Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 8 of 120
Found at i:2196334 original size:16 final size:17
Alignment explanation
Indices: 2196298--2196339 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2196288 TTGAAAAAAT
2196298 AAAT-TATTA-ATATAA
1 AAATATATTATATATAA
2196313 AAATATATTATATAT-A
1 AAATATATTATATATAA
*
2196329 ATATATATTAT
1 AAATATATTAT
2196340 TTATTTCGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATATTATATATAA
Found at i:2199839 original size:2 final size:2
Alignment explanation
Indices: 2199832--2199878 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
2199822 ACATAAATAG
*
2199832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2199872 AT AT AT A
1 AT AT AT A
2199879 GATGCATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2205749 original size:22 final size:21
Alignment explanation
Indices: 2205724--2205771 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2205714 AATTGACAAA
* *
2205724 TTAAATTCACGAAAAGTATAAT
1 TTAAA-TCACAAAAAATATAAT
*
2205746 TTAAATCCCAAAAAATATAAT
1 TTAAATCACAAAAAATATAAT
2205767 TTAAA
1 TTAAA
2205772 AATATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (21 bp):
TTAAATCACAAAAAATATAAT
Found at i:2206172 original size:6 final size:6
Alignment explanation
Indices: 2206161--2206185 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2206151 GCCAAACGTT
2206161 CTTCCC CTTCCC CTTCCC CTTCCC C
1 CTTCCC CTTCCC CTTCCC CTTCCC C
2206186 ATTCATTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTTCCC
Found at i:2229245 original size:40 final size:43
Alignment explanation
Indices: 2229189--2229279 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
2229179 TTCTCAAAAT
2229189 TATTATTTTAAATTTTTTTCAAAA-T-TT-TAATTTTCTTTATA
1 TATTATTTTAAATTTTTTT-AAAATTATTATAATTTTCTTTATA
*
2229230 TATTA-TTTAAATTTTTTTAAAATTATTATAATTTTTTTTATA
1 TATTATTTTAAATTTTTTTAAAATTATTATAATTTTCTTTATA
*
2229272 -AATATTTT
1 TATTATTTT
2229280 TTGTTGAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 4 0.09
40 14 0.32
41 10 0.23
42 16 0.36
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (43 bp):
TATTATTTTAAATTTTTTTAAAATTATTATAATTTTCTTTATA
Found at i:2229277 original size:21 final size:19
Alignment explanation
Indices: 2229199--2229278 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 19
2229189 TATTATTTTA
*
2229199 AATTTTTTTCAAAAT-TTT
1 AATTTTTTTTAAAATATTT
* *
2229217 AATTTTCTTTATATATTATTT
1 AATTTT-TTT-TAAAATATTT
*
2229238 AAATTTTTTTAAAATTATTAT
1 AATTTTTTTTAAAA-TATT-T
2229259 AATTTTTTTTATAAATATTT
1 AATTTTTTTTA-AAATATTT
2229279 TTTGTTGAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
18 6 0.12
19 6 0.12
20 11 0.22
21 23 0.47
22 3 0.06
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTTTTTAAAATATTT
Found at i:2232372 original size:20 final size:20
Alignment explanation
Indices: 2232342--2232402 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
2232332 TGATATCAAC
2232342 TAAATTAAAATTTAATAAACT
1 TAAATT-AAATTTAATAAACT
** *
2232363 TAAATTAAATTTTTTTAACT
1 TAAATTAAATTTAATAAACT
*
2232383 TATATATAAATTTATATAAA
1 TAAAT-TAAATTTA-ATAAA
2232403 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.48
21 13 0.42
22 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATTAAATTTAATAAACT
Found at i:2233557 original size:24 final size:24
Alignment explanation
Indices: 2233528--2233577 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2233518 TTCAATGACT
*
2233528 TACTTCGTCCCCTCTCCTCTCTAC
1 TACTTCATCCCCTCTCCTCTCTAC
*
2233552 TACTTCATCCCCTCTCCTCTTTAC
1 TACTTCATCCCCTCTCCTCTCTAC
2233576 TA
1 TA
2233578 TAATAGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.40
Consensus pattern (24 bp):
TACTTCATCCCCTCTCCTCTCTAC
Found at i:2233665 original size:32 final size:32
Alignment explanation
Indices: 2233629--2233694 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
2233619 AACGGTTAAC
2233629 TATTACATTGTATTCTCAGTTTTTCCCCTTTT
1 TATTACATTGTATTCTCAGTTTTTCCCCTTTT
2233661 TATTACATTGTATTCTCAGTTTTTCCCCTTTT
1 TATTACATTGTATTCTCAGTTTTTCCCCTTTT
2233693 TA
1 TA
2233695 CTTATGTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.56
Consensus pattern (32 bp):
TATTACATTGTATTCTCAGTTTTTCCCCTTTT
Found at i:2235893 original size:16 final size:16
Alignment explanation
Indices: 2235872--2235907 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2235862 TGAATTATTG
2235872 ATTACAATTCTATTCC
1 ATTACAATTCTATTCC
*
2235888 ATTACAATTCTATTTC
1 ATTACAATTCTATTCC
2235904 ATTA
1 ATTA
2235908 TAGTTATATT
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:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTACAATTCTATTCC
Found at i:2238804 original size:20 final size:20
Alignment explanation
Indices: 2238779--2238819 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2238769 AAATTTATGT
2238779 AACTTATTAAA-ATTATAAAA
1 AACTTA-TAAATATTATAAAA
2238799 AACTTATAAATATTATAAAA
1 AACTTATAAATATTATAAAA
2238819 A
1 A
2238820 TAAAAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AACTTATAAATATTATAAAA
Found at i:2240015 original size:9 final size:9
Alignment explanation
Indices: 2240001--2240063 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
2239991 ATTTTTCTCA
2240001 TAAAAATAT
1 TAAAAATAT
*
2240010 TAAAAATCTT
1 TAAAAAT-AT
2240020 TAAAAATA-
1 TAAAAATAT
2240028 T-AAAA-A-
1 TAAAAATAT
2240034 TAAAAATAT
1 TAAAAATAT
2240043 T--AAATAT
1 TAAAAATAT
2240050 TAAAACA-AT
1 TAAAA-ATAT
2240059 TAAAA
1 TAAAA
2240064 TTTATGTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 2 0.04
7 15 0.33
8 2 0.04
9 17 0.38
10 9 0.20
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAAAATAT
Found at i:2240098 original size:21 final size:21
Alignment explanation
Indices: 2240072--2240125 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
2240062 AATTTATGTG
2240072 AACTTATTAAA-ATTATAAAAA
1 AACTTA-TAAATATTATAAAAA
2240093 AACTTATAAATATTATAAAAA
1 AACTTATAAATATTATAAAAA
*
2240114 AATCTAATAAAT
1 AA-CTTATAAAT
2240126 TGTAAAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.13
21 18 0.60
22 8 0.27
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (21 bp):
AACTTATAAATATTATAAAAA
Found at i:2240103 original size:19 final size:21
Alignment explanation
Indices: 2240079--2240132 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2240069 GTGAACTTAT
*
2240079 TAAAATTATAAAAAAA-CTTA
1 TAAAATTATAAAAAAATCTAA
2240099 TAAATATTATAAAAAAATCTAA
1 TAAA-ATTATAAAAAAATCTAA
*
2240121 T-AAATTGTAAAA
1 TAAAATTATAAAA
2240133 TCAATAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
21 14 0.47
22 4 0.13
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAATTATAAAAAAATCTAA
Found at i:2240220 original size:9 final size:9
Alignment explanation
Indices: 2240208--2240265 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
2240198 AAAACTGTTA
2240208 AAAATTATT
1 AAAATTATT
2240217 AAAA-TATTT
1 AAAATTA-TT
2240226 AAAA-TATT
1 AAAATTATT
2240234 AAAATTGATAT
1 AAAATT-AT-T
* *
2240245 AAACTTATA
1 AAAATTATT
2240254 AAAATTA-T
1 AAAATTATT
2240262 AAAA
1 AAAA
2240266 AATCATAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
8 12 0.29
9 19 0.46
10 4 0.10
11 6 0.15
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTATT
Found at i:2240267 original size:77 final size:74
Alignment explanation
Indices: 2240089--2240267 Score: 175
Period size: 77 Copynumber: 2.4 Consensus size: 74
2240079 TAAAATTATA
* * *
2240089 AAAAAACTTATAAATATTATAAAAAAATCTAATAAATTGTAAAATCAATAAAACTTATTTAAAAT
1 AAAAAACTTATAAAAATTATAAAAAAATCTAAAAAACTGTAAAATCAATAAAAC-TATTTAAAAT
2240154 ATTTAAAATT
65 ATTTAAAATT
* * * * * *
2240164 AAAAAAATGTAATAGAACTCAT-AAAAAATACTAAAAAACTGTTAAAAATTATTAAAA-TATTTA
1 AAAAAACT-T-ATAAAAATTATAAAAAAAT-CTAAAAAACTG-T-AAAATCAATAAAACTATTTA
2240227 AAATA-TTAAAATT
61 AAATATTTAAAATT
*
2240240 GATATAAACTTATAAAAATTATAAAAAA
1 -A-AAAAACTTATAAAAATTATAAAAAA
2240268 TCATAACAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
75 7 0.09
76 24 0.29
77 34 0.41
78 6 0.07
79 11 0.13
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (74 bp):
AAAAAACTTATAAAAATTATAAAAAAATCTAAAAAACTGTAAAATCAATAAAACTATTTAAAATA
TTTAAAATT
Found at i:2240581 original size:13 final size:13
Alignment explanation
Indices: 2240565--2240589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2240555 TATATTAAAA
2240565 ATTTGGTTCAACC
1 ATTTGGTTCAACC
2240578 ATTTGGTTCAAC
1 ATTTGGTTCAAC
2240590 AGCTCGGTTC
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:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTTGGTTCAACC
Found at i:2241598 original size:17 final size:17
Alignment explanation
Indices: 2241576--2241614 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2241566 TAACCCAAAC
*
2241576 CTGACTCGACTCGTTGA
1 CTGACTCGACTCATTGA
2241593 CTGACTCGACTCATTGA
1 CTGACTCGACTCATTGA
*
2241610 TTGAC
1 CTGAC
2241615 CCAACCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (17 bp):
CTGACTCGACTCATTGA
Found at i:2243089 original size:8 final size:9
Alignment explanation
Indices: 2243064--2243155 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 9
2243054 TATGAAAAAA
2243064 TTATAATTT
1 TTATAATTT
* *
2243073 TTTTGATTT
1 TTATAATTT
2243082 TTAT-ATTT
1 TTATAATTT
*
2243090 TTGATAATAT
1 TT-ATAATTT
2243100 TTATAAGTTT
1 TTATAA-TTT
*
2243110 ATATCAATTT
1 TTAT-AATTT
*
2243120 TCAT-ATTT
1 TTATAATTT
2243128 TT-TAATATT
1 TTATAAT-TT
* *
2243137 TAATAATTG
1 TTATAATTT
2243146 TTAT-ATTT
1 TTATAATTT
2243154 TT
1 TT
2243156 TTGATATTTG
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
7 1 0.02
8 18 0.29
9 23 0.37
10 19 0.30
11 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:2246536 original size:30 final size:29
Alignment explanation
Indices: 2246502--2246561 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2246492 GAGGAATTCG
*
2246502 GGGATCAAAATCAAAATTTTTGGAAAATTT
1 GGGATCAAAATC-AAACTTTTGGAAAATTT
