAAAATCAC
1 CAAAAATTTAAAAATCAC
21401265 CAA
1 CAA
21401268 TTATCATGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (18 bp):
CAAAAATTTAAAAATCAC
Found at i:21409696 original size:7 final size:7
Alignment explanation
Indices: 21409684--21409721 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
21409674 TAAATCAAAT
21409684 GTGTTGA
1 GTGTTGA
21409691 GTGTTGA
1 GTGTTGA
21409698 GTGTTGA
1 GTGTTGA
21409705 GTGTTGA
1 GTGTTGA
21409712 GTGTTGA
1 GTGTTGA
21409719 GTG
1 GTG
21409722 CTAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.00, G:0.45, T:0.42
Consensus pattern (7 bp):
GTGTTGA
Found at i:21412280 original size:21 final size:21
Alignment explanation
Indices: 21412242--21412281 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21412232 GGTTCTGTTT
* *
21412242 CTTCCTTGTCTTCTTCCTTTC
1 CTTCCTCGTCTTCATCCTTTC
*
21412263 CTTCCTCGTCTTGATCCTT
1 CTTCCTCGTCTTCATCCTT
21412282 CTCTTGATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.38, G:0.07, T:0.53
Consensus pattern (21 bp):
CTTCCTCGTCTTCATCCTTTC
Found at i:21428775 original size:21 final size:19
Alignment explanation
Indices: 21428749--21428799 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
21428739 TTTTTAGTGT
21428749 CGGTAGATGCATGACTTGTAC
1 CGGTAGAT-CAT-ACTTGTAC
*
21428770 CGGTAGAAATCATACTTGTAT
1 CGGTAG--ATCATACTTGTAC
21428791 CGGTAGATC
1 CGGTAGATC
21428800 TAGCACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.11
21 19 0.70
22 3 0.11
23 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (19 bp):
CGGTAGATCATACTTGTAC
Found at i:21440476 original size:20 final size:20
Alignment explanation
Indices: 21440428--21440476 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
21440418 GAGATTCCAG
*
21440428 TTTGGTGCCTCTGTTTGCAC
1 TTTGGTGCCCCTGTTTGCAC
** *
21440448 TTTAATGCCCCTGTTTGCAT
1 TTTGGTGCCCCTGTTTGCAC
21440468 TTTGGTGCC
1 TTTGGTGCC
21440477 TCTAATTACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.08, C:0.24, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTGGTGCCCCTGTTTGCAC
Found at i:21445399 original size:92 final size:95
Alignment explanation
Indices: 21445295--21445477 Score: 309
Period size: 94 Copynumber: 2.0 Consensus size: 95
21445285 TTATAATTAT
*
21445295 TAATTATAATGATTTCGTT-AATATT-AAAACATGGAAGTTAATATCCTTTTAGAAAGGATATAA
1 TAATTATAATGATTTCATTAAATATTAAAAACATGGAAGTTAATATCCTTTTAGAAAGGATATAA
21445358 TGTTTTAATAAACCTTCCATA-ATTTAACG
66 TGTTTTAATAAACCTTCCATATATTTAACG
* * *
21445387 TAATTATCATGATTTCATTAAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAATGATATAA
1 TAATTATAATGATTTCATTAAATATTAAAAACATGGAAGTTAATATCCTTTTAGAAAGGATATAA
21445452 TGTTTTAATAAACCTTCCATATATTT
66 TGTTTTAATAAACCTTCCATATATTT
21445478 CTTTAAAGTA
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
92 17 0.20
93 6 0.07
94 57 0.68
95 4 0.05
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (95 bp):
TAATTATAATGATTTCATTAAATATTAAAAACATGGAAGTTAATATCCTTTTAGAAAGGATATAA
TGTTTTAATAAACCTTCCATATATTTAACG
Found at i:21445572 original size:123 final size:122
Alignment explanation
Indices: 21445407--21445775 Score: 553
Period size: 123 Copynumber: 3.0 Consensus size: 122
21445397 GATTTCATTA
* *
21445407 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
*
21445472 ATATTTCTTTAAAGTAATATTTCCAATTTAATATGAGATATTATATAAAAGGAAATT
66 ATATTTCTTTAAAGTAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATT
* *
21445529 GAATATTAAAAACATGAAAGTTAATATCCTTTTGGGAAGGATATAATGTTTTTAATAAATCTTCC
1 -AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATG-TTTTAATAAACCTTCC
* * *
21445594 ACATATTTCTTTAAAGGAATATTTTCATTTTAATATGAGATATTATAATAAAA--AAATT
64 ATATATTTCTTTAAAGTAATATTTCCATTTTAATATGAGATATTAT-ATAAAAGGAAATT
*
21445652 AATATTAAAAAATATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCA
1 AATATT-AAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCA
* * *
21445717 TGTATTTCTCTAAAGATATATATTTCCATTTTAATATGAGATATTAAAATAAAAGGAAA
65 TATATTTCTTTAAAG-TA-ATATTTCCATTTTAATATGAGATATT-ATATAAAAGGAAA
21445776 GATAGTAGAA
Statistics
Matches: 221, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
122 34 0.15
123 89 0.40
124 88 0.40
125 7 0.03
126 3 0.01
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (122 bp):
AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAAGTAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATT
Found at i:21451317 original size:17 final size:16
Alignment explanation
Indices: 21451274--21451320 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
21451264 CTACAGAATA
21451274 TTTTT-TCT-TTTTTC
1 TTTTTCTCTATTTTTC
*
21451288 TTTTTCTTGTATTTTTC
1 TTTTTC-TCTATTTTTC
21451305 TTTTTTCTCTATTTTT
1 -TTTTTCTCTATTTTT
21451321 TATCACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 5 0.19
16 2 0.07
17 14 0.52
18 6 0.22
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTCTCTATTTTTC
Found at i:21465756 original size:23 final size:23
Alignment explanation
Indices: 21465743--21465799 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
21465733 TTACACATTA
21465743 ATCACATTAACATTTAAGCATAT
1 ATCACATTAACATTTAAGCATAT
* *
21465766 ATTACATTAACATTTAGGCATAT
1 ATCACATTAACATTTAAGCATAT
*
21465789 AACACA-TAACA
1 ATCACATTAACA
21465800 CATTTGATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (23 bp):
ATCACATTAACATTTAAGCATAT
Found at i:21468959 original size:215 final size:216
Alignment explanation
Indices: 21467746--21471430 Score: 3524
Period size: 215 Copynumber: 17.3 Consensus size: 216
21467736 TGGGCTTGGA
* * *
21467746 CATTTTGTAAACAAC-TTTGTTCTTAT-TATTAAAAACTTATTTACGTGAGAATTGTTTCTCTGT
1 CATTTTGTAAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * *
21467809 T-GTTCTGGGATGAA-TTTCCGAACTTATCAAACTTTTACTAGCTCTTTTATAACTTCGGTT-CC
