Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 6 of 132
Found at i:1579960 original size:23 final size:23
Alignment explanation
Indices: 1579931--1579999 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1579921 TTTGAAAAAG
*
1579931 TAATAAGCGATGGATTCGTGCGA
1 TAATAAGCAATGGATTCGTGCGA
* * *
1579954 TAATAAGCAATGGGTTCGTCCAA
1 TAATAAGCAATGGATTCGTGCGA
*
1579977 T-ATAAGCAATGGAGTCGTGCGA
1 TAATAAGCAATGGATTCGTGCGA
1579999 T
1 T
1580000 CTCGTGATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (23 bp):
TAATAAGCAATGGATTCGTGCGA
Found at i:1584646 original size:23 final size:23
Alignment explanation
Indices: 1584609--1584678 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
1584599 ATATCACGAG
1584609 ATCGCACG-ACTCCATTGCTTATT
1 ATCGCACGAAC-CCATTGCTTATT
* *
1584632 ATTGGACGAACCCATTGCTTATT
1 ATCGCACGAACCCATTGCTTATT
* *
1584655 ATCGCACGAATCCATCGCTTATT
1 ATCGCACGAACCCATTGCTTATT
1584678 A
1 A
1584679 CTTTTTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (23 bp):
ATCGCACGAACCCATTGCTTATT
Found at i:1601435 original size:23 final size:23
Alignment explanation
Indices: 1601401--1601467 Score: 100
Period size: 23 Copynumber: 2.9 Consensus size: 23
1601391 TCACGAGATC
1601401 GCACG-ACTCCATTGCTTATTATT
1 GCACGAAC-CCATTGCTTATTATT
*
1601424 GGACGAACCCATTGCTTATTATT
1 GCACGAACCCATTGCTTATTATT
*
1601447 GCACGAATCCATTGCTTATTA
1 GCACGAACCCATTGCTTATTA
1601468 CTTTTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (23 bp):
GCACGAACCCATTGCTTATTATT
Found at i:1612219 original size:23 final size:23
Alignment explanation
Indices: 1612185--1612251 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
1612175 TCACGAGATC
1612185 GCACG-ACTCCATTGCTTATTATT
1 GCACGAAC-CCATTGCTTATTATT
*
1612208 GGACGAACCCATTGCTTATTATT
1 GCACGAACCCATTGCTTATTATT
* *
1612231 GCACGAATCCATCGCTTATTA
1 GCACGAACCCATTGCTTATTA
1612252 CTTTTTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 37 0.95
24 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (23 bp):
GCACGAACCCATTGCTTATTATT
Found at i:1634763 original size:25 final size:23
Alignment explanation
Indices: 1634722--1634767 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
1634712 CCAATTAGGG
1634722 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
1634745 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
1634768 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:1635041 original size:38 final size:38
Alignment explanation
Indices: 1634999--1635074 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1634989 TTCTTCATCT
1634999 TGTGGTTATATTGTCTTTGAGATGTTTTCATTTATTAG
1 TGTGGTTATATTGTCTTTGAGATGTTTTCATTTATTAG
1635037 TGTGGTTATATTGTCTTTGAGATGTTTTCATTTATTAG
1 TGTGGTTATATTGTCTTTGAGATGTTTTCATTTATTAG
1635075 CATGAACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (38 bp):
TGTGGTTATATTGTCTTTGAGATGTTTTCATTTATTAG
Found at i:1639208 original size:25 final size:25
Alignment explanation
Indices: 1639178--1639225 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1639168 TTTTGATATA
1639178 TAAAATATAAATATTAAATATTTTT
1 TAAAATATAAATATTAAATATTTTT
* * *
1639203 TAAAATTTTAATATTAATTATTT
1 TAAAATATAAATATTAAATATTT
1639226 GTAAAATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAATATAAATATTAAATATTTTT
Found at i:1639269 original size:19 final size:20
Alignment explanation
Indices: 1639237--1639274 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1639227 TAAAATTCAA
*
1639237 TTTAAATCTATAAAATATAT
1 TTTAAATATATAAAATATAT
1639257 TTTAAATAT-TAAAATATA
1 TTTAAATATATAAAATATA
1639275 ATACAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATATATAAAATATAT
Found at i:1652624 original size:18 final size:16
Alignment explanation
Indices: 1652581--1652625 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
1652571 ATTTTTTATA
1652581 TTTAATTATTATTTTCT
1 TTTAATT-TTATTTTCT
1652598 TTTATATTTTGATTTTCTT
1 TTTA-ATTTT-ATTTTC-T
1652617 TTTAATTTT
1 TTTAATTTT
1652626 TATCTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.24
18 14 0.56
19 5 0.20
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTAATTTTATTTTCT
Found at i:1656385 original size:17 final size:18
Alignment explanation
Indices: 1656359--1656392 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1656349 TATTAATTAA
*
1656359 ATAAATATTA-AAAATTC
1 ATAAACATTATAAAATTC
1656376 ATAAACATTATAAAATT
1 ATAAACATTATAAAATT
1656393 GGTTCAACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAACATTATAAAATTC
Found at i:1660095 original size:5 final size:5
Alignment explanation
Indices: 1660088--1660130 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
1660078 GTATATAAAA
*
1660088 ATAAA ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1660131 TTACAAACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:1671776 original size:39 final size:42
Alignment explanation
Indices: 1671705--1671794 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 42
1671695 TCATTAAAAA
*
1671705 TATTTATACTAAAAAACACTATCATAAATATAATAAATATTT
1 TATTTATACTAAAAAACACTATAATAAATATAATAAATATTT
*
1671747 TATTT-TATTAAAAAACAC-A-AATAAATATAATAAATATTT
1 TATTTATACTAAAAAACACTATAATAAATATAATAAATATTT
1671786 TATTATATA
1 TATT-TATA
1671795 AATATAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
39 23 0.52
40 2 0.05
41 14 0.32
42 5 0.11
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (42 bp):
TATTTATACTAAAAAACACTATAATAAATATAATAAATATTT
Found at i:1673631 original size:66 final size:66
Alignment explanation
Indices: 1673548--1673676 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
1673538 ATTATAAGTA
* * * *
1673548 ATTACATCGAAATCCAATTA-TAATGTTTAAGGTTTGGCATTTATACCTCCATCGATGAAAAAAA
1 ATTACATCCAAATCCAATTACT-AGGTTTAAGGTTTGACATTTATACCTCCATCGATCAAAAAAA
1673612 TC
65 TC
* * *
1673614 ATTACATCCAAATCCAATTACTAGGTTTAAGGTTTGACATTTGTATCTCCATCGTTCAAAAAA
1 ATTACATCCAAATCCAATTACTAGGTTTAAGGTTTGACATTTATACCTCCATCGATCAAAAAA
1673677 CTCACCTGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 54 0.98
67 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (66 bp):
ATTACATCCAAATCCAATTACTAGGTTTAAGGTTTGACATTTATACCTCCATCGATCAAAAAAAT
C
Found at i:1676315 original size:24 final size:24
Alignment explanation
Indices: 1676286--1676336 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1676276 AAAATTTTAT
1676286 AAATTGATCTTAGATAAAGTTGTC
1 AAATTGATCTTAGATAAAGTTGTC
1676310 AAATTGATCTTAGATAAAGTTGTC
1 AAATTGATCTTAGATAAAGTTGTC
1676334 AAA
1 AAA
1676337 ATTATAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (24 bp):
AAATTGATCTTAGATAAAGTTGTC
Found at i:1676519 original size:21 final size:21
Alignment explanation
Indices: 1676472--1676543 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1676462 AATAAGGGGT
*
1676472 CACCAAAACAGT-AAAAAAA-
1 CACCAAAACAATAAAAAAAAG
*
1676491 CACAAAAACAA-AAAAAAAAG
1 CACCAAAACAATAAAAAAAAG
* *
1676511 CAATCAAAACAATAAAAAATAG
1 C-ACCAAAACAATAAAAAAAAG
1676533 CACCAAAACAA
1 CACCAAAACAA
1676544 CAATATATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 16 0.37
20 1 0.02
21 17 0.40
22 9 0.21
ACGTcount: A:0.71, C:0.19, G:0.04, T:0.06
Consensus pattern (21 bp):
CACCAAAACAATAAAAAAAAG
Found at i:1679217 original size:21 final size:21
Alignment explanation
Indices: 1679193--1679255 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1679183 GTAAAAATAC
*
1679193 ATAAAAAATAACATCCAAACA
1 ATAAAAAATAACATCAAAACA
1679214 AT-AAAAATAACAATCAAAACA
1 ATAAAAAATAAC-ATCAAAACA
* *
1679235 GTAGCAAAAATAACAGCAAAA
1 ATA--AAAAATAACATCAAAA
1679256 GAACATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 9 0.26
21 11 0.31
23 6 0.17
24 9 0.26
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.13
Consensus pattern (21 bp):
ATAAAAAATAACATCAAAACA
Found at i:1679284 original size:24 final size:24
Alignment explanation
Indices: 1679266--1679323 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1679256 GAACATTAAA
1679266 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* *
1679290 AACAACAAAAATAGTAACAAAAAT
1 AACAACAAAAATAGCAACAAAAAC
*
1679314 AACAGCAAAA
1 AACAACAAAA
1679324 GCAACACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAC
Found at i:1679310 original size:36 final size:35
Alignment explanation
Indices: 1679229--1679347 Score: 120
Period size: 35 Copynumber: 3.5 Consensus size: 35
1679219 AATAACAATC
* * * *
1679229 AAAACAGTAGCAAAAATAACAGC-AAAAGAACATTA
1 AAAACAGTAACAAAAATAACAACAAAAACAACA-CA
*
1679264 AAAAC---AACAAAAATAGCAACAAAAACAACAACA
1 AAAACAGTAACAAAAATAACAACAAAAACAAC-ACA
* * *
1679297 AAAATAGTAACAAAAATAACAGCAAAAGCAACACA
1 AAAACAGTAACAAAAATAACAACAAAAACAACACA
1679332 AAAACAGTAACAAAAA
1 AAAACAGTAACAAAAA
1679348 AGTAAAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
32 12 0.17
33 12 0.17
34 1 0.01
35 23 0.33
36 21 0.30
ACGTcount: A:0.68, C:0.17, G:0.08, T:0.08
Consensus pattern (35 bp):
AAAACAGTAACAAAAATAACAACAAAAACAACACA
Found at i:1679322 original size:12 final size:12
Alignment explanation
Indices: 1679266--1679323 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
1679256 GAACATTAAA
1679266 AACAACAAAAAT
1 AACAACAAAAAT
* *
1679278 AGCAACAAAAAC
1 AACAACAAAAAT
1679290 AACAACAAAAAT
1 AACAACAAAAAT
**
1679302 AGTAACAAAAAT
