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 107 of 120
Found at i:31151661 original size:21 final size:21
Alignment explanation
Indices: 31151620--31151671 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
31151610 TTTTGTATTG
**
31151620 AATTATGTTT-TTTATGTTTTT
1 AATTAT-TTTATTTATACTTTT
31151641 AATTATTTTATTTATACTTTT
1 AATTATTTTATTTATACTTTT
31151662 -ATT-TTTTATT
1 AATTATTTTATT
31151672 GATTTAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 15 0.54
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (21 bp):
AATTATTTTATTTATACTTTT
Found at i:31155999 original size:15 final size:15
Alignment explanation
Indices: 31155978--31156219 Score: 88
Period size: 15 Copynumber: 14.9 Consensus size: 15
31155968 TTTATCGTTC
31155978 GCATTTGGTACAGCA
1 GCATTTGGTACAGCA
* *
31155993 ACATTTGGTATAAAAGCA
1 GCATTTGG--T-ACAGCA
* **
31156011 GCATTTGGAACCCCA
1 GCATTTGGTACAGCA
* * *
31156026 ACATTTGGCACAACA
1 GCATTTGGTACAGCA
*
31156041 ACATTTGGTACAGCA
1 GCATTTGGTACAGCA
* **
31156056 GCATCTGGTGTAACAATA
1 GCAT-TTG-GT-ACAGCA
*
31156074 GCATTTGGTGTAACCGCA
1 GCATTT-G-GT-ACAGCA
* *
31156092 ACATTTGGTGTTACCGCA
1 GCATTT-G-G-TACAGCA
31156110 GCATTTGGTGTAACAGCA
1 GCATTT-G-GT-ACAGCA
* * **
31156128 GTATTTGGAACCCCA
1 GCATTTGGTACAGCA
*
31156143 ACATTTGGTACAGCA
1 GCATTTGGTACAGCA
*
31156158 GCATCTGATGTAACAGCA
1 GCATTTG--GT-ACAGCA
* **
31156176 ACATTTGGTACCCCA
1 GCATTTGGTACAGCA
* *
31156191 GCATTTGGCACGGCA
1 GCATTTGGTACAGCA
31156206 GCATTTGGTACAGC
1 GCATTTGGTACAGC
31156220 GACATAAGGT
Statistics
Matches: 170, Mismatches: 45, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
15 83 0.49
16 5 0.03
17 8 0.05
18 73 0.43
19 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (15 bp):
GCATTTGGTACAGCA
Found at i:31156082 original size:18 final size:18
Alignment explanation
Indices: 31156050--31156184 Score: 102
Period size: 18 Copynumber: 7.8 Consensus size: 18
31156040 AACATTTGGT
*
31156050 ACAGCAGCATCTGGTGTA
1 ACAGCAGCATTTGGTGTA
**
31156068 ACAATAGCATTTGGTGTA
1 ACAGCAGCATTTGGTGTA
* * *
31156086 ACCGCAACATTTGGTGTT
1 ACAGCAGCATTTGGTGTA
*
31156104 ACCGCAGCATTTGGTGTA
1 ACAGCAGCATTTGGTGTA
*
31156122 ACAGCAGTATTT-G-G-A
1 ACAGCAGCATTTGGTGTA
** *
31156137 ACCCCAACATTT-G-GT-
1 ACAGCAGCATTTGGTGTA
* *
31156152 ACAGCAGCATCTGATGTA
1 ACAGCAGCATTTGGTGTA
*
31156170 ACAGCAACATTTGGT
1 ACAGCAGCATTTGGT
31156185 ACCCCAGCAT
Statistics
Matches: 89, Mismatches: 24, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
15 19 0.21
16 1 0.01
17 3 0.03
18 66 0.74
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (18 bp):
ACAGCAGCATTTGGTGTA
Found at i:31156100 original size:51 final size:48
Alignment explanation
Indices: 31156039--31156214 Score: 172
Period size: 48 Copynumber: 3.5 Consensus size: 48
31156029 TTTGGCACAA
* *
31156039 CAACATTTGGTACAGCAGCATCTGGTGTAACAATAGCATTTGGTGTAACCG
1 CAACATTTGGTACAGCAGCATCTGGTGTAACAACAGCATTT-G-G-AACCC
* * * *
31156090 CAACATTTGGTGTTACCGCAGCATTTGGTGTAACAGCAGTATTTGGAACCC
1 CAACATTT-G-G-TACAGCAGCATCTGGTGTAACAACAGCATTTGGAACCC
* * * *
31156141 CAACATTTGGTACAGCAGCATCTGATGTAACAGCAACATTTGGTACCC
1 CAACATTTGGTACAGCAGCATCTGGTGTAACAACAGCATTTGGAACCC
* * * *
31156189 CAGCATTTGGCACGGCAGCATTTGGT
1 CAACATTTGGTACAGCAGCATCTGGT
31156215 ACAGCGACAT
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
48 53 0.50
49 1 0.01
50 1 0.01
51 20 0.19
52 2 0.02
53 2 0.02
54 26 0.25
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
CAACATTTGGTACAGCAGCATCTGGTGTAACAACAGCATTTGGAACCC
Found at i:31157565 original size:20 final size:20
Alignment explanation
Indices: 31157535--31157573 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31157525 ATACTTTTAC
31157535 CTTCTTTTGTTGT-TTGCTT
1 CTTCTTTTGTTGTGTTGCTT
31157554 CTTCTATTTGTTGTGTTGCT
1 CTTCT-TTTGTTGTGTTGCT
31157574 GTATGCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.03, C:0.15, G:0.18, T:0.64
Consensus pattern (20 bp):
CTTCTTTTGTTGTGTTGCTT
Found at i:31163134 original size:20 final size:20
Alignment explanation
Indices: 31163104--31163158 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
31163094 CTTTTAATGT
*
31163104 AATTACAAGCAATTATAACCA
1 AATT-CAAGCAATTACAACCA
31163125 AATTCAAGCAATTACAACCA
1 AATTCAAGCAATTACAACCA
31163145 AATTCAAGCAATTA
1 AATTCAAGCAATTA
31163159 AGTGATTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (20 bp):
AATTCAAGCAATTACAACCA
Found at i:31166150 original size:24 final size:24
Alignment explanation
Indices: 31166095--31166164 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
31166085 AGATTACTTT
*
31166095 ATATTTTATATATAATTATATTAA
1 ATATTTTATATATCATTATATTAA
* *
31166119 ATATTTTATGTATCATTATATTGA
1 ATATTTTATATATCATTATATTAA
*
31166143 AT-TATTTAAATATCATT-TATTA
1 ATAT-TTTATATATCATTATATTA
31166165 TTATAGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 5 0.13
24 34 0.87
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (24 bp):
ATATTTTATATATCATTATATTAA
Found at i:31166182 original size:31 final size:30
Alignment explanation
Indices: 31166133--31166213 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
31166123 TTTATGTATC
31166133 ATTATATTGAATTATTTAAATATCATTTATT
1 ATTATATTGAATT-TTTAAATATCATTTATT
* * * *
31166164 ATTATAGTAAATTGTTTAAATCTTATTTATT
1 ATTATATTGAATT-TTTAAATATCATTTATT
31166195 ATTATATTGAATTTTTAAA
1 ATTATATTGAATTTTTAAA
31166214 ATATTTTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 6 0.14
31 37 0.86
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.54
Consensus pattern (30 bp):
ATTATATTGAATTTTTAAATATCATTTATT
Found at i:31166634 original size:2 final size:2
Alignment explanation
Indices: 31166627--31166651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31166617 AGCACTCTTT
31166627 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31166652 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31168946 original size:3 final size:3
Alignment explanation
Indices: 31168938--31168965 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31168928 TAGCTGGCAA
31168938 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
31168966 TTTATTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:31170934 original size:188 final size:188
Alignment explanation
Indices: 31170578--31170975 Score: 514
Period size: 188 Copynumber: 2.1 Consensus size: 188
31170568 TTAAAATATC
* * * *
31170578 TATTTTTATTATTAATGATATTTGATGATCTGATTCACTAAAAACTCATACAATTATACATCGTC
1 TATTTTTATTATTAATGATATCTCATGATCTGATTCACTAAAAACTCATAAAATCATACATCGTC
* *
31170643 AGTGCATCAAACATTAACCATTTCAGAATGGATCAATACTTGATGCACTAACGAATATAATTTTA
66 AGTGCATCAAACATTAACCATTTCAGAATGGATCAATACTTGATACACTAACGAATATAATTCTA
* * * * *
31170708 TGCATTATAAGTGAAGTAAAATATGACACATCATAAAAAAATTAAAACAT-AATTCACT
131 TACACTATAAGAGAAGTAAAATATAACACATAATAAAAAAATTAAAAC-TGAATTCACT
* * **
31170766 TATTTTTATTATTAATGATGTCTCATGA-CATGATTCATTAAAAACTCATAAAATCATATTTCGT
1 TATTTTTATTATTAATGATATCTCATGATC-TGATTCACTAAAAACTCATAAAATCATACATCGT
* * * *
31170830 CATTGCATCAAACATTAACCATTTCGGAATGGATCAATTCTT-ATACACTAACAGTATATAATTC
65 CAGTGCATCAAACATTAACCATTTCAGAATGGATCAATACTTGATACACTAAC-GAATATAATTC
* * * * * *
31170894 TATATACTATTAGAGAATTAGATTATAAGACATAATAAAAAAATTAAAACTGAATTCACT
129 TATACACTATAAGAGAAGTAAAATATAACACATAATAAAAAAATTAAAACTGAATTCACT
31170954 TATTTTTCATTATTAATGATAT
1 TATTTTT-ATTATTAATGATAT
31170976 GTTAATAATT
Statistics
Matches: 180, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
187 11 0.06
188 156 0.87
189 13 0.07
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (188 bp):
TATTTTTATTATTAATGATATCTCATGATCTGATTCACTAAAAACTCATAAAATCATACATCGTC
AGTGCATCAAACATTAACCATTTCAGAATGGATCAATACTTGATACACTAACGAATATAATTCTA
TACACTATAAGAGAAGTAAAATATAACACATAATAAAAAAATTAAAACTGAATTCACT
Found at i:31176405 original size:20 final size:20
Alignment explanation
Indices: 31176380--31176421 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31176370 AATACTCTCA
31176380 CAAACATTTAGAACAAACTC
1 CAAACATTTAGAACAAACTC
31176400 CAAACATTTAGAACAAACTC
1 CAAACATTTAGAACAAACTC
31176420 CA
1 CA
31176422 GAAACTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.19
Consensus pattern (20 bp):
CAAACATTTAGAACAAACTC
Found at i:31178486 original size:31 final size:31
Alignment explanation
Indices: 31178451--31178516 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
31178441 GTAATTAAAT
*
31178451 TATTCTAAAGTTTTCATTTAAGTCACT-GAAC
1 TATTCAAAAGTTTTCATTTAAGTCACTAG-AC
*
31178482 TATTCAAAAGTTTTTATTTAAGTCACTAGAC
1 TATTCAAAAGTTTTCATTTAAGTCACTAGAC
31178513 TATT
1 TATT
31178517 ACATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAGTCACTAGAC
Found at i:31181866 original size:20 final size:19
Alignment explanation
Indices: 31181835--31181872 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
31181825 TATCTATTTG
31181835 TTTTATTTAATTATAATAT
1 TTTTATTTAATTATAATAT
31181854 TTTTATGTTAATTATAATA
1 TTTTAT-TTAATTATAATA
31181873 ATATGGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTATTTAATTATAATAT
Found at i:31183312 original size:37 final size:37
Alignment explanation
Indices: 31183267--31183357 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 37
31183257 TTCCAAAAAT
31183267 AATATTATTTTAATAGT-TTAATATTGAA-TTAA-ATTA
1 AATATTATTTTAATAGTATT-ATATT-AATTTAATATTA
*
31183303 AATACTTATTTTAATAGTATTTTATTAATTTAATATTA
1 AATA-TTATTTTAATAGTATTATATTAATTTAATATTA
31183341 AAGTAATTATTTTAATA
1 AA-T-ATTATTTTAATA
31183358 TTAAATTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
36 6 0.12
37 21 0.44
38 8 0.17
39 12 0.25
40 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (37 bp):
AATATTATTTTAATAGTATTATATTAATTTAATATTA
Found at i:31183931 original size:27 final size:29
Alignment explanation
Indices: 31183893--31183947 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