65 TGGTTCTTGGCTGAACTTT-CGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCC
* * **
21467871 TGAAAGTATTCAATACGATCCATTCCTTCGAGCAA-TTTTCTGAACATTCTATGCTCTAGAAATC
129 T-AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATC
*
21467935 GCATCATTTGGTTTAAATAGTTTGT
192 GCATCATTTGGTCTAAATAGTTTGT
*
21467960 CATTTTGTAAACAACTTTTGGTCTTAT-AATTAAAAACTTATTTACATGAGAATTGTTTCTCTCT
1 CATTTTGTAAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * * * *
21468024 T-GTTCTT-GCACGAACTTTCAAACTTCTCACACTTTTTCGAGTTCTTTTATAACTTCGATTCCT
65 TGGTTCTTGGC-TGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCC
* * *
21468087 TCAAGTATTCAAGACGATCCA--------AGC-ATTTTTCCAGACATTCCATGCAT-GAGAAATC
129 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGA-ACATTCCATGC-TCGGGAAATC
* * ***
21468142 GCATAATTTGATCTAAATAGTTAAC
192 GCATCATTTGGTCTAAATAGTTTGT
* * * * *
21468167 CATTTTGTAAACAACTTTTTGTCTTTAAATTAATAACTTATTTACGTTAGAA----TT-TATCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * *
21468227 GGTT-TTGGAC-GAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTGGTT-CCT
66 GGTTCTTGG-CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT
* * * *
21468289 GAGAGTATTCAAGATGATCCATTCCTTTGA-CAAATTTTAT-GAACATTCCATGCTCGAGAAATC
130 -AAAGTATTCAAGACGATCCATTCCTTCGAGC-AATTTT-TCGAACATTCCATGCTCGGGAAATC
*
21468352 ACAT-ATCGTTGAGTCTAAATAGTTTGT
192 GCATCAT--TTG-GTCTAAATAGTTTGT
*
21468379 CATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGATTT-TCTCT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTTCTCTCT
* * * * *
21468443 TGGTCCTTGGCCT-AAC-TTCTTAACTTGTCAAACTTTTACGAGTTCTTTTACAACTTTGATTCT
65 TGGTTCTTGG-CTGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC-
* * * ** * * * *
21468506 TCT-AAGTATTCAAGACGACCCATTCCTTCAAGCAACCTTCCAAACATTTCATGCTCGGGAAATT
127 CCTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATC
**
21468570 GCATCATTTGGTCTAAATAGCATGT
192 GCATCATTTGGTCTAAATAGTTTGT
* *
21468595 CATTTTGTAAACAACTTTTCGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * * * **
21468660 GGTCCTTGGCCT-AAC-TTCTTAACTTGTCAAACTTTTACGAGTTCTTTTACAACTTCGATTTTT
66 GGTTCTTGG-CTGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG-GTTCC
* * * * *
21468723 CT-AAGTATT-AAGAGGATCCATTCATTTGAGCAATTTTTCGAACTTTCCATGCTTGGGAAATCG
128 CTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCG
21468786 CATCATTTGGTCTAAATAGTTTGT
193 CATCATTTGGTCTAAATAGTTTGT
* * *
21468810 TATTTTGTAAACAACTTTTGGTCTATGAATTAAAAACTTA-TTAAGTGAGAATTGTTTCTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * *
21468874 GGTACTTGGCTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATTACTTTGGTTCCCTA
66 GGTTCTTGGCTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCTA
* * * * *
21468939 AAGTAATCAAGACTATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTTGGGAAATCGTAT
131 AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT
* * *
21469004 CATTTGGTTTAAATTGTTAGT
196 CATTTGGTCTAAATAGTTTGT
* * * *
21469025 CATTTTGTAAAAAACTTTTGGTTTTTGAATTAAAAACTTATTTACGTAATAATTGTTTCTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * * * * * **
21469090 -GTTCTTGGAC-AAACTTCCGAACTTGTCAAAATTTTACTAGTTCTTTTACAACTTCGATTCATT
66 GGTTCTTGG-CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT
* * * * * **
21469153 AAAGTATTCAAGACGATCCATTACTTCGAGCAAATTTCCAAACATTCCTTGCTTTGGAAATCGCA
130 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCA
*
21469218 TCATTTGATCTAAATAGTTTGT
195 TCATTTGGTCTAAATAGTTTGT
* * * *
21469240 CATTTTGCAAACAAATTTTGGTCTTAT-AATTAAAAACTTATTTACGTGACAATCGTTTCTCTCT
1 CATTTTGTAAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * * * * *
21469304 TGGTTCTTCGCCGAATTTTCGAACTTGCCAAAATTTTATGAGTTCTTTTATAACTTTGGTTCCAT
65 TGGTTCTTGGCTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT
* * * *
21469369 AAAATATTCAAGACGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCAGAAAATCGCA
130 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCA
* *
21469434 TCATTTGGTCCAAATAGTTAGT
195 TCATTTGGTCTAAATAGTTTGT
* **
21469456 CATTTTGTAAACAAC-TTTGGTCTTAT-TATTAAAAACTTATTTATATGAGAATTGTTTCTCTCT
1 CATTTTGTAAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * *
21469519 T-GTTCTTGGAC-AAACTTCCGAACTTATCAAACTTTTACTAGATCTTTTATAACTTCGGTT-CC
65 TGGTTCTTGG-CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCC
* *
21469581 TGAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCTGGAAATCG
129 T-AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCG
21469646 CATCATTTGGTCTAAATAGTTTGT
193 CATCATTTGGTCTAAATAGTTTGT
*
21469670 CATTTTGTAAACAACTTTTGGTCTTAT-AATTAAAAACCTATTTACGTGAGAATTGTTTCTCTCT
1 CATTTTGTAAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * * ** *
21469734 T-GTTCTT-GCACGAACTTTCAAACTTCTCACACTTTTACGAGTTCTTTTATAACTTTGAATCCT
65 TGGTTCTTGGC-TGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCC
* * * * * * * *
21469797 TTAAGTTTTCAAGACGATCCAGTCCTTCAAGTAA-TTTTCCAGACATTACATGCACGGGAAATCG
129 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGA-ACATTCCATGCTCGGGAAATCG
* * *
21469861 CATAATTTGATCTAAATAGTTTGC
193 CATCATTTGGTCTAAATAGTTTGT
* * * * *
21469885 CATTTTGTAAATAGCTTTTTGTCTTTAAATTAATAACTTATTTACGTGAGAA----TT-TCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * * *
21469945 AGTT-TTGGATGAACTTTCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTT-CCTG
66 GGTTCTTGGCTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT-
* * * * ** *
21470008 AGAGTATTCAAGATGATCTATTCCTTTGA-CAAATTTTAT-GAACATTCCATGCTCAAGAAATCA
130 AAAGTATTCAAGACGATCCATTCCTTCGAGC-AATTTT-TCGAACATTCCATGCTCGGGAAATCG
*
21470071 CATCA-TTGAATCTAAATAGTTTGT
193 CATCATTTG-GTCTAAATAGTTTGT
* * * *
21470095 CATTTTGTAAATAACTTTTGGTCTTTAAATTAAAAACTTATTTACATGAGAATTGTTTGTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * * * *
21470160 GGTCCTTAGCCT-AAC-TTCTTAACTTGTCAAACTTTTACGAGTTCTTTTACAACTTCGGTTCTT
66 GGTTCTT-GGCTGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC-C
* * * * * *
21470223 CT-AAGTATTCAAGACGATCCATTCATTTGAGTAATTTTTTGAACTTTCCATGCTCGAGAAATCG
128 CTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCG
* * *
21470287 CATTATTTTGTCCAAATAGTTTGT
193 CATCATTTGGTCTAAATAGTTTGT
* * * * * * * *** * * **
21470311 CAATTTGTAAAAAAC---T--T-ATT-AAGTGAGAA-TTGTTT-C-T--CTCTTGGTTC-ATGGT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* ** * * * *
21470363 CGAACTT-TC-GAACTTGTCAAACTT-T--------TACGAGTTCTTTTATAACTTTGGTTCCTT
66 GGTTCTTGGCTGAACTT-TCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT
* * * *
21470417 GAAGTAATCAAGATGATCCATTCGTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCA
130 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCA
* *
21470482 TCATTTGGTCTAAATTGTTAGT
195 TCATTTGGTCTAAATAGTTTGT
* * * * * * *
21470504 CTTTTTGTAAACAACTTTTGGTTTTTGAACTCAAAACTTGTTTATGTAAGAATTGTTTCTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * * * * * * **
21470569 -GATCATGGATGAACTTCCAAACTTGTCAATA-TTTTACTAGTTCTATTATAACTTCGGTTCATT
66 GGTTCTTGGCTGAACTTTCGAACTTGTCAA-ACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT
* * *
21470632 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCTGGAAATTGCA
130 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCA
21470697 TCATTTGGTCTAAATAGTTTGT
195 TCATTTGGTCTAAATAGTTTGT
* * * *
21470719 CATTTTGTAAACAAATTTTAGTCTTAT-AATTAAACACTTATTTACGTGAGAATTATTTC-CTCT
1 CATTTTGTAAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * **
21470782 T-GTTCTT-GCATGAAC-TTCTGAACTTCTCACACTTTTATGACTTCTTTTATAACTTCTATTCC
65 TGGTTCTTGGC-TGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCC
* * * * * *
21470844 TTAAAGTAATCAAGATGATCC-TGTCCTTCGAG-AAATTTTCTAGACATTCCATGCAT-AGGAAA
128 CTAAAGTATTCAAGACGATCCAT-TCCTTCGAGCAATTTTTCGA-ACATTCCATGC-TCGGGAAA
* **
21470906 TCGCATAATTTGGTCTAAATAGTTTAC
190 TCGCATCATTTGGTCTAAATAGTTTGT
* * *
21470933 CATTTTGTAAACAACTTTTTGTCTTTAAATTAATAACTTATTTACGTGAGAA----TT-TCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
** * *
21470993 GGTTCTTGGAAGAACTTTCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTT-CTTG
66 GGTTCTTGGCTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCT-
* * *
21471057 AGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTAT-GAACATTCCATGCTCGGGAAATCAC
130 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-TCGAACATTCCATGCTCGGGAAATCGC
*
21471121 ATCATTTGGTCTAAATAGTATGT
194 ATCATTTGGTCTAAATAGTTTGT
* * * * *
21471144 CATTTTGTAAATAACTTTTCGTCTTTGAATTAAAAACTTTTTTACGTGAG-ATTTTTTTTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* * * * * * *
21471208 GGTCCTCGACCT-AAC-TTCTTAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCT
66 GGTTCTTG-GCTGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCC
* * * * *
21471271 TAAAGTATTCAAAACGATCCATTCCTTCAAGC-AGTTTTCTGAACATTTCATGCTCGGGAAATAG
129 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCG
*
21471335 CATTATTTGG-CTTAAATAGTATT-T
193 CATCATTTGGTC-TAAATAGT-TTGT
* * * * * *
21471359 CATCTTGTAAGCAACTTTTAGTCTTTGAATTAAAAACATATTTTCATGAGAATTGTTTCTCTCTT
1 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
21471424 GGTTCTT
66 GGTTCTT
21471431 AAGCTTACAG
Statistics
Matches: 2875, Mismatches: 459, Indels: 272
0.80 0.13 0.08
Matches are distributed among these distances:
192 1 0.00
193 109 0.04
196 1 0.00
198 1 0.00
199 2 0.00
200 6 0.00
201 13 0.00
202 71 0.02
203 15 0.01
204 6 0.00
205 10 0.00
206 13 0.00
207 98 0.03
208 6 0.00
209 15 0.01
210 194 0.07
211 171 0.06
212 71 0.02
213 25 0.01
214 408 0.14
215 1068 0.37
216 449 0.16
217 21 0.01
218 96 0.03
219 3 0.00
220 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (216 bp):
CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
GGTTCTTGGCTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCCTA
AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT
CATTTGGTCTAAATAGTTTGT
Found at i:21470470 original size:193 final size:194
Alignment explanation
Indices: 21470126--21470729 Score: 504
Period size: 193 Copynumber: 3.0 Consensus size: 194
21470116 TCTTTAAATT
* * * *
21470126 AAAAACTTATTTACATGAGAATTGTTTGTCTCTTGGTCCTTAGCCTAACTTCTTAACTTGTCAAA
1 AAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGTCCATAGCCGAACTTCTGAACTTGTCAAA
* * * *
21470191 CTTTTACGAGTTCTTTTACAACTTCGGTTCTTCTAAGTATTCAAGACGATCCATTCATTTGAGTA
66 CTTTTACGAGTTCTTTTACAACTTCGGTTCTTCGAAGTAATCAAGACGATCCATTCATTCGAGCA
* * * * *
21470256 ATTTTTTGAACTTTCCATGCTCGAGAAATCGCATTATTTTGTCCAAATAGTTTGTCAATTTGTA
131 ATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTAGTCAATTTGTA
* * *
21470320 AAAAACTTA-TTA-AGTGAGAATTGTTTCTCTCTTGGTTCATGGTCGAACTT-TCGAACTTGTCA
1 AAAAACTTATTTACA-TGAGAATTGTTTCTCTCTTGGTCCATAGCCGAACTTCT-GAACTTGTCA
* * * *
21470382 AACTTTTACGAGTTCTTTTATAACTTTGGTTCCTT-GAAGTAATCAAGATGATCCATTCGTTCGA
64 AACTTTTACGAGTTCTTTTACAACTTCGGTT-CTTCGAAGTAATCAAGACGATCCATTCATTCGA
* * * **
21470446 GCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATTGTTAGTCTTTTTG
128 GCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTAGTCAATTTG
21470511 TA
193 TA
* * * *
21470513 AACAACTTTTGGTTTTTGAACTCAAAACTTGTTTATGTAAGAATTGTTTCTCTCTTGAT-CATGG
1 AAAAAC------TTATT----T----AC------ATG--AGAATTGTTTCTCTCTTGGTCCATAG
** ** * * * * *
21470577 ATGAACTTCCAAACTTGTCAATA-TTTTACTAGTTCTATTATAACTTCGGTTCATT-AAAGTATT
44 CCGAACTTCTGAACTTGTCAA-ACTTTTACGAGTTCTTTTACAACTTCGGTTC-TTCGAAGTAAT
* * *
21470640 CAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCTG-GAAATTGCATCATTTG
107 CAAGACGATCCATTCATTCGAGCAATTTTTCGAACATTCCATGCTC-GAGAAATCGCATCATTTG
* * *
21470704 GTCTAAATAGTTTGTCATTTTGTA
171 GTCCAAATAGTTAGTCAATTTGTA
21470728 AA