1 AACAACAAAAAT
*
1679314 AACAGCAAAA
1 AACAACAAAA
1679324 GCAACACAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:1679344 original size:12 final size:12
Alignment explanation
Indices: 1679268--1679347 Score: 63
Period size: 12 Copynumber: 6.8 Consensus size: 12
1679258 ACATTAAAAA
*
1679268 CAACAAAAATAG
1 CAACAAAAACAG
*
1679280 CAACAAAAACAA
1 CAACAAAAACAG
*
1679292 CAACAAAAATAG
1 CAACAAAAACAG
* * *
1679304 TAACAAAAATAA
1 CAACAAAAACAG
* * *
1679316 CAGCAAAAGCAA
1 CAACAAAAACAG
1679328 C-ACAAAAACAG
1 CAACAAAAACAG
*
1679339 TAACAAAAA
1 CAACAAAAA
1679348 AGTAAAAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 7 0.13
12 46 0.87
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (12 bp):
CAACAAAAACAG
Found at i:1679369 original size:18 final size:18
Alignment explanation
Indices: 1679342--1679414 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
1679332 AAAACAGTAA
*
1679342 CAAAAAAGTAAAAAAAAC
1 CAAAACAGTAAAAAAAAC
1679360 CAAAACAGTAAAAAAATAC
1 CAAAACAGTAAAAAAA-AC
* * *
1679379 AAAAACAGGAAAAAAAGCAAT
1 CAAAACA-GTAAAAAA--AAC
1679400 CAAAACAGTAAAAAA
1 CAAAACAGTAAAAAA
1679415 TAGCACCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 15 0.33
19 8 0.18
20 14 0.31
21 7 0.16
22 1 0.02
ACGTcount: A:0.73, C:0.12, G:0.08, T:0.07
Consensus pattern (18 bp):
CAAAACAGTAAAAAAAAC
Found at i:1679373 original size:19 final size:19
Alignment explanation
Indices: 1679342--1679414 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1679332 AAAACAGTAA
*
1679342 CAAAAAAGT-AAAAAAAAC
1 CAAAACAGTAAAAAAAAAC
*
1679360 CAAAACAGTAAAAAAATAC
1 CAAAACAGTAAAAAAAAAC
* * *
1679379 AAAAACAGGAAAAAAAGCAAT
1 CAAAACAGTAAAAAAA--AAC
1679400 CAAAACAGTAAAAAA
1 CAAAACAGTAAAAAA
1679415 TAGCACCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 8 0.18
19 22 0.50
21 14 0.32
ACGTcount: A:0.73, C:0.12, G:0.08, T:0.07
Consensus pattern (19 bp):
CAAAACAGTAAAAAAAAAC
Found at i:1679403 original size:22 final size:22
Alignment explanation
Indices: 1679380--1679427 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1679370 AAAAAATACA
1679380 AAAACAGGAAAAAA-AGCAATC
1 AAAACAGGAAAAAATAGCAATC
* *
1679401 AAAACAGTAAAAAATAGC-ACC
1 AAAACAGGAAAAAATAGCAATC
1679422 AAAACA
1 AAAACA
1679428 ACAATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.06
Consensus pattern (22 bp):
AAAACAGGAAAAAATAGCAATC
Found at i:1685178 original size:210 final size:208
Alignment explanation
Indices: 1684723--1685201 Score: 771
Period size: 210 Copynumber: 2.3 Consensus size: 208
1684713 TTCTCAACAA
* * * **
1684723 ACAACCACAAGTTCCACAGCTTGAGCCAAAAAGCTTTGATGA-TTGCATATAACTCAAAAACCAC
1 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGAT-ATTTGCACATAATTTGAAAACCAC
** *
1684787 ATTAAAATAAACTTTTGGTTGTTCTCATTCAACATGAAAATAGGATTGAAATGCTAGAAAACAAC
65 ATTAAAATAAACTTTTGGTCATTCTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAAC
*
1684852 TTAGGAACAACAAACAAGAACATAAACTATGCTACCATACTATTGGCACCAAAAGAAGCAACCAA
130 TTAGGAACAACAAACAAGAACATAAACTATGCTACCATACTATCGGCACCAAAAGAAGCAACCAA
*
1684917 CATAATATTATGAC
195 CATAATATTATAAC
1684931 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAACCACC
1 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAACCA-C
*
1684996 ATTAAAATAAACTTTTGGTCATTTTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAAC
65 ATTAAAATAAACTTTTGGTCATTCTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAAC
* * * *
1685061 TTAGGAACAACAAACAAGAACGTAAAGGTATGCTACTATACTATCGGCATCAAAAGAAGCAACCA
130 TTAGGAACAACAAACAAGAACATAAA-CTATGCTACCATACTATCGGCACCAAAAGAAGCAACCA
1685126 ACATAATATTATAAC
194 ACATAATATTATAAC
* *
1685141 ACAACCACAAGTTACGCAGCTTGAGCCAAAAAGCTTTGCTATTTGCACATAATTTGAAAAC
1 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAAC
1685202 TGCATCCAAC
Statistics
Matches: 251, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
207 1 0.00
208 56 0.22
209 87 0.35
210 107 0.43
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.24
Consensus pattern (208 bp):
ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAACCACA
TTAAAATAAACTTTTGGTCATTCTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAACT
TAGGAACAACAAACAAGAACATAAACTATGCTACCATACTATCGGCACCAAAAGAAGCAACCAAC
ATAATATTATAAC
Found at i:1693522 original size:16 final size:18
Alignment explanation
Indices: 1693498--1693536 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1693488 AACATAAAAA
*
1693498 TAATCAACGAA-A-AATT
1 TAATTAACGAACATAATT
1693514 TAATTAACGAACATAATT
1 TAATTAACGAACATAATT
1693532 TAATT
1 TAATT
1693537 CAATTGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
TAATTAACGAACATAATT
Found at i:1702218 original size:41 final size:41
Alignment explanation
Indices: 1702174--1702302 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 41
1702164 AAAATTCACT
* * *
1702174 TTTAGCGGCGCTTTTCTATAAGCGCCGCTAATGCCCCGATT
1 TTTAGCGGCGCTTCTCCATAAGCGCCGCTAATGCCCCGATC
* * * *
1702215 TTTAACGGCGCTTCTCCATAAGCACGGCTAATGACCCGATC
1 TTTAGCGGCGCTTCTCCATAAGCGCCGCTAATGCCCCGATC
* **
1702256 TTTAGCGGCGCTTCTCCATAAACGTTGCTAATGCCCCGATC
1 TTTAGCGGCGCTTCTCCATAAGCGCCGCTAATGCCCCGATC
1702297 TTTAGC
1 TTTAGC
1702303 AGGCCTGTCC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGCTTCTCCATAAGCGCCGCTAATGCCCCGATC
Found at i:1709760 original size:6 final size:6
Alignment explanation
Indices: 1709749--1709788 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
1709739 TCTTGGCTTC
1709749 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT -TCCC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCC
1709789 CCATATCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:1710204 original size:20 final size:22
Alignment explanation
Indices: 1710181--1710223 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1710171 GGAAATATTT
1710181 TTTTTTAA-A-TATTAATATAA
1 TTTTTTAATAGTATTAATATAA
1710201 TTTTTTAATTAGTATTAATATAA
1 TTTTTTAA-TAGTATTAATATAA
1710224 ATAAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTTTAATAGTATTAATATAA
Found at i:1712719 original size:16 final size:18
Alignment explanation
Indices: 1712695--1712733 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1712685 AACATAAAAA
*
1712695 TAATCAACGAA-A-AATT
1 TAATTAACGAACATAATT
1712711 TAATTAACGAACATAATT
1 TAATTAACGAACATAATT
1712729 TAATT
1 TAATT
1712734 CAATTGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
TAATTAACGAACATAATT
Found at i:1714451 original size:6 final size:6
Alignment explanation
Indices: 1714431--1714489 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
1714421 TTAAATGGGT
* **
1714431 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTAA TTTAAA TTT-CC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
1714479 TTTAAG TTTAA
1 TTTAAA TTTAA
1714490 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 7 0.17
6 29 0.69
8 6 0.14
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:1715318 original size:16 final size:17
Alignment explanation
Indices: 1715275--1715319 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
1715265 TAGCATTAAA
*
1715275 TATTAATAATTAATAAT
1 TATTAATAAATAATAAT
1715292 TATTAACATAAATAATAAT
1 TATT-A-ATAAATAATAAT
1715311 TA-TAATAAA
1 TATTAATAAA
1715320 AAACGAAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 5 0.20
18 2 0.08
19 13 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TATTAATAAATAATAAT
Found at i:1716209 original size:33 final size:31
Alignment explanation
Indices: 1716137--1716213 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 31
1716127 CTATTTTGGC
*
1716137 TTATTTTGTAA-TTAGTCCTTTTTATTTTTAA
1 TTATTTT-TAATTTAGTCCTTTTTACTTTTAA
*
1716168 TT-TGTTTTAATTTAGTCTTTTTCGTACTTTTAA
1 TTAT-TTTTAATTTAGTCCTTTT--TACTTTTAA
1716201 TTATTTTTAATTT
1 TTATTTTTAATTT
1716214 GGCCCAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.10
31 15 0.38
33 19 0.49
34 1 0.03
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (31 bp):
TTATTTTTAATTTAGTCCTTTTTACTTTTAA
Found at i:1716275 original size:160 final size:161
Alignment explanation
Indices: 1716009--1716341 Score: 519
Period size: 160 Copynumber: 2.1 Consensus size: 161
1715999 GCTTTTTTTA
*
1716009 TTGTTTTAATTTAGTTCTTTTCATACTTTTAATTATTTTTAATTTGGCCCATTAATTTTGTTTAA
1 TTGTTTTAATTTAGTTCTTTTCATACTTTTAATTATTTTTAATTTGGCCCAATAATTTTGTTTAA
* ***
1716074 TTTTCAATTTGATCTTTTAACTTTTCGAATGCACCAGAGGCTGCCACGTGGCACTATTTTGGCTT
66 TTTTCAATTTGATCCTTTAACTTTTCGAATGCACCAGAGGCTGCCACGTGGCACTATTTCAACTT
* *
1716139 ATTT-TGTAATTAGTCCTTTTTATTTTTAAT
131 ATTTGTGCAATTAGTCCCTTTTATTTTTAAT
*
1716169 TTGTTTTAATTTAG-TCTTTTTCGTACTTTTAATTATTTTTAATTTGGCCCAATAATTTTGTTTA
1 TTGTTTTAATTTAGTTC-TTTTCATACTTTTAATTATTTTTAATTTGGCCCAATAATTTTGTTTA
* * * *
1716233 CTTTTCAATTTGATCCTTTGACATTTT-GAATGCACTAGAGGCTGCCATGTGGCACTATTTCAAC
65 ATTTTCAATTTGATCCTTTAAC-TTTTCGAATGCACCAGAGGCTGCCACGTGGCACTATTTCAAC
1716297 TTATTTGTGCAATTAGTCCCTTTTATTTTTAAT
129 TTATTTGTGCAATTAGTCCCTTTTATTTTTAAT
1716330 TTGTTTTAATTT
1 TTGTTTTAATTT
1716342 GGTCCCTAAA
Statistics
Matches: 158, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
159 2 0.01
160 116 0.73
161 40 0.25
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.52
Consensus pattern (161 bp):
TTGTTTTAATTTAGTTCTTTTCATACTTTTAATTATTTTTAATTTGGCCCAATAATTTTGTTTAA