31183883 AGTAAAATAG
*
31183893 ATTTAGATATATTTAATT-TTT-TTTAAA
1 ATTTAGATATATTGAATTATTTATTTAAA
31183920 ATTTATGA-ATATTGAATTATTTATTTAA
1 ATTTA-GATATATTGAATTATTTATTTAA
31183948 TTATTGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 14 0.58
28 5 0.21
29 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (29 bp):
ATTTAGATATATTGAATTATTTATTTAAA
Found at i:31195093 original size:16 final size:16
Alignment explanation
Indices: 31195082--31195135 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
31195072 ATTATTTTTA
31195082 ATTTAATGTATTATTT
1 ATTTAATGTATTATTT
* *
31195098 ATTTAATTTGTTATTT
1 ATTTAATGTATTATTT
*
31195114 TTTTACATGTAATTATCTT
1 ATTTA-ATGT-ATTAT-TT
31195133 ATT
1 ATT
31195136 AGGTTATCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 18 0.62
17 3 0.10
18 4 0.14
19 4 0.14
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.63
Consensus pattern (16 bp):
ATTTAATGTATTATTT
Found at i:31206724 original size:16 final size:18
Alignment explanation
Indices: 31206699--31206741 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
31206689 ATTATTAAGG
31206699 TATAAT-TTATG-ATTTT
1 TATAATATTATGTATTTT
31206715 TAT-ATATTATGTTATTTT
1 TATAATATTATG-TATTTT
31206733 TATAATATT
1 TATAATATT
31206742 TATTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 8 0.35
18 8 0.35
19 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TATAATATTATGTATTTT
Found at i:31208140 original size:2 final size:2
Alignment explanation
Indices: 31208133--31208194 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
31208123 AACCCCAATC
31208133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
31208175 AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
31208195 GAACTAACTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31225884 original size:20 final size:20
Alignment explanation
Indices: 31225859--31225900 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31225849 ACTGTGAAGA
31225859 ATTTCAAGCTTCAGGTTGAG
1 ATTTCAAGCTTCAGGTTGAG
31225879 ATTTCAAGCTTCAGGTTGAG
1 ATTTCAAGCTTCAGGTTGAG
31225899 AT
1 AT
31225901 AGTTTGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (20 bp):
ATTTCAAGCTTCAGGTTGAG
Found at i:31230213 original size:31 final size:31
Alignment explanation
Indices: 31230166--31230295 Score: 115
Period size: 31 Copynumber: 4.3 Consensus size: 31
31230156 AAAATATTAA
* **
31230166 GTACCAACTTAAGAAAAAGTGTTGAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
* *
31230197 GTACCAAATTAGGAAAAGGTGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
* *
31230228 GTACCAAATTGAACAAAAA----AAAGTTTAG
1 GTACCAAATT-AAGAAAAAGTGTCAAGTTTAG
* * *
31230256 ATATCAAATTAAGAAAAAGTATCAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
* *
31230287 ATGCCAAAT
1 GTACCAAAT
31230296 GTTATATTAA
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.09
28 16 0.20
31 51 0.65
32 5 0.06
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
Found at i:31230249 original size:90 final size:91
Alignment explanation
Indices: 31230104--31230275 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 91
31230094 AAAAAAGATC
***
31230104 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACCCCAAAAA-TATTA-AG
1 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACAAAAAAAAGT-TTAGA-
*
31230167 TACCAACTTAAGAAAAAGTGTTGAGTTT
64 TACCAAATTAAGAAAAAGTGTTGAGTTT
* *** * *
31230195 AGGTACCAAATTAG-GAAAAGGTGTCAAGTTTAGGTACCAAATTGAACAAAAAAAAGTTTAGATA
1 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACAAAAAAAAGTTTAGATA
*
31230259 TCAAATTAAGAAAAAGT
66 CCAAATTAAGAAAAAGT
31230276 ATCAAGTTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
90 52 0.76
91 16 0.24
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.23
Consensus pattern (91 bp):
AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACAAAAAAAAGTTTAGATA
CCAAATTAAGAAAAAGTGTTGAGTTT
Found at i:31230263 original size:28 final size:27
Alignment explanation
Indices: 31230220--31230273 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
31230210 AAAAGGTGTC
*
31230220 AAGTTTAGGTACCAAATTGAACAAAAAA
1 AAGTTTAGATACCAAATT-AACAAAAAA
* *
31230248 AAGTTTAGATATCAAATTAAGAAAAA
1 AAGTTTAGATACCAAATTAACAAAAA
31230274 GTATCAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (27 bp):
AAGTTTAGATACCAAATTAACAAAAAA
Found at i:31230284 original size:90 final size:91
Alignment explanation
Indices: 31230104--31230295 Score: 201
Period size: 90 Copynumber: 2.1 Consensus size: 91
31230094 AAAAAAGATC
***
31230104 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACCCCAAAAATATTAAGTA
1 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACAAAAAAAATATTAAGTA
* * **
31230169 CCAACTTAAGAAAAAGTGTTGAGTTT
66 CCAAATTAAGAAAAAGTATCAAGTTT
* *** * *
31230195 AGGTACCAAATTAG-GAAAAGGTGTCAAGTTTAGGTACCAAATTGAACAAAAAAAAGT-TT-AGA
1 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACAAAAAAAA-TATTAAG-
*
31230257 TATCAAATTAAGAAAAAGTATCAAGTTT
64 TACCAAATTAAGAAAAAGTATCAAGTTT
* *
31230285 AGATGCCAAAT
1 AGGTACCAAAT
31230296 GTTATATTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
89 2 0.02
90 66 0.80
91 15 0.18
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.24
Consensus pattern (91 bp):
AGGTACCAAATTAGAAAAAAAAAGTCAAGTTTAAGTACCAAATAGAACAAAAAAAATATTAAGTA
CCAAATTAAGAAAAAGTATCAAGTTT
Found at i:31230729 original size:29 final size:28
Alignment explanation
Indices: 31230695--31230782 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 28
31230685 AAACTTCAAT
* *
31230695 TTTTAAATTAAAAAAATTGAGGACTAAA
1 TTTTAAATTAAAAAAATTAAGAACTAAA
*
31230723 TTCTTAAAAGT-AAAAAA-TAAGAACTAAA
1 TT-TT-AAATTAAAAAAATTAAGAACTAAA
* *
31230751 TTTTAAATATATAAAAATATAAAAACTTAAA
1 TTTTAAAT-TAAAAAAAT-TAAGAAC-TAAA
31230782 T
1 T
31230783 CATATTGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 18 0.38
29 8 0.17
30 10 0.21
31 5 0.11
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.32
Consensus pattern (28 bp):
TTTTAAATTAAAAAAATTAAGAACTAAA
Found at i:31230766 original size:28 final size:27
Alignment explanation
Indices: 31230695--31230769 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
31230685 AAACTTCAAT
* *
31230695 TTTTAAAT-TAAAAAAATTGAGGACTAAA
1 TTTTAAATAT-AAAAAA-TAAGAACTAAA
31230723 TTCTTAAA-AGTAAAAAATAAGAACTAAA
1 TT-TTAAATA-TAAAAAATAAGAACTAAA
31230751 TTTTAAATATATAAAAATA
1 TTTTAAATATA-AAAAATA
31230770 TAAAAACTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 7 0.17
28 21 0.52
29 11 0.28
30 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTTAAATATAAAAAATAAGAACTAAA
Found at i:31230933 original size:15 final size:15
Alignment explanation
Indices: 31230915--31230981 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
31230905 TTTACCGCGC
*
31230915 TCTTTTCCATTCTTT
1 TCTTTTCCTTTCTTT
*
31230930 TCTTTTCTTTTCTTT
1 TCTTTTCCTTTCTTT
* *
31230945 TCATCTCCTTTCTTT
1 TCTTTTCCTTTCTTT
**
31230960 AATTTTCCTTTCTTT
1 TCTTTTCCTTTCTTT
31230975 TCCTTTT
1 T-CTTTT
31230982 ATTATTAGTT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
15 36 0.90
16 4 0.10
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTTTCCTTTCTTT
Found at i:31230934 original size:5 final size:5
Alignment explanation
Indices: 31230924--31230981 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
31230914 CTCTTTTCCA
* * * ** *
31230924 TTCTT TTCTT TTCTT TTCTT TTCAT CTCCT TTCTT TAATT TTCCT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
31230974 TTCCTT TT
1 TT-CTT TT
31230982 ATTATTAGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
5 36 0.88
6 5 0.12
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (5 bp):
TTCTT
Found at i:31235214 original size:21 final size:21
Alignment explanation
Indices: 31235166--31235214 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
31235156 GCAATATGAT
31235166 AGCAAAATGGAAGCAAACAAC
1 AGCAAAATGGAAGCAAACAAC
31235187 ATG-AAAATGGCAA-CAAACAAC
1 A-GCAAAATGG-AAGCAAACAAC
31235208 AGCAAAA
1 AGCAAAA
31235215 CAGCAGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.59, C:0.18, G:0.16, T:0.06
Consensus pattern (21 bp):
AGCAAAATGGAAGCAAACAAC
Found at i:31248943 original size:5 final size:5
Alignment explanation
Indices: 31248933--31248961 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31248923 TCAAGAGAGA
31248933 AACCC AACCC AACCC AACCC AACCC AACC
1 AACCC AACCC AACCC AACCC AACCC AACC
31248962 GCATTAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:31254421 original size:68 final size:68
Alignment explanation
Indices: 31254292--31254421 Score: 158
Period size: 69 Copynumber: 1.9 Consensus size: 68
31254282 TGGAAGCAAC
* ***
31254292 AAAAGCTTGATTTAGTTCCACACATTCTTCCACCTCATGTTCTCTCTACCTCCGTTGTTCCCTTT
1 AAAAGCTTGATTTAGTTCCACACATTCTTCCACCCCATGTTCTCTCTACCTCCGAACTTCCCTTT
31254357 TAT
66 TAT
**
31254360 AAAAGCTTGATTTAGTTCTCACTA-ATTCTTCTGCCCCATGTTCTCTC-ATCCTCC-AACTTCCC
1 AAAAGCTTGATTTAGTTC-CAC-ACATTCTTCCACCCCATGTTCTCTCTA-CCTCCGAACTTCCC
31254422 ACTCATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
68 24 0.45
69 28 0.53
70 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.08, T:0.39
Consensus pattern (68 bp):
AAAAGCTTGATTTAGTTCCACACATTCTTCCACCCCATGTTCTCTCTACCTCCGAACTTCCCTTT
TAT
Found at i:31258603 original size:2 final size:2
Alignment explanation
Indices: 31258596--31258629 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31258586 TATATGAGCA
31258596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31258630 TTTTTTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31264270 original size:23 final size:23
Alignment explanation
Indices: 31264223--31264272 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
31264213 ACATTGTCGA
* *
31264223 TTTAGTTCTTATACTTTAGTCAT