1 AA
21470730 CAAATTTTAG
Statistics
Matches: 335, Mismatches: 44, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
192 2 0.01
193 156 0.47
194 12 0.04
199 2 0.01
200 1 0.00
204 1 0.00
208 1 0.00
214 3 0.01
215 136 0.41
216 21 0.06
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (194 bp):
AAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGTCCATAGCCGAACTTCTGAACTTGTCAAA
CTTTTACGAGTTCTTTTACAACTTCGGTTCTTCGAAGTAATCAAGACGATCCATTCATTCGAGCA
ATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTAGTCAATTTGTA
Found at i:21474113 original size:15 final size:16
Alignment explanation
Indices: 21474084--21474118 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
21474074 TTTAACAGAT
21474084 TAAAAGTAAAATAAAC
1 TAAAAGTAAAATAAAC
*
21474100 TAAAA-TAAATTAAAC
1 TAAAAGTAAAATAAAC
21474115 TAAA
1 TAAA
21474119 GCTTAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAAAGTAAAATAAAC
Found at i:21475032 original size:20 final size:20
Alignment explanation
Indices: 21475007--21475046 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21474997 AACATGGAGG
* *
21475007 TATTGATACTTATGCCCAAA
1 TATTGATACCTATGCACAAA
21475027 TATTGATACCTATGCACAAA
1 TATTGATACCTATGCACAAA
21475047 CTGACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (20 bp):
TATTGATACCTATGCACAAA
Found at i:21478383 original size:17 final size:18
Alignment explanation
Indices: 21478355--21478567 Score: 79
Period size: 17 Copynumber: 12.0 Consensus size: 18
21478345 TATGCTATGT
*
21478355 CAAAGTAATAAATATATA
1 CAAAGTAATAAAAATATA
21478373 CAAAG-AATAAAAATATA
1 CAAAGTAATAAAAATATA
** * *
21478390 GTAACTAATAGAAATAT-
1 CAAAGTAATAAAAATATA
* * *
21478407 -ATA-T-ATATATATATA
1 CAAAGTAATAAAAATATA
* *
21478422 TAAAG-AATGAAAATATA
1 CAAAGTAATAAAAATATA
21478439 -ATAAGTAATAGAAATATATA
1 CA-AAGTAATA-AAA-ATATA
* *
21478459 TAAAG-AATGAAAATATA
1 CAAAGTAATAAAAATATA
** *
21478476 TTAAGTAATAGAAATATGTA
1 CAAAGTAATA-AAA-ATATA
* *
21478496 TAAAG-AATGAAAATATA
1 CAAAGTAATAAAAATATA
**
21478513 TTAAGTAATAGAAATATATA
1 CAAAGTAATA-AAA-ATATA
*
21478533 TAAAG-AATAAAAATATA
1 CAAAGTAATAAAAATATA
* *
21478550 -ATAAGTATTAAATATATA
1 CA-AAGTAATAAAAATATA
21478568 TATATATAGT
Statistics
Matches: 151, Mismatches: 26, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
14 8 0.05
15 1 0.01
16 5 0.03
17 49 0.32
18 43 0.28
19 19 0.13
20 25 0.17
21 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (18 bp):
CAAAGTAATAAAAATATA
Found at i:21478421 original size:49 final size:49
Alignment explanation
Indices: 21478366--21478460 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
21478356 AAAGTAATAA
*
21478366 ATATATACAAAGAATAAAAATATAGTAACTAATAGAAATATATATATAT
1 ATATATACAAAGAATAAAAATATAATAACTAATAGAAATATATATATAT
* * *
21478415 ATATATATAAAGAATGAAAATATAATAAGTAATAGAAATATATATA
1 ATATATACAAAGAATAAAAATATAATAACTAATAGAAATATATATA
21478461 AAGAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (49 bp):
ATATATACAAAGAATAAAAATATAATAACTAATAGAAATATATATATAT
Found at i:21478456 original size:37 final size:37
Alignment explanation
Indices: 21478415--21478571 Score: 253
Period size: 37 Copynumber: 4.2 Consensus size: 37
21478405 ATATATATAT
21478415 ATATATATAAAGAATGAAAATATAATAAGTAATAGAA
1 ATATATATAAAGAATGAAAATATAATAAGTAATAGAA
*
21478452 ATATATATAAAGAATGAAAATATATTAAGTAATAGAA
1 ATATATATAAAGAATGAAAATATAATAAGTAATAGAA
* *
21478489 ATATGTATAAAGAATGAAAATATATTAAGTAATAGAA
1 ATATATATAAAGAATGAAAATATAATAAGTAATAGAA
* *
21478526 ATATATATAAAGAATAAAAATATAATAAGTATTA-AA
1 ATATATATAAAGAATGAAAATATAATAAGTAATAGAA
21478562 TATATATATA
1 -ATATATATA
21478572 TATAGTTGCT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
36 2 0.02
37 111 0.98
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (37 bp):
ATATATATAAAGAATGAAAATATAATAAGTAATAGAA
Found at i:21478561 original size:18 final size:18
Alignment explanation
Indices: 21478357--21478567 Score: 120
Period size: 18 Copynumber: 11.9 Consensus size: 18
21478347 TGCTATGTCA
*
21478357 AAGTAATAAATATATACA-
1 AAGTAATAAAAATATA-AT
*
21478375 AAG-AATAAAAATATAGT
1 AAGTAATAAAAATATAAT
* *
21478392 AACTAATAGAAATAT-AT
1 AAGTAATAAAAATATAAT
* *
21478409 -A-T-ATATATATAT-AT
1 AAGTAATAAAAATATAAT
*
21478423 AAAG-AATGAAAATATAAT
1 -AAGTAATAAAAATATAAT
*
21478441 AAGTAATAGAAATATATAT
1 AAGTAATAAAAATATA-AT
* *
21478460 AAAG-AATGAAAATATATT
1 -AAGTAATAAAAATATAAT
* *
21478478 AAGTAATAGAAATATGTAT
1 AAGTAATAAAAATAT-AAT
* *
21478497 AAAG-AATGAAAATATATT
1 -AAGTAATAAAAATATAAT
*
21478515 AAGTAATAGAAATATATAT
1 AAGTAATAAAAATATA-AT
21478534 AAAG-AATAAAAATATAAT
1 -AAGTAATAAAAATATAAT
* *
21478552 AAGTATTAAATATATA
1 AAGTAATAAAAATATA
21478568 TATATATAGT
Statistics
Matches: 147, Mismatches: 29, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
14 10 0.07
15 1 0.01
16 2 0.01
17 33 0.22
18 58 0.39
19 34 0.23
20 9 0.06
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (18 bp):
AAGTAATAAAAATATAAT
Found at i:21480528 original size:12 final size:12
Alignment explanation
Indices: 21480511--21480545 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21480501 TTTTAAGAGC
21480511 ATAAAATAAAAG
1 ATAAAATAAAAG
*
21480523 ATAAAATAAAAT
1 ATAAAATAAAAG
*
21480535 AGAAAATAAAA
1 ATAAAATAAAA
21480546 AGTTTGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:21480533 original size:17 final size:17
Alignment explanation
Indices: 21480511--21480545 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21480501 TTTTAAGAGC
21480511 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
21480528 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
21480545 A
1 A
21480546 AGTTTGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:21493129 original size:12 final size:12
Alignment explanation