TTTTCAATTTGATCCTTTAACTTTTCGAATGCACCAGAGGCTGCCACGTGGCACTATTTCAACTT
ATTTGTGCAATTAGTCCCTTTTATTTTTAAT
Found at i:1716538 original size:29 final size:28
Alignment explanation
Indices: 1716499--1716647 Score: 105
Period size: 28 Copynumber: 5.2 Consensus size: 28
1716489 CCAAAAATTA
1716499 CCATTTTACCCCTAAACTTTCCAAAACT
1 CCATTTTACCCCTAAACTTTCCAAAACT
* * *
1716527 CCATTTTAACCC--GA-TTTCACTAAAAATT
1 CCATTTTACCCCTAAACTTTC-C--AAAACT
1716555 ACCATTTTACCCCTAAACTTTCCAAAACT
1 -CCATTTTACCCCTAAACTTTCCAAAACT
* *
1716584 CCATTTTAACCCC--GA-TTTCACCAAAATT
1 CCATTTT-ACCCCTAAACTTT--CCAAAACT
* *
1716612 ACCATTTTA-CCCTCGAACTTTCCAAAATT
1 -CCATTTTACCCCT-AAACTTTCCAAAACT
1716641 CCATTTT
1 CCATTTT
1716648 TAACCTCGAT
Statistics
Matches: 97, Mismatches: 9, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
25 4 0.04
26 5 0.05
27 4 0.04
28 38 0.39
29 36 0.37
30 1 0.01
31 5 0.05
32 4 0.04
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (28 bp):
CCATTTTACCCCTAAACTTTCCAAAACT
Found at i:1716648 original size:29 final size:29
Alignment explanation
Indices: 1716482--1716854 Score: 227
Period size: 29 Copynumber: 12.8 Consensus size: 29
1716472 ATAGGTCCTT
*
1716482 GAACTGTCCAAAAATTACCATTTTACCC-C
1 GAACTTTCC-AAAATTACCATTTTACCCTC
* * *
1716511 TAAACTTTCCAAAACT-CCATTTTAACC-C
1 -GAACTTTCCAAAATTACCATTTTACCCTC
1716539 G-A-TTTCACTAAAAATTACCATTTTACCC-C
1 GAACTTTC-C--AAAATTACCATTTTACCCTC
* *
1716568 TAAACTTTCCAAAACT-CCATTTTAACCC-C
1 -GAACTTTCCAAAATTACCATTTT-ACCCTC
1716597 G-A-TTTCACCAAAATTACCATTTTACCCTC
1 GAACTTT--CCAAAATTACCATTTTACCCTC
*
1716626 GAACTTTCCAAAATT-CCATTTTTAACCTC
1 GAACTTTCCAAAATTACCA-TTTTACCCTC
* *
1716655 G-A-TTTCACCAAAATTACCATTTCACCCCC
1 GAACTTT--CCAAAATTACCATTTTACCCTC
1716684 GAACTTTCCAAAATT-CCATTTTTGA-CCTC
1 GAACTTTCCAAAATTACCA-TTTT-ACCCTC
1716713 -AA-TTTCACCAAAAATTACCATTTTACCCTC
1 GAACTTT--CC-AAAATTACCATTTTACCCTC
* *
1716743 GAACTTTCCAAAATT-TCATTTTTAACCTC
1 GAACTTTCCAAAATTACCA-TTTTACCCTC
1716772 G-A-TTTCACCAAAAATTACCATTTTACCC-C
1 GAACTTT--CC-AAAATTACCATTTTACCCTC
* *
1716801 TAAACTTTCCAAAATT-CCATTTTCAACCTC
1 -GAACTTTCCAAAATTACCATTTT-ACCCTC
1716831 G-A-TTTCACCAAAAATTACCATTTT
1 GAACTTT--CC-AAAATTACCATTTT
1716855 GCCCCCGCGA
Statistics
Matches: 276, Mismatches: 24, Indels: 85
0.72 0.06 0.22
Matches are distributed among these distances:
25 4 0.01
26 5 0.02
27 13 0.05
28 54 0.20
29 116 0.42
30 51 0.18
31 23 0.08
32 10 0.04
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
GAACTTTCCAAAATTACCATTTTACCCTC
Found at i:1716756 original size:59 final size:59
Alignment explanation
Indices: 1716489--1716859 Score: 549
Period size: 59 Copynumber: 6.4 Consensus size: 59
1716479 CTTGAACTGT
*
1716489 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAACTCCA-TTTTAACC-CGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
1716546 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAACTCCA-TTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
*
1716604 CC-AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* ** * *
1716662 CC-AAAATTACCATTTCACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCAATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
1716720 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
*
1716779 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTCAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
*
1716838 CCAAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
1716860 CGCGAGTCCA
Statistics
Matches: 289, Mismatches: 18, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
56 4 0.01
57 79 0.27
58 80 0.28
59 122 0.42
60 4 0.01
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:1722292 original size:23 final size:23
Alignment explanation
Indices: 1722259--1722345 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 23
1722249 ATTTATACAA
*
1722259 GGTTCGGATGTGATACATATAAG
1 GGTTCGCATGTGATACATATAAG
* *
1722282 GGTTTGCATGTGATGTATATATAAATAG
1 GGTTCGCATGTGA--TACATAT--A-AG
* *
1722310 GGTTCACATGTGATACATATGAG
1 GGTTCGCATGTGATACATATAAG
1722333 GGTTCGCATGTGA
1 GGTTCGCATGTGA
1722346 CATATAGATA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 25 0.49
25 6 0.12
26 6 0.12
27 1 0.02
28 13 0.25
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.33
Consensus pattern (23 bp):
GGTTCGCATGTGATACATATAAG
Found at i:1722297 original size:28 final size:28
Alignment explanation
Indices: 1722265--1722345 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
1722255 ACAAGGTTCG
1722265 GATGTGATACATATAAGGGTTTGCATGT
1 GATGTGATACATATAAGGGTTTGCATGT
* *
1722293 GATGT-ATATATAAATAGGG-TT-CA---
1 GATGTGATACATATA-AGGGTTTGCATGT
* * *
1722316 CATGTGATACATATGAGGGTTCGCATGT
1 GATGTGATACATATAAGGGTTTGCATGT
1722344 GA
1 GA
1722346 CATATAGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
23 8 0.21
24 7 0.18
25 2 0.05
26 2 0.05
27 9 0.24
28 10 0.26
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (28 bp):
GATGTGATACATATAAGGGTTTGCATGT
Found at i:1722350 original size:21 final size:22
Alignment explanation
Indices: 1722308--1722350 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1722298 ATATATAAAT
1722308 AGGGTTCACATGTGATACATATG
1 AGGGTTCACATGTGA-ACATATG
*
1722331 AGGGTTCGCATGTG-ACATAT
1 AGGGTTCACATGTGAACATAT
1722351 AGATAGGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (22 bp):
AGGGTTCACATGTGAACATATG
Found at i:1725674 original size:16 final size:16
Alignment explanation
Indices: 1725655--1725688 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1725645 TAAAGTATTA
1725655 TAAACTTAAAACGGGT
1 TAAACTTAAAACGGGT
1725671 TAAACTTAAAACGGGT
1 TAAACTTAAAACGGGT
1725687 TA
1 TA
1725689 GGTTAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (16 bp):
TAAACTTAAAACGGGT
Found at i:1726644 original size:6 final size:6
Alignment explanation
Indices: 1726633--1726666 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1726623 GTAGTGCCAA
1726633 CACCCT CACCCT CACCCT CACCCT CACCCT CACC
1 CACCCT CACCCT CACCCT CACCCT CACCCT CACC
1726667 ATTTCCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.68, G:0.00, T:0.15
Consensus pattern (6 bp):
CACCCT
Found at i:1727371 original size:18 final size:19
Alignment explanation
Indices: 1727334--1727374 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1727324 ATTAATAATA
*
1727334 TAAAAGATTGTTTAAATTT
1 TAAAAGATTATTTAAATTT
*
1727353 TAAAA-ATTATTTTAATTT
1 TAAAAGATTATTTAAATTT
1727371 TAAA
1 TAAA
1727375 CTTGTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TAAAAGATTATTTAAATTT
Found at i:1729626 original size:29 final size:30
Alignment explanation
Indices: 1729559--1729627 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
1729549 GGAGAAGAAG
* *
1729559 AAATGTAAACATATTGGGTCATTTACGCAA
1 AAATGTAAAAATATTGGGTCATTTACGAAA
* **
1729589 AAA-GTAAAAATATTTGGTCATTTATTAAA
1 AAATGTAAAAATATTGGGTCATTTACGAAA
1729618 AAATG-AAAAA
1 AAATGTAAAAA
1729628 GGAGGGACGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.30
Consensus pattern (30 bp):
AAATGTAAAAATATTGGGTCATTTACGAAA
Found at i:1729893 original size:20 final size:21
Alignment explanation
Indices: 1729851--1729893 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1729841 AACGTGACAA
*
1729851 GTTAATTAGCCACGTCAACTT
1 GTTAACTAGCCACGTCAACTT
*
1729872 GTTAACTAGCCGCGTC-ACTT
1 GTTAACTAGCCACGTCAACTT
1729892 GT
1 GT
1729894 CTCATTAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
GTTAACTAGCCACGTCAACTT
Found at i:1732683 original size:39 final size:39
Alignment explanation
Indices: 1732629--1732703 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
1732619 GGACAACAAC
* *
1732629 GAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* ** *
1732668 GAGCACATAAAGTGCTAATTAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
1732704 GCTAATAACG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:1732777 original size:23 final size:23
Alignment explanation
Indices: 1732668--1732779 Score: 77
Period size: 23 Copynumber: 4.8 Consensus size: 23
1732658 ACAAAGTACT
* * **
1732668 GAGCACATAAAGTGCTAATTAGA
1 GAGCACACAGAGTGCTAAACAGA
*
1732691 GAGCACAC-GAAGTGCTAATAACGGA
1 GAGCACACAG-AGTGCT-A-AACAGA
** *
1732716 GAGCA-TGAGACGTGCTAAACGGA
1 GAGCACACAGA-GTGCTAAACAGA
*
1732739 GAGCACACATAGTGCTAAACAGA
1 GAGCACACAGAGTGCTAAACAGA
1732762 GAGCACACACGA-TGCTAA
1 GAGCACACA-GAGTGCTAA
1732780 TAGGAGAGCA
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
23 50 0.71
24 6 0.09
25 14 0.20
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (23 bp):
GAGCACACAGAGTGCTAAACAGA
Found at i:1732786 original size:23 final size:23
Alignment explanation
Indices: 1732689--1732789 Score: 91
Period size: 23 Copynumber: 4.3 Consensus size: 23
1732679 GTGCTAATTA
*
1732689 GAGAGCACACGAAGTGCTAATAACG
1 GAGAGCACAC-ACGTGCTAAT-ACG
* *
1732714 GAGAGCATGAGACGTGCTAA-ACG
1 GAGAGCA-CACACGTGCTAATACG
* *
1732737 GAGAGCACACATAGTGCTAA-ACA
1 GAGAGCACACA-CGTGCTAATACG
1732760 GAGAGCACACACGATGCTAATA-G
1 GAGAGCACACACG-TGCTAATACG
1732783 GAGAGCA
1 GAGAGCA
1732790 TGTTAGTGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 3 0.05
23 43 0.68
24 1 0.02
25 15 0.24
26 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.29, T:0.12