* * *
2246532 GGGATTAAAATCGAACTTTTGGAACATTT
1 GGGATCAAAATCAAACTTTTGGAAAATTT
2246561 G
1 G
2246562 AGGTCGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (29 bp):
GGGATCAAAATCAAACTTTTGGAAAATTT
Found at i:2246610 original size:29 final size:28
Alignment explanation
Indices: 2246578--2246668 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
2246568 ATAATGTGAC
*
2246578 TTTTGAAAATTTGAGGGCAAAATGGTAAT
1 TTTTG-AAATTTAAGGGCAAAATGGTAAT
*
2246607 TTTT-AGATGTTCAAGGGCAAAATGGTAAT
1 TTTTGAAAT-TT-AAGGGCAAAATGGTAAT
**
2246636 TTTTGGATGTTTAAGGGC-AAATGGTAAT
1 TTTT-GAAATTTAAGGGCAAAATGGTAAT
2246664 TTTTG
1 TTTTG
2246669 GATGTTCGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 4 0.07
28 16 0.30
29 30 0.56
30 2 0.04
31 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.38
Consensus pattern (28 bp):
TTTTGAAATTTAAGGGCAAAATGGTAAT
Found at i:2246667 original size:28 final size:29
Alignment explanation
Indices: 2246591--2246675 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
2246581 TGAAAATTTG
*
2246591 AGGGCAAAATGGTAATTTTTAGATGTTCA
1 AGGGCAAAATGGTAATTTTTGGATGTTCA
*
2246620 AGGGCAAAATGGTAATTTTTGGATGTTTA
1 AGGGCAAAATGGTAATTTTTGGATGTTCA
2246649 AGGGC-AAATGGTAATTTTTGGATGTTC
1 AGGGCAAAATGGTAATTTTTGGATGTTC
2246676 GGGGTTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 21 0.40
29 32 0.60
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (29 bp):
AGGGCAAAATGGTAATTTTTGGATGTTCA
Found at i:2246686 original size:57 final size:56
Alignment explanation
Indices: 2246578--2246723 Score: 147
Period size: 57 Copynumber: 2.6 Consensus size: 56
2246568 ATAATGTGAC
* *
2246578 TTTTGA-AAATTTGAGGGCAAAATGGTAATTTTTAGATGTTCAAGGGCAAAATGGTAAT
1 TTTTGAGAAGTTT-AGGGC-AAATGGTAATTTTTGGATGTTCAAGGGCAAAAT-GTAAT
* * * *
2246636 TTTTG-GATGTTTAAGGGCAAATGGTAATTTTTGGATGTTC-GGGGTTAAAATGTGAT
1 TTTTGAGAAGTTT-AGGGCAAATGGTAATTTTTGGATGTTCAAGGG-CAAAATGTAAT
* *
2246692 TTTTGAGAAGTTTAGGGGAAAT-ATAATTTTTG
1 TTTTGAGAAGTTTAGGGCAAATGGTAATTTTTG
2246724 TAAAGCTTAG
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
55 9 0.12
56 20 0.27
57 32 0.43
58 14 0.19
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (56 bp):
TTTTGAGAAGTTTAGGGCAAATGGTAATTTTTGGATGTTCAAGGGCAAAATGTAAT
Found at i:2246687 original size:29 final size:27
Alignment explanation
Indices: 2246591--2246723 Score: 108
Period size: 29 Copynumber: 4.7 Consensus size: 27
2246581 TGAAAATTTG
*
2246591 AGGGCAAAATGGTAATTTTTAGATGTTC
1 AGGG-AAAATGGTAATTTTTGGATGTTC
*
2246619 AAGGGCAAAATGGTAATTTTTGGATGTTTA
1 -AGGG-AAAATGGTAATTTTTGGATG-TTC
*
2246649 AGGGCAAATGGTAATTTTTGGATGTTC
1 AGGGAAAATGGTAATTTTTGGATGTTC
* * * *
2246676 GGGGTTAAAAT-GTGATTTTTGAGAAGTTT
1 AGGG--AAAATGGTAATTTTTG-GATGTTC
* *
2246705 AGGGGAAAT-ATAATTTTTG
1 AGGGAAAATGGTAATTTTTG
2246724 TAAAGCTTAG
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
27 17 0.20
28 28 0.32
29 40 0.46
30 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.38
Consensus pattern (27 bp):
AGGGAAAATGGTAATTTTTGGATGTTC
Found at i:2246713 original size:27 final size:29
Alignment explanation
Indices: 2246677--2246808 Score: 94
Period size: 29 Copynumber: 4.6 Consensus size: 29
2246667 TGGATGTTCG
* *
2246677 GGGTTAAAATGTGATTTTTG-AGAAGTTTA
1 GGGTGAAAATGTGATTTTTGTA-AAGCTTA
* *
2246706 GGG-G-AAATATAATTTTTGTAAAGCTTA
1 GGGTGAAAATGTGATTTTTGTAAAGCTTA
* *
2246733 GGGTGAAAATGTGATTTTAG-AAAGGTTCGA
1 GGGTGAAAATGTGATTTTTGTAAAGCTT--A
* * * * *
2246763 AGGTGAAAATGTAATTTTGGAAAAG-TTT
1 GGGTGAAAATGTGATTTTTGTAAAGCTTA
2246791 GAGGTGAAAATGTGATTT
1 G-GGTGAAAATGTGATTT
2246809 GGGAAAAGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
27 21 0.26
28 8 0.10
29 29 0.35
30 20 0.24
31 4 0.05
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
GGGTGAAAATGTGATTTTTGTAAAGCTTA
Found at i:2246750 original size:29 final size:27
Alignment explanation
Indices: 2246677--2246943 Score: 97
Period size: 30 Copynumber: 9.1 Consensus size: 27
2246667 TGGATGTTCG
*
2246677 GGGTTAAAATGTGATTTTTGAGAAGTTTA
1 GGGTGAAAATGTGATTTTTGA-AAG-TTA
* *
2246706 GGG-G-AAATATAATTTTTGTAAAGCTTA
1 GGGTGAAAATGTGATTTTTG-AAAG-TTA
*
2246733 GGGTGAAAATGTGATTTTAGAAAGGTTCGA
1 GGGTGAAAATGTGATTTTTGAAA-GTT--A
* * * *
2246763 AGGTGAAAATGTAATTTTGGAAAAGTTT
1 GGGTGAAAATGTGATTTTTG-AAAGTTA
**
2246791 GAGGTGAAAATGTGATTTGGGAAAAGTTTAA
1 G-GGTGAAAATGTGATTTTTG-AAAG-TT-A
* * **
2246822 GGGTTAAAATGTAATTTTAAAGAAGTTTAA
1 GGGTGAAAATGTGATTTTTGA-AAG-TT-A
* * * *
2246852 GGGTTAAAATGTAATTATAGAGAAGTTTA
1 GGGTGAAAATGTGATTTTTGA-AAG-TTA
* * * *
2246881 GGGGTCAAAATGTAATTTTGGAAAAGTTTG
1 -GGGTGAAAATGTGATTTTTG-AAAG-TTA
* *
2246911 GGAGTCAAAATATGATTTTTGAAAAGTTTA
1 GG-GTGAAAATGTGATTTTTG-AAAG-TTA
2246941 GGG
1 GGG
2246944 ACCTCCTGTG
Statistics
Matches: 194, Mismatches: 30, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
27 21 0.11
28 7 0.04
29 42 0.22
30 119 0.61
31 5 0.03
ACGTcount: A:0.37, C:0.01, G:0.27, T:0.34
Consensus pattern (27 bp):
GGGTGAAAATGTGATTTTTGAAAGTTA
Found at i:2246770 original size:30 final size:29
Alignment explanation
Indices: 2246734--2246938 Score: 115
Period size: 30 Copynumber: 6.9 Consensus size: 29
2246724 TAAAGCTTAG
*
2246734 GGTGAAAATGTGATTTTAGAAAGGTTCGAA
1 GGTGAAAATGTGATTTTAGAAAAGTTCG-A
* * *
2246764 GGTGAAAATGTAATTTTGGAAAAGTTTGA
1 GGTGAAAATGTGATTTTAGAAAAGTTCGA
** **
2246793 GGTGAAAATGTGATTTGGGAAAAGTTTAA
1 GGTGAAAATGTGATTTTAGAAAAGTTCGA
* * **
2246822 GGGTTAAAATGTAATTTTA-AAGAAGTTTAA
1 -GGTGAAAATGTGATTTTAGAA-AAGTTCGA
* * * * * *
2246852 GGGTTAAAATGTAATTATAGAGAAGTTTAGG
1 -GGTGAAAATGTGATTTTAGAAAAG-TTCGA
* * * * *
2246883 GGTCAAAATGTAATTTTGGAAAAGTTTGG
1 GGTGAAAATGTGATTTTAGAAAAGTTCGA
* * *
2246912 GAGTCAAAATATGATTTTTGAAAAGTT
1 G-GTGAAAATGTGATTTTAGAAAAGTT
2246939 TAGGGACCTC
Statistics
Matches: 146, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
29 34 0.23
30 109 0.75
31 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (29 bp):
GGTGAAAATGTGATTTTAGAAAAGTTCGA
Found at i:2246921 original size:60 final size:59
Alignment explanation
Indices: 2246710--2246940 Score: 171
Period size: 59 Copynumber: 3.9 Consensus size: 59
2246700 AGTTTAGGGG
* * * * * * * * * * *
2246710 AAATATAATTTTTGTAAAGCTTAGGGTGAAAATGTGATTTTAGAAAGGTTCGAA-GGTGA
1 AAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTGAGAAAAGTT-TAAGGGTCA
* * * * *
2246769 AAATGTAATTTTGGAAAAGTTTGAGGTGAAAATGTGATTTGGGAAAAGTTTAAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTGAGAAAAGTTTAAGGGTCA
* * * * *
2246828 AAATGTAATTTT-AAAGAAGTTTAAGGGTTAAAATGTAATTAT-AGAGAAGTTTAGGGGTCA
1 AAATGTAATTTTGGAA-AAGTTT-GGGGTCAAAATGTAATT-TGAGAAAAGTTTAAGGGTCA
* * **
2246888 AAATGTAATTTTGGAAAAGTTTGGGAGTCAAAATATGATTTTTGAAAAGTTTA
1 AAATGTAATTTTGGAAAAGTTTGGG-GTCAAAATGTAATTTGAGAAAAGTTTA
2246941 GGGACCTCCT
Statistics
Matches: 138, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
58 4 0.03
59 66 0.48
60 65 0.47
61 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (59 bp):
AAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTGAGAAAAGTTTAAGGGTCA
Found at i:2246939 original size:30 final size:31
Alignment explanation
Indices: 2246768--2246944 Score: 125
Period size: 30 Copynumber: 5.9 Consensus size: 31
2246758 TTCGAAGGTG
* * *
2246768 AAAATGTAATTTTGGAAAAGTTT-GAG-GTG
1 AAAATATAATTTTGGAAAAGTTTAGGGAGTC
* * * * *
2246797 AAAATGTGATTTGGGAAAAGTTTAAGG-GTT
1 AAAATATAATTTTGGAAAAGTTTAGGGAGTC
* * * *
2246827 AAAATGTAATTTT-AAAGAAGTTTAAGG-GTT
1 AAAATATAATTTTGGAA-AAGTTTAGGGAGTC
* * * *
2246857 AAAATGTAATTATAGAGAAGTTTAGGG-GTC
1 AAAATATAATTTTGGAAAAGTTTAGGGAGTC
*
2246887 AAAATGTAATTTTGGAAAAGTTT-GGGAGTC
1 AAAATATAATTTTGGAAAAGTTTAGGGAGTC
* *
2246917 AAAATATGATTTTTGAAAAGTTTAGGGA
1 AAAATATAATTTTGGAAAAGTTTAGGGA
2246945 CCTCCTGTGT
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
29 26 0.21
30 93 0.75
31 5 0.04
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.34
Consensus pattern (31 bp):
AAAATATAATTTTGGAAAAGTTTAGGGAGTC
Found at i:2246941 original size:60 final size:58
Alignment explanation
Indices: 2246677--2246943 Score: 229
Period size: 60 Copynumber: 4.6 Consensus size: 58
2246667 TGGATGTTCG
* * * * * * *
2246677 GGGTTAAAATGTGATTTTTGAGAAGTTTAGGGG--AAATATAATTTTTGTAAAGCTTA
1 GGGTGAAAATGTGATTTTAGAAAAGTTTAGGGGTAAAATGTAATTTTGGAAAAGTTTA
* * *
2246733 GGGTGAAAATGTGATTTTAG-AAAGGTTCGAAGGTGAAAATGTAATTTTGGAAAAGTTT-
1 GGGTGAAAATGTGATTTTAGAAAAGTTTAG-GGGT-AAAATGTAATTTTGGAAAAGTTTA
** * *
2246791 GAGGTGAAAATGTGATTTGGGAAAAGTTTAAGGGTTAAAATGTAATTTT-AAAGAAGTTTAA
1 G-GGTGAAAATGTGATTTTAGAAAAGTTT-AGGGGTAAAATGTAATTTTGGAA-AAGTTT-A
* * * * *
2246852 GGGTTAAAATGTAATTATAGAGAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTG
1 GGGTGAAAATGTGATTTTAGAAAAGTTTAGGGGT-AAAATGTAATTTTGGAAAAGTTTA
* * *
2246911 GGAGTCAAAATATGATTTTTGAAAAGTTTAGGG
1 GG-GTGAAAATGTGATTTTAGAAAAGTTTAGGG
2246944 ACCTCCTGTG
Statistics
Matches: 166, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
55 6 0.04
56 20 0.12
58 3 0.02
59 61 0.37
60 72 0.43
61 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.27, T:0.34
Consensus pattern (58 bp):
GGGTGAAAATGTGATTTTAGAAAAGTTTAGGGGTAAAATGTAATTTTGGAAAAGTTTA
Found at i:2250180 original size:51 final size:51
Alignment explanation
Indices: 2250096--2250288 Score: 262
Period size: 51 Copynumber: 3.8 Consensus size: 51
2250086 GCTATAAACG
* *
2250096 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAG-GTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
2250148 AAACGT-TCGATGACTAAGTGTCATCGTGAGTAAATGAATTCTTTACGGATT
1 AAAGGTCT-GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * ** *
2250199 AAAGGTCTGATGACTAAGTGTCATAGTGAGTAAATGAATCCATGCCGAATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
2250250 AAAGGTCTGATGACTCAGTGTCATCGTGAGTATATGAAT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAAT
2250289 TCCTATATGA
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
51 121 0.97