1 TTTAGTCCTTATACTTTAGTAAT
31264246 TTTAGTCCTTATACTTTAAG-AAT
1 TTTAGTCCTTATACTTT-AGTAAT
31264269 TTTA
1 TTTA
31264273 AAATTCTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (23 bp):
TTTAGTCCTTATACTTTAGTAAT
Found at i:31264698 original size:18 final size:17
Alignment explanation
Indices: 31264647--31264698 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
31264637 ACCCGACCTG
* *
31264647 TTTTAAATT-TATAATA
1 TTTTATATTATATAATT
* *
31264663 TTTTATATTATGTTATT
1 TTTTATATTATATAATT
31264680 TTTATATATTATATAATT
1 TTT-TATATTATATAATT
31264698 T
1 T
31264699 CGAATACATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATATTATATAATT
Found at i:31272642 original size:5 final size:6
Alignment explanation
Indices: 31272616--31272646 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
31272606 TTAGGTCTAA
31272616 CCCGAC CCCGAC CCCGAC CCCGA- CCCGAC CC
1 CCCGAC CCCGAC CCCGAC CCCGAC CCCGAC CC
31272647 ATGATCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CCCGAC
Found at i:31273963 original size:18 final size:18
Alignment explanation
Indices: 31273945--31273979 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31273935 GGTTTAGAAT
31273945 TTAAATTT-TTTAATTAA
1 TTAAATTTATTTAATTAA
31273962 TTAAATTTATTTAATTAA
1 TTAAATTTATTTAATTAA
31273980 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTTATTTAATTAA
Found at i:31274468 original size:18 final size:18
Alignment explanation
Indices: 31274445--31274482 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31274435 TTGGTGTTTC
31274445 CTATTTCTTTTCTTCTTT
1 CTATTTCTTTTCTTCTTT
*
31274463 CTATTTCTTTTTTTCTTT
1 CTATTTCTTTTCTTCTTT
31274481 CT
1 CT
31274483 TCCTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
CTATTTCTTTTCTTCTTT
Found at i:31274481 original size:25 final size:25
Alignment explanation
Indices: 31274448--31274507 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
31274438 GTGTTTCCTA
31274448 TTTCTTTTCTT-CTTTCTATTTCTTTT
1 TTTC-TTTCTTCCTTT-TATTTCTTTT
*
31274474 TTTCTTTCTTCCTTTTGTTTCTTTT
1 TTTCTTTCTTCCTTTTATTTCTTTT
31274499 TTTCTTTCT
1 TTTCTTTCT
31274508 GTTTCTGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 24 0.75
26 8 0.25
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTCTTTCTTCCTTTTATTTCTTTT
Found at i:31277215 original size:21 final size:21
Alignment explanation
Indices: 31277186--31277227 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31277176 CTACAACTTA
*
31277186 AAGCGGAGGCAACAGCAAGAG
1 AAGCAGAGGCAACAGCAAGAG
* *
31277207 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAACAGCAAGAG
31277228 CCGCGAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.00
Consensus pattern (21 bp):
AAGCAGAGGCAACAGCAAGAG
Found at i:31277597 original size:43 final size:43
Alignment explanation
Indices: 31277549--31277721 Score: 202
Period size: 43 Copynumber: 4.0 Consensus size: 43
31277539 ATCTGTTAAT
* * * * *
31277549 TTTAGCGGTGTTTATGGGGAAAACGCAGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTATGGGGAAAGCACCGCTAAAGACCATGTTC
* * * *
31277592 TTTAGCAGCGTTTGTGTGTAAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTATGGGGAAAGCACCGCTAAAGACCATGTTC
* * *
31277635 TTTAGCGGCGTTTATGGGGAAGGCACTGCTAAAGACCATGGTC
1 TTTAGCGGCGTTTATGGGGAAAGCACCGCTAAAGACCATGTTC
* * * *
31277678 TTTAGTGGCGCTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTATGGGGAAAGCACCGCTAAAGACCATGTTC
31277721 T
1 T
31277722 ATAACAGCGT
Statistics
Matches: 107, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 107 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTATGGGGAAAGCACCGCTAAAGACCATGTTC
Found at i:31277701 original size:86 final size:86
Alignment explanation
Indices: 31277549--31277721 Score: 229
Period size: 86 Copynumber: 2.0 Consensus size: 86
31277539 ATCTGTTAAT
* * * * * * *
31277549 TTTAGCGGTGTTTATGGGGAAAACGCAGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGTGTAAA
1 TTTAGCGGCGTTTATGGGGAAAACACAGCTAAAGACCATGGTCTTTAGCAGCGCTTGTGGGGAAA
31277614 GCACCGCTAAAGACCATGTTC
66 GCACCGCTAAAGACCATGTTC
** * **
31277635 TTTAGCGGCGTTTATGGGGAAGGCACTGCTAAAGACCATGGTCTTTAGTGGCGCTTGTGGGGAAA
1 TTTAGCGGCGTTTATGGGGAAAACACAGCTAAAGACCATGGTCTTTAGCAGCGCTTGTGGGGAAA
*
31277700 GCGCCGCTAAAGACCATGTTC
66 GCACCGCTAAAGACCATGTTC
31277721 T
1 T
31277722 ATAACAGCGT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTATGGGGAAAACACAGCTAAAGACCATGGTCTTTAGCAGCGCTTGTGGGGAAA
GCACCGCTAAAGACCATGTTC
Found at i:31287667 original size:12 final size:12
Alignment explanation
Indices: 31287650--31287677 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31287640 GGAGGGATTT
31287650 GAGACATCGGCG
1 GAGACATCGGCG
31287662 GAGACATCGGCG
1 GAGACATCGGCG
31287674 GAGA
1 GAGA
31287678 TGGTAGCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.43, T:0.07
Consensus pattern (12 bp):
GAGACATCGGCG
Found at i:31301774 original size:33 final size:32
Alignment explanation
Indices: 31301695--31301784 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 32
31301685 ATTAAGCTAC
*
31301695 ATTTATATTAATATTATTTAA-ATA-TAAAAAT
1 ATTTATTTTAATATT-TTTAATATATTAAAAAT
*
31301726 -TTTA-TTTAATTTATTTTTAATTTATTAAAAAAT
1 ATTTATTTTAA--TATTTTTAATATATT-AAAAAT
31301759 ATTTATTTTAATATTTTTAATATATT
1 ATTTATTTTAATATTTTTAATATATT
31301785 TAATAGATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
29 4 0.08
30 9 0.18
31 6 0.12
32 1 0.02
33 20 0.41
34 4 0.08
35 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTATTTTAATATTTTTAATATATTAAAAAT
Found at i:31304694 original size:1 final size:1
Alignment explanation
Indices: 31304690--31304716 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
31304680 CCGAAAAAGC
31304690 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
31304717 CCCATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:31307461 original size:14 final size:14
Alignment explanation
Indices: 31307442--31307485 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
31307432 AAAAAAATTC
31307442 AATACTTAATTTTT
1 AATACTTAATTTTT
*
31307456 AATACTTATTTCTTTT
1 AATACTTA-AT-TTTT
*
31307472 AGTACTTAATTTTT
1 AATACTTAATTTTT
31307486 TAATTTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (14 bp):
AATACTTAATTTTT
Found at i:31307483 original size:17 final size:16
Alignment explanation
Indices: 31307452--31307489 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31307442 AATACTTAAT
31307452 TTTTAATACTTATTTC
1 TTTTAATACTTATTTC
* *
31307468 TTTTAGTACTTAATT-
1 TTTTAATACTTATTTC
31307483 TTTTAAT
1 TTTTAAT
31307490 TTATCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTAATACTTATTTC
Found at i:31308145 original size:17 final size:17
Alignment explanation
Indices: 31308119--31308160 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
31308109 GATATTCAAC
31308119 AAATTAGTTCCTTTAAA
1 AAATTAGTTCCTTTAAA
*
31308136 AAATTGGTTCCTTTAAA
1 AAATTAGTTCCTTTAAA
31308153 AAAGTTAG
1 AAA-TTAG
31308161 AGCAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
AAATTAGTTCCTTTAAA
Found at i:31321962 original size:7 final size:6
Alignment explanation
Indices: 31321926--31321973 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
31321916 AATATATATT
* * *
31321926 ATTT-A ATTTAA ATTTAA ATTTTA GTGTAAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA ATTTAA
31321974 GATAACTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
5 4 0.11
6 28 0.80
7 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:31324006 original size:18 final size:18
Alignment explanation
Indices: 31323933--31324024 Score: 68
Period size: 19 Copynumber: 5.2 Consensus size: 18
31323923 ATTTTAACTT
*
31323933 TTTTATATATATTTTAGAA
1 TTTTATAAATATTTTA-AA
*
31323952 TTTT-TATAT-TTTTAAA
1 TTTTATAAATATTTTAAA
* *
31323968 --ATATAAA-ATTTGAAA
1 TTTTATAAATATTTTAAA
31323983 TTTTTATAAATATTTTAAA
1 -TTTTATAAATATTTTAAA
* *
31324002 TTTTAAAAATCATTTTTAA
1 TTTTATAAAT-ATTTTAAA
31324021 TTTT
1 TTTT
31324025 TGAAAATTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
16 2 0.03
17 5 0.08
18 20 0.34
19 22 0.37
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTATAAATATTTTAAA
Found at i:31324020 original size:20 final size:20
Alignment explanation
Indices: 31323995--31324037 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31323985 TTTATAAATA
31323995 TTTTAAATTTTAAAAATCAT
1 TTTTAAATTTTAAAAATCAT
* * *
31324015 TTTTAATTTTTGAAAATTAT
1 TTTTAAATTTTAAAAATCAT
31324035 TTT
1 TTT
31324038 GAATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTAAATTTTAAAAATCAT
Found at i:31324042 original size:20 final size:19
Alignment explanation
Indices: 31323976--31324042 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
31323966 AAATATAAAA
31323976 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTA-AAATTAT
* * *
31323996 TTTAAATTTTAAAAATCAT
1 TTTGAATTTTTAAAATTAT
*
31324015 TTTTAATTTTTGAAAATTAT
1 TTTGAATTTTT-AAAATTAT
31324035 TTTGAATT
1 TTTGAATT
31324043 ATTTTGTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.08
19 18 0.47
20 17 0.45
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:31328360 original size:35 final size:30
Alignment explanation
Indices: 31328309--31328385 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 30
31328299 TATTTTTGAG
*
31328309 AAATAAAATA-ATTATTTTAAATATTATATTATA
1 AAATAAAAAATATTA-TTTAAATA--ATATT-TA
31328342 AAATAAAAAATATGTATTTAAATAATATTTA
1 AAATAAAAAATAT-TATTTAAATAATATTTA
* *
31328373 AATTAAATAATAT
1 AAATAAAAAATAT
31328386 CATGATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 13 0.33
32 5 0.13
33 9 0.23
34 10 0.26
35 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
AAATAAAAAATATTATTTAAATAATATTTA
Found at i:31328395 original size:35 final size:32
Alignment explanation
Indices: 31328324--31328385 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