Consensus pattern (23 bp):
GAGAGCACACACGTGCTAATACG
Found at i:1739975 original size:23 final size:22
Alignment explanation
Indices: 1739916--1740138 Score: 109
Period size: 23 Copynumber: 9.9 Consensus size: 22
1739906 GAGAGTACCG
* *
1739916 AAGTACTAAACAGAGAGCACAT
1 AAGTGCTAAACAGAGAGCACAC
*
1739938 AAGTGCTGGGCAACAGAGAGCACAC
1 AAGTGCT---AAACAGAGAGCACAC
*
1739963 ACAGTGCTAAACAGAGAGTACAC
1 A-AGTGCTAAACAGAGAGCACAC
* * *
1739986 AA-AG-T--AC-TA-AGCACATA
1 AAGTGCTAAACAGAGAGCACA-C
** *
1740003 AAGTGCTAATTAGAGAGCACATG
1 AAGTGCTAAACAGAGAGCACA-C
* *
1740026 AAGTGCTAATAACGGAGAGCACGAG
1 AAGTGCT-A-AACAGAGAGCAC-AC
* *
1740051 ATGTGCTAAATAGAGAGCACAC
1 AAGTGCTAAACAGAGAGCACAC
*
1740073 ATAGTGC-AAGACGGAGAGCACAC
1 A-AGTGCTAA-ACAGAGAGCACAC
** *
1740096 ACAGTGCTAAATGGAGAGTACAC
1 A-AGTGCTAAACAGAGAGCACAC
*
1740119 ACAGTGCTAATCAGAGAGCA
1 A-AGTGCTAAACAGAGAGCA
1740139 TGCTAGTGTT
Statistics
Matches: 153, Mismatches: 31, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
16 5 0.03
17 3 0.02
18 3 0.02
19 1 0.01
20 1 0.01
21 1 0.01
22 12 0.08
23 86 0.56
24 4 0.03
25 30 0.20
26 7 0.05
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (22 bp):
AAGTGCTAAACAGAGAGCACAC
Found at i:1740104 original size:46 final size:46
Alignment explanation
Indices: 1740003--1740129 Score: 132
Period size: 46 Copynumber: 2.7 Consensus size: 46
1739993 TAAGCACATA
* * *
1740003 AAGTGCTAATTAGAGAGCACATGAAGTGCTAATAACGGAGAGCACGAG
1 AAGTGCTAAATAGAGAGCACA-CAAGTGCTAATAACGGAGAGCAC-AC
* *
1740051 ATGTGCTAAATAGAGAGCACACATAGTGC-AA-GACGGAGAGCACAC
1 AAGTGCTAAATAGAGAGCACACA-AGTGCTAATAACGGAGAGCACAC
* *
1740096 ACAGTGCTAAATGGAGAGTACACACAGTGCTAAT
1 A-AGTGCTAAATAGAGAGCACACA-AGTGCTAAT
1740130 CAGAGAGCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
45 2 0.03
46 35 0.53
47 5 0.08
48 24 0.36
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (46 bp):
AAGTGCTAAATAGAGAGCACACAAGTGCTAATAACGGAGAGCACAC
Found at i:1746103 original size:72 final size:74
Alignment explanation
Indices: 1745961--1746113 Score: 224
Period size: 72 Copynumber: 2.1 Consensus size: 74
1745951 CTTATTTTAG
*
1745961 TTTATTGTTGTAATTTTATAACATTTTTTTCAATTAAAATTTATTAACTATTTATTTTTATCACA
1 TTTATTGTTATAATTTTATAACATTTTTTTCAATTAAAATTTATTAACTATTTATTTTTATCACA
1746026 TATTAGAAA
66 TATTAGAAA
** *
1746035 TTTATTGTTATAATTTTATAACATTTTTTT-AATT-TGA-TTATCTAACTATTTATTTTTATTTA
1 TTTATTGTTATAATTTTATAACATTTTTTTCAATTAAAATTTAT-TAACTATTTATTTTTA-TCA
1746097 -ATATTAGAAA
64 CATATTAGAAA
1746107 TTTATTG
1 TTTATTG
1746114 CAATAATGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
71 4 0.05
72 34 0.47
73 6 0.08
74 29 0.40
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (74 bp):
TTTATTGTTATAATTTTATAACATTTTTTTCAATTAAAATTTATTAACTATTTATTTTTATCACA
TATTAGAAA
Found at i:1746298 original size:23 final size:23
Alignment explanation
Indices: 1746272--1746347 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
1746262 TACATTTTAG
*
1746272 TTGTTTTTTGTGCATATTTGGTA
1 TTGTTTTTGGTGCATATTTGGTA
* * *
1746295 TTGTTTTTGGTG-TTGATTTGATG
1 TTGTTTTTGGTGCAT-ATTTGGTA
**
1746318 TTGTTTTTGGTGCAGCTTTGGTA
1 TTGTTTTTGGTGCATATTTGGTA
*
1746341 CTGTTTT
1 TTGTTTT
1746348 CGATGTTGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.09, C:0.05, G:0.26, T:0.59
Consensus pattern (23 bp):
TTGTTTTTGGTGCATATTTGGTA
Found at i:1746305 original size:12 final size:12
Alignment explanation
Indices: 1746288--1746329 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1746278 TTTGTGCATA
*
1746288 TTTGGTATTGTT
1 TTTGGTGTTGTT
*
1746300 TTTGGTGTTG-A
1 TTTGGTGTTGTT
*
1746311 TTTGATGTTGTT
1 TTTGGTGTTGTT
1746323 TTTGGTG
1 TTTGGTG
1746330 CAGCTTTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.07, C:0.00, G:0.31, T:0.62
Consensus pattern (12 bp):
TTTGGTGTTGTT
Found at i:1746323 original size:46 final size:47
Alignment explanation
Indices: 1746271--1746366 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 47
1746261 TTACATTTTA
* * * * *
1746271 GTTGTTTTTTGTGCATATTTGGTATTGTTTTTGGTGTTGATTTG-AT
1 GTTGTTTTTGGTGCAGATTTGGTACTGTTTTCGATGTTGATTTGAAT
* *
1746317 GTTGTTTTTGGTGCAGCTTTGGTACTGTTTTCGATGTTGTTTTGAAT
1 GTTGTTTTTGGTGCAGATTTGGTACTGTTTTCGATGTTGATTTGAAT
1746364 GTT
1 GTT
1746367 TTGGTGCTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 37 0.88
47 5 0.12
ACGTcount: A:0.10, C:0.05, G:0.27, T:0.57
Consensus pattern (47 bp):
GTTGTTTTTGGTGCAGATTTGGTACTGTTTTCGATGTTGATTTGAAT
Found at i:1746601 original size:41 final size:41
Alignment explanation
Indices: 1746539--1746618 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
1746529 TCTTATTGTA
1746539 TTTTCAATTTATTTGTTGTTTT-ATGAATTGTTTTAATATCG
1 TTTTCAATTTATTTGTTGTTTTAAT-AATTGTTTTAATATCG
* * *
1746580 TTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATAT
1 TTTTCAATTTATTTGTTGTTTTAATAATTGTTTTAATAT
1746619 TTTTAAGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.21, C:0.03, G:0.11, T:0.65
Consensus pattern (41 bp):
TTTTCAATTTATTTGTTGTTTTAATAATTGTTTTAATATCG
Found at i:1746612 original size:12 final size:12
Alignment explanation
Indices: 1746595--1746620 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1746585 AATTTGTTTG
1746595 TTGTTTTAATAT
1 TTGTTTTAATAT
1746607 TTGTTTTAATAT
1 TTGTTTTAATAT
1746619 TT
1 TT
1746621 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:1754940 original size:29 final size:29
Alignment explanation
Indices: 1754891--1754957 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
1754881 CAAAATAATG
*
1754891 ATTTTA-CCCTAAACATTCAAAAATTACC
1 ATTTTACCCCTAAACATCCAAAAATTACC
*
1754919 ATTTTACCCCTAAACATCCAAAAATTATC
1 ATTTTACCCCTAAACATCCAAAAATTACC
*
1754948 ATTTTGCCCC
1 ATTTTACCCC
1754958 CAGATTTCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.33
Consensus pattern (29 bp):
ATTTTACCCCTAAACATCCAAAAATTACC
Found at i:1755029 original size:29 final size:29
Alignment explanation
Indices: 1754976--1755058 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
1754966 CCAAAATCAT
*
1754976 ATTTTCAACCTCAAATTTTC-CAAAAGTTC-
1 ATTTT-AACC-CAAATTTTCAAAAAAGTTCA
*
1755005 ATTTTAATCCCAAATTTTCAAAAAATTTCA
1 ATTTTAA-CCCAAATTTTCAAAAAAGTTCA
* *
1755035 ATTTTGACCCAAATTCCTCAAAAA
1 ATTTTAACCCAAATT-TTCAAAAA
1755059 TTACGTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 11 0.24
29 22 0.48
30 13 0.28
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (29 bp):
ATTTTAACCCAAATTTTCAAAAAAGTTCA
Found at i:1756814 original size:17 final size:17
Alignment explanation
Indices: 1756785--1756874 Score: 128
Period size: 17 Copynumber: 5.4 Consensus size: 17
1756775 CATTATTTAT
1756785 TTTAAATTT-AAATAAA
1 TTTAAATTTAAAATAAA
1756801 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
** *
1756818 TTTAAGCTTAAAATAAG
1 TTTAAATTTAAAATAAA
*
1756835 CTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
1756852 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
1756869 TTTAAA
1 TTTAAA
1756875 ATGGGTTCAG
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
16 9 0.14
17 55 0.86
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1757377 original size:39 final size:39
Alignment explanation
Indices: 1757334--1757904 Score: 325
Period size: 39 Copynumber: 14.7 Consensus size: 39
1757324 GATGGTTGCA
* *
1757334 ATCTGCCCTAGGCTCCGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* **
1757373 ATCTG-CCTAGGCTCAGGGTAAGAGATTGATTGATGGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * *
1757411 ATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGGCT-GTA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCT-GATGGTG
* * * * *
1757450 ATCTGCCCCAGGCTCGAGGTAAAAGATTGGCCGATAGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** *
1757489 ATCTGTCCTTTGCTCGGGGTAAGAGA-T--CAGATGGCTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGG-TG
*
1757526 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * *
1757567 ATCTGCCC-AAGCTCAGGGTAAAAGA-T--CTAATGGTTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGG-TG
*
1757603 TAATCTG-CCTCAGGCTCGGGGTAAGAGATTGGCAGATGGTG
1 --ATCTGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * *
1757644 ATCTGTCCC-AAGCTCAGGGTAAAAGATT-G--AATGGCTG
1 ATCTG-CCCTAGGCTCGGGGTAAGAGATTGGCTGATGG-TG
* * *
1757681 CAATCTGCCCCAGGTTCGGGGTAAGAGATTGGCTGATAGTG
1 --ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** * * * * *
1757722 ATCTG-CCTCAAGCTCAAGCTAAAAGA-TAG--AATGGCTACA
1 ATCTGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGG-T--G
* *
1757761 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** * * * ***
1757800 ATCTGTCCTAGGCTCAAGGTAAAAGATCGGATGACT-ACA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* * * * * *
1757839 ATTTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGATG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
*
1757878 ATCTGCCCCAGGCTCGGGGTAAGAGAT
1 ATCTGCCCTAGGCTCGGGGTAAGAGAT
1757905 CGGAATCTTC
Statistics
Matches: 398, Mismatches: 98, Indels: 72
0.70 0.17 0.13
Matches are distributed among these distances:
35 6 0.02
36 14 0.04
37 8 0.02
38 65 0.16
39 269 0.68
40 10 0.03
41 9 0.02
42 17 0.04
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:1757504 original size:78 final size:78
Alignment explanation