52 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:2251089 original size:21 final size:22
Alignment explanation
Indices: 2251065--2251124 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
2251055 TAGTTGCATG
2251065 ACTTGTATCGGTAAAAATTA-T
1 ACTTGTATCGGTAAAAATTAGT
* *
2251086 ACTTGTATTGGT-AGAATTAGT
1 ACTTGTATCGGTAAAAATTAGT
***
2251107 AAAAGTATCGGTAAAAAT
1 ACTTGTATCGGTAAAAAT
2251125 CTGCACAGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 6 0.20
21 20 0.67
22 4 0.13
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (22 bp):
ACTTGTATCGGTAAAAATTAGT
Found at i:2251589 original size:49 final size:50
Alignment explanation
Indices: 2251528--2251848 Score: 169
Period size: 50 Copynumber: 6.5 Consensus size: 50
2251518 CTAGGTTTGT
* * *
2251528 CGTTGCGGCCTCAACCTTTCCCTTTATATCTTC-ATGTTA-TAGGATTCGC
1 CGTTGCGACCTCAACCTTTCCCTTTATATCTTCTAAGGTACT-GGATTCGC
* * *** *
2251577 CGTTGTGACCTCAATCC-TTCCCATCGCATCTTCTAAGGTACTGGGTTCGC
1 CGTTGCGACCTCAA-CCTTTCCCTTTATATCTTCTAAGGTACTGGATTCGC
* * * * *
2251627 CGTTGCGGCCTCAACCTTTCCCTCTATATCTCCGT--GGTA-TCGGGTTTGC
1 CGTTGCGACCTCAACCTTTCCCTTTATATCTTC-TAAGGTACT-GGATTCGC
* * * * * * * * *
2251676 CATTGCAACCTCAACGTTTCCCATCACATCTTCTTAGGTA-TCGAGTTTGC
1 CGTTGCGACCTCAACCTTTCCCTTTATATCTTCTAAGGTACTGGA-TTCGC
* * ** * *
2251726 CATTGCGGCCTCAACCTTTCCCTTCGTATCTTC-ATGGTACT-GAGTTCTC
1 CGTTGCGACCTCAACCTTTCCCTTTATATCTTCTAAGGTACTGGA-TTCGC
* * * * *
2251775 CGTTGC-AGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCAC
1 CGTTGCGA-CCTCAACCTTTCCCTTTATATCTTCTAAGGTACTGGATTCGC
* *
2251825 CGTCGCGGCCTCAATCC-TTCCCTT
1 CGTTGCGACCTCAA-CCTTTCCCTT
2251849 CGCCAAGTAT
Statistics
Matches: 207, Mismatches: 50, Indels: 29
0.72 0.17 0.10
Matches are distributed among these distances:
48 2 0.01
49 99 0.48
50 100 0.48
51 6 0.03
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (50 bp):
CGTTGCGACCTCAACCTTTCCCTTTATATCTTCTAAGGTACTGGATTCGC
Found at i:2251639 original size:50 final size:50
Alignment explanation
Indices: 2251474--2251843 Score: 238
Period size: 49 Copynumber: 7.5 Consensus size: 50
2251464 GGGTATAAGA
* * * * * * * *
2251474 TTCGCCATTGTGGCTTCAATCTTTCCCGTCAC-TTTTCTAAGGTGCTAGG
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACTGGG
* * * * * * * *
2251523 TTTGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTC-ATGTTA-TAGGA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACT-GGG
* * *
2251572 TTCGCCGTTGTGACCTCAATCC-TTCCCATCGCATCTTCTAAGGTACTGGG
1 TTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACTGGG
* *
2251622 TTCGCCGTTGCGGCCTCAACCTTTCCC-TCTATATCTCCGT--GGTA-TCGGG
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATC-ACATCTTC-TAAGGTACT-GGG
* * ** * * *
2251671 TTTGCCATTGCAACCTCAACGTTTCCCATCACATCTTCTTAGGTA-TCGAG
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACT-GGG
* * * ** * *
2251721 TTTGCCATTGCGGCCTCAACCTTTCCCTTCGTATCTTC-ATGGTACTGAG
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACTGGG
* * * *
2251770 TTCTCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACTGGG
* *
2251820 TTCACCGTCGCGGCCTCAATCCTT
1 TTCGCCGTTGCGGCCTCAA-CCTT
2251844 CCCTTCGCCA
Statistics
Matches: 245, Mismatches: 61, Indels: 28
0.73 0.18 0.08
Matches are distributed among these distances:
48 3 0.01
49 131 0.53
50 105 0.43
51 6 0.02
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (50 bp):
TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACTGGG
Found at i:2251642 original size:99 final size:98
Alignment explanation
Indices: 2251465--2251848 Score: 330
Period size: 99 Copynumber: 3.9 Consensus size: 98
2251455 TCGACTTTAG
* * * * * * * * * *
2251465 GGTATAAGATTCGCCATTGTGGCTTCAATCTTTCCCGTCAC-TTTTCTAAGGTGCTAGGTTTGTC
1 GGTATAGGATTCGCCATTGTGACCTCAA-CCTTCCCATCACATCTTCTAAGGTACTGGGTTCGCC
2251529 GTTGCGGCCTCAACCTTTCCCTTTATATCTTCAT
65 GTTGCGGCCTCAACCTTTCCCTTTATATCTTCAT
* * *
2251563 GTTATAGGATTCGCCGTTGTGACCTCAATCCTTCCCATCGCATCTTCTAAGGTACTGGGTTCGCC
1 GGTATAGGATTCGCCATTGTGACCTCAA-CCTTCCCATCACATCTTCTAAGGTACTGGGTTCGCC
* * *
2251628 GTTGCGGCCTCAACCTTTCCCTCTATATCTCCGT
65 GTTGCGGCCTCAACCTTTCCCTTTATATCTTCAT
* * * ** * * * *
2251662 GGTATCGGGTTTGCCATTGCAACCTCAACGTTTCCCATCACATCTTCTTAGGTA-TCGAGTTTGC
1 GGTATAGGATTCGCCATTGTGACCTCAAC-CTTCCCATCACATCTTCTAAGGTACT-GGGTTCGC
* **
2251726 CATTGCGGCCTCAACCTTTCCCTTCGTATCTTCAT
64 CGTTGCGGCCTCAACCTTTCCCTTTATATCTTCAT
* * * * *
2251761 GGTACT--GAGTTCTCCGTTG-CAGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTC
1 GGTA-TAGGA-TTCGCCATTGTGA-CCTCAACC-TTCCCATCACATCTTCTAAGGTACTGGGTTC
* *
2251823 ACCGTCGCGGCCTCAATCC-TTCCCTT
62 GCCGTTGCGGCCTCAA-CCTTTCCCTT
2251849 CGCCAAGTAT
Statistics
Matches: 229, Mismatches: 48, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
98 37 0.16
99 189 0.83
100 3 0.01
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (98 bp):
GGTATAGGATTCGCCATTGTGACCTCAACCTTCCCATCACATCTTCTAAGGTACTGGGTTCGCCG
TTGCGGCCTCAACCTTTCCCTTTATATCTTCAT
Found at i:2255607 original size:25 final size:25
Alignment explanation
Indices: 2255579--2255629 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2255569 TGGTATGAGT
2255579 ATGAGTATGTTTATCAAATTGGACA
1 ATGAGTATGTTTATCAAATTGGACA
2255604 ATGAGTATGTTTATCAAATTGGACA
1 ATGAGTATGTTTATCAAATTGGACA
2255629 A
1 A
2255630 GAATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGAGTATGTTTATCAAATTGGACA
Found at i:2259002 original size:30 final size:30
Alignment explanation
Indices: 2258963--2259025 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2258953 CATTTTTTGG
2258963 CCCCCAAAGTCTTCAAAAATTAAAATTTAA
1 CCCCCAAAGTCTTCAAAAATTAAAATTTAA
* *
2258993 CCCCTAAAGTTTTCAAAAATTAAAATTTAA
1 CCCCCAAAGTCTTCAAAAATTAAAATTTAA
2259023 CCC
1 CCC
2259026 TGTTTTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (30 bp):
CCCCCAAAGTCTTCAAAAATTAAAATTTAA
Found at i:2269948 original size:85 final size:85
Alignment explanation
Indices: 2269853--2270022 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
2269843 TCTCGAAGCC
*
2269853 TAAAGAGATTTGAACTAAAAACCTGAAAGGGCAGTTCAGATTTGGATCAAAGATCGGGCATGAAA
1 TAAAGAGATTTGAACTAAAAACCTGAAAGGGCAGTTCAAATTTGGATCAAAGATCGGGCATGAAA
2269918 TGAGCTTCTTTCTAAAAAAT
66 TGAGCTTCTTTCTAAAAAAT
2269938 TAAAGAGATTTGAACTAAAAACCTGAAAGGGCAGTTCAAATTTGGATCAAAGATCGGGCATGAAA
1 TAAAGAGATTTGAACTAAAAACCTGAAAGGGCAGTTCAAATTTGGATCAAAGATCGGGCATGAAA
2270003 TGAGCTTCTTTCTAAAAAAT
66 TGAGCTTCTTTCTAAAAAAT
2270023 AATAAGATGG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (85 bp):
TAAAGAGATTTGAACTAAAAACCTGAAAGGGCAGTTCAAATTTGGATCAAAGATCGGGCATGAAA
TGAGCTTCTTTCTAAAAAAT
Found at i:2270876 original size:50 final size:50
Alignment explanation
Indices: 2270807--2270931 Score: 187
Period size: 50 Copynumber: 2.5 Consensus size: 50
2270797 CTTTTACCCT
* * * *
2270807 TAAAGCTTTGGAGGTGCAGATTGAAACCGCAATGGCAAATCTCATACACC
1 TAAAGCTGTAGAGGGGCAGATTGAAACCACAATGGCAAATCTCATACACC
* *
2270857 TAAAGCTGTAGAGGGGCAGAATGAAACCACAATGGCAAATCTCATTCACC
1 TAAAGCTGTAGAGGGGCAGATTGAAACCACAATGGCAAATCTCATACACC
*
2270907 TAAAGCTGTAGAGGGGAAGATTGAA
1 TAAAGCTGTAGAGGGGCAGATTGAA
2270932 GTCACAAGGA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (50 bp):
TAAAGCTGTAGAGGGGCAGATTGAAACCACAATGGCAAATCTCATACACC
Found at i:2271041 original size:39 final size:39
Alignment explanation
Indices: 2270985--2271236 Score: 294
Period size: 39 Copynumber: 6.4 Consensus size: 39
2270975 AAGTTACAAC
*
2270985 ATCCAATC-TTTACCCTAACCAGAGGGTAGATTGAAGCA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
* * *
2271023 ATCCAGTCTTTTACCCTAACCAGAGGGCAGATTAAAGACC
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CA
* * * *
2271063 ATCCGATCTTTTACCCTAATCAGAGAGTAGATTGAAGCA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
** * * **
2271102 ATCCAATCTTTTACCCCGATCATG-GGGCTGATT-AAAAA
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCA
2271140 TTATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
1 --ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
* *
2271181 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAGGACA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CA
2271221 ATCCAATCTTTTACCC
1 ATCCAATCTTTTACCC
2271237 CTAAAGTTAT
Statistics
Matches: 179, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
38 10 0.06
39 88 0.49
40 78 0.44
41 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (39 bp):
ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCA
Found at i:2271087 original size:79 final size:79
Alignment explanation
Indices: 2270984--2271236 Score: 348
Period size: 79 Copynumber: 3.2 Consensus size: 79
2270974 GAAGTTACAA
* *
2270984 CATCCAATC-TTTACCCTAACCAGAGGGTAGATTGAAGCAATCCAGTCTTTTACCCTAACCAGAG
1 CATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAG
2271048 GGCAGATTAAAGAC
66 GGCAGATTAAAGAC
* * * **
2271062 CATCCGATCTTTTACCCTAATCAGAGAGTAGATTGAAGCAATCCAATCTTTTACCCCGATCATG-
1 CATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAAGCAATCCAATCTTTTACCCTAATCA-GA
* * *
2271126 GGGCTGATTAAAAAT
65 GGGCAGATTAAAGAC
* *
2271141 TATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAG
1 CATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAG
* *
2271206 GGCAGATTGAGGAC
66 GGCAGATTAAAGAC
*
2271220 AATCCAATCTTTTACCC
1 CATCCAATCTTTTACCC
2271237 CTAAAGTTAT
Statistics
Matches: 149, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
78 9 0.06
79 139 0.93
80 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (79 bp):
CATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAG
GGCAGATTAAAGAC
Found at i:2272707 original size:28 final size:27
Alignment explanation
Indices: 2272659--2272720 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
2272649 GATAAGGGAA
*
2272659 TTTTAAAAATAAAAATCGGTTTTGTTTT
1 TTTTAAAAATAAAAATCGGTTGT-TTTT
* *
2272687 TTTTAATAAA-AAGAATGGGTTGTTTTT
1 TTTTAA-AAATAAAAATCGGTTGTTTTT
2272714 TTTTAAA
1 TTTTAAA