31328314 AAATAATTAT
31328324 TTTAAATATTATATTATAAAATAAAAAATATGTA
1 TTTAAATA--ATATTATAAAATAAAAAATATGTA
* *
31328358 TTTAAATAATATT-TAAATTAAATAATAT
1 TTTAAATAATATTATAAAATAAAAAATAT
31328386 CATGATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 13 0.50
32 5 0.19
34 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTAAATAATATTATAAAATAAAAAATATGTA
Found at i:31329644 original size:30 final size:30
Alignment explanation
Indices: 31329588--31329711 Score: 162
Period size: 30 Copynumber: 4.2 Consensus size: 30
31329578 TCAAAAACAA
* * *
31329588 AATTTTGG-AAGGTTTGGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
31329617 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
*
31329647 AATATTGGAAAAGTTTTGGGGTC-AAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
* ** *
31329676 AATATTGGAAAAGTTTTAAGGTTAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
31329706 AATTTT
1 AATTTT
31329712 TGGATAGTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
29 34 0.40
30 51 0.60
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.38
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTTGGGGTCAAAATGT
Found at i:31330911 original size:36 final size:37
Alignment explanation
Indices: 31330844--31330915 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
31330834 TATTAATGGC
* *
31330844 TATTGATTGCTGTTATTAATACTATATTTATTATTAT
1 TATTGATTGCTGTTATTAATACTAGAATTATTATTAT
** *
31330881 TATTGA-TGCTGTTATTGTTATTAGAATTATTATTA
1 TATTGATTGCTGTTATTAATACTAGAATTATTATTA
31330916 ATACTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 24 0.80
37 6 0.20
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (37 bp):
TATTGATTGCTGTTATTAATACTAGAATTATTATTAT
Found at i:31331557 original size:17 final size:16
Alignment explanation
Indices: 31331535--31331617 Score: 85
Period size: 17 Copynumber: 4.9 Consensus size: 16
31331525 TTGGACATTG
*
31331535 AATTTATAATAATTTTA
1 AATTTA-AATAAATTTA
*
31331552 AATTTAAATTAAATCTA
1 AATTTAAA-TAAATTTA
*
31331569 AATTTAAATTAAATTCA
1 AATTTAAA-TAAATTTA
31331586 AATTTAAAATAAATTTA
1 AATTT-AAATAAATTTA
*
31331603 ATTTTAAAATAAATT
1 AATTT-AAATAAATT
31331618 CAAAATGATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 2 0.03
17 53 0.91
18 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATAAATTTA
Found at i:31331559 original size:6 final size:6
Alignment explanation
Indices: 31331548--31331610 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
31331538 TTATAATAAT
* *
31331548 TTTAAA TTTAAA -TTAAA TCTAAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
31331594 -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
31331611 ATAAATTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 14 0.30
6 32 0.70
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:31331563 original size:11 final size:11
Alignment explanation
Indices: 31331549--31331603 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
31331539 TATAATAATT
31331549 TTAAATTTAAA
1 TTAAATTTAAA
*
31331560 TTAAATCTAAA
1 TTAAATTTAAA
31331571 TTTAAA-TTAAA
1 -TTAAATTTAAA
31331582 TTCAAATTTAAA
1 TT-AAATTTAAA
*
31331594 ATAAATTTAA
1 TTAAATTTAA
31331604 TTTTAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 2 0.05
11 25 0.66
12 11 0.29
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:31331573 original size:34 final size:33
Alignment explanation
Indices: 31331535--31331621 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 33
31331525 TTGGACATTG
* * *
31331535 AATTTATAATAATTTTAAATTTAAATTAAATCTA
1 AATTTA-AATAAATTCAAATTTAAAATAAATCTA
*
31331569 AATTTAAATTAAATTCAAATTTAAAATAAATTTA
1 AATTTAAA-TAAATTCAAATTTAAAATAAATCTA
*
31331603 ATTTTAAAATAAATTCAAA
1 AATTT-AAATAAATTCAAA
31331622 ATGATTTGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 2 0.04
34 41 0.89
35 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (33 bp):
AATTTAAATAAATTCAAATTTAAAATAAATCTA
Found at i:31342486 original size:15 final size:16
Alignment explanation
Indices: 31342468--31342500 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31342458 ACCGACTAAT
*
31342468 AAAAAAA-GTAAAAAA
1 AAAAAAAGGCAAAAAA
31342483 AAAAAAAGGCAAAAAA
1 AAAAAAAGGCAAAAAA
31342499 AA
1 AA
31342501 TTTAAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAAGGCAAAAAA
Found at i:31348153 original size:43 final size:43
Alignment explanation
Indices: 31348087--31348359 Score: 150
Period size: 43 Copynumber: 6.3 Consensus size: 43
31348077 CATATACTTG
* * *
31348087 GGTTTAGTCGATGATGCATTATGTGTGCCAGTATTTTTGCTTC
1 GGTTTAGTCGATGATGCACTATGTGTGCCAATATATTTGCTTC
*
31348130 GGTTTA-TCCGATGATGCACTATGTGTGTCAATATATTTGCTTC
1 GGTTTAGT-CGATGATGCACTATGTGTGCCAATATATTTGCTTC
** * * * ** * *
31348173 AATTTATTTGA-GAACGCACTATGTGTGTTAATATGA-TTGTTTT
1 GGTTTAGTCGATG-ATGCACTATGTGTGCCAATAT-ATTTGCTTC
* * * * *
31348216 GATTTA-TCTAATGATGCACTATGTGTGCTAATATAATTGTTTC
1 GGTTTAGTC-GATGATGCACTATGTGTGCCAATATATTTGCTTC
* *
31348259 GG-TTCGTCCGATGATGCACCTCT-TGTGCCAATATAATTT-CTTC
1 GGTTTAGT-CGATGATGCA-CTATGTGTGCCAATAT-ATTTGCTTC
* * * * ** * *
31348302 AGCTT-GCCTGACGATGCAAGATGTGTGCCAATATATTTCCTTT
1 GGTTTAGTC-GATGATGCACTATGTGTGCCAATATATTTGCTTC
31348345 GGTTTA-TCCGATGAT
1 GGTTTAGT-CGATGAT
31348360 ACACCACGGT
Statistics
Matches: 178, Mismatches: 35, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
42 12 0.07
43 153 0.86
44 13 0.07
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (43 bp):
GGTTTAGTCGATGATGCACTATGTGTGCCAATATATTTGCTTC
Found at i:31356050 original size:15 final size:15
Alignment explanation
Indices: 31356032--31356072 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
31356022 TAATCTTCTC
*
31356032 TATAATAATTTTTTT
1 TATAATAATTTTTGT
31356047 TATAATAATATTTTGT
1 TATAATAAT-TTTTGT
*
31356063 TATAACAATT
1 TATAATAATT
31356073 AAACATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TATAATAATTTTTGT
Found at i:31360213 original size:2 final size:2
Alignment explanation
Indices: 31360206--31360231 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31360196 TTACATATTC
31360206 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31360232 TTAATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31364008 original size:17 final size:17
Alignment explanation
Indices: 31363986--31364024 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
31363976 AGGTGGAGAA
* *
31363986 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
31364003 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
31364020 CTTGT
1 CTTGT
31364025 CAAGGTGGAG
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:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:31372382 original size:15 final size:15
Alignment explanation
Indices: 31372364--31372415 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
31372354 GCAGGAGAAG
31372364 GAGCAGGAGCCACAA
1 GAGCAGGAGCCACAA
* *
31372379 GAGCCACAGGAGCCGCAG
1 GAG---CAGGAGCCACAA
31372397 GAGCAGGAGCCACAA
1 GAGCAGGAGCCACAA
31372412 GAGC
1 GAGC
31372416 CACAGGAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.35, C:0.29, G:0.37, T:0.00
Consensus pattern (15 bp):
GAGCAGGAGCCACAA
Found at i:31372384 original size:9 final size:9
Alignment explanation
Indices: 31372367--31372451 Score: 95
Period size: 9 Copynumber: 9.8 Consensus size: 9
31372357 GGAGAAGGAG
31372367 CAGGAGCCA
1 CAGGAGCCA
*
31372376 CAAGAGCCA
1 CAGGAGCCA
*
31372385 CAGGAGCCG
1 CAGGAGCCA
31372394 CAGGAG---
1 CAGGAGCCA
31372400 CAGGAGCCA
1 CAGGAGCCA
*
31372409 CAAGAGCCA
1 CAGGAGCCA
31372418 CAGGAGCCA
1 CAGGAGCCA
*
31372427 CAGGAGCCG
1 CAGGAGCCA
* *
31372436 CAGGGGCCG
1 CAGGAGCCA
31372445 CAGGAGC
1 CAGGAGC
31372452 AGGAGCAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
6 6 0.09
9 59 0.91
ACGTcount: A:0.31, C:0.32, G:0.38, T:0.00
Consensus pattern (9 bp):
CAGGAGCCA
Found at i:31372403 original size:33 final size:33
Alignment explanation
Indices: 31372362--31372433 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
31372352 CAGCAGGAGA
*
31372362 AGGAGCAGGAGCCACAAGAGCCACAGGAGCCGC
1 AGGAGCAGGAGCCACAAGAGCCACAGGAGCCAC
31372395 AGGAGCAGGAGCCACAAGAGCCACAGGAGCCAC
1 AGGAGCAGGAGCCACAAGAGCCACAGGAGCCAC
31372428 AGGAGC
1 AGGAGC
31372434 CGCAGGGGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.35, C:0.29, G:0.36, T:0.00
Consensus pattern (33 bp):
AGGAGCAGGAGCCACAAGAGCCACAGGAGCCAC
Found at i:31372482 original size:18 final size:18
Alignment explanation
Indices: 31372460--31372502 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
31372450 GCAGGAGCAG
* *
31372460 CAGCCGGAGCCAGAGCCA
1 CAGCCGCAGCCACAGCCA
* *
31372478 GAGCCTCAGCCACAGCCA
1 CAGCCGCAGCCACAGCCA
31372496 CAGCCGC
1 CAGCCGC
31372503 CTGCCAACGA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.44, G:0.28, T:0.02
Consensus pattern (18 bp):
CAGCCGCAGCCACAGCCA
Found at i:31377582 original size:18 final size:19
Alignment explanation
Indices: 31377559--31377596 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31377549 TTTTTTGGTG
*
31377559 TATGATGG-TTCATCCCTA
1 TATGATGGTTTCAACCCTA
31377577 TATGATGGTTTCAACCCTA
1 TATGATGGTTTCAACCCTA
31377596 T
1 T
31377597 CTTTTGCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (19 bp):
TATGATGGTTTCAACCCTA
Found at i:31379448 original size:161 final size:160
Alignment explanation
Indices: 31379158--31379945 Score: 890
Period size: 162 Copynumber: 4.9 Consensus size: 160
31379148 CATCATTTAG
* *
31379158 GATTTGTTTTCATTGTTAAAACAGTAGTGTGCA-TAAGTGGTTAATTACATAAGCATTTT-ACAA
1 GATTTGTATTCATTGTTAAAACAGTAGTG-GCAGTAA-TGGTTAATTGCATAAGCATTTTAAC-A
* * * *
31379221 CGTCTTGCTTGTTTATAAAAATTTAAAATTGTTACTTTATCTCTTCTTTTTAAGTTAATCGTAAG
63 CGTCTTGCTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAG
* *
31379286 TCAATATTAT-AAAAGTGTAGGTGACTCTTTTAA