Indices: 1757373--1757908 Score: 603
Period size: 78 Copynumber: 6.9 Consensus size: 78
1757363 GCTGATGGTG
* * ** * * * *
1757373 ATCTG-CCTAGGCTCAGGGTAAGAGATTGATTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCCAAGCTCAGGGTAAAAGA
*
1757437 TCGGATGGCTGTA
66 TCGGATGGCTGCA
* * * *** * *
1757450 ATCTGCCCCAGGCTCGAGGTAAAAGATTGGCCGATAGTGATCTGTCCTTTGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCCAAGCTCAGGGTAAAAGA
*
1757515 TCAGATGGCTGCA
66 TCGGATGGCTGCA
*
1757528 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCAGGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCCAAGCTCAGGGTAAAAGA
** * *
1757592 TCTAATGGTTGTA
66 TCGGATGGCTGCA
* * *
1757605 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCAGATGGTGATCTGTCCCAAGCTCAGGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCCAAGCTCAGGGTAAAAGA
* *
1757670 TTGAATGGCTGCA
66 TCGGATGGCTGCA
* * *
1757683 ATCTGCCCCAGGTTCGGGGTAAGAGATTGGCTGATAGTGATCTG-CCTCAAGCTCAAGCTAAAAG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCC-CAAGCTCAGGGTAAAAG
* * *
1757747 ATAGAATGGCTACA
65 ATCGGATGGCTGCA
* * *
1757761 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCTAGGCTCAAGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCCAAGCTCAGGGTAAAAGA
* *
1757826 TCGGATGACTACA
66 TCGGATGGCTGCA
* * * * * * * *
1757839 ATTTACCCCAAGCTCGAGGTAAGAGATTGGCTGAT-GATGATCTGCCCCAGGCTCGGGGTAAGAG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAG-TGATCTGTCCCAAGCTCAGGGTAAAAG
1757903 ATCGGA
65 ATCGGA
1757909 ATCTTCAACT
Statistics
Matches: 397, Mismatches: 57, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
77 74 0.19
78 321 0.81
79 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (78 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGTCCCAAGCTCAGGGTAAAAGA
TCGGATGGCTGCA
Found at i:1768182 original size:30 final size:29
Alignment explanation
Indices: 1768143--1768231 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
1768133 GAGGAATCTG
1768143 GGGTC-AAAATTGAAATTTTTGGAAAATTT
1 GGGTCTAAAATTG-AATTTTTGGAAAATTT
* *
1768172 GGGAT-TAAAATCGAACTTTTGGAAAATTT
1 GGG-TCTAAAATTGAATTTTTGGAAAATTT
1768201 GTGGTCTAAAATGTG-ATTTTTGG-AAATTT
1 G-GGTCTAAAAT-TGAATTTTTGGAAAATTT
1768230 GG
1 GG
1768232 TGGCAAAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
28 1 0.02
29 27 0.53
30 22 0.43
31 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
GGGTCTAAAATTGAATTTTTGGAAAATTT
Found at i:1768268 original size:29 final size:27
Alignment explanation
Indices: 1768236--1768306 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 27
1768226 ATTTGGTGGC
1768236 AAAACAATAATTTTTGGATGTTCGGGGGG
1 AAAAC-ATAATTTTTGGATGTTC-GGGGG
*
1768265 AAAATGATAATTTTTGGATGTTCGGGGG
1 AAAA-CATAATTTTTGGATGTTCGGGGG
1768293 AAAATCATAATTTT
1 AAAA-CATAATTTT
1768307 GGAGAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 18 0.46
29 21 0.54
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (27 bp):
AAAACATAATTTTTGGATGTTCGGGGG
Found at i:1768292 original size:28 final size:29
Alignment explanation
Indices: 1768242--1768306 Score: 114
Period size: 28 Copynumber: 2.3 Consensus size: 29
1768232 TGGCAAAACA
*
1768242 ATAATTTTTGGATGTTCGGGGGGAAAATG
1 ATAATTTTTGGATGTTCGGGGGGAAAATC
1768271 ATAATTTTTGGATGTTC-GGGGGAAAATC
1 ATAATTTTTGGATGTTCGGGGGGAAAATC
1768299 ATAATTTT
1 ATAATTTT
1768307 GGAGAAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (29 bp):
ATAATTTTTGGATGTTCGGGGGGAAAATC
Found at i:1768364 original size:30 final size:30
Alignment explanation
Indices: 1768300--1768489 Score: 147
Period size: 30 Copynumber: 6.5 Consensus size: 30
1768290 GGGAAAATCA
* *
1768300 TAATTTTGGAGAAGTTTGA--GTCAAAATG
1 TAATTTTGGAAAAATTTGAGGGTCAAAATG
** * *
1768328 GGATTTT-GAAGAAGTTTGAGGGTGAAAATG
1 TAATTTTGGAA-AAATTTGAGGGTCAAAATG
* * * **
1768358 TAATTTT-TAAAAAATTAAGGGTTGAAATG
1 TAATTTTGGAAAAATTTGAGGGTCAAAATG
* *
1768387 TAATTTTGGAAAAATTCGAGGGTCAAAATA
1 TAATTTTGGAAAAATTTGAGGGTCAAAATG
* * *
1768417 TAATTTTGGAAAAGTTT-AGGGTAAAAATA
1 TAATTTTGGAAAAATTTGAGGGTCAAAATG
* * * *
1768446 TGATTTTAGAAAAATTTAAGGGTTAAAATG
1 TAATTTTGGAAAAATTTGAGGGTCAAAATG
*
1768476 TAATATTGGAAAAA
1 TAATTTTGGAAAAA
1768490 ATTAGGGGTT
Statistics
Matches: 127, Mismatches: 30, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
27 2 0.02
28 13 0.10
29 46 0.36
30 66 0.52
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.34
Consensus pattern (30 bp):
TAATTTTGGAAAAATTTGAGGGTCAAAATG
Found at i:1768386 original size:59 final size:59
Alignment explanation
Indices: 1768322--1768506 Score: 174
Period size: 59 Copynumber: 3.1 Consensus size: 59
1768312 AGTTTGAGTC
* * * *
1768322 AAAATGGGATTTT-GAAGAAGTTTGAGGGTGAAAATGTAATTTTTAAAAAATTAAGGGTT
1 AAAATGTGATTTTAGAA-AAATTTGAGGGTCAAAATGTAATTTTGAAAAAATTAAGGGTT
* * * * * * * * *
1768381 GAAATGTAATTTTGGAAAAATTCGAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGTA
1 AAAATGTGATTTTAGAAAAATTTGAGGGTCAAAATGTAATTTTGAAAAAATTAAGGGTT
* * * * *
1768440 AAAATATGATTTTAGAAAAATTTAAGGGTTAAAATGTAATATTGGAAAAAATTAGGGGTT
1 AAAATGTGATTTTAGAAAAATTTGAGGGTCAAAATGTAAT-TTTGAAAAAATTAAGGGTT
*
1768500 ACAATGT
1 AAAATGT
1768507 AGTTTTTAAA
Statistics
Matches: 96, Mismatches: 28, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
59 75 0.78
60 21 0.22
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.33
Consensus pattern (59 bp):
AAAATGTGATTTTAGAAAAATTTGAGGGTCAAAATGTAATTTTGAAAAAATTAAGGGTT
Found at i:1768499 original size:30 final size:30
Alignment explanation
Indices: 1768346--1768512 Score: 151
Period size: 30 Copynumber: 5.6 Consensus size: 30
1768336 AAGAAGTTTG
* *
1768346 AGGGTGAAAATGTAATTTT-TAAAAAATTA
1 AGGGTTAAAATGTAATTTTGGAAAAAATTA
* *
1768375 AGGGTTGAAATGTAATTTTGG-AAAAATTCG
1 AGGGTTAAAATGTAATTTTGGAAAAAATT-A
* * * *
1768405 AGGGTCAAAATATAATTTTGG-AAAAGTTT
1 AGGGTTAAAATGTAATTTTGGAAAAAATTA
* * * * *
1768434 AGGGTAAAAATATGATTTTAGAAAAATTTA
1 AGGGTTAAAATGTAATTTTGGAAAAAATTA
*
1768464 AGGGTTAAAATGTAATATTGGAAAAAATTA
1 AGGGTTAAAATGTAATTTTGGAAAAAATTA
* * *
1768494 GGGGTTACAATGTAGTTTT
1 AGGGTTAAAATGTAATTTT
1768513 TAAACAAAAC
Statistics
Matches: 111, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
29 42 0.38
30 69 0.62
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.34
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTGGAAAAAATTA
Found at i:1769955 original size:10 final size:10
Alignment explanation
Indices: 1769937--1769966 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1769927 TTATTTATTT
1769937 TAAATTTAAA
1 TAAATTTAAA
*
1769947 TAAACTTAAA
1 TAAATTTAAA
1769957 TAAATTTAAA
1 TAAATTTAAA
1769967 CTTAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:1769966 original size:16 final size:17
Alignment explanation
Indices: 1769947--1769983 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1769937 TAAATTTAAA
1769947 TAAACTT-AAATAAATT
1 TAAACTTAAAATAAATT
1769963 TAAACTTAAAATAAATT
1 TAAACTTAAAATAAATT
1769980 TAAA
1 TAAA
1769984 AATGGGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAACTTAAAATAAATT
Found at i:1777300 original size:43 final size:42
Alignment explanation
Indices: 1777248--1777337 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 42
1777238 ACTTAAAATA
*
1777248 AATAAATTTAGTCAAAATAAAATTAAGAAAATAACAACTTTT
1 AATAAATTTAGTCAAAATAAAATTAAGAAAATAACAACTTTG
*
1777290 AATATAATTTAGTCAAAATAAAATTAAGAAAATAACAGCTTTG
1 AATA-AATTTAGTCAAAATAAAATTAAGAAAATAACAACTTTG
1777333 AATAA
1 AATAA
1777338 GCTTATTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 5 0.11
43 40 0.89
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (42 bp):
AATAAATTTAGTCAAAATAAAATTAAGAAAATAACAACTTTG
Found at i:1781305 original size:74 final size:74
Alignment explanation
Indices: 1781184--1781332 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
1781174 TTTGGTTAAT
1781184 TCTGTAAAATCAATTCTTAAGCTTCTTCTGTACATCCTTCTGCTATTTATGGATTCTCATCACTA
1 TCTGTAAAATCAATTCTTAAGCTTCTTCTGTACATCCTTCTGCTATTTATGGATTCTCATCACTA
1781249 ACAACCTGA
66 ACAACCTGA
*
1781258 TCTGTAAAATCATTTCTTAAGCTTCTTCTGTACATCCTTCTGCTATTTATGGATTCTCATCACTA
1 TCTGTAAAATCAATTCTTAAGCTTCTTCTGTACATCCTTCTGCTATTTATGGATTCTCATCACTA
1781323 ACAACCTGA
66 ACAACCTGA
1781332 T
1 T
1781333 AACCAAATAC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.40
Consensus pattern (74 bp):
TCTGTAAAATCAATTCTTAAGCTTCTTCTGTACATCCTTCTGCTATTTATGGATTCTCATCACTA
ACAACCTGA
Found at i:1782661 original size:20 final size:20
Alignment explanation
Indices: 1782627--1782686 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1782617 TCTTAAAAGA
1782627 TATAAAT-TTTT-AATTTTT
1 TATAAATATTTTGAATTTTT
*
1782645 TATAAATATTTTGAATTTTA
1 TATAAATATTTTGAATTTTT
* *
1782665 AAAAAATATTTTGAATTATTT
1 TATAAATATTTTGAATT-TTT
1782686 T
1 T
1782687 GTAATTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 21 0.62
21 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TATAAATATTTTGAATTTTT
Found at i:1784322 original size:21 final size:22
Alignment explanation
Indices: 1784280--1784322 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1784270 TAAAAGGAAC
*
1784280 TAACAGAAAGTACCAAAGTACT
1 TAACAGAAAGTACCAAACTACT
1784302 TAACA-AAAGTA-CATAACTACT
1 TAACAGAAAGTACCA-AACTACT