2272721 TGGAAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 10 0.33
28 16 0.53
29 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (27 bp):
TTTTAAAAATAAAAATCGGTTGTTTTT
Found at i:2273067 original size:32 final size:30
Alignment explanation
Indices: 2273028--2273155 Score: 94
Period size: 31 Copynumber: 4.1 Consensus size: 30
2273018 CAAAGTCTTC
* * *
2273028 AAAAATTCAAATTTGACCCACGAATTTTTAAA
1 AAAAATTCAAATTTCACCC-CCAAATTTT-AA
**
2273060 AAAAATTCAAATTTCACCCCCAAATTTTCC
1 AAAAATTCAAATTTCACCCCCAAATTTTAA
* * * **
2273090 AAAAATTCAAATTTAATCCCTAAAGTTTTCC
1 AAAAATTCAAATTTCACCCCCAAA-TTTTAA
* * * *
2273121 AAGAATTCAAATTTAACCCCTAAAATTTTCA
1 AAAAATTCAAATTTCACCCC-CAAATTTTAA
2273152 AAAA
1 AAAA
2273156 TTAAAATCTA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
30 21 0.26
31 39 0.48
32 21 0.26
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATTCAAATTTCACCCCCAAATTTTAA
Found at i:2273119 original size:31 final size:30
Alignment explanation
Indices: 2273027--2273170 Score: 146
Period size: 30 Copynumber: 4.7 Consensus size: 30
2273017 CCAAAGTCTT
* * * *
2273027 CAAAAATTCAAATTTGACCCACGAATTTTTAA
1 CAAAAATTCAAATTTAACCC-CTAAATTTT-C
* * *
2273059 AAAAAATTCAAATTTCACCCCCAAATTTTC
1 CAAAAATTCAAATTTAACCCCTAAATTTTC
*
2273089 CAAAAATTCAAATTTAATCCCTAAAGTTTTC
1 CAAAAATTCAAATTTAACCCCTAAA-TTTTC
*
2273120 CAAGAATTCAAATTTAACCCCTAAAATTTT-
1 CAAAAATTCAAATTTAACCCCT-AAATTTTC
* *
2273150 CAAAAATTAAAATCTAACCCC
1 CAAAAATTCAAATTTAACCCC
2273171 ATTTTAATGT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
30 39 0.41
31 36 0.38
32 21 0.22
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (30 bp):
CAAAAATTCAAATTTAACCCCTAAATTTTC
Found at i:2276081 original size:30 final size:28
Alignment explanation
Indices: 2276045--2276100 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
2276035 TTAGAATCGA
*
2276045 ACTTTTGGAACATTTGAGGTCGAAAATGTG
1 ACTTTTGGAA-ATTTGAGGGC-AAAATGTG
2276075 ACTTTTGGAAATTTGAGGGCAAAATG
1 ACTTTTGGAAATTTGAGGGCAAAATG
2276101 GTAATTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (28 bp):
ACTTTTGGAAATTTGAGGGCAAAATGTG
Found at i:2276109 original size:29 final size:29
Alignment explanation
Indices: 2276047--2276436 Score: 214
Period size: 29 Copynumber: 13.3 Consensus size: 29
2276037 AGAATCGAAC
* *
2276047 TTTTGGAACATTTGA-GGTCGAAAATGTGAC
1 TTTTGGAA-ATTTGAGGGTC-AAAATGTAAT
2276077 TTTTGGAAATTTGAGGG-CAAAATGGTAAT
1 TTTTGGAAATTTGAGGGTCAAAAT-GTAAT
*
2276106 TTTT-G-AATGCTCGAGGGT-AAAATGGTAA-
1 TTTTGGAAAT--TTGAGGGTCAAAAT-GTAAT
** *
2276134 TTTTGGATGTTTGGGGGT-AAAATGGTAAT
1 TTTTGGAAATTTGAGGGTCAAAAT-GTAAT
**
2276163 TTTTGGATGTTTG-GGGTCAAAATGAGTAAT
1 TTTTGGAAATTTGAGGGTCAAAAT--GTAAT
** *
2276193 TTTTGGATGTTCGAGGG-CAAAATGGTAAT
1 TTTTGGAAATTTGAGGGTCAAAAT-GTAAT
* * * * *
2276222 TTTTGGATA-TTCAAGGTTAAAATGTTAT
1 TTTTGGAAATTTGAGGGTCAAAATGTAAT
***
2276250 TTTTGGTTTGTTTG-GGGTCAAAATGTAAT
1 TTTTGG-AAATTTGAGGGTCAAAATGTAAT
* * * *
2276279 TTTTGCAAAGTTT-AGGGTGAAAATATGAT
1 TTTTGGAAA-TTTGAGGGTCAAAATGTAAT
* * * *
2276308 TTTAGAAAAGTTTAAGGGTTAAAATGTAAT
1 TTTTGGAAA-TTTGAGGGTCAAAATGTAAT
* *
2276338 TTTAGAGAAGTTTGAGGGTCAAAATGTAA-
1 TTTTG-GAAATTTGAGGGTCAAAATGTAAT
*
2276367 TTTTGGAAAAGTTTAAGGGTCAAAATGTAAT
1 TTTTGG-AAA-TTTGAGGGTCAAAATGTAAT
* * * *
2276398 TTTAGAAAAGTTT-AGGGGTCAAAATATGAT
1 TTTTGGAAA-TTTGA-GGGTCAAAATGTAAT
2276428 TTTTGGAAA
1 TTTTGGAAA
2276437 GTTTAGAGAC
Statistics
Matches: 291, Mismatches: 47, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.01
28 45 0.15
29 118 0.41
30 116 0.40
31 9 0.03
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
TTTTGGAAATTTGAGGGTCAAAATGTAAT
Found at i:2276138 original size:57 final size:59
Alignment explanation
Indices: 2276077--2276226 Score: 198
Period size: 57 Copynumber: 2.6 Consensus size: 59
2276067 AAAATGTGAC
**
2276077 TTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGAATGCTCGAGGGT-AAAATG-GTAA-
1 TTTTGGATGTTTGAGGGCAAAATGGTAATTTTTGAATGCTCG-GGGTCAAAATGAGTAAT
* * * * *
2276134 TTTTGGATGTTTGGGGGTAAAATGGTAATTTTTGGATGTTTGGGGTCAAAATGAGTAAT
1 TTTTGGATGTTTGAGGGCAAAATGGTAATTTTTGAATGCTCGGGGTCAAAATGAGTAAT
*
2276193 TTTTGGATGTTCGAGGGCAAAATGGTAATTTTTG
1 TTTTGGATGTTTGAGGGCAAAATGGTAATTTTTG
2276227 GATATTCAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 4 0.05
57 41 0.51
58 4 0.05
59 31 0.39
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.38
Consensus pattern (59 bp):
TTTTGGATGTTTGAGGGCAAAATGGTAATTTTTGAATGCTCGGGGTCAAAATGAGTAAT
Found at i:2276332 original size:30 final size:30
Alignment explanation
Indices: 2276264--2276441 Score: 223
Period size: 30 Copynumber: 6.0 Consensus size: 30
2276254 GGTTTGTTTG
* *
2276264 GGGTCAAAATGTAATTTTTGCAAAGTTT-A
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAA
* * *
2276293 GGGTGAAAATATGATTTTAGAAAAGTTTAA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAA
* * *
2276323 GGGTTAAAATGTAATTTTAGAGAAGTTTGA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAA
*
2276353 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAA
*
2276383 GGGTCAAAATGTAATTTTAGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAA
* * * *
2276413 GGGTCAAAATATGATTTTTGGAAAGTTTA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTA
2276442 GAGACCTCCT
Statistics
Matches: 128, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
29 23 0.18
30 105 0.82
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAGAAAAGTTTAA
Found at i:2276442 original size:30 final size:29
Alignment explanation
Indices: 2276240--2276442 Score: 160
Period size: 30 Copynumber: 6.8 Consensus size: 29
2276230 ATTCAAGGTT
***
2276240 AAAATGTTATTTTTGGTTTGTTT-GGGGTC
1 AAAATG-TATTTTTGGAAAGTTTAGGGGTC
* *
2276269 AAAATGTAATTTTTGCAAAGTTTA-GGGTG
1 AAAATGT-ATTTTTGGAAAGTTTAGGGGTC
* * * * *
2276298 AAAATATGATTTTAGAAAAGTTTAAGGGTT
1 AAAATGT-ATTTTTGGAAAGTTTAGGGGTC
* *
2276328 AAAATGTAATTTTAGAGAAGTTT-GAGGGTC
1 AAAATGTATTTTTGGA-AAGTTTAG-GGGTC
* *
2276358 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTATTTTTGG-AAAGTTTAGGGGTC
* *
2276388 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
1 AAAATGT-ATTTTTGGAAAGTTTAGGGGTC
*
2276418 AAAATATGATTTTTGGAAAGTTTAG
1 AAAATGT-ATTTTTGGAAAGTTTAG
2276443 AGACCTCCTA
Statistics
Matches: 139, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.01
29 46 0.33
30 86 0.62
31 6 0.04
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGTATTTTTGGAAAGTTTAGGGGTC
Found at i:2278576 original size:16 final size:15
Alignment explanation
Indices: 2278536--2278579 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2278526 CCTTTTTAAA
2278536 TATAAAATTTTAATT
1 TATAAAATTTTAATT
*
2278551 TA-AATTATTTATAATT
1 TATAA-AATTT-TAATT
2278567 TATAAAATTTTAA
1 TATAAAATTTTAA
2278580 ATTAATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 11 0.46
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAAAATTTTAATT
Found at i:2278672 original size:17 final size:18
Alignment explanation
Indices: 2278647--2278683 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2278637 TCTTTTAAAA
2278647 ATTATAAAT-ATATAAATT
1 ATTATAAATGATA-AAATT
2278665 ATTA-AAATGATAAAATT
1 ATTATAAATGATAAAATT
2278682 AT
1 AT
2278684 ATTTTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATAAAATT
Found at i:2283063 original size:24 final size:24
Alignment explanation
Indices: 2283018--2283063 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2283008 ACGTGTGTTT
***
2283018 TGAATTATATTTAAATTTTTTTGG
1 TGAATTATATTTAAAAAATTTTGG
2283042 TGAATTATATTTAAAAAATTTT
1 TGAATTATATTTAAAAAATTTT
2283064 AAAATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (24 bp):
TGAATTATATTTAAAAAATTTTGG
Found at i:2283400 original size:36 final size:35
Alignment explanation
Indices: 2283330--2283410 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 35
2283320 TATGAAAAAA
* *
2283330 TTATAATTTATTCGATTTTTATATTTTTGATAATAT
1 TTATAATTTATTCAATTTTCATATTTTT-ATAATAT
2283366 TTATAAGTTTATATCAATTTTCATATTTTT-TAATAT
1 TTATAA-TTTAT-TCAATTTTCATATTTTTATAATAT
2283402 TTAATAATT
1 TT-ATAATT
2283411 GTTATATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 16 0.40
37 9 0.22
38 15 0.38
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (35 bp):
TTATAATTTATTCAATTTTCATATTTTTATAATAT
Found at i:2283428 original size:36 final size:36
Alignment explanation
Indices: 2283344--2283429 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 36
2283334 AATTTATTCG
2283344 ATTTTTATATTTTTGATAATATTTATAAGTTTATATCA
1 ATTTTTATATTTTT-ATAATATTTATAAGTTTATAT-A
* *
2283382 ATTTTCATATTTTT-TAATATTTAATAATTGTTATAT-
1 ATTTTTATATTTTTATAATATTT-ATAAGT-TTATATA
*
2283418 TTTTTTATATTT
1 ATTTTTATATTT
2283430 GATTTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
36 18 0.43
37 5 0.12
38 19 0.45
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (36 bp):
ATTTTTATATTTTTATAATATTTATAAGTTTATATA
Found at i:2285196 original size:16 final size:15
Alignment explanation
Indices: 2285156--2285199 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2285146 TCTTTTTAAA
2285156 TATAAAATTTTAATT
1 TATAAAATTTTAATT
*
2285171 TA-AATTATTTATAATT
1 TATAA-AATTT-TAATT
2285187 TATAAAATTTTAA
1 TATAAAATTTTAA
2285200 ATTAATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 11 0.46
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAAAATTTTAATT
Found at i:2288598 original size:10 final size:10
Alignment explanation
Indices: 2288585--2288609 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2288575 ATATATAAAA
2288585 ATAAAATATT
1 ATAAAATATT
2288595 ATAAAATATT
1 ATAAAATATT
2288605 ATAAA
1 ATAAA
2288610 CTTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAATATT
Found at i:2289699 original size:24 final size:24
Alignment explanation
Indices: 2289655--2289700 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2289645 ACGTTTGTTT
**
2289655 TGAATTATATTTAAATTTTTTTGG
1 TGAATTATATTTAAAAATTTTTGG
2289679 TGAATTATATTTAAAAATTTTT