128 TCAATATTATGAAAA-TGTAAGTGACTCTCTTAA
* * *
31379319 TATTTGTATTCATTTTTAAAACAGTAGTGGACAGTAATGGTTAATTGCATAAGCATTTTAACATG
1 GATTTGTATTCATTGTTAAAACAGTAGTGG-CAGTAATGGTTAATTGCATAAGCATTTTAACACG
* * * * *
31379384 CCTTGCTTGTTTATAAGAATCTAATATTGTAACTTTATCTCTTCTTCTTAAACTAATTGTAAGTC
65 TCTTGCTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAGTC
* *
31379449 AATATTATGAAAGTGTAACTGACTCTCTTAA
130 AATATTATGAAAATGTAAGTGACTCTCTTAA
* * * *
31379480 AATTTGTATTCATTGTTAAAACAATAGTGACAGTAGTGGTTAATTGCATAAGCATTTTAACACAC
1 GATTTGTATTCATTGTTAAAACAGTAGTGGCAGTAATGGTTAATTGCATAAGCATTTT-A-ACAC
* * *
31379545 GTCTTGTTTGTTTATAAGAATCTAAAATTATAACTTTATCTCTTCTTTTTAAGCTAATTGTAAGT
64 GTCTTGCTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAGT
* * * *
31379610 TAGA-ATTGTGAAAATGTAAGTAACTCTCTTAG
129 CA-ATATTATGAAAATGTAAGTGACTCTCTTAA
31379642 GATTTGTATTCATTGTTAAAACAGTAGT----G--A---TT-ATTGCATAAGCATTTTAACACAC
1 GATTTGTATTCATTGTTAAAACAGTAGTGGCAGTAATGGTTAATTGCATAAGCATTTT-A-ACAC
* * * * *
31379697 TTCTTGTTTGTTTATAATAAGAATCTAAAATTGTTATTTTATCTATTCTTTTTAAACTAATTGTA
64 GTCTTGCTTG-TT-T-ATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTA
* * * *
31379762 ACTCAGTATTATGAAAATATAAGTGACTCTCTTAG
126 AGTCAATATTATGAAAATGTAAGTGACTCTCTTAA
* *
31379797 GATTTGTATTCATTGTTAAAACAGTAGTGGGTAGTAGTGGTTAATTGCATAAGCATTTTAACACA
1 GATTTGTATTCATTGTTAAAACAGTAGT-GGCAGTAATGGTTAATTGCATAAGCATTTTAACAC-
* * *
31379862 TGTCTTG-TATGTTTATAAGATTCTAAAATTTTTACTTGT-T-TTTTCTTTTTAAGCTAATTGTA
64 -GTCTTGCT-TGTTTATAAGAATCTAAAATTGTTACTT-TATCTCTTCTTTTTAAGCTAATTGTA
**
31379924 AGTCGGTATTATGAAAATGTAA
126 AGTCAATATTATGAAAATGTAA
31379946 ATGATTTTTT
Statistics
Matches: 540, Mismatches: 61, Indels: 51
0.83 0.09 0.08
Matches are distributed among these distances:
152 32 0.06
153 4 0.01
154 1 0.00
155 100 0.19
158 1 0.00
160 29 0.05
161 157 0.29
162 159 0.29
163 22 0.04
164 6 0.01
165 6 0.01
166 23 0.04
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (160 bp):
GATTTGTATTCATTGTTAAAACAGTAGTGGCAGTAATGGTTAATTGCATAAGCATTTTAACACGT
CTTGCTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAGTCA
ATATTATGAAAATGTAAGTGACTCTCTTAA
Found at i:31379638 original size:162 final size:162
Alignment explanation
Indices: 31379158--31379945 Score: 914
Period size: 161 Copynumber: 4.9 Consensus size: 162
31379148 CATCATTTAG
* * *
31379158 GATTTGTTTTCATTGTTAAAACAGTAGTGTGCA-TAAGTGGTTAATTACATAAGCATTTT-ACA-
1 GATTTGTATTCATTGTTAAAACAGTAGTG-ACAGT-AGTGGTTAATTGCATAAGCATTTTAACAC
* * * * *
31379220 ACGTCTTGCTTGTTTATAAAAATTTAAAATTGTTACTTTATCTCTTCTTTTTAAGTTAATCGTAA
64 ACGTCTTGTTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAA
* *
31379285 GTCA-ATATTAT-AAAAGTGTAGGTGACTCTTTTAA
129 GTCAGA-ATTATGAAAA-TGTAAGTGACTCTCTTAA
* * *
31379319 TATTTGTATTCATTTTTAAAACAGTAGTGGACAGTAATGGTTAATTGCATAAGCATTTT-A-ACA
1 GATTTGTATTCATTGTTAAAACAGTAGT-GACAGTAGTGGTTAATTGCATAAGCATTTTAACACA
* * * * * * *
31379382 TGCCTTGCTTGTTTATAAGAATCTAATATTGTAACTTTATCTCTTCTTCTTAAACTAATTGTAAG
65 CGTCTTGTTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAG
* *
31379447 TCA-ATATTATGAAAGTGTAACTGACTCTCTTAA
130 TCAGA-ATTATGAAAATGTAAGTGACTCTCTTAA
* *
31379480 AATTTGTATTCATTGTTAAAACAATAGTGACAGTAGTGGTTAATTGCATAAGCATTTTAACACAC
1 GATTTGTATTCATTGTTAAAACAGTAGTGACAGTAGTGGTTAATTGCATAAGCATTTTAACACAC
* *
31379545 GTCTTGTTTGTTTATAAGAATCTAAAATTATAACTTTATCTCTTCTTTTTAAGCTAATTGTAAGT
66 GTCTTGTTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAGT
* * * *
31379610 TAGAATTGTGAAAATGTAAGTAACTCTCTTAG
131 CAGAATTATGAAAATGTAAGTGACTCTCTTAA
31379642 GATTTGTATTCATTGTTAAAACAGTAGT----G-A----TT-ATTGCATAAGCATTTTAACACAC
1 GATTTGTATTCATTGTTAAAACAGTAGTGACAGTAGTGGTTAATTGCATAAGCATTTTAACACAC
* * * *
31379697 TTCTTGTTTGTTTATAATAAGAATCTAAAATTGTTATTTTATCTATTCTTTTTAAACTAATTGTA
66 GTCTTGTTTG-TT-T-ATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTA
* * * *
31379762 ACTCAGTATTATGAAAATATAAGTGACTCTCTTAG
128 AGTCAGAATTATGAAAATGTAAGTGACTCTCTTAA
**
31379797 GATTTGTATTCATTGTTAAAACAGTAGTGGGTAGTAGTGGTTAATTGCATAAGCATTTTAACACA
1 GATTTGTATTCATTGTTAAAACAGTAGT-GACAGTAGTGGTTAATTGCATAAGCATTTTAACACA
* * * * *
31379862 TGTCTTGTATGTTTATAAGATTCTAAAATTTTTACTTGT-T-TTTTCTTTTTAAGCTAATTGTAA
65 CGTCTTGTTTGTTTATAAGAATCTAAAATTGTTACTT-TATCTCTTCTTTTTAAGCTAATTGTAA
* *
31379925 GTCGGTATTATGAAAATGTAA
129 GTCAGAATTATGAAAATGTAA
31379946 ATGATTTTTT
Statistics
Matches: 543, Mismatches: 62, Indels: 43
0.84 0.10 0.07
Matches are distributed among these distances:
152 32 0.06
153 4 0.01
154 1 0.00
155 101 0.19
157 1 0.00
158 1 0.00
160 31 0.06
161 158 0.29
162 156 0.29
163 22 0.04
164 2 0.00
165 4 0.01
166 30 0.06
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (162 bp):
GATTTGTATTCATTGTTAAAACAGTAGTGACAGTAGTGGTTAATTGCATAAGCATTTTAACACAC
GTCTTGTTTGTTTATAAGAATCTAAAATTGTTACTTTATCTCTTCTTTTTAAGCTAATTGTAAGT
CAGAATTATGAAAATGTAAGTGACTCTCTTAA
Found at i:31379762 original size:155 final size:152
Alignment explanation
Indices: 31379509--31379945 Score: 511
Period size: 155 Copynumber: 2.8 Consensus size: 152
31379499 AACAATAGTG
*
31379509 ACAGTAGTGGTTAATTGCATAAGCATTTTAACACACGTCTTGTTTGTTTATAAGAATCTAAAATT
1 ACAGTAGTGATTAATTGCATAAGCATTTTAACACAC-TCTTGTTTGTTTATAAGAATCTAAAATT
* * * * *
31379574 ATAACTTTATCTCTTCTTTTTAAGCTAATTGTAAGTTAGAATTGTGAAAATGTAAGTAACTCTCT
65 GTAACTTTATCTCTTCTTTTTAAACTAATTGTAAGTCAGAATTATGAAAATGTAAGTGACTCTCT
31379639 TAGGATTTGTATTCATTGTTAAA
130 TAGGATTTGTATTCATTGTTAAA
31379662 ACAGTAGTGATT-ATTGCATAAGCATTTTAACACACTTCTTGTTTGTTTATAATAAGAATCTAAA
1 ACAGTAGTGATTAATTGCATAAGCATTTTAACACAC-TCTTGTTTG-TT-T-ATAAGAATCTAAA
* * * * * *
31379726 ATTGTTATTTTATCTATTCTTTTTAAACTAATTGTAACTCAGTATTATGAAAATATAAGTGACTC
62 ATTGTAACTTTATCTCTTCTTTTTAAACTAATTGTAAGTCAGAATTATGAAAATGTAAGTGACTC
31379791 TCTTAGGATTTGTATTCATTGTTAAA
127 TCTTAGGATTTGTATTCATTGTTAAA
* *
31379817 ACAGTAGTGGGTAGTAGTGGTTAATTGCATAAGCATTTTAACACATGTCTTGTATGTTTATAAGA
1 ACAGTA----GT-G-A----TTAATTGCATAAGCATTTTAACACA-CTCTTGTTTGTTTATAAGA
* * * * * * *
31379882 TTCTAAAATTTTTACTTGT-T-TTTTCTTTTTAAGCTAATTGTAAGTCGGTATTATGAAAATGTA
55 ATCTAAAATTGTAACTT-TATCTCTTCTTTTTAAACTAATTGTAAGTCAGAATTATGAAAATGTA
31379945 A
119 A
31379946 ATGATTTTTT
Statistics
Matches: 245, Mismatches: 23, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
152 32 0.13
153 13 0.05
154 1 0.00
155 99 0.40
159 2 0.01
160 1 0.00
161 1 0.00
162 39 0.16
163 21 0.09
164 2 0.01
165 4 0.02
166 30 0.12
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (152 bp):
ACAGTAGTGATTAATTGCATAAGCATTTTAACACACTCTTGTTTGTTTATAAGAATCTAAAATTG
TAACTTTATCTCTTCTTTTTAAACTAATTGTAAGTCAGAATTATGAAAATGTAAGTGACTCTCTT
AGGATTTGTATTCATTGTTAAA
Found at i:31379815 original size:317 final size:316
Alignment explanation
Indices: 31379154--31379945 Score: 967
Period size: 317 Copynumber: 2.5 Consensus size: 316
31379144 CATACATCAT
* *
31379154 TTAGGATTTGTTTTCATTGTTAAAACAGTAGTGTGCA-TAAGTGGTTAATTACATAAGCATTTT-
1 TTAGGATTTGTATTCATTGTTAAAACAGTAGTG-GCAGT-AGTGGTTAATTGCATAAGCATTTTA
* * * * * *
31379217 ACA-ACGTCTTGCTTGTTTATAAAAATTTAAAATTGTTACTTTATCTCTTCTTTTTAAGTTAATC
64 ACACACGTCTTGTTTGTTTATAAGAATCTAAAATTATTACTTTATCTCTTCTTTTTAAGCTAATT
* * * * *
31379281 GTAAGTCA-ATATTAT-AAAAGTGTAGGTGACTCTTTTAATATTTGTATTCATTTTTAAAACAGT
129 GTAAGTCAGA-ATTATGAAAA-TGTAAGTAACTCTCTTAAGATTTGTATTCATTGTTAAAACAGT
** *
31379344 AGTGGACAGTAATGGTTAATTGCATAAGCATTTTAACATGCCTTGCTTGTTTATAAGAATCTAAT
192 AGT----AG-AA--GTTAATTGCATAAGCATTTTAACACACCTTGCTTGTTTATAAGAATCTAAA
* * * *
31379409 ATTGTAACTTTATCTCTTCTTCTTAAACTAATTGTAAGTCAATATTATGAAAGTGTAACTGACTC
250 ATTGTAACTTTATCTATTCTTCTTAAACTAATTGTAACTCAATATTATGAAAATATAACTGACTC
31379474 TC
315 TC
** * *
31379476 TTAAAATTTGTATTCATTGTTAAAACAATAGTGACAGTAGTGGTTAATTGCATAAGCATTTTAAC
1 TTAGGATTTGTATTCATTGTTAAAACAGTAGTGGCAGTAGTGGTTAATTGCATAAGCATTTTAAC
*
31379541 ACACGTCTTGTTTGTTTATAAGAATCTAAAATTATAACTTTATCTCTTCTTTTTAAGCTAATTGT
66 ACACGTCTTGTTTGTTTATAAGAATCTAAAATTATTACTTTATCTCTTCTTTTTAAGCTAATTGT
* * *
31379606 AAGTTAGAATTGTGAAAATGTAAGTAACTCTCTTAGGATTTGTATTCATTGTTAAAACAGTAGT-
131 AAGTCAGAATTATGAAAATGTAAGTAACTCTCTTAAGATTTGTATTCATTGTTAAAACAGTAGTA
* *
31379670 G-A-TT-ATTGCATAAGCATTTTAACACACTTCTTGTTTGTTTATAATAAGAATCTAAAATTGTT
196 GAAGTTAATTGCATAAGCATTTTAACACAC--CTTGCTTG-TT-T-ATAAGAATCTAAAATTGTA
* * * *
31379732 ATTTTATCTATTCTTTTTAAACTAATTGTAACTCAGTATTATGAAAATATAAGTGACTCTC
256 ACTTTATCTATTCTTCTTAAACTAATTGTAACTCAATATTATGAAAATATAACTGACTCTC
*
31379793 TTAGGATTTGTATTCATTGTTAAAACAGTAGTGGGTAGTAGTGGTTAATTGCATAAGCATTTTAA
1 TTAGGATTTGTATTCATTGTTAAAACAGTAGT-GGCAGTAGTGGTTAATTGCATAAGCATTTTAA
* * * * *
31379858 CACATGTCTTGTATGTTTATAAGATTCTAAAATTTTTACTTGT-T-TTTTCTTTTTAAGCTAATT
65 CACACGTCTTGTTTGTTTATAAGAATCTAAAATTATTACTT-TATCTCTTCTTTTTAAGCTAATT
* *
31379921 GTAAGTCGGTATTATGAAAATGTAA
129 GTAAGTCAGAATTATGAAAATGTAA
31379946 ATGATTTTTT
Statistics
Matches: 409, Mismatches: 49, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
312 21 0.05
313 2 0.00
314 7 0.02
315 2 0.00
316 2 0.00
317 138 0.34
318 68 0.17
319 1 0.00
321 25 0.06
322 33 0.08
323 105 0.26
324 5 0.01
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (316 bp):
TTAGGATTTGTATTCATTGTTAAAACAGTAGTGGCAGTAGTGGTTAATTGCATAAGCATTTTAAC
ACACGTCTTGTTTGTTTATAAGAATCTAAAATTATTACTTTATCTCTTCTTTTTAAGCTAATTGT
AAGTCAGAATTATGAAAATGTAAGTAACTCTCTTAAGATTTGTATTCATTGTTAAAACAGTAGTA
GAAGTTAATTGCATAAGCATTTTAACACACCTTGCTTGTTTATAAGAATCTAAAATTGTAACTTT
ATCTATTCTTCTTAAACTAATTGTAACTCAATATTATGAAAATATAACTGACTCTC
Found at i:31387937 original size:21 final size:21
Alignment explanation
Indices: 31387898--31387937 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31387888 AAATTCTCAA
** *
31387898 TTCTTTTCTTTTGGTTTTTCC
1 TTCTTTTCTTCAGGGTTTTCC
31387919 TTCTTTTCTTCAGGGTTTT
1 TTCTTTTCTTCAGGGTTTT
31387938 ATAGTTAGCC