1784323 GGGGAAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (22 bp):
TAACAGAAAGTACCAAACTACT
Found at i:1784353 original size:22 final size:22
Alignment explanation
Indices: 1784328--1784450 Score: 156
Period size: 22 Copynumber: 5.4 Consensus size: 22
1784318 CTACTGGGGA
*
1784328 AACAGAAGCATACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
1784350 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
1784372 AACAGAAGCACACATAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* **
1784394 ATCAGAAAAACACACAGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
*
1784418 AAATAGAAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
1784441 AACAGTAAGC
1 AACAG-AAGC
1784451 GCGCTAACGT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
22 63 0.73
23 5 0.06
24 1 0.01
25 17 0.20
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:1787243 original size:15 final size:15
Alignment explanation
Indices: 1787219--1787249 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1787209 CAAGGGAATA
*
1787219 GGCAAGAGCAGCACC
1 GGCAACAGCAGCACC
1787234 GGCAACAGCAGCACC
1 GGCAACAGCAGCACC
1787249 G
1 G
1787250 ACTATGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.35, G:0.32, T:0.00
Consensus pattern (15 bp):
GGCAACAGCAGCACC
Found at i:1793449 original size:20 final size:21
Alignment explanation
Indices: 1793407--1793449 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1793397 AATGTGACAA
*
1793407 GTTAACTGGCCACGTCAACTT
1 GTTAACTAGCCACGTCAACTT
*
1793428 GTTAACTAGCCGCGTC-ACTT
1 GTTAACTAGCCACGTCAACTT
1793448 GT
1 GT
1793450 CTCATTAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (21 bp):
GTTAACTAGCCACGTCAACTT
Found at i:1793527 original size:174 final size:174
Alignment explanation
Indices: 1793224--1793549 Score: 463
Period size: 174 Copynumber: 1.9 Consensus size: 174
1793214 GCCTTGTCTG
* * * * * * *
1793224 ATGTGGCAATTTAACTGGCCACATCAGCTAATTTACTGGCCACGTCACTTGTCCCGTTAGGCCTG
1 ATGTGACAAGTTAACTGGCCACATCAACTAATTAACTAGCCACGTCACTTGTCCCATTAAGCCTG
* * *
1793289 TAACGGAAAATGTTAATGAGTGACTAATTTATCACTTTTCGATAACATTAGTGACTGGTTTGTTA
66 TAACGAAAAATGTTAATGAGTAACTAATTTATCACTTTTCGATAACATTAGTGACTGATTTGTTA
1793354 TTTTTTGAAAGTTGAGTGACTGGAGTGAAATTTTGTCTCGTCCA
131 TTTTTTGAAAGTTGAGTGACTGGAGTGAAATTTTGTCTCGTCCA
* ** * *
1793398 ATGTGACAAGTTAACTGGCCACGTCAACTTGTTAACTAGCCGCGTCACTTGTCTCATTAAGCCTG
1 ATGTGACAAGTTAACTGGCCACATCAACTAATTAACTAGCCACGTCACTTGTCCCATTAAGCCTG
* * * * * *
1793463 TAACGAAAAATGTTAATGGGTAATTGATTTGTCACTTTTCGATAACGTTAGTGATTGATTTGTTA
66 TAACGAAAAATGTTAATGAGTAACTAATTTATCACTTTTCGATAACATTAGTGACTGATTTGTTA
1793528 TTTTTTGAAAGTTGAGTGACTG
131 TTTTTTGAAAGTTGAGTGACTG
1793550 AATTTAAATC
Statistics
Matches: 131, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
174 131 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (174 bp):
ATGTGACAAGTTAACTGGCCACATCAACTAATTAACTAGCCACGTCACTTGTCCCATTAAGCCTG
TAACGAAAAATGTTAATGAGTAACTAATTTATCACTTTTCGATAACATTAGTGACTGATTTGTTA
TTTTTTGAAAGTTGAGTGACTGGAGTGAAATTTTGTCTCGTCCA
Found at i:1796394 original size:14 final size:14
Alignment explanation
Indices: 1796375--1796409 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1796365 TACACTTCGT
1796375 CAAGATAAAACCAA
1 CAAGATAAAACCAA
1796389 CAAGATAAAACCAA
1 CAAGATAAAACCAA
1796403 CAA-ATAA
1 CAAGATAA
1796410 TCGAGACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.66, C:0.20, G:0.06, T:0.09
Consensus pattern (14 bp):
CAAGATAAAACCAA
Found at i:1803024 original size:9 final size:9
Alignment explanation
Indices: 1803010--1803038 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1803000 TATTTTTTCA
1803010 AATTCGAAT
1 AATTCGAAT
1803019 AATTCGAAT
1 AATTCGAAT
1803028 AATTCGAAT
1 AATTCGAAT
1803037 AA
1 AA
1803039 ATCAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1803046 original size:18 final size:18
Alignment explanation
Indices: 1803010--1803046 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1803000 TATTTTTTCA
* *
1803010 AATTCGAATAATTCGAAT
1 AATTCGAATAAATCAAAT
1803028 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
1803046 A
1 A
1803047 TAAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:1811261 original size:36 final size:38
Alignment explanation
Indices: 1811182--1811263 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 38
1811172 TATATTTTTT
* *
1811182 TATAATTTTTTACACTTTTCAATTTTTTTATAATATTG
1 TATAATTTTTTACACTTTTCAATTTTTTCATAATATTA
* *
1811220 T-TAATTTTTTTCA-TGTTTCTA-TTTTTCATAAT-TTA
1 TATAATTTTTTACACT-TTTCAATTTTTTCATAATATTA
1811255 TATAATTTT
1 TATAATTTT
1811264 CCATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 3 0.08
36 18 0.47
37 16 0.42
38 1 0.03
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (38 bp):
TATAATTTTTTACACTTTTCAATTTTTTCATAATATTA
Found at i:1811263 original size:18 final size:17
Alignment explanation
Indices: 1811242--1811335 Score: 50
Period size: 19 Copynumber: 5.2 Consensus size: 17
1811232 ATGTTTCTAT
1811242 TTTTCATAATTTATATAA
1 TTTTCATAATTT-TATAA
*
1811260 TTTTCCAT--TTTTATTA
1 TTTT-CATAATTTTATAA
*
1811276 TTTTAATAATTTTTATATA
1 TTTTCATAA-TTTTATA-A
** *
1811295 TTTTTGTCATTTGTAATAAA
1 TTTTCATAATTT-T-AT-AA
1811315 TTTT-ATAATTTTATATA
1 TTTTCATAATTTTATA-A
1811332 TTTT
1 TTTT
1811336 TTCACTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
15 2 0.03
16 9 0.15
17 10 0.17
18 14 0.24
19 16 0.27
20 7 0.12
21 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTCATAATTTTATAA
Found at i:1811269 original size:26 final size:25
Alignment explanation
Indices: 1811235--1811288 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1811225 TTTTTTCATG
*
1811235 TTTCTATTTTTCATAA-TTTATATAAT
1 TTTCCATTTTT-ATAATTTTA-ATAAT
*
1811261 TTTCCATTTTTATTATTTTAATAAT
1 TTTCCATTTTTATAATTTTAATAAT
1811286 TTT
1 TTT
1811289 TATATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTCCATTTTTATAATTTTAATAAT
Found at i:1811344 original size:18 final size:17
Alignment explanation
Indices: 1811241--1811370 Score: 75
Period size: 17 Copynumber: 7.2 Consensus size: 17
1811231 CATGTTTCTA
*
1811241 TTTTTCATAATTTATATAA
1 TTTTTCAT--TTTATATAT
*
1811260 TTTTCCATTTT-TATTAT
1 TTTTTCATTTTATA-TAT
* *
1811277 TTTAATAATTTTTATATAT
1 TTT-TTCA-TTTTATATAT
*
1811296 TTTTGTCATTTGTAATAAAT
1 TTTT-TCATTT-T-ATATAT
* *
1811316 TTTATAATTTTATATAT
1 TTTTTCATTTTATATAT
1811333 TTTTTCACTTTTATAT-T
1 TTTTTCA-TTTTATATAT
** *
1811350 TTTTAAATTTTAAATAT
1 TTTTTCATTTTATATAT
1811367 TTTT
1 TTTT
1811371 ATATTTTTAT
Statistics
Matches: 86, Mismatches: 16, Indels: 20
0.70 0.13 0.16
Matches are distributed among these distances:
16 9 0.10
17 29 0.34
18 13 0.15
19 25 0.29
20 10 0.12
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTCATTTTATATAT
Found at i:1811352 original size:26 final size:26
Alignment explanation
Indices: 1811266--1811386 Score: 79
Period size: 26 Copynumber: 4.5 Consensus size: 26
1811256 ATAATTTTCC
*
1811266 ATTTTTAT-TATTTTAATAATTTTTAT
1 ATTTTTATATATTTTAAT-ACTTTTAT
* *
1811292 ATATTTT-TGTCATTTGTAATAAATTTTAT
1 AT-TTTTATAT-ATTT-TAAT-ACTTTTAT
* *
1811321 AATTTTATATATTTT-TTCACTTTTAT
1 ATTTTTATATATTTTAAT-ACTTTTAT
* *
1811347 ATTTTT-TAAATTTTAAATATTTTTAT
1 ATTTTTATATATTTT-AATACTTTTAT
1811373 ATTTTTATGATATT
1 ATTTTTAT-ATATT
1811387 CTATATTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
25 7 0.09
26 29 0.39
27 8 0.11
28 16 0.21
29 15 0.20
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTTTTATATATTTTAATACTTTTAT
Found at i:1811378 original size:18 final size:19
Alignment explanation
Indices: 1811251--1811386 Score: 92
Period size: 18 Copynumber: 7.5 Consensus size: 19
1811241 TTTTTCATAA
* *
1811251 TTTATATAATTTT-CCATT
1 TTTATATATTTTTATCATT
* *
1811269 TTTAT-TATTTTAATAATT
1 TTTATATATTTTTATCATT
*
1811287 TTTATATATTTTTGTCATT
1 TTTATATATTTTTATCATT
* * *
1811306 TGTA-ATAAATTTTAT-AAT
1 TTTATAT-ATTTTTATCATT
*
1811324 TTTATATATTTTT-TCACT
1 TTTATATATTTTTATCATT
*
1811342 TTTATAT-TTTTTA--AAT
1 TTTATATATTTTTATCATT
*
1811358 TTTAAATATTTTTAT-ATT
1 TTTATATATTTTTATCATT
1811376 TTTATGATATT
1 TTTAT-ATATT
1811387 CTATATTTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 17
0.72 0.14 0.13
Matches are distributed among these distances:
16 8 0.09
17 17 0.19
18 40 0.44
19 26 0.29
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTATATATTTTTATCATT
Found at i:1811380 original size:34 final size:35
Alignment explanation
Indices: 1811186--1811370 Score: 116
Period size: 34 Copynumber: 5.2 Consensus size: 35
1811176 TTTTTTTATA
*
1811186 ATTTTTTACACTTTTCA-ATTTTTTTATAATATTGTTAAT
1 ATTTTTT-CACTTTT-ATA-TTTTTTATAAT-TT-TAAAT
* * *
1811225 -TTTTTTCA-TGTTTCTATTTTTCATAA-TTTATAT
1 ATTTTTTCACT-TTTATATTTTTTATAATTTTAAAT
* * *
1811258 AATTTTCCA-TTTT-TATTATTTTAATAATTTTTATAT
1 ATTTTTTCACTTTTATATT-TTTT-ATAA-TTTTAAAT
** *
1811294 ATTTTTGTCA-TTTGTAATAAATTTTATAATTTTATAT
1 ATTTTT-TCACTTT-T-ATATTTTTTATAATTTTAAAT
1811331 ATTTTTTCACTTTTATATTTTTTA-AATTTTAAAT
1 ATTTTTTCACTTTTATATTTTTTATAATTTTAAAT
1811365 ATTTTT
1 ATTTTT
1811371 ATATTTTTAT
Statistics
Matches: 120, Mismatches: 14, Indels: 29
0.74 0.09 0.18
Matches are distributed among these distances:
32 4 0.03
33 9 0.08
34 28 0.23
35 8 0.07
36 26 0.22
37 28 0.23
38 11 0.09
39 4 0.03
40 2 0.02