1 TGAATTATATTTAAAAATTTTT
2289701 AAAATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TGAATTATATTTAAAAATTTTTGG
Found at i:2290037 original size:37 final size:36
Alignment explanation
Indices: 2289966--2290047 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 36
2289956 TATGAAAAAA
* *
2289966 TTATAATTTATTCGATTTTTATATTTTTGATAATAT
1 TTATAATTTATTCAATTTTCATATTTTTGATAATAT
*
2290002 TTATAAGTTTATATCAATTTTCATATTTTT-TTAATAT
1 TTATAA-TTTAT-TCAATTTTCATATTTTTGATAATAT
2290039 TTAATAATT
1 TT-ATAATT
2290048 GTTATGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 6 0.15
37 15 0.38
38 19 0.47
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (36 bp):
TTATAATTTATTCAATTTTCATATTTTTGATAATAT
Found at i:2290078 original size:26 final size:27
Alignment explanation
Indices: 2290026--2290085 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
2290016 CAATTTTCAT
2290026 ATTTTTTTAATATTTAATAATTGTTATG
1 ATTTTTTTAATATTTAAT-ATTGTTATG
* * *
2290054 TTTTTTTTAATATTTGAT-TTTTTATG
1 ATTTTTTTAATATTTAATATTGTTATG
2290080 ATTTTT
1 ATTTTT
2290086 ATGGAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 12 0.43
28 16 0.57
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (27 bp):
ATTTTTTTAATATTTAATATTGTTATG
Found at i:2291521 original size:15 final size:16
Alignment explanation
Indices: 2291493--2291550 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 16
2291483 ATCAATCTAT
2291493 TATAATATAAATTTGAAA
1 TATAATA-AAATTT-AAA
2291511 -ATAA-AAAATTTAAA
1 TATAATAAAATTTAAA
2291525 TATAATAAAAATTATAAA
1 TATAAT-AAAATT-TAAA
2291543 TATTAATA
1 TA-TAATA
2291551 TAAGTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 1 0.03
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TATAATAAAATTTAAA
Found at i:2291533 original size:18 final size:20
Alignment explanation
Indices: 2291510--2291550 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
2291500 TAAATTTGAA
2291510 AATAAAAAATT-TAAATA-T
1 AATAAAAAATTATAAATATT
2291528 AAT-AAAAATTATAAATATT
1 AATAAAAAATTATAAATATT
2291547 AATA
1 AATA
2291551 TAAGTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAAAAAATTATAAATATT
Found at i:2291943 original size:17 final size:18
Alignment explanation
Indices: 2291918--2291954 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2291908 TCTTTTAAAA
2291918 ATTATAAATATAT-AAATT
1 ATTATAAATA-ATGAAATT
2291936 ATTA-AAATAATGAAATT
1 ATTATAAATAATGAAATT
2291953 AT
1 AT
2291955 ATTTTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.67
18 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATGAAATT
Found at i:2300554 original size:32 final size:31
Alignment explanation
Indices: 2300511--2300574 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
2300501 CCACTTGTCA
*
2300511 AAAAATTTAAAATCC-AAAAATATTATAATTT
1 AAAAATTTAAAAACCAAAAAAT-TTATAATTT
*
2300542 AAAAATTATAAAAACTAAAAAATTTATAATTT
1 AAAAATT-TAAAAACCAAAAAATTTATAATTT
2300574 A
1 A
2300575 TTTTTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.24
32 16 0.55
33 6 0.21
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAAATTTAAAAACCAAAAAATTTATAATTT
Found at i:2300716 original size:19 final size:20
Alignment explanation
Indices: 2300688--2300727 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2300678 TCGATTTTTA
2300688 GAAAAATTT-AGAATCTTAT
1 GAAAAATTTAAGAATCTTAT
* *
2300707 GAAAATTTTAAGAATTTTAT
1 GAAAAATTTAAGAATCTTAT
2300727 G
1 G
2300728 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (20 bp):
GAAAAATTTAAGAATCTTAT
Found at i:2300726 original size:20 final size:19
Alignment explanation
Indices: 2300673--2300727 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
2300663 GTTTGTTTGG
* *
2300673 AAATTTCGATTTTTA-GAA
1 AAATTTAGAATTTTATGAA
*
2300691 AAATTTAGAATCTTATGAA
1 AAATTTAGAATTTTATGAA
*
2300710 AATTTTAAGAATTTTATG
1 AAATTT-AGAATTTTATG
2300728 GTTTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 12 0.40
19 8 0.27
20 10 0.33
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (19 bp):
AAATTTAGAATTTTATGAA
Found at i:2301813 original size:17 final size:17
Alignment explanation
Indices: 2301793--2301840 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2301783 TATTTATTGA
2301793 ATTTTTAATCTTTTAG-T
1 ATTTTTAAT-TTTTAGAT
* * *
2301810 ATTTGTAAATATTAGAT
1 ATTTTTAATTTTTAGAT
2301827 ATTTTTAATTTTTA
1 ATTTTTAATTTTTA
2301841 AATTCAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (17 bp):
ATTTTTAATTTTTAGAT
Found at i:2310414 original size:2 final size:2
Alignment explanation
Indices: 2310407--2310435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2310397 TTTGAAAAAG
2310407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2310436 TAAAAACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2316604 original size:21 final size:23
Alignment explanation
Indices: 2316553--2316608 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
2316543 CTCTATGACT
* *
2316553 TCCTCCTCCTCTTCACTTCTTCTT
1 TCCTCCTCATCTTCACTTC-TCTC
*
2316577 TCTTCCTCATCTTCACTTC-C-C
1 TCCTCCTCATCTTCACTTCTCTC
2316598 TCCTCCTCATC
1 TCCTCCTCATC
2316609 GACTATGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.36
22 1 0.04
24 17 0.61
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.45
Consensus pattern (23 bp):
TCCTCCTCATCTTCACTTCTCTC
Found at i:2317465 original size:21 final size:24
Alignment explanation
Indices: 2317411--2317467 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 24
2317401 CAAGCATGCA
2317411 AACTACCGATACTTCTATACATAC
1 AACTACCGATACTTCTATACATAC
* **
2317435 AACTATCGATAC-TC-ATA-ATTT
1 AACTACCGATACTTCTATACATAC
2317456 AACTACCGATAC
1 AACTACCGATAC
2317468 AACTCAAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.45
22 3 0.10
23 2 0.07
24 11 0.38
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (24 bp):
AACTACCGATACTTCTATACATAC
Found at i:2318180 original size:51 final size:51
Alignment explanation
Indices: 2318101--2318242 Score: 221
Period size: 51 Copynumber: 2.8 Consensus size: 51
2318091 CCGTATAGAA
* * * * *
2318101 ATTCATATACTCACGATGACACTGAGTCATCGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
2318152 ATTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
2318203 ATTCATTTACTCACGATGACACTTAGTCATCGGACTCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
2318243 CGTTTATAGC
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 79 0.95
52 4 0.05
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:2322512 original size:97 final size:96
Alignment explanation
Indices: 2322327--2322515 Score: 224
Period size: 97 Copynumber: 2.0 Consensus size: 96
2322317 CAATTTGGAG
* * * *
2322327 AAGGATATTTGATTATCTCGATTTGAAAAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAAAAAGATAGCACCTAGTAAGTTAAGGAGTAAATTTTCA
* *
2322392 TAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* *
2322423 AAGGGTATTCGATTATTTCGATTTTGAAGAAAA-ATAGCACCTAGTAAGTTAAGGAGTAAAATTT
1 AAGGATATTCGATTATCTCGA-TTTGAA-AAAAGATAGCACCTAGTAAGTTAAGGAGT-AAATTT
*
2322487 T-AGAACTCGAA-ATAAA-AGAATATTGCCTC
63 TCAGAA-TCGAAGATAAAGA-AACATTGCCTC
2322516 TATTTTAAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
96 19 0.24
97 44 0.56
98 16 0.20
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAAAAAGATAGCACCTAGTAAGTTAAGGAGTAAATTTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:2322839 original size:28 final size:28
Alignment explanation
Indices: 2322735--2322841 Score: 85
Period size: 28 Copynumber: 3.8 Consensus size: 28
2322725 TTTGGATACC
*
2322735 CGAGGGTAAAA-GAGTAATTTTAGACTTT
1 CGAGGGTAAAATG-GTAATTTTAGACATT
* * * *
2322763 CAAGGGCAAAATGGTAATTTTTGGAAATTT
1 CGAGGGTAAAATGGTAA-TTTTAGACA-TT
* *
2322793 TG-GGGTTAAAAAT-GAAATTTTAGACATT
1 CGAGGG-T-AAAATGGTAATTTTAGACATT
2322821 CGAGGGTAAAATGGTAATTTT
1 CGAGGGTAAAATGGTAATTTT
2322842 TGAAAAAATC
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
27 5 0.08
28 24 0.41
29 20 0.34
30 5 0.08
31 5 0.08
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (28 bp):
CGAGGGTAAAATGGTAATTTTAGACATT
Found at i:2323084 original size:29 final size:29
Alignment explanation
Indices: 2322897--2323085 Score: 211
Period size: 29 Copynumber: 6.5 Consensus size: 29
2322887 AGAATAGTAA
* *
2322897 TTTTGAAAGTTTCAGGGTTAAAAATGGAAT
1 TTTTGGAAGTTTGAGGG-TAAAAATGGAAT
* *
2322927 TTTTGGAAGTTTCAGGGTTAAAATGGAATT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAA-T
* * *
2322957 TTTTAGAATTTTTAGGGTTAAAAATGGAAT
1 TTTTGGAAGTTTGAGGG-TAAAAATGGAAT
* *
2322987 TTTTGGAAATTTAAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAAT
*
2323016 TTTTGGAAGTTTG-GGGT-AAAATGTAAT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAAT
* * * *
2323043 TTTTGAAAGTTTGAGGGCAAAAATGCATT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAAT
2323072 TTTTGGAAGTTTGA
1 TTTTGGAAGTTTGA
2323086 ATATAATTTT
Statistics
Matches: 138, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
27 21 0.15
28 7 0.05
29 54 0.39
30 46 0.33
31 10 0.07
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (29 bp):
TTTTGGAAGTTTGAGGGTAAAAATGGAAT
Found at i:2325032 original size:5 final size:5
Alignment explanation
Indices: 2325000--2325062 Score: 63
Period size: 5 Copynumber: 11.6 Consensus size: 5
2324990 TTACAATAAT
*
2325000 ATTAA ATTTAA ATTAA ACTCAA ACTTAA ATTAA ATTAA ATTAAA ATTTAA
1 ATTAA A-TTAA ATTAA A-TTAA A-TTAA ATTAA ATTAA ATT-AA A-TTAA
*
2325050 ATTAA ATTTA ATT
1 ATTAA ATTAA ATT
2325063 TCAAAGTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 29 0.57
6 20 0.39
7 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:2325035 original size:22 final size:22
Alignment explanation
Indices: 2325001--2325057 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
2324991 TACAATAATA
*
2325001 TTAAATTTAAATTAAACTCAAAC
1 TTAAA-TTAAATTAAACTAAAAC
* *
2325024 TTAAATTAAATTAAATTAAAAT
1 TTAAATTAAATTAAACTAAAAC
2325046 TTAAATTAAATT