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:0.17, G:0.12, T:0.68
Consensus pattern (21 bp):
TTCTTTTCTTCAGGGTTTTCC
Found at i:31414231 original size:60 final size:60
Alignment explanation
Indices: 31414137--31414407 Score: 375
Period size: 60 Copynumber: 4.5 Consensus size: 60
31414127 ATACTTTCGT
* * *
31414137 TAATATTTTCAAGATTGTCTGTTTTCATCGCTAAACTTTAAAAAGTTACAATTTGGTCAC
1 TAATATTTTCAAGATTGTCTGTTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
* *
31414197 TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTATAATTTGCTCAC
1 TAATATTTTCAAGATTGTCTGTTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
* *
31414257 TAATATTTTCAAGGTTGTCTGTTTTGATCATTAAACTTTTAAAAA-TTACAATTTGCTCAC
1 TAATATTTTCAAGATTGTCTGTTTTGATCACTAAAC-TTTAAAAAGTTACAATTTGCTCAC
* * * *
31414317 TAACATTTTCAAGATTATCTGTTTTGATCACTAAA-TTTAAAAAGTTATAATTTGATCAC
1 TAATATTTTCAAGATTGTCTGTTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
* * * * *
31414376 CAATATTTTCAATATGGTTTGTTTTGGTCACT
1 TAATATTTTCAAGATTGTCTGTTTTGATCACT
31414408 TGACCGATTC
Statistics
Matches: 187, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
58 8 0.04
59 38 0.20
60 133 0.71
61 8 0.04
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (60 bp):
TAATATTTTCAAGATTGTCTGTTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
Found at i:31414256 original size:29 final size:29
Alignment explanation
Indices: 31414167--31414375 Score: 102
Period size: 29 Copynumber: 7.0 Consensus size: 29
31414157 GTTTTCATCG
* *
31414167 CTAAACTTTAAAAAGTTACAATTTGGTCA
1 CTAAACTTTAAAAAGTTATAATTTGATCA
* * * * * *
31414196 CTAATATTTTCAAGATTGTCTATTTTGATCA
1 CTAA-ACTTTAAAAAGT-TATAATTTGATCA
*
31414227 CTAAACTTTAAAAAGTTATAATTTGCTCA
1 CTAAACTTTAAAAAGTTATAATTTGATCA
** * * **
31414256 CTAATA-TTTTCAAGGTTGTCTGTTTTGATCA
1 CTAA-ACTTTAAAAAG-T-TATAATTTGATCA
* * *
31414287 TTAAACTTTTAAAAA-TTACAATTTGCTCA
1 CTAAAC-TTTAAAAAGTTATAATTTGATCA
* * * **
31414316 CTAACATTTTCAAGA-TTATCTGTTTTGATCA
1 CTAA-ACTTTAAAAAGTTA--TAATTTGATCA
31414347 CTAAA-TTTAAAAAGTTATAATTTGATCA
1 CTAAACTTTAAAAAGTTATAATTTGATCA
31414375 C
1 C
31414376 CAATATTTTC
Statistics
Matches: 126, Mismatches: 43, Indels: 23
0.66 0.22 0.12
Matches are distributed among these distances:
28 10 0.08
29 50 0.40
30 25 0.20
31 36 0.29
32 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (29 bp):
CTAAACTTTAAAAAGTTATAATTTGATCA
Found at i:31418440 original size:4 final size:4
Alignment explanation
Indices: 31418433--31418457 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31418423 TAGAGAGGAT
31418433 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
31418458 AGGATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:31419579 original size:17 final size:16
Alignment explanation
Indices: 31419544--31419586 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
31419534 CTCTCTTGAC
*
31419544 CTTTAATCTTTTATCTT
1 CTTTAA-CTTTTATATT
31419561 CTTTAACTTTTCATATT
1 CTTTAACTTTT-ATATT
31419578 CTTGTAACT
1 CTT-TAACT
31419587 ATCCTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (16 bp):
CTTTAACTTTTATATT
Found at i:31424925 original size:17 final size:17
Alignment explanation
Indices: 31424899--31424938 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
31424889 CTCTTGACCA
*
31424899 TTAACATTTCATTTTCT
1 TTAACATTTCATATTCT
*
31424916 TTAACCTTTCATATTCT
1 TTAACATTTCATATTCT
31424933 TGTAAC
1 T-TAAC
31424939 TATCCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAACATTTCATATTCT
Found at i:31425026 original size:13 final size:13
Alignment explanation
Indices: 31425008--31425032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31424998 TGCTACTTTT
31425008 AAATATAGAATGA
1 AAATATAGAATGA
31425021 AAATATAGAATG
1 AAATATAGAATG
31425033 CAATACATAT
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
AAATATAGAATGA
Found at i:31426688 original size:29 final size:28
Alignment explanation
Indices: 31426635--31426800 Score: 103
Period size: 29 Copynumber: 5.7 Consensus size: 28
31426625 ATCCGGGGGC
31426635 AAAAATGGAATTTTGATGAAATTGGGGTT
1 AAAAATGGAATTTTG-TGAAATTGGGGTT
*
31426664 AAAAATGGGATTTTG-GAAAGTTTGGGGGTT
1 AAAAATGGAATTTTGTGAAA--TT-GGGGTT
* *
31426694 --AAATGGTAATTTTGGGTGAAACTGAGGTT
1 AAAAATGG-AATTTT--GTGAAATTGGGGTT
31426723 AAAAATGGAATTTTG-GAAAGTTTAGGGG-T
1 AAAAATGGAATTTTGTGAAA--TT-GGGGTT
* * * *
31426752 -AAATTGGTATTTTTTGGTGAAATCGAGGTT
1 AAAAATGG-A-ATTTT-GTGAAATTGGGGTT
31426782 AAAAATGGAATTTTG-GAAA
1 AAAAATGGAATTTTGTGAAA
31426801 GTTTGGGGAC
Statistics
Matches: 107, Mismatches: 12, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
27 12 0.11
28 14 0.13
29 36 0.34
30 23 0.21
31 14 0.13
32 8 0.07
ACGTcount: A:0.35, C:0.01, G:0.30, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTGTGAAATTGGGGTT
Found at i:31426729 original size:59 final size:56
Alignment explanation
Indices: 31426637--31426808 Score: 229
Period size: 59 Copynumber: 3.0 Consensus size: 56
31426627 CCGGGGGCAA
* * *
31426637 AAATGG-AATTTTGATGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTT
1 AAATGGTAATTTTGGTGAAA-TGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGG-T
*
31426694 AAATGGTAATTTTGGGTGAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAATGGTAATTTT-GGTGAAA-TGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
*
31426752 AAATTGGTATTTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGG
1 AAA-TGGTA-ATTTTGGTGAAAT-GAGGTTAAAAATGGAATTTTGGAAAGTTTGGGG
31426809 ACTAGAGAGC
Statistics
Matches: 103, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
57 6 0.06
58 11 0.11
59 82 0.80
60 4 0.04
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.35
Consensus pattern (56 bp):
AAATGGTAATTTTGGTGAAATGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:31428807 original size:18 final size:19
Alignment explanation
Indices: 31428770--31428808 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
31428760 GTCTTTTGAC
*
31428770 AAAATATTTTCAATAAATT
1 AAAATATTTTCAAAAAATT
*
31428789 AAAATA-TTTGAAAAAATT
1 AAAATATTTTCAAAAAATT
31428807 AA
1 AA
31428809 CAAGAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAATATTTTCAAAAAATT
Found at i:31429106 original size:19 final size:21
Alignment explanation
Indices: 31429066--31429107 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31429056 GTGATTTGAC
31429066 AAAAAATACAAATTTAAGAAT
1 AAAAAATACAAATTTAAGAAT
*
31429087 AAAAAATA-AAGTTTAA-AAT
1 AAAAAATACAAATTTAAGAAT
31429106 AA
1 AA
31429108 CTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAAATACAAATTTAAGAAT
Found at i:31441662 original size:30 final size:31
Alignment explanation
Indices: 31441594--31441674 Score: 105
Period size: 30 Copynumber: 2.6 Consensus size: 31
31441584 GAGACATTTG
31441594 CAATTGTAGTTGCTGCA-TGTAAGAACGATCA
1 CAATTGTAGTTGCTG-ATTGTAAGAACGATCA
* *
31441625 CAATTGTATTTGCTGATTGTAAGAA-TATC-
1 CAATTGTAGTTGCTGATTGTAAGAACGATCA
31441654 CTAATTGTAGTTGCTGATTGT
1 C-AATTGTAGTTGCTGATTGT
31441675 TAACCAAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.02
30 22 0.49
31 22 0.49
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.38
Consensus pattern (31 bp):
CAATTGTAGTTGCTGATTGTAAGAACGATCA
Found at i:31465795 original size:15 final size:15
Alignment explanation
Indices: 31465775--31465826 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 15
31465765 ATAAGAAGCT
31465775 ATAAATTATATAAAC
1 ATAAATTATATAAAC
31465790 ATAAATTATATTATTAAAAC
1 ATAAA-T-TA-TA-T-AAAC
31465810 ATAAATTATATAAAC
1 ATAAATTATATAAAC
31465825 AT
1 AT
31465827 TTAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
17 4 0.12
18 4 0.12
19 2 0.06
20 9 0.28
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATTATATAAAC
Found at i:31474234 original size:7 final size:7
Alignment explanation
Indices: 31474222--31474258 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
31474212 GAACCCCTTG
31474222 CCATTCA
1 CCATTCA
31474229 CCATTCA
1 CCATTCA
31474236 CCATTCA
1 CCATTCA
31474243 CCATTCA
1 CCATTCA
31474250 CCATTCA
1 CCATTCA
31474257 CC
1 CC
31474259 GTTGTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.27
Consensus pattern (7 bp):
CCATTCA
Found at i:31477374 original size:25 final size:25
Alignment explanation
Indices: 31477346--31477396 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
31477336 AATTTAAGTA
**
31477346 AATCTATACTTTGTAGTTAAATTTT
1 AATCTATACTTCATAGTTAAATTTT
31477371 AATCTATACTTCATAGTTAAATTTT
1 AATCTATACTTCATAGTTAAATTTT
31477396 A
1 A
31477397 TTAGGGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (25 bp):
AATCTATACTTCATAGTTAAATTTT
Found at i:31491175 original size:63 final size:63
Alignment explanation
Indices: 31491076--31491201 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
31491066 CATTTCATTG
*
31491076 AAGTTCTATTAGGTTCCATTTCTCTTTTTCCATAATTGATACTAAAAGCATTATACATTGCTT
1 AAGTTCTATTAGGTTCCATTTCTCTTTATCCATAATTGATACTAAAAGCATTATACATTGCTT
* * * * ** *
31491139 AAGTTCTATTTGGTTGC-TTGTTTCTTTATCCGTAATTGATGGTAAAAGCATTATAGATTGCTT
1 AAGTTCTATTAGGTTCCATT-TCTCTTTATCCATAATTGATACTAAAAGCATTATACATTGCTT
31491202 GCTTCATGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
62 2 0.04
63 52 0.96
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (63 bp):
AAGTTCTATTAGGTTCCATTTCTCTTTATCCATAATTGATACTAAAAGCATTATACATTGCTT
Found at i:31493427 original size:14 final size:14
Alignment explanation
Indices: 31493408--31493434 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31493398 TTTGTTTGGG
31493408 GTAAAATATTTTTC
1 GTAAAATATTTTTC
31493422 GTAAAATATTTTT
1 GTAAAATATTTTT
31493435 TTATTTTACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (14 bp):
GTAAAATATTTTTC
Found at i:31496540 original size:127 final size:127
Alignment explanation