Indices: 21493112--21493150 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
21493102 TTCTCAAGAG
21493112 GAAAAAGAAAAT
1 GAAAAAGAAAAT
*
21493124 GAAAAACAAGAA-
1 GAAAAAGAA-AAT
21493136 GAAAAAGAAAAT
1 GAAAAAGAAAAT
21493148 GAA
1 GAA
21493151 TAACAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (12 bp):
GAAAAAGAAAAT
Found at i:21493133 original size:24 final size:24
Alignment explanation
Indices: 21493106--21493161 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
21493096 GGAGAGTTCT
*
21493106 CAAGAGGAAAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
*
21493130 CAAGAAGAAAAAGAAAATGAATAA
1 CAAGAAGAAAAAGAAAATGAAAAA
21493154 CAAGAAGA
1 CAAGAAGA
21493162 TACCCATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.70, C:0.05, G:0.20, T:0.05
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAATGAAAAA
Found at i:21495182 original size:17 final size:18
Alignment explanation
Indices: 21495162--21495200 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
21495152 CTACTTCTTG
21495162 TTTAGATTAATT-AGAGT
1 TTTAGATTAATTAAGAGT
*
21495179 TTTAGTTTAATTAAGAGT
1 TTTAGATTAATTAAGAGT
21495197 TTTA
1 TTTA
21495201 TTTAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (18 bp):
TTTAGATTAATTAAGAGT
Found at i:21500437 original size:17 final size:17
Alignment explanation
Indices: 21500415--21500453 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
21500405 GAGAGTTTAA
21500415 GTCCTTGTGCTGTTCCT
1 GTCCTTGTGCTGTTCCT
21500432 GTCCTTGTGCTGTTCCT
1 GTCCTTGTGCTGTTCCT
21500449 GTCCT
1 GTCCT
21500454 ATTGGTGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.31, G:0.23, T:0.46
Consensus pattern (17 bp):
GTCCTTGTGCTGTTCCT
Found at i:21512605 original size:323 final size:323
Alignment explanation
Indices: 21512018--21512974 Score: 1799
Period size: 323 Copynumber: 3.0 Consensus size: 323
21512008 AACACACAAA
* *
21512018 TGAGTCCCGAGTATGAAGCATCATTGTAAACCACAA-TTTTTTTTCTGGGCACCGATTGAGTCAA
1 TGAGTCCCGAGTATGAAGCATCATTGTAAACCATAATTTTTTTTTCTGGGCTCCGATTGAGTCAA
* * *
21512082 CACAGGTGCCTTCGTTAAAACTGCTTTAATTTGTTCAAAACTTTTCTGTCTTTCATAGTCTATTC
66 CACAGGTGCCTTCGTCAAAACTGCTTTAAGTTGTTCAAAACTTTTATGTCTTTCATAGTCTATTC
*
21512147 AAACACCACATTATTTTGAAGTAGTTTCTTTAAAGGTGCAACAATAAGGGAAAATTCTTCAACAA
131 AAACACCACATTATTTTGAAGTAGTTTCGTTAAAGGTGCAACAATAAGGGAAAATTCTTCAACAA
21512212 ACCTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAACACTTTTTGGCAGCTTCT
196 ACCTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAACACTTTTTGGCAGCTTCT
21512277 ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACACGGATTCGATCTACTGATAATAACCAAC
261 ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACACGGATTCGATCTACTGATAATAACCAAC
*
21512340 TGAGTCCCGAGTATGAAGCATCATTGTAAACCATAATTTTTTTTTCTGGGCTCCAATTGAGTCAA
1 TGAGTCCCGAGTATGAAGCATCATTGTAAACCATAATTTTTTTTTCTGGGCTCCGATTGAGTCAA
*
21512405 CACAGGTGCCTTCGTCAAAACTGCTTTAAGTTGTTCAAAACTTTTATGTCTTTCATAATCTATTC
66 CACAGGTGCCTTCGTCAAAACTGCTTTAAGTTGTTCAAAACTTTTATGTCTTTCATAGTCTATTC
21512470 AAACACCACATTATTTTGAAGTAGTTTCGTTAAAGGTGCAACAATAAGGGAAAATTCTTCAACAA
131 AAACACCACATTATTTTGAAGTAGTTTCGTTAAAGGTGCAACAATAAGGGAAAATTCTTCAACAA
21512535 ACCTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAACACTTTTTGGCAGCTTCT
196 ACCTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAACACTTTTTGGCAGCTTCT
21512600 ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACACGGATTCGATCTACTGATAATAACCAAC
261 ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACACGGATTCGATCTACTGATAATAACCAAC
21512663 TGAGTCCCGAGTATGAAGCATCATTGTAAACCATAATTTTTTTTTCTGGGCTCCGATTGAGTCAA
1 TGAGTCCCGAGTATGAAGCATCATTGTAAACCATAATTTTTTTTTCTGGGCTCCGATTGAGTCAA
21512728 CACAGGTGCCTTCGTCAAAACTGCTTTAAGTTGTTCAAAACTTTTATGTCTTTCATAGTCTATTC
66 CACAGGTGCCTTCGTCAAAACTGCTTTAAGTTGTTCAAAACTTTTATGTCTTTCATAGTCTATTC
*
21512793 AAACACCACATTATTTTGAAGTAGTTTCGTTAAAGGTGAAACAATAAGGGAAAATTCTTCAACAA
131 AAACACCACATTATTTTGAAGTAGTTTCGTTAAAGGTGCAACAATAAGGGAAAATTCTTCAACAA
* *
21512858 ACTTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAATACTTTTTGGCAGCTTCT
196 ACCTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAACACTTTTTGGCAGCTTCT
*
21512923 ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACATGGATTCGATCTACTGA
261 ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACACGGATTCGATCTACTGA
21512975 CAAAATATGG
Statistics
Matches: 620, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
322 35 0.06
323 585 0.94
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (323 bp):
TGAGTCCCGAGTATGAAGCATCATTGTAAACCATAATTTTTTTTTCTGGGCTCCGATTGAGTCAA
CACAGGTGCCTTCGTCAAAACTGCTTTAAGTTGTTCAAAACTTTTATGTCTTTCATAGTCTATTC
AAACACCACATTATTTTGAAGTAGTTTCGTTAAAGGTGCAACAATAAGGGAAAATTCTTCAACAA
ACCTACGATAATAACCAACTAAACGTAAGAAATCTAAACCTCGGTAACACTTTTTGGCAGCTTCT
ACTCCAAGGTCGCTTCAATTTTCTTCAGATCCACACGGATTCGATCTACTGATAATAACCAAC
Found at i:21514402 original size:51 final size:51
Alignment explanation
Indices: 21514341--21514478 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 51
21514331 TGCATGACTT
*
21514341 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATG-TCAG
* * * *
21514393 GATTTATGATGCATA-TTTAACGAACATGTA-AGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAACTTTAACTAACATG-AGAGTTACATAATGCATGTCAG
*
21514443 TATTTATGATGCAAAC-TTAACTAATCATGAGAGTTA
1 GATTTATGATGCAAACTTTAACTAA-CATGAGAGTTA
21514479 ATGGATGTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
49 1 0.01
50 49 0.67
51 18 0.25
52 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (51 bp):
GATTTATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATGTCAG
Found at i:21514463 original size:50 final size:50
Alignment explanation
Indices: 21514298--21514463 Score: 142
Period size: 50 Copynumber: 3.3 Consensus size: 50
21514288 ATGGTTTAAA
* * * *