1 TTAAATTAAATT
2325058 TAATTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATTAAATTAAACTAAAAC
Found at i:2325049 original size:17 final size:16
Alignment explanation
Indices: 2324984--2325075 Score: 87
Period size: 17 Copynumber: 5.5 Consensus size: 16
2324974 TAATGGACAT
2324984 TTAAATTTACAA-TAATA
1 TTAAATTTA-AATTAA-A
2325001 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
* *
2325017 CTCAAACTTAAATTAAA
1 -TTAAATTTAAATTAAA
*
2325034 TTAAATTAAAATTTAAA
1 TTAAATTTAAA-TTAAA
*
2325051 TTAAATTTAATTTCAAA
1 TTAAATTTAAATT-AAA
*
2325068 GTAAATTT
1 TTAAATTT
2325076 TAAAATGGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
16 13 0.21
17 50 0.79
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:2325788 original size:92 final size:92
Alignment explanation
Indices: 2325683--2325989 Score: 491
Period size: 92 Copynumber: 3.4 Consensus size: 92
2325673 TTTTATCCTG
*
2325683 CTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATA
1 CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATA
2325748 GGGATTGATGTTTGAAGCTTCATCTTA
66 GGGATTGATGTTTGAAGCTTCATCTTA
* *
2325775 CTCTTACTGCAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTTCTACAACTTCAAGAGGATA
1 CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATA
*
2325840 GGGATTGATGTTTGAAACTTCATCTTA
66 GGGATTGATGTTTGAAGCTTCATCTTA
* * * *
2325867 CTCTTACTAAAAATTCAGAGAGATAAAGACTTGTTATCTAACTTTACTACAACTTCAAGAGGATA
1 CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATA
*
2325932 GGAATTGATGTTTGAAGC-T--TC--A
66 GGGATTGATGTTTGAAGCTTCATCTTA
2325954 -TCTTACTACAACTTCAGAGAGATAAAGACTTGCTAT
1 CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTAT
2325990 TATTTATTTT
Statistics
Matches: 200, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
86 33 0.17
87 1 0.00
89 2 0.01
91 1 0.00
92 163 0.81
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (92 bp):
CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATA
GGGATTGATGTTTGAAGCTTCATCTTA
Found at i:2326155 original size:50 final size:50
Alignment explanation
Indices: 2326096--2326358 Score: 196
Period size: 50 Copynumber: 5.2 Consensus size: 50
2326086 CGACTTAAAC
** *
2326096 CTTTCCCTTCAAATCTTTGTGGTACTGGATCCACCGTTGCGGTCTTAGAT
1 CTTTCCCTTCGTATCTTTGAGGTACTGGATCCACCGTTGCGGTCTTAGAT
* * * * *
2326146 CTTTCCCTTC--ATGCTTCTAAGGTACACGG-TCCACCGTTGC-GACCTAGAC
1 CTTTCCCTTCGTAT-CTT-TGAGGTAC-TGGATCCACCGTTGCGGTCTTAGAT
* * * * *
2326195 CTTTCCCTTTTGTGTCTTTGCGGTACTGGATCCACCGTCGCGATCTTAGAT
1 CTTTCCC-TTCGTATCTTTGAGGTACTGGATCCACCGTTGCGGTCTTAGAT
* * * * * *
2326246 CTTTCCCTTCGTGTCTTCTGAGGTACACGG-TCCGCCGTTGC-GACTTAAAC
1 CTTTCCCTTCGTATCTT-TGAGGTAC-TGGATCCACCGTTGCGGTCTTAGAT
* * * * *
2326296 CTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGGTCATAGAT
1 CTTTCCC-TTCGTATCTTTGAGGTACTGGATCCACCGTTGCGGTCTTAGAT
*
2326347 CTTTCCCATCGT
1 CTTTCCCTTCGT
2326359 GTTTCATGGT
Statistics
Matches: 164, Mismatches: 36, Indels: 26
0.73 0.16 0.12
Matches are distributed among these distances:
48 2 0.01
49 20 0.12
50 86 0.52
51 53 0.32
52 3 0.02
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (50 bp):
CTTTCCCTTCGTATCTTTGAGGTACTGGATCCACCGTTGCGGTCTTAGAT
Found at i:2326306 original size:101 final size:101
Alignment explanation
Indices: 2326086--2326360 Score: 392
Period size: 101 Copynumber: 2.7 Consensus size: 101
2326076 TTCGTCATTA
*** *
2326086 CGACTTAAACCTTTCCC-TTCAAATCTTTGTGGTACTGGATCCACCGTTGCGGTCTTAGATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTT
*
2326150 CCCTTCATG-CTTCTAAGGTACACGGTCCACCGTTG
66 CCCTTCGTGTCTTCTAAGGTACACGGTCCACCGTTG
* * * * *
2326185 CGACCTAGACCTTTCCCTTTTGTGTCTTTGCGGTACTGGATCCACCGTCGCGATCTTAGATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTT
* *
2326250 CCCTTCGTGTCTTCTGAGGTACACGGTCCGCCGTTG
66 CCCTTCGTGTCTTCTAAGGTACACGGTCCACCGTTG
* * *
2326286 CGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTACGGTCATAGATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTT
*
2326351 CCCATCGTGT
66 CCCTTCGTGT
2326361 TTCATGGTGC
Statistics
Matches: 153, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 15 0.10
100 48 0.31
101 90 0.59
ACGTcount: A:0.15, C:0.29, G:0.20, T:0.35
Consensus pattern (101 bp):
CGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTT
CCCTTCGTGTCTTCTAAGGTACACGGTCCACCGTTG
Found at i:2332253 original size:12 final size:12
Alignment explanation
Indices: 2332236--2332260 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2332226 CAGAAAAACA
2332236 GGTTCGAGAGTC
1 GGTTCGAGAGTC
2332248 GGTTCGAGAGTC
1 GGTTCGAGAGTC
2332260 G
1 G
2332261 TTTAAAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.44, T:0.24
Consensus pattern (12 bp):
GGTTCGAGAGTC
Found at i:2334257 original size:28 final size:27
Alignment explanation
Indices: 2334242--2334327 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
2334232 TTACAATAAT
2334242 ATTAAATTTAAATTAAATTCAAACTTAA
1 ATTAAATTTAAATTAAATTCAAAC-TAA
* *
2334270 ATTAAATTTAAATAAAATT-AAATTAAA
1 ATTAAATTTAAATTAAATTCAAACT-AA
* * *
2334297 ATTTAAA-ATAAATTTAATTTCAAAGTAA
1 A-TTAAATTTAAA-TTAAATTCAAACTAA
2334325 ATT
1 ATT
2334328 TTAAAATGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.02
27 12 0.25
28 31 0.65
29 4 0.08
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (27 bp):
ATTAAATTTAAATTAAATTCAAACTAA
Found at i:2334258 original size:11 final size:11
Alignment explanation
Indices: 2334243--2334313 Score: 74
Period size: 11 Copynumber: 6.4 Consensus size: 11
2334233 TACAATAATA
2334243 TTAAATTTAAA-
1 TTAAA-TTAAAT
*
2334254 TTAAATTCAAAC
1 TTAAATT-AAAT
2334266 TTAAATTAAAT
1 TTAAATTAAAT
*
2334277 TTAAA-TAAAA
1 TTAAATTAAAT
2334287 TTAAATTAAAAT
1 TTAAATT-AAAT
*
2334299 TTAAAATAAAT
1 TTAAATTAAAT
2334310 TTAA
1 TTAA
2334314 TTTCAAAGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
10 11 0.21
11 25 0.48
12 16 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:2334259 original size:5 final size:5
Alignment explanation
Indices: 2334242--2334315 Score: 67
Period size: 5 Copynumber: 13.6 Consensus size: 5
2334232 TTACAATAAT
*
2334242 ATTAA ATTTAA ATTAA ATTCAA ACTTAA ATTAA ATTTAA ATAAA ATTAA
1 ATTAA A-TTAA ATTAA ATT-AA A-TTAA ATTAA A-TTAA ATTAA ATTAA
* *
2334291 ATTAAA ATTTAA AATAA ATTTA ATT
1 ATT-AA A-TTAA ATTAA ATTAA ATT
2334316 TCAAAGTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
5 32 0.55
6 22 0.38
7 4 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:2334289 original size:33 final size:33
Alignment explanation
Indices: 2334251--2334313 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2334241 TATTAAATTT
* *
2334251 AAATTAAATTCAAACTTAAATTAAATTTAAATA
1 AAATTAAATTAAAACTTAAAATAAATTTAAATA
*
2334284 AAATTAAATTAAAATTTAAAATAAATTTAA
1 AAATTAAATTAAAACTTAAAATAAATTTAA
2334314 TTTCAAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (33 bp):
AAATTAAATTAAAACTTAAAATAAATTTAAATA
Found at i:2334325 original size:17 final size:16
Alignment explanation
Indices: 2334224--2334328 Score: 68
Period size: 17 Copynumber: 6.2 Consensus size: 16
2334214 ATTAATGGAC
*
2334224 ATTTAAATTTACAATAA
1 ATTT-AATTTAAAATAA
* *
2334241 TATTAAATTTAAATTAA
1 -ATTTAATTTAAAATAA
* * *
2334258 ATTCAAACTTAAATTAA
1 ATT-TAATTTAAAATAA
*
2334275 ATTTAA-ATAAAATTAA
1 ATTTAATTTAAAA-TAA
*
2334291 ATTAAAATTTAAAATAA
1 ATT-TAATTTAAAATAA
*
2334308 ATTTAATTTCAAAGTAA
1 ATTTAATTT-AAAATAA
2334325 ATTT
1 ATTT
2334329 TAAAATGGTT
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
15 4 0.06
16 16 0.23
17 43 0.61
18 8 0.11
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTTAATTTAAAATAA
Found at i:2335061 original size:51 final size:50
Alignment explanation
Indices: 2334988--2335224 Score: 289
Period size: 51 Copynumber: 4.6 Consensus size: 50
2334978 ATTCATTTAA
* * * *
2334988 TACTCACGATGACA-TATTGTCATCGGACCTTGT-TCCGTATAGAAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCTT-TATCCGTAAAG-GATTCATT
* * * *
2335039 TACTCACGATGACACTGAGTCATCGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTT-ATCCGTAAAGGATTCATT
* * *
2335090 TACTCACGATGACTCTTAGTCATCAGACCTTCAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTT-TATCCGTAAAGGATTCATT
2335141 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTT-ATCCGTAAAGGATTCATT
*
2335192 TACTCACGATGACACTTAATCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
2335225 CGTTTATAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
51 150 0.93
52 10 0.06
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTATCCGTAAAGGATTCATT
Found at i:2340264 original size:5 final size:5
Alignment explanation
Indices: 2340224--2340260 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
2340214 TGAGCATTCG
* *
2340224 ATCGA ATCGA ATAGA ATCGA ATCGA ATCGA ATGGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA AT
2340261 GGAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:2341527 original size:37 final size:37
Alignment explanation
Indices: 2341470--2341571 Score: 186
Period size: 37 Copynumber: 2.8 Consensus size: 37
2341460 ATTCTTAGAT
* *
2341470 CACCGGCACGAAGCCTACTAGGCACATAGCCTAAAAA
1 CACCTGCACGAAGCCGACTAGGCACATAGCCTAAAAA
2341507 CACCTGCACGAAGCCGACTAGGCACATAGCCTAAAAA
1 CACCTGCACGAAGCCGACTAGGCACATAGCCTAAAAA
2341544 CACCTGCACGAAGCCGACTAGGCACATA
1 CACCTGCACGAAGCCGACTAGGCACATA
2341572 ACTTGAAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.36, C:0.33, G:0.20, T:0.11
Consensus pattern (37 bp):
CACCTGCACGAAGCCGACTAGGCACATAGCCTAAAAA
Found at i:2342928 original size:42 final size:42
Alignment explanation
Indices: 2342881--2342964 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
2342871 AAAAGGAATT
* *
2342881 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGATTTA
1 GTTTATGAGTATT-TTTGAAGAATAAAATTATATTTGGATTTA
* *
2342923 GTTTATGAGTATTTTTGAAGAATGAAATTATATTTGGGTTTA
1 GTTTATGAGTATTTTTGAAGAATAAAATTATATTTGGATTTA