Indices: 31496388--31496619 Score: 419
Period size: 127 Copynumber: 1.8 Consensus size: 127
31496378 TAATTTAAAC
* *
31496388 CAACTGGTTGTATTAATTCAATTATTGAACTACAATATTAGAAGCTTACTCCATGTTTGTGATCT
1 CAACTGGTTGTATTAATTCAATTATTGAACCACAATAGTAGAAGCTTACTCCATGTTTGTGATCT
*
31496453 ATTATTTTGGGAAATTCTTCATTTGTTAGAAGCTCTAACAAACATGGTGAATTTCCCAAAAT
66 ATTATTTTGGGAAATTCTTCATTTGTTAGAAGATCTAACAAACATGGTGAATTTCCCAAAAT
* *
31496515 CAACTGGTTGTATTAATTGAATTATTGAACCACAATAGTAGAAGCTTACTCCATTTTTGTGATCT
1 CAACTGGTTGTATTAATTCAATTATTGAACCACAATAGTAGAAGCTTACTCCATGTTTGTGATCT
31496580 ATTATTTTGGGAAATTCTTCATTTGTTAGAAGATCTAACA
66 ATTATTTTGGGAAATTCTTCATTTGTTAGAAGATCTAACA
31496620 TGGTGAATTT
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 100 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (127 bp):
CAACTGGTTGTATTAATTCAATTATTGAACCACAATAGTAGAAGCTTACTCCATGTTTGTGATCT
ATTATTTTGGGAAATTCTTCATTTGTTAGAAGATCTAACAAACATGGTGAATTTCCCAAAAT
Found at i:31497606 original size:916 final size:907
Alignment explanation
Indices: 31495760--31497442 Score: 2405
Period size: 916 Copynumber: 1.8 Consensus size: 907
31495750 CCATGTTTGT
* * * * ** * *
31495760 TCAATAATTCAATTAATACAACCAGTTGGTTTAAATTATTAAACATGGTGTAAGCTTTTAACATT
1 TCAATAATTC-ATT-ATACAACCAATTGGATTCAATTAATAAACATGGCATAAGATTTTAACATG
* * * *
31495825 GAAAAAAAAA-ATACAAGATAAAGCAAAAACAATTCCTTGAAAATAATTTCATTGTAACATTTGC
64 GAAAAAAAAATA-ACAAAAAAAAACAAAAGCAATTCCTTGAAAATAATTTCATTGTAACATTTGC
*
31495889 AGGATTCAATTAAATAAAAACCAGAAGTCTACTTATGAATAACCCAACTAATAATGCTAATGATG
128 AGGATTCAATTAAATAAAAACCAGAAGCCTACTTATGAATAACCCAACTAATAATGCTAATGATG
* *
31495954 TATTGAACAAAGATAATGAGATATTGTGGTTCAATAATCCGATTGCAAGAATAGTTCAACATAAA
193 TATTGAACAAAGACAATGAGATATTGTGGTTCAACAATCCGATTGCAAGAATAGTTCAACATAAA
* * * * *
31496019 AGACAACATTGAACAATGCTGTGAAACCTTTGAAATCTTTGAGTACAGATACCGTGAAATCTTTG
258 AAACAACATTGAACAAAGCTATGAAACCTTTGAAATCTTTGAGCACAGATACCATGAAATCTTTG
31496084 TTTGTCAAATGCTCCACCAAAGCTCCTTCCATTGCTAATGATTTCAAAGGTTTCATAGCTTTGCT
323 TTTGTCAAATGCTCCACCAAAGCTCCTTCCATTGCTAATGATTTCAAAGGTTTCATAGCTTTGCT
*
31496149 CAATGTTTTGTTTTATGTTAAACTATTCTTGCAATCGAATTATTGAACCATAATATCTTAGTGCT
388 CAATGTTTTGTTTTATGTTAAACTATTCTTGCAATCGAATTATTGAACCATAATATCTCAGTGCT
* *
31496214 TTTGTTCAATAGGTCATTAGCATTATTGGTAGGATTATTCATAAGCAGGCTTCTGGTTTTTTTAT
453 TTTGTTCAATACGTCATTAGCATTATTAGTAGGATTATTCATAAGCAGGCTTCTGGTTTTTTTAT
31496279 TGAATCCTGCAAATGTTACAATGAAATTATTATCAAGGGATTGCTTTTACTTTATCTTGTGTTTT
518 TGAATCCTGCAAATGTTACAATGAAATTATTATCAAGGGATTGCTTTTACTTTATCTTGTGTTTT
* *
31496344 TATTTTCAATGTTAAAAGCTTGCGCCATGTTTAATAATTTAAACCAACTGGTTGTATTAATTCAA
583 TATTTTCAATGTTAAAAGCTTACGCCATGCTTAATAATTTAAACCAACTGGTTGTATTAATTCAA
* *
31496409 TTATTGAACTACAATATTAGAAGCTTACTCCATGTTTGTGATCTATTATTTTGGGAAATTCTTCA
648 TTATTGAACCACAATATTAGAAGCTTACTCCATGTTTATGATCTATTATTTTGGGAAATTCTTCA
* * * ** *
31496474 TTTGTTAGAAGCTCTAACAAACATGGTGAATTTCCCAAAATCAACTGGTTGTATTAATTGAATTA
713 TTTGTTAGAAGCTCTAACAAACATGGTGAATTTCCCAAAATCAACTAGATGCACAAAATGAATTA
* * * ** * * ** * * * **
31496539 TTGAACCACAATAGTAGAAGCTTACTCCATTTTTGTGATCTATTATTTTGGGAAATTCTTCATTT
778 TAGAACCACAATAGTAGAAGCTTAATCAATTAATGTAATCAACCATGTTGGGAAATTATTAACAT
* *** **
31496604 GTTAGAAGATCTAACATGGTGAATTTCCCCAAATATTAGATCATAAACATGGAGTAAGCTTCTAA
843 GATAGAAGATCTAACAT-GTGAA--T-AAAAAATACAAGATCATAAACA--GAG-AAG--TCTAA
** * *
31496669 TATTGTGGT
899 TATCCTCGA
* * * * *
31496678 TCAATAATTCAATTAATACAACCAATTGGTTTAAATTATTAAACATGGCATAAGCTTTTAACATT
1 TCAATAATTC-ATT-ATACAACCAATTGGATTCAATTAATAAACATGGCATAAGATTTTAACATG
* * * *
31496743 GAAAAAAAAAT-ACAAGATAAAGCAAAAGCAATTCCTTGAAAATAATTTCATTGTAACATTTGTA
64 GAAAAAAAAATAACAAAAAAAAACAAAAGCAATTCCTTGAAAATAATTTCATTGTAACATTTGCA
*
31496807 GGATTCAATTGAAA-AAAAA-TAGAAGCCTACTTATGAATAACCCAACTAATAATGCTAATGATG
129 GGATTCAATT-AAATAAAAACCAGAAGCCTACTTATGAATAACCCAACTAATAATGCTAATGATG
31496870 TATTGAACAAAGACAATGAGATATTGTGGTTCAACAATCCGATTGCAAGAATAGTTCAACATAAA
193 TATTGAACAAAGACAATGAGATATTGTGGTTCAACAATCCGATTGCAAGAATAGTTCAACATAAA
* *
31496935 AAATAACATTGAACAAAGCTATGAAACCTTTGAAATCTTTGAGCACAGGTACCATGAAATCTTTG
258 AAACAACATTGAACAAAGCTATGAAACCTTTGAAATCTTTGAGCACAGATACCATGAAATCTTTG
*
31497000 TTTGTCAAATGCTCCATCC-GAGCTCC-TCTCATTGCTAATGATTTCAAAGGTTTCATAGCTTTG
323 TTTGTCAAATGCTCCA-CCAAAGCTCCTTC-CATTGCTAATGATTTCAAAGGTTTCATAGCTTTG
* *
31497063 CTCAATGTTTTGTTTTATGTTGAACTATTCTTGCAATCGGATTATTGAACCATAATATCTCAGTG
386 CTCAATGTTTTGTTTTATGTTAAACTATTCTTGCAATCGAATTATTGAACCATAATATCTCAGTG
*
31497128 CTTTTGTTCAATACGTCATTAGCATTATTAGTAGGGTTATTCATAAGCAGGCTTCTGGTTTTTTT
451 CTTTTGTTCAATACGTCATTAGCATTATTAGTAGGATTATTCATAAGCAGGCTTCTGGTTTTTTT
* *
31497193 ATTGAATCTTGCAAATGTTACAATGAAATTATTATCAAGGGATTGCTTTTGCTTTATCTTGTGTT
516 ATTGAATCCTGCAAATGTTACAATGAAATTATTATCAAGGGATTGCTTTTACTTTATCTTGTGTT
* * * *
31497258 TTTATTTTCACTGTTAAAAGCTTACGTCATGCTTAATAATTTAAATCAACTGGTTGTATTAATTG
581 TTTATTTTCAATGTTAAAAGCTTACGCCATGCTTAATAATTTAAACCAACTGGTTGTATTAATTC
* *
31497323 AATTATTGTACCACAATATTTGAAGCTTACTCCATGTTTATGATCTATTATTTTGGGAAATTCTT
646 AATTATTGAACCACAATATTAGAAGCTTACTCCATGTTTATGATCTATTATTTTGGGAAATTCTT
*
31497388 CA-TTGTTAGAAGCTCTAACAAACATGGTGAATTTTCCAAAAT-AA-TAGAT-CACAAA
711 CATTTGTTAGAAGCTCTAACAAACATGGTGAATTTCCCAAAATCAACTAGATGCACAAA
31497443 CATGGTGTAA
Statistics
Matches: 720, Mismatches: 41, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
912 3 0.00
913 3 0.00
914 2 0.00
915 41 0.06
916 528 0.73
917 68 0.09
918 75 0.10
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (907 bp):
TCAATAATTCATTATACAACCAATTGGATTCAATTAATAAACATGGCATAAGATTTTAACATGGA
AAAAAAAATAACAAAAAAAAACAAAAGCAATTCCTTGAAAATAATTTCATTGTAACATTTGCAGG
ATTCAATTAAATAAAAACCAGAAGCCTACTTATGAATAACCCAACTAATAATGCTAATGATGTAT
TGAACAAAGACAATGAGATATTGTGGTTCAACAATCCGATTGCAAGAATAGTTCAACATAAAAAA
CAACATTGAACAAAGCTATGAAACCTTTGAAATCTTTGAGCACAGATACCATGAAATCTTTGTTT
GTCAAATGCTCCACCAAAGCTCCTTCCATTGCTAATGATTTCAAAGGTTTCATAGCTTTGCTCAA
TGTTTTGTTTTATGTTAAACTATTCTTGCAATCGAATTATTGAACCATAATATCTCAGTGCTTTT
GTTCAATACGTCATTAGCATTATTAGTAGGATTATTCATAAGCAGGCTTCTGGTTTTTTTATTGA
ATCCTGCAAATGTTACAATGAAATTATTATCAAGGGATTGCTTTTACTTTATCTTGTGTTTTTAT
TTTCAATGTTAAAAGCTTACGCCATGCTTAATAATTTAAACCAACTGGTTGTATTAATTCAATTA
TTGAACCACAATATTAGAAGCTTACTCCATGTTTATGATCTATTATTTTGGGAAATTCTTCATTT
GTTAGAAGCTCTAACAAACATGGTGAATTTCCCAAAATCAACTAGATGCACAAAATGAATTATAG
AACCACAATAGTAGAAGCTTAATCAATTAATGTAATCAACCATGTTGGGAAATTATTAACATGAT
AGAAGATCTAACATGTGAATAAAAAATACAAGATCATAAACAGAGAAGTCTAATATCCTCGA
Found at i:31517219 original size:18 final size:18
Alignment explanation
Indices: 31517192--31517234 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31517182 TATTTATATT
*
31517192 TAAT-ATAAAAATAATTA
1 TAATAATAAAAATAAATA
*
31517209 TAATAATAAAATTAAATA
1 TAATAATAAAAATAAATA
*
31517227 TTATAATA
1 TAATAATA
31517235 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAAAAATAAATA
Found at i:31519595 original size:11 final size:12
Alignment explanation
Indices: 31519573--31519606 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
31519563 AAATTTATTA
*
31519573 TTAAATTTAAAT
1 TTAAATTAAAAT
31519585 TT-AATTAAAAT
1 TTAAATTAAAAT
31519596 TTAAATTAAAA
1 TTAAATTAAAA
31519607 AGTCCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATTAAAAT
Found at i:31519597 original size:17 final size:17
Alignment explanation
Indices: 31519560--31519602 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
31519550 ATTTTTTAGG
31519560 TTTAAATTTATTATTAAA
1 TTTAAATTTATTA-TAAA
31519578 TTTAAATTTAATTA-AAA
1 TTTAAATTT-ATTATAAA
31519595 TTTAAATT
1 TTTAAATT
31519603 AAAAAGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
18 9 0.38
19 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTATAAA
Found at i:31521386 original size:29 final size:30
Alignment explanation
Indices: 31521306--31521383 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
31521296 TGCTTATAGG
* * *
31521306 TCCCTAAACTGTTCAAAAATTATGTTTGTGA
1 TCCCAAAACT-TTAAAAAATTATATTTGTGA
31521337 TCCCAAAACTTTAAAAAATTATATTT-TGA
1 TCCCAAAACTTTAAAAAATTATATTTGTGA
31521366 -CCCTAAAACTTCTAAAAA
1 TCCC-AAAACTT-TAAAAA
31521384 TTACCGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.07
29 10 0.24
30 20 0.48
31 9 0.21
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (30 bp):
TCCCAAAACTTTAAAAAATTATATTTGTGA
Found at i:31521412 original size:29 final size:30
Alignment explanation
Indices: 31521380--31521450 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
31521370 AAAACTTCTA
*
31521380 AAAATTACCGTTTT-ACCCCTAAACTTT-CC
1 AAAATTACCATTTTGACCCC-AAACTTTCCC
*
31521409 AAAATT-CCATTTTGACCCCAAATTTTCCC
1 AAAATTACCATTTTGACCCCAAACTTTCCC
*
31521438 GAAATTA-CATTTT
1 AAAATTACCATTTT
31521451 TGCCATCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTGACCCCAAACTTTCCC
Found at i:31523684 original size:18 final size:17
Alignment explanation
Indices: 31523657--31523690 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31523647 AAGATAGACG
*
31523657 AAAACGTGCCATAAGAT
1 AAAACGTGCCACAAGAT
31523674 AAAAGCGTGCCACAAGA
1 AAAA-CGTGCCACAAGA
31523691 CAGAGGCGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (17 bp):
AAAACGTGCCACAAGAT
Found at i:31526794 original size:17 final size:18
Alignment explanation
Indices: 31526772--31526805 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31526762 CTCAAAATTT
*
31526772 CTTT-AATTTTTTAAAAG
1 CTTTAAATTTTCTAAAAG
31526789 CTTTAAATTTTCTAAAA
1 CTTTAAATTTTCTAAAA
31526806 TTTCTGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (18 bp):
CTTTAAATTTTCTAAAAG
Found at i:31529622 original size:18 final size:18
Alignment explanation
Indices: 31529599--31529640 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
31529589 AGATAACACA
31529599 TTAATA-TTTGATTATTTT
1 TTAATATTTTGA-TATTTT
31529617 TTAATATTTTTGATATTTT
1 TTAATA-TTTTGATATTTT