21514298 GATGCAAACTGAATGAACTAATGG-A-TTACTAAATGCATGAC-TTGATTTAAT
1 GATGCAAACTTAACGAAC--ATGGAAGTTACTTAATGCATGTCATT-ATTT-AT
* * * **
21514349 GATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AGGATTTAT
1 GATGCAAAC-TTAACGAACATGGAAGTTACTTAATGCATG-TCATTATTTAT
* * *
21514400 GATGCATATTTAACGAACATGTAAGTTACTTAATGCATGTCATTATTTAT
1 GATGCAAACTTAACGAACATGGAAGTTACTTAATGCATGTCATTATTTAT
21514450 GATGCAAACTTAAC
1 GATGCAAACTTAAC
21514464 TAATCATGAG
Statistics
Matches: 91, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
49 1 0.01
50 49 0.54
51 19 0.21
52 22 0.24
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (50 bp):
GATGCAAACTTAACGAACATGGAAGTTACTTAATGCATGTCATTATTTAT
Found at i:21516040 original size:21 final size:21
Alignment explanation
Indices: 21515999--21516052 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
21515989 CTGCTTGATC
21515999 ACTTTCTTCTTT-TTCAATCTT
1 ACTTTCTT-TTTCTTCAATCTT
**
21516020 ACTTTCTTTTTCTTCTTTCTT
1 ACTTTCTTTTTCTTCAATCTT
* *
21516041 GCTCTCTTTTTC
1 ACTTTCTTTTTC
21516053 AATTTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.07, C:0.26, G:0.02, T:0.65
Consensus pattern (21 bp):
ACTTTCTTTTTCTTCAATCTT
Found at i:21516100 original size:18 final size:17
Alignment explanation
Indices: 21516079--21516112 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21516069 TCACAATTTC
21516079 TTTCAGTCTCTCTTTCTT
1 TTTCAGTCTCT-TTTCTT
*
21516097 TTTCATTCTCTTTTCT
1 TTTCAGTCTCTTTTCT
21516113 CACACACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTCAGTCTCTTTTCTT
Found at i:21516171 original size:21 final size:22
Alignment explanation
Indices: 21516129--21516189 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 22
21516119 CTCTCTTTTT
*
21516129 ATTTCCTTTTCTTT-TTCCCTC-
1 ATTT-CTTTTTTTTCTTCCCTCA
*
21516150 ATTTCTTTTTTTTCTTCTCTCA
1 ATTTCTTTTTTTTCTTCCCTCA
*
21516172 ATCTCCTTTATTTTTCTT
1 AT-TTCTTT-TTTTTCTT
21516190 TCATTTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 8 0.24
21 10 0.30
22 2 0.06
23 5 0.15
24 8 0.24
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTCTTTTTTTTCTTCCCTCA
Found at i:21518484 original size:50 final size:50
Alignment explanation
Indices: 21518407--21518528 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 50
21518397 ACTTGATTTA
*
21518407 ATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AGGATTTATG
1 ATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAGGATTTATG
* * * **
21518458 ATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCATTATTTATG
1 ATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAGGATTTATG
*
21518508 ATGCAAACTTAACTAATCATG
1 ATGCAAATTTAACTAA-CATG
21518529 AGAGTTAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.02
50 50 0.82
51 10 0.16
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (50 bp):
ATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAGGATTTATG
Found at i:21518761 original size:17 final size:17
Alignment explanation
Indices: 21518730--21518762 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21518720 CAAACACTTA
21518730 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
21518747 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
21518763 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:21542029 original size:2 final size:2
Alignment explanation
Indices: 21542022--21542053 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
21542012 TTGTACAGTA
21542022 AT AT AT AT AT -T AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21542054 TATGTGACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:21542040 original size:13 final size:13
Alignment explanation
Indices: 21542022--21542053 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
21542012 TTGTACAGTA
21542022 ATATATATATTAT
1 ATATATATATTAT
21542035 ATATATATATTAT
1 ATATATATATTAT
21542048 ATATAT
1 ATATAT
21542054 TATGTGACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:21542056 original size:9 final size:8
Alignment explanation
Indices: 21542022--21542053 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
21542012 TTGTACAGTA
21542022 ATATATAT
1 ATATATAT
21542030 AT-TATAT
1 ATATATAT
21542037 ATATATAT
1 ATATATAT
21542045 -TATATAT
1 ATATATAT
21542052 AT
1 AT
21542054 TATGTGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.64
8 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATATATAT
Found at i:21549660 original size:17 final size:17
Alignment explanation
Indices: 21549629--21549661 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21549619 TTAAGGACTT
21549629 TTTTAATTTTATTTAAG
1 TTTTAATTTTATTTAAG
21549646 TTTT-ATTTTAGTTTAA
1 TTTTAATTTTA-TTTAA
21549662 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTATTTAAG
Found at i:21549932 original size:50 final size:50
Alignment explanation
Indices: 21549866--21550001 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 50
21549856 TATCATGATC
* *
21549866 AGTTAAGTTTGCATCATAAATAATGACATGCATTATGTAACTTACATGTT
1 AGTTAAATTTGCATCATAAATAATGACATGCATTATGTAACTCACATGTT
* ** *
21549916 AGTTAAATATGCATCATAAATCCT-ATCATGCATTATGTAACTCCCATGTT
1 AGTTAAATTTGCATCATAAATAATGA-CATGCATTATGTAACTCACATGTT
*
21549966 AGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATT
1 AGTTAAA-TTTGCATCA-TAAAT-AATGACATGCATT
21550002 TAGTAATCCA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
49 1 0.01
50 49 0.69
51 8 0.11
52 13 0.18
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (50 bp):
AGTTAAATTTGCATCATAAATAATGACATGCATTATGTAACTCACATGTT
Found at i:21551210 original size:20 final size:19
Alignment explanation
Indices: 21551187--21551236 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
21551177 TCGAAAAGGT
21551187 GAAAAAAATTCGAAAAAAAA
1 GAAAAAAATT-GAAAAAAAA