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (35 bp):
ATTTTTTCACTTTTATATTTTTTATAATTTTAAAT
Found at i:1813161 original size:19 final size:19
Alignment explanation
Indices: 1813133--1813169 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1813123 GAAAGTTAAT
*
1813133 AACAATTTTGATTACGATA
1 AACAAATTTGATTACGATA
1813152 AACAAATTTGATTACGAT
1 AACAAATTTGATTACGAT
1813170 GAGTAACAAT
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:0.11, G:0.11, T:0.35
Consensus pattern (19 bp):
AACAAATTTGATTACGATA
Found at i:1822163 original size:30 final size:30
Alignment explanation
Indices: 1822126--1822327 Score: 253
Period size: 30 Copynumber: 6.6 Consensus size: 30
1822116 GGAAGGTTCA
1822126 AGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTT
* *
1822156 GGGGTTAAAATGTAATTTTGAAAAAGTTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTT
*
1822186 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTT
***
1822216 -GTGGTTAAAATGTAATTTTGGAAAAAAAAATT
1 AG-GGTTAAAATGTAATTTTGG--AAAAGTTTT
* *
1822248 AGGGGTCAAAATGTAATTTTAGAAAAGTTTT
1 A-GGGTTAAAATGTAATTTTGGAAAAGTTTT
* **
1822279 AGGGTTAAAATATAATTTTCAAAAAGTTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTT
*
1822309 AGGGTTAAAATATAATTTT
1 AGGGTTAAAATGTAATTTT
1822328 TAGACAGTTT
Statistics
Matches: 149, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.01
30 117 0.79
31 7 0.05
32 6 0.04
33 17 0.11
34 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.38
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTTT
Found at i:1822210 original size:15 final size:15
Alignment explanation
Indices: 1822192--1822240 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1822182 TTTTAGGGTC
1822192 AAAATGTAATTTTGG
1 AAAATGTAATTTTGG
1822207 AAAA-GT--TTTGTGG
1 AAAATGTAATTT-TGG
1822220 TTAAAATGTAATTTTGG
1 --AAAATGTAATTTTGG
1822237 AAAA
1 AAAA
1822241 AAAAATTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 3 0.11
13 3 0.11
14 2 0.07
15 12 0.43
16 2 0.07
17 3 0.11
18 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (15 bp):
AAAATGTAATTTTGG
Found at i:1822274 original size:93 final size:90
Alignment explanation
Indices: 1822126--1822327 Score: 264
Period size: 93 Copynumber: 2.2 Consensus size: 90
1822116 GGAAGGTTCA
** * *
1822126 AGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGAAAAAGTTTTAGGGT
1 AGGGTTAAAATGTAATTTTGGAAAAAATTAGGGGTCAAAATGTAATTTTGAAAAAGTTTTAGGGT
* **
1822191 CAAAATGTAATTTTGGAAAAGTTTT
66 CAAAATATAATTTTCAAAAAGTTTT
1822216 -GTGGTTAAAATGTAATTTTGGAAAAAAAAATTAGGGGTCAAAATGTAATTTT-AGAAAAGTTTT
1 AG-GGTTAAAATGTAATTTTGG---AAAAAATTAGGGGTCAAAATGTAATTTTGA-AAAAGTTTT
*
1822279 AGGGTTAAAATATAATTTTCAAAAAGTTTT
61 AGGGTCAAAATATAATTTTCAAAAAGTTTT
*
1822309 AGGGTTAAAATATAATTTT
1 AGGGTTAAAATGTAATTTT
1822328 TAGACAGTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
89 1 0.01
90 19 0.20
92 1 0.01
93 75 0.77
94 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.38
Consensus pattern (90 bp):
AGGGTTAAAATGTAATTTTGGAAAAAATTAGGGGTCAAAATGTAATTTTGAAAAAGTTTTAGGGT
CAAAATATAATTTTCAAAAAGTTTT
Found at i:1823445 original size:3 final size:3
Alignment explanation
Indices: 1823437--1823464 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1823427 TATTTAAACC
1823437 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1823465 ATGGCTATTG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1824204 original size:6 final size:6
Alignment explanation
Indices: 1824193--1824255 Score: 78
Period size: 6 Copynumber: 11.0 Consensus size: 6
1824183 TTATAATAAT
* *
1824193 TTTAAA TTTAAA -TTAAA TCTAAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1824239 -TTAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
1824256 ACAAATTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:1824208 original size:11 final size:11
Alignment explanation
Indices: 1824194--1824248 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
1824184 TATAATAATT
1824194 TTAAATTTAAA
1 TTAAATTTAAA
*
1824205 TTAAATCTAAA
1 TTAAATTTAAA
1824216 TTTAAA-TTAAA
1 -TTAAATTTAAA
1824227 TTCAAATTTAAA
1 TT-AAATTTAAA
1824239 TTAAATTTAA
1 TTAAATTTAA
1824249 TTTTAAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 2 0.05
11 25 0.64
12 12 0.31
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1824253 original size:17 final size:17
Alignment explanation
Indices: 1824180--1824266 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
1824170 TTGGACATTG
*
1824180 AATTTATAA-TAATTTTA
1 AATTTA-AATTAAATTTA
*
1824197 AATTTAAATTAAATCTA
1 AATTTAAATTAAATTTA
*
1824214 AATTTAAATTAAATTCA
1 AATTTAAATTAAATTTA
1824231 AATTTAAATTAAATTTA
1 AATTTAAATTAAATTTA
* **
1824248 ATTTTAAAACAAATTTA
1 AATTTAAATTAAATTTA
1824265 AA
1 AA
1824267 ATGGTTTGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
16 2 0.03
17 58 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:1829220 original size:110 final size:111
Alignment explanation
Indices: 1829026--1829246 Score: 417
Period size: 110 Copynumber: 2.0 Consensus size: 111
1829016 TTTACCCAGG
*
1829026 TATACATATAATAGCTAGAAAATTTGTCTGCTAAATGGCAGAGTTGTTGAGTAGCTTTGATTTTA
1 TATACATATAATAGCTAGAAAATTTGTCTGCTAAAAGGCAGAGTTGTTGAGTAGCTTTGATTTTA
1829091 GCTGAAGTAAGATTAGACTAAGGACGATAGCTGATTGAATATCTAT
66 GCTGAAGTAAGATTAGACTAAGGACGATAGCTGATTGAATATCTAT
1829137 TATACATATAATAGCTAGAAAATTTGT-TGCTAAAAGGCAGAGTTGTTGAGTAGCTTTGATTTTA
1 TATACATATAATAGCTAGAAAATTTGTCTGCTAAAAGGCAGAGTTGTTGAGTAGCTTTGATTTTA
*
1829201 GCTGAAGTAAGATTAGACTAAGGATGATAGCTGATTGAATATCTAT
66 GCTGAAGTAAGATTAGACTAAGGACGATAGCTGATTGAATATCTAT
1829247 AATTTTTTTA
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 81 0.75
111 27 0.25
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (111 bp):
TATACATATAATAGCTAGAAAATTTGTCTGCTAAAAGGCAGAGTTGTTGAGTAGCTTTGATTTTA
GCTGAAGTAAGATTAGACTAAGGACGATAGCTGATTGAATATCTAT
Found at i:1832483 original size:65 final size:65
Alignment explanation
Indices: 1832399--1832522 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 65
1832389 GATAATGTTT
* * * * * * *
1832399 TTTTTTTTATGTACTTTTATGTTACCTGC-ATATTAAATGGCTTCGATAATATGAATCTGATCAT
1 TTTTTTTCACGTACCTTTATGTTACCTACGACATT-AATAGCTTCAATAATATGAATCTGATCAT
1832463 A
65 A
*
1832464 TTTTTTTCACGTACCTTTATGTTACCTACGACCTTAATAGCTTCAATAATATGAATCTG
1 TTTTTTTCACGTACCTTTATGTTACCTACGACATTAATAGCTTCAATAATATGAATCTG
1832523 GTCAAGTACT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
65 47 0.94
66 3 0.06
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (65 bp):
TTTTTTTCACGTACCTTTATGTTACCTACGACATTAATAGCTTCAATAATATGAATCTGATCATA
Found at i:1833398 original size:12 final size:13
Alignment explanation
Indices: 1833381--1833410 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1833371 TATAGTTATC
1833381 TTAAAAAATTGT-
1 TTAAAAAATTGTA
1833393 TTAAAAAATTGTA
1 TTAAAAAATTGTA
1833406 TTAAA
1 TTAAA
1833411 TAAAGGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
TTAAAAAATTGTA
Found at i:1834443 original size:17 final size:18
Alignment explanation
Indices: 1834421--1834458 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
1834411 TTCTATTTGG
1834421 ATTATTATAATATC-TCA
1 ATTATTATAATATCATCA
1834438 ATTATTATAATATCATCA
1 ATTATTATAATATCATCA
1834456 ATT
1 ATT
1834459 GGTCTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTATAATATCATCA
Found at i:1835600 original size:23 final size:23
Alignment explanation
Indices: 1835574--1835673 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 23
1835564 AGTGTTGGGC
1835574 AACAGAGAGCACACACAATGCTA
1 AACAGAGAGCACACACAATGCTA
* *
1835597 AACAGAGAGTACACA-AAGTACTA
1 AACAGAGAGCACACACAA-TGCTA
* *
1835620 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAATGCT-A
* *
1835644 TAACAGAGAGCAC-CAGACGTGCTA
1 -AACAGAGAGCACACACA-ATGCTA
1835668 AACAGA
1 AACAGA
1835674 AAGTGCGCTA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
22 2 0.03
23 40 0.62
24 6 0.09
25 16 0.25
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAATGCTA
Found at i:1835654 original size:25 final size:25
Alignment explanation
Indices: 1835574--1835656 Score: 102
Period size: 23 Copynumber: 3.5 Consensus size: 25
1835564 AGTGTTGGGC
*
1835574 AACAGAGAGCACACACAATGCT-A-
1 AACAGAGAGCACACACAGTGCTAAT
* * *
1835597 AACAGAGAGTACACAAAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAAT
1835622 --CAGAGAGCACACACAGTGCTAAT
1 AACAGAGAGCACACACAGTGCTAAT
1835645 AACAGAGAGCAC
1 AACAGAGAGCAC
1835657 CAGACGTGCT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 38 0.78
24 1 0.02
25 10 0.20
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (25 bp):
AACAGAGAGCACACACAGTGCTAAT
Found at i:1837396 original size:14 final size:14
Alignment explanation
Indices: 1837379--1837405 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1837369 TTAGAGTTTA
1837379 GATTTTGAATTTTG
1 GATTTTGAATTTTG
1837393 GATTTTGAATTTT
1 GATTTTGAATTTT
1837406 AAATATGATT
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:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (14 bp):
GATTTTGAATTTTG
Found at i:1837965 original size:18 final size:18
Alignment explanation
Indices: 1837939--1837974 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1837929 AGTGTGTTCT
*