31529636 TTAAT
1 TTAAT
31529641 TTAAAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 11 0.50
20 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTAATATTTTGATATTTT
Found at i:31531000 original size:22 final size:21
Alignment explanation
Indices: 31530945--31531001 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
31530935 TCGTTGATTC
*
31530945 ATGTCTCGAGACAATCTGCCA
1 ATGTCTCAAGACAATCTGCCA
* *
31530966 ATTGCCTCTAGACATAT-TGCACA
1 A-TGTCTCAAGACA-ATCTGC-CA
31530989 ATGTCTCAAGACA
1 ATGTCTCAAGACA
31531002 GACACCTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 23 0.79
23 5 0.17
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (21 bp):
ATGTCTCAAGACAATCTGCCA
Found at i:31538647 original size:47 final size:49
Alignment explanation
Indices: 31538560--31538657 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 49
31538550 TTTTTTAAAA
* * * *
31538560 ATAATAAAATATGAAATTAATCTTAATATTAAATATTTTTATAT-AATT
1 ATAATAAAATATGAAATAAAACTTAATAATAAATATTTTTAGATAAATT
* * *
31538608 ATAATTAAATAT-AAATAAAACTTACTAATAAATTTTTTTAGATAAATT
1 ATAATAAAATATGAAATAAAACTTAATAATAAATATTTTTAGATAAATT
31538656 AT
1 AT
31538658 CCTAAATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 25 0.60
48 17 0.40
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (49 bp):
ATAATAAAATATGAAATAAAACTTAATAATAAATATTTTTAGATAAATT
Found at i:31558936 original size:23 final size:23
Alignment explanation
Indices: 31558910--31558956 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
31558900 ATTAGATCTT
31558910 TATTCTTTAAAACGATATAAAAA
1 TATTCTTTAAAACGATATAAAAA
31558933 TATTCTTTAAAACGATATAAAAA
1 TATTCTTTAAAACGATATAAAAA
31558956 T
1 T
31558957 TTTAACAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (23 bp):
TATTCTTTAAAACGATATAAAAA
Found at i:31559140 original size:21 final size:21
Alignment explanation
Indices: 31559102--31559142 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31559092 TCTATTTAAT
* * *
31559102 ATTCAAGGTTCGATATTTGAA
1 ATTCAAGATTCAAAATTTGAA
31559123 ATTCAAGATTCAAAATTTGA
1 ATTCAAGATTCAAAATTTGA
31559143 GATCGAGTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
ATTCAAGATTCAAAATTTGAA
Found at i:31562369 original size:31 final size:31
Alignment explanation
Indices: 31562332--31562391 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
31562322 GGATTGACTA
*
31562332 TGCTTGCTAAAAAATTACTCCCTTTGCCATT
1 TGCTTGCTAAAAAATTACTCCATTTGCCATT
*
31562363 TGCTTGCTAAAAAATTACTTCATTTGCCA
1 TGCTTGCTAAAAAATTACTCCATTTGCCA
31562392 CATGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (31 bp):
TGCTTGCTAAAAAATTACTCCATTTGCCATT
Found at i:31565459 original size:31 final size:32
Alignment explanation
Indices: 31565410--31565478 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
31565400 CTTATTTGAA
* * *
31565410 CTAATTTGAACAACAAAGCTAATTTTAGGTG-
1 CTAATTTGAACAACAAAGCCAAGTTTAAGTGC
*
31565441 CTAATTTGAATTAA-AAAGCCAAGTTTAAGTGC
1 CTAATTTGAA-CAACAAAGCCAAGTTTAAGTGC
31565473 CTAATT
1 CTAATT
31565479 AGACAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (32 bp):
CTAATTTGAACAACAAAGCCAAGTTTAAGTGC
Found at i:31567213 original size:24 final size:24
Alignment explanation
Indices: 31567185--31567232 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31567175 TTGTACGGTT
31567185 TAATTAAATAAAT-TATTAAAATAA
1 TAATT-AATAAATATATTAAAATAA
* *
31567209 TAATTTATAAATATTTTAAAATAA
1 TAATTAATAAATATATTAAAATAA
31567233 AAAATTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATTAATAAATATATTAAAATAA
Found at i:31577787 original size:3 final size:3
Alignment explanation
Indices: 31577779--31577807 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31577769 GCAGTGACTC
31577779 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
31577808 TTGATCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:31578243 original size:35 final size:34
Alignment explanation
Indices: 31578204--31578269 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
31578194 AATTATTGAA
* *
31578204 TATAATAAAAAATATTAATTTATCAATTAAAATAT
1 TATAATAAAAAATATTAAATAAT-AATTAAAATAT
*
31578239 TATAATAAAAAATTTTAAATAATAATTAAAA
1 TATAATAAAAAATATTAAATAATAATTAAAA
31578270 CATTTTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (34 bp):
TATAATAAAAAATATTAAATAATAATTAAAATAT
Found at i:31584886 original size:13 final size:13
Alignment explanation
Indices: 31584851--31584923 Score: 64
Period size: 13 Copynumber: 5.7 Consensus size: 13
31584841 TTAGACTTAT
*
31584851 GAAAGAAGA-AGA
1 GAAAGAAGAGAAA
*
31584863 GAAA-AAAAGAAA
1 GAAAGAAGAGAAA
31584875 GAAAGAAGAGAAGA
1 GAAAGAAGAGAA-A
31584889 GAAGAGAAG-GAAAA
1 GAA-AGAAGAG-AAA
*
31584903 GAAAAAAGAGAAA
1 GAAAGAAGAGAAA
31584916 GAAA-AAGA
1 GAAAGAAGA
31584924 AAAAAATTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
11 3 0.06
12 14 0.27
13 17 0.33
14 10 0.20
15 7 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
GAAAGAAGAGAAA
Found at i:31584891 original size:18 final size:18
Alignment explanation
Indices: 31584857--31584925 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
31584847 TTATGAAAGA
*
31584857 AGAAGAGAAAAAAAGAA-
1 AGAAGAGAAAGAAAGAAG
31584874 AGAA-AGAAGAGAAGAGAAG
1 AGAAGAGAA-AGAA-AGAAG
*
31584893 AGAAG-GAAAAGAAAAAAG
1 AGAAGAG-AAAGAAAGAAG
*
31584911 AGAAAGAAAAAGAAA
1 AG-AAGAGAAAGAAA
31584926 AAAATTGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
18 10 0.24
19 19 0.45
20 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAGAGAAAGAAAGAAG
Found at i:31587180 original size:19 final size:19
Alignment explanation
Indices: 31587156--31587192 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31587146 TTTTAGAGAT
*
31587156 TCTAATTAGGAGATATTAA
1 TCTAATTAAGAGATATTAA
31587175 TCTAATTAAGAGATATTA
1 TCTAATTAAGAGATATTA
31587193 TTTCCTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TCTAATTAAGAGATATTAA
Found at i:31606710 original size:22 final size:22
Alignment explanation
Indices: 31606684--31606730 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
31606674 GAATTTTTTT
31606684 TATAAAAT-TACAAAAAAAACAA
1 TATAAAATATA-AAAAAAAACAA
* *
31606706 TATAAAATATAAAAAATAATAA
1 TATAAAATATAAAAAAAAACAA
31606728 TAT
1 TAT
31606731 TTACTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (22 bp):
TATAAAATATAAAAAAAAACAA
Found at i:31613010 original size:17 final size:19
Alignment explanation
Indices: 31612977--31613011 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31612967 TTCACCATTG
31612977 ATTCAACATTCTATGTTTC
1 ATTCAACATTCTATGTTTC
31612996 ATTC-ACATT-TATGTTT
1 ATTCAACATTCTATGTTT
31613012 ATATCTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTCAACATTCTATGTTTC
Found at i:31618619 original size:38 final size:37
Alignment explanation
Indices: 31618549--31618621 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
31618539 AATATCCAAT
* *
31618549 TTTTAGGGACTGAATTGTAAAACTATGTAAATTTAGGA
1 TTTTAAGGACTGAATCGTAAAAC-ATGTAAATTTAGGA
31618587 TTTTAAGGACTGAATCGTAAAA-ACTGTAAAATTTA
1 TTTTAAGGACTGAATCGTAAAACA-TGT-AAATTTA
31618622 AATTTCAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 1 0.03
37 3 0.10
38 27 0.87
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (37 bp):
TTTTAAGGACTGAATCGTAAAACATGTAAATTTAGGA
Found at i:31622261 original size:29 final size:29
Alignment explanation
Indices: 31622204--31622261 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31622194 AAAATTTATT
* * **
31622204 ATTTAATCATTCATTTTTTTTTTGGAAAA
1 ATTTAATCATTCATTTTTTATATACAAAA
*
31622233 ATTTAATGATTCATTTTTTATATACAAAA
1 ATTTAATCATTCATTTTTTATATACAAAA
31622262 GAGCAATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTAATCATTCATTTTTTATATACAAAA
Found at i:31622639 original size:18 final size:18
Alignment explanation
Indices: 31622605--31622642 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
31622595 TACAAAAAAA
31622605 AAAAATTCAAATTATTTAT
1 AAAAATTCAAA-TATTTAT
31622624 AAAAATTCTAAA-ATTTAT
1 AAAAATTC-AAATATTTAT
31622642 A
1 A
31622643 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTCAAATATTTAT
Found at i:31622702 original size:9 final size:9
Alignment explanation
Indices: 31622647--31622694 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
31622637 TTTATATTTT
31622647 TTAAAAAAA
1 TTAAAAAAA
31622656 CTATAAAAAAA
1 -T-TAAAAAAA
*
31622667 TTCAAAAAA
1 TTAAAAAAA
*
31622676 TTCAAAAAA
1 TTAAAAAAA
31622685 TATAAAAAAA
1 T-TAAAAAAA
31622695 AATTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 17 0.50
10 9 0.26
11 8 0.24
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:31622710 original size:28 final size:29
Alignment explanation
Indices: 31622645--31622710 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
31622635 AATTTATATT
*
31622645 TTTTAAAAAAACTATAAAAAAATTCAAAAA
1 TTTTAAAAAAACTAAAAAAAAATT-AAAAA
* *
31622675 ATTCAAAAAATA-TAAAAAAAAATT-AAAA
1 TTTTAAAAAA-ACTAAAAAAAAATTAAAAA
31622703 TTTTAAAA
1 TTTTAAAA
31622711 TTTTCTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 10 0.33
30 19 0.63
31 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
TTTTAAAAAAACTAAAAAAAAATTAAAAA
Found at i:31634159 original size:60 final size:59
Alignment explanation
Indices: 31634050--31634161 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
31634040 CCAAATTGAA
* * *
31634050 CAAAAAATTAGGTACCAAATTAAAAAACAGAGTAAAATTTAGGTGTCAAATTGAACTTT
1 CAAAAAATTAAGTACCAAATTAAAAAAAAGAGTAAAATTTAGGTATCAAATTGAACTTT
* * *
31634109 CAAAAAGATTAAGTA-CAAATATAAAAAAAAGTGTCAAGTTTAGGTATCAAATT
1 CAAAAA-ATTAAGTACCAAAT-TAAAAAAAAGAGTAAAATTTAGGTATCAAATT
31634162 ATAAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
59 11 0.24
60 34 0.76
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (59 bp):
CAAAAAATTAAGTACCAAATTAAAAAAAAGAGTAAAATTTAGGTATCAAATTGAACTTT
Done.