21551207 GAAAAAATATTGAAAAAAAA
1 GAAAAAA-ATTGAAAAAAAA
*
21551227 AAAAAAAATT
1 GAAAAAAATT
21551237 TTGAAGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (19 bp):
GAAAAAAATTGAAAAAAAA
Found at i:21551212 original size:21 final size:19
Alignment explanation
Indices: 21551188--21551236 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
21551178 CGAAAAGGTG
21551188 AAAAAAATTCGAAAAAAAAGA
1 AAAAAAATT-GAAAAAAAA-A
*
21551209 AAAAATATTGAAAAAAAAA
1 AAAAAAATTGAAAAAAAAA
21551228 AAAAAAATT
1 AAAAAAATT
21551237 TTGAAGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 9 0.35
21 8 0.31
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (19 bp):
AAAAAAATTGAAAAAAAAA
Found at i:21551240 original size:21 final size:21
Alignment explanation
Indices: 21551199--21551241 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21551189 AAAAAATTCG
*
21551199 AAAAAAAAGAAAAAATATTGA
1 AAAAAAAAAAAAAAATATTGA
*
21551220 AAAAAAAAAAAAAAATTTTGA
1 AAAAAAAAAAAAAAATATTGA
21551241 A
1 A
21551242 GTTTAAAAAA
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:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAAAAAAAAAAAATATTGA
Found at i:21551281 original size:22 final size:20
Alignment explanation
Indices: 21551189--21551288 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 20
21551179 GAAAAGGTGA
21551189 AAAAAATTCGAAAAAAAA-G
1 AAAAAATTCGAAAAAAAAGG
* **
21551208 AAAAAATATTGAAAAAAAAAA
1 AAAAAAT-TCGAAAAAAAAGG
*
21551229 AAAAAATTTTGAAGTTTAAAAAAAGG
1 AAAAAA-TTCG-A----AAAAAAAGG
21551255 -AAAAATTCGAATTAAAAAAGG
1 AAAAAATTCGAA--AAAAAAGG
*
21551276 AAAAAAATCGAAA
1 AAAAAATTCGAAA
21551289 GAAGAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
19 8 0.12
20 11 0.17
21 17 0.27
22 12 0.19
23 1 0.02
24 3 0.05
25 5 0.08
26 7 0.11
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (20 bp):
AAAAAATTCGAAAAAAAAGG
Found at i:21552307 original size:18 final size:17
Alignment explanation
Indices: 21552275--21552308 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21552265 AAAAGTTGTG
21552275 AGAAAAGAGAATGAAAA
1 AGAAAAGAGAATGAAAA
*
21552292 AGAAAGAGAGACTGAAA
1 AGAAA-AGAGAATGAAA
21552309 GAAATTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.03, G:0.26, T:0.06
Consensus pattern (17 bp):
AGAAAAGAGAATGAAAA
Found at i:21552371 original size:21 final size:21
Alignment explanation
Indices: 21552335--21552388 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
21552325 AAAGAAAATT
* *
21552335 GAAAAAGAGAGCAAGAGAGAA
1 GAAAAAGAAAGTAAGAGAGAA
**
21552356 GAAAAAGAAAGTAAGATTGAA
1 GAAAAAGAAAGTAAGAGAGAA
21552377 -AAAGAAGAAAGT
1 GAAA-AAGAAAGT
21552389 GATCAAGCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.63, C:0.02, G:0.28, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAGTAAGAGAGAA
Found at i:21553701 original size:17 final size:17
Alignment explanation
Indices: 21553681--21553713 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21553671 TTTAAGGACT
21553681 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
21553698 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
21553714 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:21553853 original size:33 final size:34
Alignment explanation
Indices: 21553805--21553869 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
21553795 AAGATTGTGA
* *
21553805 TTTAATTATGTCATGCATTAT-TAATCTACATCT
1 TTTAAATATGACATGCATTATGTAATCTACATCT
*
21553838 TTTAAATATGACATGCATTATGTGATCTACAT
1 TTTAAATATGACATGCATTATGTAATCTACAT
21553870 TTAATAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (34 bp):
TTTAAATATGACATGCATTATGTAATCTACATCT
Found at i:21553986 original size:50 final size:50
Alignment explanation
Indices: 21553926--21554039 Score: 122
Period size: 50 Copynumber: 2.2 Consensus size: 50
21553916 TCATTAAGTT
*
21553926 TGCATCATAAATAATGA-CATACATTAAGTAACTTACATGTTAGTTAAATA
1 TGCATCATAAATAAT-ATCATACATTAAGTAACTCACATGTTAGTTAAATA
* ** * * * *
21553976 TGCATTATAAATCCTATCATGCATTATGTAACTCCCATGTTAGTTAAAGTT
1 TGCATCATAAATAATATCATACATTAAGTAACTCACATGTTAGTTAAA-TA
21554027 TGCATCATTAAAT
1 TGCATCA-TAAAT
21554040 CAAGTCATGC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.02
50 39 0.75
51 7 0.13
52 5 0.10
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (50 bp):
TGCATCATAAATAATATCATACATTAAGTAACTCACATGTTAGTTAAATA
Found at i:21557774 original size:18 final size:18
Alignment explanation
Indices: 21557732--21557860 Score: 159
Period size: 18 Copynumber: 7.1 Consensus size: 18
21557722 GGGATCCAAT
* *
21557732 TGCTCTCACAAGCCAGTA
1 TGCTCTAACGAGCCAGTA
*
21557750 TTGCTCTCACGAGCCAGTA
1 -TGCTCTAACGAGCCAGTA
21557769 TGCTCTAACGAGCCAGTA
1 TGCTCTAACGAGCCAGTA
* *
21557787 TGCTCAAACGAGTCAGTA
1 TGCTCTAACGAGCCAGTA
* *
21557805 TGCTCAAACGAGCCAATA
1 TGCTCTAACGAGCCAGTA
* *
21557823 TGCTCAAACGAGCTAGTA
1 TGCTCTAACGAGCCAGTA
*
21557841 TGCTCTAACGAGTCAGTA
1 TGCTCTAACGAGCCAGTA
21557859 TG
1 TG
21557861 TTATTCCTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
18 82 0.83
19 17 0.17
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (18 bp):
TGCTCTAACGAGCCAGTA
Found at i:21558603 original size:20 final size:21
Alignment explanation
Indices: 21558573--21558615 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
21558563 AGGTTTGTCT
* *
21558573 TGAAGAAGAAGAAGAAGATGA
1 TGAAGAAGAAGAACAAAATGA
21558594 TGAA-AAGAAGAACAAAATGA
1 TGAAGAAGAAGAACAAAATGA
21558614 TG
1 TG
21558616 TTTAATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.58, C:0.02, G:0.28, T:0.12
Consensus pattern (21 bp):
TGAAGAAGAAGAACAAAATGA
Found at i:21568915 original size:27 final size:28
Alignment explanation
Indices: 21568835--21568918 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 28
21568825 AATATTTAAA
*
21568835 TATAAATATTTAATGATTATATTAAATATT