2342965 AAAATATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTATTTTTGAAGAATAAAATTATATTTGGATTTA
Found at i:2346280 original size:23 final size:23
Alignment explanation
Indices: 2346254--2346370 Score: 148
Period size: 23 Copynumber: 5.0 Consensus size: 23
2346244 TAGCGCGCTA
2346254 TCTGATTAGCACTGTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCTC
* *
2346277 TCTGTTTAGCAC-GTCTCGTGCTC
1 TCTGATTAGCACTGTGT-GTGCTC
2346300 TCTGTTATTAGCACTGTGTGTGCTC
1 TCTG--ATTAGCACTGTGTGTGCTC
*
2346325 TCCGATTAGCACT-TCGTGTGCTC
1 TCTGATTAGCACTGT-GTGTGCTC
*
2346348 TCTGATTAGCACTTTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCTC
2346371 AGTACTTTGT
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 58 0.71
24 1 0.01
25 16 0.20
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
TCTGATTAGCACTGTGTGTGCTC
Found at i:2346356 original size:46 final size:46
Alignment explanation
Indices: 2346254--2346370 Score: 164
Period size: 48 Copynumber: 2.5 Consensus size: 46
2346244 TAGCGCGCTA
* *
2346254 TCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTC
1 TCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCTC
*
2346300 TCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGT-GTGCTC
1 TCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTC-TCGTGCTC
*
2346348 TCTGATTAGCACTTTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCTC
2346371 AGTACTTTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
46 22 0.34
48 41 0.64
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
TCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCTC
Found at i:2346399 original size:39 final size:39
Alignment explanation
Indices: 2346335--2346409 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
2346325 TCCGATTAGC
*
2346335 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
2346374 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
2346410 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:2346404 original size:23 final size:23
Alignment explanation
Indices: 2346369--2346462 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
2346359 CTTTGTGTGC
*
2346369 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
2346392 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
2346415 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
2346440 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
2346462 T
1 T
2346463 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:2347964 original size:21 final size:21
Alignment explanation
Indices: 2347938--2347986 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2347928 AGAATCCCAG
*
2347938 AACCCTAATAAACCC-AACTCT
1 AACCCTAAT-AACCCAAACCCT
*
2347959 AACCCTAATCACCCAAACCCT
1 AACCCTAATAACCCAAACCCT
2347980 AACCCTA
1 AACCCTA
2347987 TTCATTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (21 bp):
AACCCTAATAACCCAAACCCT
Found at i:2353877 original size:51 final size:51
Alignment explanation
Indices: 2353755--2353936 Score: 231
Period size: 51 Copynumber: 3.5 Consensus size: 51
2353745 TAAACGAAAG
* * *
2353755 GGTCCGATGACTAAGTGTTATCGTGAGCAAATGAATCCTTTATGGATTACAG
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTA-AA
* * * **
2353807 GGTCTGATGATTAAGTGTCATCATGAGTAAATGAATCCTTTACAGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* *
2353858 GGTCTGATGACTAAGTGTCATCGTGAGTAAATGAAT-CTATGATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCT-TTATGGATTAAA
* *
2353909 CGTCCGATGACTTAGTGTCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
2353937 GTATGAATTT
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
50 2 0.02
51 69 0.61
52 42 0.37
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
Found at i:2354703 original size:21 final size:21
Alignment explanation
Indices: 2354676--2354735 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2354666 TAGATGCATG
*
2354676 ACATGTATCGGTAGAAATTAT
1 ACATGTATCGGTAGAAATAAT
*
2354697 ACTTGTATCGGTA-AAACTAAT
1 ACATGTATCGGTAGAAA-TAAT
* *
2354718 ACAAGTACCGGTAGAAAT
1 ACATGTATCGGTAGAAAT
2354736 CTACTCTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 26 0.81
22 3 0.09
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (21 bp):
ACATGTATCGGTAGAAATAAT
Found at i:2361008 original size:24 final size:24
Alignment explanation
Indices: 2360981--2361033 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2360971 CAGACGATAT
2360981 TTAGCCCACACAAGCCCAAAATGA
1 TTAGCCCACACAAGCCCAAAATGA
* ** * *
2361005 TTAGCTCTTACGAGCCCAGAATGA
1 TTAGCCCACACAAGCCCAAAATGA
2361029 TTAGC
1 TTAGC
2361034 TCTTACGATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (24 bp):
TTAGCCCACACAAGCCCAAAATGA
Found at i:2361034 original size:24 final size:24
Alignment explanation
Indices: 2360993--2361120 Score: 211
Period size: 24 Copynumber: 5.3 Consensus size: 24
2360983 AGCCCACACA
*
2360993 AGCCCAAAATGATTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACG
2361017 AGCCCAGAATGATTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACG
*
2361041 ATCCCAGAATGATTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACG
* *
2361065 ATCCCAGAATAATTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACG
*
2361089 AGCCCAAAATGATTAGCTCTTACG
1 AGCCCAGAATGATTAGCTCTTACG
2361113 AGCCCAGA
1 AGCCCAGA
2361121 CAGAATTTAA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 97 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (24 bp):
AGCCCAGAATGATTAGCTCTTACG
Found at i:2363533 original size:51 final size:51
Alignment explanation
Indices: 2363400--2363638 Score: 257
Period size: 51 Copynumber: 4.6 Consensus size: 51
2363390 CTATAAATGA
* * * *
2363400 AAAGGTCCAATGATTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
2363451 ACAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTTTTACGGATT
1 A-AAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
2363503 AAAGATCCGATGACTAACTGTCATCGTGAGTAAATGAAT-CTATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCT-TTACGGATT
* ** * **
2363554 AAAGGTCCGATGACTTAGTGTCATCGTGAGTGTATGAATTCCTATACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
* *
2363606 AAGAGATCTGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
2363639 TTAAATGAAA
Statistics
Matches: 156, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
50 1 0.01
51 76 0.49
52 52 0.33
53 26 0.17
54 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:2363602 original size:103 final size:102
Alignment explanation
Indices: 2363400--2363638 Score: 284
Period size: 103 Copynumber: 2.3 Consensus size: 102
2363390 CTATAAATGA
* * * * * *
2363400 AAAGGTCCAATGATTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTACAGGGTCCGATGA
1 AAAGATCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTGATGGATTACAAGGTCCGATGA
* * **
2363465 CTAAGTGTCATCGTGAGTAAATGAATCTTTTACGGATT
65 CTAAGTGTCATCGTGAGTAAATGAATCCTATACGGAAC
2363503 AAAGATCCGATGACTAACTGTCATCGTGAGTAAATGAAT-CTATGATGGATTA-AAGGTCCGATG
1 AAAGATCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCT-TGATGGATTACAAGGTCCGATG
* **
2363566 ACTTAGTGTCATCGTGAGTGTATGAATTCCTATACGGAAC
64 ACTAAGTGTCATCGTGAGTAAATGAA-TCCTATACGGAAC
*
2363606 AAGAGATCTGATGACTATATGTCATCGTGAGTA
1 AA-AGATCCGATGACTA-ATGTCATCGTGAGTA
2363639 TTAAATGAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
102 35 0.30
103 54 0.46
104 27 0.23
105 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (102 bp):
AAAGATCCGATGACTAATGTCATCGTGAGTAAATGAATCCTTGATGGATTACAAGGTCCGATGAC
TAAGTGTCATCGTGAGTAAATGAATCCTATACGGAAC
Found at i:2364379 original size:21 final size:22
Alignment explanation
Indices: 2364352--2364411 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
2364342 TAGATGCATG
2364352 ACATGTATCGGTAGAAATTA-T
1 ACATGTATCGGTAGAAATTAGT
* *
2364373 ACTTGTATCGGTA-AAACTAGT
1 ACATGTATCGGTAGAAATTAGT
* *
2364394 ACAAGTACCGGTAGAAAT
1 ACATGTATCGGTAGAAAT
2364412 CTACTTTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.16
21 23 0.74
22 3 0.10
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (22 bp):
ACATGTATCGGTAGAAATTAGT
Found at i:2366887 original size:41 final size:41
Alignment explanation
Indices: 2366830--2366919 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
2366820 TATTTTATGA
2366830 TTGCCCAAGCCCGGCCTGACTCAAAATTTGGACCTAAAGTT
1 TTGCCCAAGCCCGGCCTGACTCAAAATTTGGACCTAAAGTT
2366871 TTGCCCAAGCCCGGCCTGACTCAAAATTTGGACCTAAAGTT
1 TTGCCCAAGCCCGGCCTGACTCAAAATTTGGACCTAAAGTT
2366912 TTGCCCAA
1 TTGCCCAA
2366920 ACCTGCCCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (41 bp):
TTGCCCAAGCCCGGCCTGACTCAAAATTTGGACCTAAAGTT
Found at i:2367030 original size:31 final size:34
Alignment explanation
Indices: 2366969--2367031 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
2366959 TAGGCTTGCC
* *
2366969 ATATTATTTTTAATTTTTTTAAAATATTTATATT
1 ATATTATTTTTAATTATTTAAAAATATTTATATT
2367003 ATATTA-TTTTAA-TATTTAAAAAT-TTTATA
1 ATATTATTTTTAATTATTTAAAAATATTTATA
2367032 CATTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 9 0.33
33 6 0.22
34 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
ATATTATTTTTAATTATTTAAAAATATTTATATT
Found at i:2369117 original size:4 final size:4
Alignment explanation
Indices: 2369108--2369145 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
2369098 TCTCTTGCTT
2369108 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
2369146 TTAATTATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2370353 original size:2 final size:2
Alignment explanation
Indices: 2370348--2370382 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2370338 TGTGTGTGTG
2370348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2370383 GAGTAAAAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2375368 original size:24 final size:24
Alignment explanation
Indices: 2375323--2375373 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2375313 TGATAATTAC
**
2375323 TTATTTTATTTTAACTTGAAATAA