1837939 AAATTACATAATAAATAA
1 AAATAACATAATAAATAA
*
1837957 AAATAACATAATATATAA
1 AAATAACATAATAAATAA
1837975 TATTATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAACATAATAAATAA
Found at i:1838570 original size:17 final size:18
Alignment explanation
Indices: 1838545--1838581 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1838535 TTTTTTAAAA
1838545 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
1838563 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
1838580 AT
1 AT
1838582 ATTTTTATTA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:1841449 original size:32 final size:31
Alignment explanation
Indices: 1841412--1841490 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
1841402 GATTAGTGAG
1841412 AATTTTCAAAAATTTTAAAACAGCT-TAATTAA-
1 AATTTTCAAAAATTTT-AAA-AGCTATAA-TAAT
* *
1841444 AATTTTCAAAAAATATTAAAAGGTATAATAAT
1 AATTTTC-AAAAATTTTAAAAGCTATAATAAT
1841476 AATTTTCAAAAATTT
1 AATTTTCAAAAATTT
1841491 GGGACCTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 13 0.32
32 20 0.49
33 8 0.20
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (31 bp):
AATTTTCAAAAATTTTAAAAGCTATAATAAT
Found at i:1844954 original size:70 final size:67
Alignment explanation
Indices: 1844822--1844954 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
1844812 ATAAACAATA
* * *
1844822 TAATGATTTTGACTTTTAACTTAATGGGTAAACATTTATCAAAATGATATAATTTTATCTTTTAA
1 TAATGATTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1844887 CT
66 CT
* * * * *
1844889 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAATATTTATCAAAATGACGTAGTTTTGCCTTT
1 TAATGATTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAATGACATAATTTTACCTTT
1844954 T
63 T
1844955 CTTATTCGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 19 0.35
68 2 0.04
70 34 0.62
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
CT
Found at i:1851366 original size:2 final size:2
Alignment explanation
Indices: 1851354--1851393 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1851344 TTTATAAAAC
* *
1851354 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1851394 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1851398 original size:2 final size:2
Alignment explanation
Indices: 1851393--1851435 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1851383 TATATAGATA
1851393 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1851435 T
1 T
1851436 TTATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1854619 original size:12 final size:12
Alignment explanation
Indices: 1854602--1854627 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1854592 GGGGCCTCCA
1854602 TGATACTTTTAC
1 TGATACTTTTAC
1854614 TGATACTTTTAC
1 TGATACTTTTAC
1854626 TG
1 TG
1854628 TCTTAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (12 bp):
TGATACTTTTAC
Found at i:1865749 original size:80 final size:80
Alignment explanation
Indices: 1865614--1865778 Score: 294
Period size: 80 Copynumber: 2.1 Consensus size: 80
1865604 ACTGAAGAAT
* * *
1865614 TAGGACTTTATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACTCTCTTGAGTTAATA
1 TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
*
1865679 TTTGTAGAATCACCG
66 TTTGTAGAATCACCA
1865694 TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
1 TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
1865759 TTTGTAGAATCACCA
66 TTTGTAGAATCACCA
1865774 TAGGA
1 TAGGA
1865779 TTTTAGAAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (80 bp):
TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
TTTGTAGAATCACCA
Found at i:1867260 original size:36 final size:35
Alignment explanation
Indices: 1867220--1867288 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1867210 TTGATCCCAG
* *
1867220 TTTATAAGTACTACTAAAAATGCCTTTGATGGTTAT
1 TTTATAA-TACTACTAAAAATACCTTTAATGGTTAT
** *
1867256 TTTATAATTTTACTATAAATACCTTTAATGGTT
1 TTTATAATACTACTAAAAATACCTTTAATGGTT
1867289 GGCTTAGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 21 0.75
36 7 0.25
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTATAATACTACTAAAAATACCTTTAATGGTTAT
Found at i:1872950 original size:15 final size:15
Alignment explanation
Indices: 1872930--1872981 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1872920 AATAAGACCT
1872930 TTTCCATTGGTTGTA
1 TTTCCATTGGTTGTA
** **
1872945 TTTCCATAAGTACCT-
1 TTTCCATTGGT-TGTA
1872960 TTTCCATTGGTTGTA
1 TTTCCATTGGTTGTA
1872975 TTTCCAT
1 TTTCCAT
1872982 AAGTTTTCTT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.50
Consensus pattern (15 bp):
TTTCCATTGGTTGTA
Found at i:1872960 original size:30 final size:30
Alignment explanation
Indices: 1872921--1872985 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1872911 GCATATCGAA
1872921 ATAAG-ACCTTTTCCATTGGTTGTATTTCC
1 ATAAGTACCTTTTCCATTGGTTGTATTTCC
1872950 ATAAGTACCTTTTCCATTGGTTGTATTTCC
1 ATAAGTACCTTTTCCATTGGTTGTATTTCC
1872980 ATAAGT
1 ATAAGT
1872986 TTTCTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (30 bp):
ATAAGTACCTTTTCCATTGGTTGTATTTCC
Found at i:1876008 original size:12 final size:12
Alignment explanation
Indices: 1875973--1876022 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
1875963 CTAAAAACCT
*
1875973 ATACATATATAT
1 ATACATATATAC
1875985 ATACATATATAC
1 ATACATATATAC
*
1875997 ATACACATATAC
1 ATACATATATAC
* *
1876009 ATGCATACATAC
1 ATACATATATAC
1876021 AT
1 AT
1876023 CCCTGGCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (12 bp):
ATACATATATAC
Found at i:1876016 original size:20 final size:20
Alignment explanation
Indices: 1875973--1876021 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1875963 CTAAAAACCT
* * *
1875973 ATACATATATATATACATAT
1 ATACATACACATATACATAC
*
1875993 ATACATACACATATACATGC
1 ATACATACACATATACATAC
1876013 ATACATACA
1 ATACATACA
1876022 TCCCTGGCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (20 bp):
ATACATACACATATACATAC
Found at i:1889280 original size:24 final size:24
Alignment explanation
Indices: 1889253--1889301 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1889243 AAACATTATT
1889253 AAAATAGAGAAAA-ATCAGAAAAAA
1 AAAATAGA-AAAAGATCAGAAAAAA
*
1889277 AAAATCGAAAAAGATCAGAAAAAA
1 AAAATAGAAAAAGATCAGAAAAAA
1889301 A
1 A
1889302 TGTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.08
Consensus pattern (24 bp):
AAAATAGAAAAAGATCAGAAAAAA
Found at i:1899407 original size:11 final size:11
Alignment explanation
Indices: 1899376--1899496 Score: 64
Period size: 11 Copynumber: 10.5 Consensus size: 11
1899366 ACTCAGACTT
*
1899376 TTAATTTTTAA
1 TTAATTTTAAA
*
1899387 TTGAAGTTTAAA
1 TT-AATTTTAAA
1899399 TTAATTTTAAA
1 TTAATTTTAAA
* **
1899410 TTTAAATTTATC
1 -TTAATTTTAAA
*
1899422 TTAAATTTAAA
1 TTAATTTTAAA
*
1899433 TTTACTTATTTAAA
1 -TTA-AT-TTTAAA
*
1899447 TTTATTTTAAA
1 TTAATTTTAAA
* *
1899458 TTTAAATTTAAT
1 -TTAATTTTAAA
1899470 TTAA-TTTAAA
1 TTAATTTTAAA
* *
1899480 ATAATATTAAA
1 TTAATTTTAAA
1899491 CTTAAT
1 -TTAAT
1899497 ATAAAAATAC
Statistics
Matches: 83, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
10 8 0.10
11 34 0.41
12 33 0.40
13 2 0.02
14 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:1899413 original size:6 final size:6
Alignment explanation
Indices: 1899393--1899479 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
1899383 TTAATTGAAG
* *
1899393 TTTAAA -TTAAT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTACTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
*
1899441 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1899480 ATAATATTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.03
5 20 0.30
6 38 0.57
7 2 0.03
8 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:1899415 original size:17 final size:17
Alignment explanation
Indices: 1899393--1899495 Score: 90
Period size: 17 Copynumber: 6.3 Consensus size: 17
1899383 TTAATTGAAG
1899393 TTTAAATTAATTTTAAA
1 TTTAAATTAATTTTAAA
* *
1899410 TTTAAATTTATCTTAAA
1 TTTAAATTAATTTTAAA
* *
1899427 TTTAAATTTA-CTT--A
1 TTTAAATTAATTTTAAA
*
1899441 TTTAAATTTATTTTAAA
1 TTTAAATTAATTTTAAA
1899458 TTTAAATTTAA-TTT-AA
1 TTTAAA-TTAATTTTAAA
* *
1899474 TTTAAAATAATATTAAA
1 TTTAAATTAATTTTAAA
*
1899491 CTTAA
1 TTTAA
1899496 TATAAAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.15
15 5 0.07
16 13 0.18
17 41 0.56
18 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:1899447 original size:31 final size:31
Alignment explanation
Indices: 1899409--1899467 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1899399 TTAATTTTAA
1899409 ATTTAAATTTATCTTAAATTTAAATTTACTT
1 ATTTAAATTTATCTTAAATTTAAATTTACTT
*
1899440 ATTTAAATTTATTTTAAATTTAAATTTA
1 ATTTAAATTTATCTTAAATTTAAATTTA
1899468 ATTTAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTATCTTAAATTTAAATTTACTT
Found at i:1900770 original size:30 final size:31
Alignment explanation
Indices: 1900734--1900800 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1900724 TTCTTTTTTT
* * *
1900734 TAAAAAAATAATAATAAA-GAACAAATGAAA
1 TAAAAAAAAAAGAACAAAGGAACAAATGAAA
* *
1900764 TAAAAAAAAAAGAACAAAGGAAGAAATGGAA
1 TAAAAAAAAAAGAACAAAGGAACAAATGAAA
1900795 TAAAAA
1 TAAAAA
1900801 TGGAAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (31 bp):
TAAAAAAAAAAGAACAAAGGAACAAATGAAA
Done.