1 TATAAATAATTAAT-ATTA-ATTAAATATT
* *
21568865 TAAAATATAATTTATTTATTTTAATTAAAT-TT
1 TATAA-ATAA-TTA---ATATTAATTAAATATT
21568897 TATAAATAATTAATATTAATTA
1 TATAAATAATTAATATTAATTA
21568919 CTTATAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
27 9 0.20
30 7 0.16
31 7 0.16
32 9 0.20
33 7 0.16
34 3 0.07
35 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TATAAATAATTAATATTAATTAAATATT
Found at i:21569044 original size:22 final size:23
Alignment explanation
Indices: 21569019--21569069 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
21569009 ATATTAATTA
21569019 ATTTAAATATTATTA-AATAT-AT
1 ATTTAAATATT-TTATAATATAAT
*
21569041 ATTT-ATTATTTTATAATATAAT
1 ATTTAAATATTTTATAATATAAT
21569063 ATTTAAA
1 ATTTAAA
21569070 ATAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 10 0.42
22 10 0.42
23 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTAAATATTTTATAATATAAT
Found at i:21576989 original size:26 final size:27
Alignment explanation
Indices: 21576960--21577010 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21576950 TGCAGCTTAA
*
21576960 CTGGCGAACTC-AACTCGCCAAACATG
1 CTGGCGAACCCTAACTCGCCAAACATG
*
21576986 CTGGCGAACCCTAGCTCGCCAAACA
1 CTGGCGAACCCTAACTCGCCAAACA
21577011 CATTGGCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.29, C:0.37, G:0.20, T:0.14
Consensus pattern (27 bp):
CTGGCGAACCCTAACTCGCCAAACATG
Found at i:21589834 original size:24 final size:26
Alignment explanation
Indices: 21589807--21589860 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
21589797 GAGAGGACAT
21589807 AAAAGTGGAAGAAG-AAGA-AGG-AGG
1 AAAAGT-GAAGAAGAAAGAGAGGAAGG
21589831 AAAA--GAAGAAGAAAGAGAGGAAGG
1 AAAAGTGAAGAAGAAAGAGAGGAAGG
21589855 AAAAGT
1 AAAAGT
21589861 AGTCGAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 7 0.28
22 4 0.16
23 3 0.12
24 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.37, T:0.04
Consensus pattern (26 bp):
AAAAGTGAAGAAGAAAGAGAGGAAGG
Found at i:21591230 original size:13 final size:13
Alignment explanation
Indices: 21591212--21591236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21591202 CCCATTTAGT
21591212 CATTTTTAGCATA
1 CATTTTTAGCATA
21591225 CATTTTTAGCAT
1 CATTTTTAGCAT
21591237 TTTTTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATA
Found at i:21593584 original size:32 final size:32
Alignment explanation
Indices: 21593543--21593605 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
21593533 GCCATCCATA
* * *
21593543 CATGTACCTGAAATATATTAATTAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
21593575 CATGTACCTGAAACACATTAATCAGCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
21593606 AATTTCAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:21593701 original size:39 final size:39
Alignment explanation
Indices: 21593658--21593748 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
21593648 TCTAAAACTT
*
21593658 AGACACCTTAAAAACAACTATTAAATATGTATCAAAATA
1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
*
21593697 AGACACATTAAAAACAACTATTAAATATGTATCAAACTA
1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
21593736 AGACACATTAAAA
1 AGACACATTAAAA
21593749 CCCTATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.24
Consensus pattern (39 bp):
AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
Found at i:21596923 original size:22 final size:21
Alignment explanation
Indices: 21596898--21596972 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 21
21596888 TTCTTTTCAC
21596898 TTTCTTTGCTTTTTCTCTCATT
1 TTTCTTT-CTTTTTCTCTCATT
* *
21596920 TTTCCTCTCTTTTT-T-TCAAT
1 TTT-CTTTCTTTTTCTCTCATT
21596940 TTTCTTTCCTTTTTCATTCTCACTCT
1 TTTCTTT-CTTTTTC--TCTCA-T-T
21596966 TTTCTTT
1 TTTCTTT
21596973 TTCCCTCGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 3 0.07
20 13 0.32
21 1 0.02
22 9 0.22
23 4 0.10
24 3 0.07
26 8 0.20
ACGTcount: A:0.07, C:0.25, G:0.01, T:0.67
Consensus pattern (21 bp):
TTTCTTTCTTTTTCTCTCATT
Found at i:21599848 original size:10 final size:10
Alignment explanation
Indices: 21599835--21599864 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
21599825 AATTAAGTAA
21599835 GGAGCTGAAT
1 GGAGCTGAAT
21599845 GGAGCTGAAT
1 GGAGCTGAAT
*
21599855 GGAACTGAAT
1 GGAGCTGAAT
21599865 AGACTAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.20
Consensus pattern (10 bp):
GGAGCTGAAT
Found at i:21600196 original size:32 final size:32
Alignment explanation
Indices: 21600160--21600222 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
21600150 GCCATCCATA
* * *
21600160 CATGTACCTGAAATATATTAATCATCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
21600192 CATGTACCTGAAACACATTAATCAGCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
21600223 AATTTCGGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:21600311 original size:39 final size:39
Alignment explanation
Indices: 21600268--21600366 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
21600258 TTAATTTGTC
*
21600268 TCAAACTTAGACACCTTAAAAACAACTATTAAATATGTA
1 TCAAACTTAGACACATTAAAAACAACTATTAAATATGTA
*
21600307 TCAAAATTAGACACATTAAAAACAACTATTAAATATGTA
1 TCAAACTTAGACACATTAAAAACAACTATTAAATATGTA
*
21600346 TCAAACTGAGACACATTAAAA
1 TCAAACTTAGACACATTAAAA
21600367 CCCTATTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (39 bp):
TCAAACTTAGACACATTAAAAACAACTATTAAATATGTA
Found at i:21601546 original size:15 final size:16
Alignment explanation
Indices: 21601510--21601545 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
21601500 GAATAACATG
*
21601510 TTTTTGAGACTTTTAA
1 TTTTTGAGACTTGTAA
21601526 TTTTTGAGACTTGTAA
1 TTTTTGAGACTTGTAA
21601542 TTTT
1 TTTT
21601546 GGATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.58
Consensus pattern (16 bp):
TTTTTGAGACTTGTAA
Done.