1 TTATTTTATTTTAACTACAAATAA
*
2375347 TTATTTTATTTTATA-TACAAATTA
1 TTATTTTATTTTA-ACTACAAATAA
2375371 TTA
1 TTA
2375374 AAAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTTAACTACAAATAA
Found at i:2386897 original size:56 final size:56
Alignment explanation
Indices: 2386825--2387015 Score: 251
Period size: 56 Copynumber: 3.4 Consensus size: 56
2386815 AGCTCCGATC
*
2386825 TGCTTACATCTCGGTTAAAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
1 TGCTTACATCTTGGTTAAAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
* * **
2386881 TGCTTACGTCTTGGTTAGAGCGTAATGCTATTATAGCTTAGGTAGAGCTTTGGACA
1 TGCTTACATCTTGGTTAAAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
* * * *
2386937 TGCTTACATCTCT-GTTAAAGCGTAAAGCTATTATATCTCGGGTAGAGC-TCGGACT
1 TGCTTACATCT-TGGTTAAAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
* * *
2386992 TTCTTACATCTCGGTTAGAGCGTA
1 TGCTTACATCTTGGTTAAAGCGTA
2387016 TGGTTATTTC
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
55 25 0.21
56 91 0.78
57 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (56 bp):
TGCTTACATCTTGGTTAAAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
Found at i:2394084 original size:2 final size:2
Alignment explanation
Indices: 2394077--2394105 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2394067 CCATTCGACA
2394077 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 A
2394106 AACTTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2397684 original size:12 final size:12
Alignment explanation
Indices: 2397667--2397700 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
2397657 AGTGTTCAAA
2397667 CAGTTAATCGTT
1 CAGTTAATCGTT
2397679 CAGTTAATCGTT
1 CAGTTAATCGTT
2397691 CAGTTAATCG
1 CAGTTAATCG
2397701 AATCGAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (12 bp):
CAGTTAATCGTT
Found at i:2403329 original size:42 final size:42
Alignment explanation
Indices: 2403270--2403353 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
2403260 TAAATATTTT
*
2403270 TAAACCTAAATATAATTTCATTCTTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATT-TTCAAATAACACTCATAAAC
* *
2403312 TAAACCCAAATATAATTTTATTTTTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTTTCAAATAACACTCATAAAC
2403354 AACTCTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 5 0.13
42 33 0.87
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTTTCAAATAACACTCATAAAC
Found at i:2412888 original size:96 final size:96
Alignment explanation
Indices: 2412724--2412919 Score: 374
Period size: 96 Copynumber: 2.0 Consensus size: 96
2412714 ACAATGCCGA
*
2412724 AAACATATACCAAACGCTGAACAATATATTTATCAGTGAATTGAGCCATACCCTTCCCCTAGTGA
1 AAACATATACAAAACGCTGAACAATATATTTATCAGTGAATTGAGCCATACCCTTCCCCTAGTGA
2412789 ATATACATGATAAAACATATTCGCCACTGCT
66 ATATACATGATAAAACATATTCGCCACTGCT
2412820 AAACATATACAAAACGCTGAACAATATATTTATCAGTGAATTGAGCCATACCCTTCCCCTAGTGA
1 AAACATATACAAAACGCTGAACAATATATTTATCAGTGAATTGAGCCATACCCTTCCCCTAGTGA
*
2412885 ATATACATGATAAGACATATTCGCCACTGCT
66 ATATACATGATAAAACATATTCGCCACTGCT
2412916 AAAC
1 AAAC
2412920 CAAGGGGGTC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (96 bp):
AAACATATACAAAACGCTGAACAATATATTTATCAGTGAATTGAGCCATACCCTTCCCCTAGTGA
ATATACATGATAAAACATATTCGCCACTGCT
Found at i:2416222 original size:60 final size:62
Alignment explanation
Indices: 2416111--2416244 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 62
2416101 TTTTTGAAAC
** ***
2416111 TTTTAGATTTAGAACTAAATTAAAAAATTTTGTAAATGTTGAGGGTTAAATTTATT-GAATT
1 TTTTAGATTTAGAACTAAATTAAAAAATTTTGTAAACATTGAGACCTAAATTTATTGGAATT
* * * * *
2416172 TTTTAGAATTAGAATTAAA-TGATAAATTTTGTAAACATTGAGACCTAAATTTATTGGATTT
1 TTTTAGATTTAGAACTAAATTAAAAAATTTTGTAAACATTGAGACCTAAATTTATTGGAATT
2416233 TTTTAGATTTAG
1 TTTTAGATTTAG
2416245 GATCAAGTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 29 0.48
61 32 0.52
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (62 bp):
TTTTAGATTTAGAACTAAATTAAAAAATTTTGTAAACATTGAGACCTAAATTTATTGGAATT
Found at i:2418136 original size:33 final size:32
Alignment explanation
Indices: 2418069--2418136 Score: 75
Period size: 33 Copynumber: 2.1 Consensus size: 32
2418059 ATTATAAATT
* * *
2418069 TTAATATTTAATTTTTTTTATATATCTCAAAA
1 TTAATATTTAATATTATTTATATATCTAAAAA
*
2418101 TTAATATCTTAATATTATTTATCTAT-TAAATAA
1 TTAATAT-TTAATATTATTTATATATCTAAA-AA
2418134 TTA
1 TTA
2418137 TTATGTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (32 bp):
TTAATATTTAATATTATTTATATATCTAAAAA
Found at i:2423159 original size:14 final size:14
Alignment explanation
Indices: 2423140--2423169 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2423130 GAATAAATTT
2423140 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
2423154 TTAATTAATTAAAA
1 TTAATTAAATAAAA
2423168 TT
1 TT
2423170 TTTAAACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:2425804 original size:6 final size:6
Alignment explanation
Indices: 2425787--2425820 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
2425777 ACAAATCTTG
2425787 TATTTAA TATTTA TATTTA TATTTA TATTTA TAT
1 TATTT-A TATTTA TATTTA TATTTA TATTTA TAT
2425821 GTGTTCGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTTA
Found at i:2426908 original size:20 final size:20
Alignment explanation
Indices: 2426872--2426909 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2426862 CATAAATATA
*
2426872 AATATTATATTTAAAATTTT
1 AATATTATATTCAAAATTTT
2426892 AATATTAT-TTCACAAATT
1 AATATTATATTCA-AAATT
2426910 GCACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATTATATTCAAAATTTT
Found at i:2434380 original size:444 final size:446
Alignment explanation
Indices: 2433547--2434443 Score: 1753
Period size: 444 Copynumber: 2.0 Consensus size: 446
2433537 ATGAACAGCG
2433547 TTGCAAGTCATTGACAAATTAGAAGGCCAACAACATAAATTAGCAGTGATTAATTAAACACCTTA
1 TTGCAAGTCATTGACAAATTAGAAGGCCAACAACATAAATTAGCAGTGATTAATTAAACACCTTA
2433612 CTGGCACCCCAGTGATTCCCCTCTCCCAATTTGAAATATATACCAAAGATGCCAAAAAAAAAAAA
66 CTGGCACCCCAGTGATTCCCCTCTCCCAATTTGAAATATATACCAAAGATGCC--AAAAAAAAAA
2433677 AAAACAAATTAAAAGGCCTTTTTTTCCAGTGTTTTGGTAGAAATGGCAACTTGAAACATGAAATA
129 AAAACAAATTAAAAGGCCTTTTTTTCCAGTGTTTTGGTAGAAATGGCAACTTGAAACATGAAATA
2433742 TGAATTGGCTTTTAGTCTCAAAGGAGACAAAGGAAGGCGATTCTTTCAAGAACTGAATGATGTAG
194 TGAATTGGCTTTTAGTCTCAAAGGAGACAAAGGAAGGCGATTCTTTCAAGAACTGAATGATGTAG
2433807 ATATCCACTTTTATTTGGGGGAAGACAAATATAATGTTTAAATTCAGGTGCCAACCAATCTGAAG
259 ATATCCACTTTTATTTGGGGGAAGACAAATATAATGTTTAAATTCAGGTGCCAACCAATCTGAAG
2433872 AAACAAGGTTATGGACAAGCAACAAGATAAAAATTTAAGTGCTGCTATTTTTCTTAAAATATCTG
324 AAACAAGGTTATGGACAAGCAACAAGATAAAAATTTAAGTGCTGCTATTTTTCTTAAAATATCTG
2433937 AAGAGAATTGTTAATCAGAAATACTGCATTCAGTATTATTAAATCATCTCAGAATAAT
389 AAGAGAATTGTTAATCAGAAATACTGCATTCAGTATTATTAAATCATCTCAGAATAAT
2433995 TTGCAAGTCATTGACAAATTAGAAGGCCAACAACATAAATTAGCAGTGATTAATTAAACACCTTA
1 TTGCAAGTCATTGACAAATTAGAAGGCCAACAACATAAATTAGCAGTGATTAATTAAACACCTTA
2434060 CTGGCACCCCAGTGATTCCCCTCTCCCAATTTGAAATATATACCAAAGATGCC-AAAAAAAAAAA
66 CTGGCACCCCAGTGATTCCCCTCTCCCAATTTGAAATATATACCAAAGATGCCAAAAAAAAAAAA
*
2434124 GACAAATTAAAAGGCC-TTTTTTCCAGTGTTTTGGTAGAAATGGCAACTTGAAACATGAAATATG
131 AACAAATTAAAAGGCCTTTTTTTCCAGTGTTTTGGTAGAAATGGCAACTTGAAACATGAAATATG
2434188 AATTGGCTTTTAGTCTCAAAGGAGACAAAGGAAGGCGATTCTTTCAAGAACTGAATGATGTAGAT
196 AATTGGCTTTTAGTCTCAAAGGAGACAAAGGAAGGCGATTCTTTCAAGAACTGAATGATGTAGAT
2434253 ATCCACTTTTATTTGGGGGAAGACAAATATAATGTTTAAATTCAGGTGCCAACCAATCTGAAGAA
261 ATCCACTTTTATTTGGGGGAAGACAAATATAATGTTTAAATTCAGGTGCCAACCAATCTGAAGAA
2434318 ACAAGGTTATGGACAAGCAACAAGATAAAAATTTAAGTGCTGCTATTTTTCTTAAAATATCTGAA
326 ACAAGGTTATGGACAAGCAACAAGATAAAAATTTAAGTGCTGCTATTTTTCTTAAAATATCTGAA
2434383 GAGAATTGTTAATCAGAAATACTGCATTCAGTATTATTAAATCATCTCAGAATAAT
391 GAGAATTGTTAATCAGAAATACTGCATTCAGTATTATTAAATCATCTCAGAATAAT
2434439 TTGCA
1 TTGCA
2434444 GATTATGATG
Statistics
Matches: 448, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
444 304 0.68
445 26 0.06
448 118 0.26
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (446 bp):
TTGCAAGTCATTGACAAATTAGAAGGCCAACAACATAAATTAGCAGTGATTAATTAAACACCTTA
CTGGCACCCCAGTGATTCCCCTCTCCCAATTTGAAATATATACCAAAGATGCCAAAAAAAAAAAA
AACAAATTAAAAGGCCTTTTTTTCCAGTGTTTTGGTAGAAATGGCAACTTGAAACATGAAATATG
AATTGGCTTTTAGTCTCAAAGGAGACAAAGGAAGGCGATTCTTTCAAGAACTGAATGATGTAGAT
ATCCACTTTTATTTGGGGGAAGACAAATATAATGTTTAAATTCAGGTGCCAACCAATCTGAAGAA
ACAAGGTTATGGACAAGCAACAAGATAAAAATTTAAGTGCTGCTATTTTTCTTAAAATATCTGAA
GAGAATTGTTAATCAGAAATACTGCATTCAGTATTATTAAATCATCTCAGAATAAT
Found at i:2445826 original size:16 final size:16
Alignment explanation
Indices: 2445797--2445827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2445787 ATTTTATCTT
*
2445797 TATTTATTTTTATGTC
1 TATTTATATTTATGTC
2445813 TATTTATATTTATGT
1 TATTTATATTTATGT
2445828 TTTTTTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTATATTTATGTC
Found at i:2446171 original size:23 final size:24
Alignment explanation
Indices: 2446142--2446213 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 24
2446132 TAAAAATGAT
2446142 TAAAAAATCTTAAAATTA-TAAATA
1 TAAAAAAT-TTAAAATTATTAAATA
* *
2446166 T-AAAAATATAAAATTATTAAAAA
1 TAAAAAATTTAAAATTATTAAATA
2446189 TAAAAATATTTTAAAATTATTAAAT
1 TAAAAA-A-TTTAAAATTATTAAAT
2446214 TTAATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 8 0.20
23 12 0.30
24 5 0.12
25 1 0.03
26 14 0.35
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAAATTTAAAATTATTAAATA
Found at i:2446188 original size:17 final size:17
Alignment explanation
Indices: 2446166--2446214 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2446156 ATTATAAATA
2446166 TAAAAATATAAAATTAT
1 TAAAAATATAAAATTAT
*
2446183 TAAAAATA-AAAATATTT
1 TAAAAATATAAAAT-TAT
* *
2446200 TAAAATTATTAAATT
1 TAAAAATATAAAATT
2446215 TAATATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 18 0.67
18 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATATAAAATTAT
Done.