Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 114 of 205
Found at i:34237550 original size:40 final size:40
Alignment explanation
Indices: 34237452--34237714 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
34237442 TCCTCGTTCA
* * * * *
34237452 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34237491 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
34237531 AATGCCTTCGGGACTTAACCCGGATTTAATAACTGGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
34237571 AATGCCTTCGGGGCTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34237611 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
34237651 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
34237691 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34237715 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 37 0.19
40 151 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34239280 original size:47 final size:47
Alignment explanation
Indices: 34239211--34239333 Score: 174
Period size: 47 Copynumber: 2.6 Consensus size: 47
34239201 GGCTGTCACA
* * *
34239211 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACG
* * *
34239258 TGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACG
* *
34239305 TGATGGATGTGAAAGTGTATAAATGTGAT
1 TGATGAATGTGAAAGTGTATATATGTGAT
34239334 GAGTCCCGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (47 bp):
TGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAACG
Found at i:34244767 original size:18 final size:18
Alignment explanation
Indices: 34244670--34244773 Score: 66
Period size: 18 Copynumber: 5.6 Consensus size: 18
34244660 CATGTTGTAA
*
34244670 TGAAAAAGAAAAAGAGAT
1 TGAAAAAGAAAAAGAAAT
*
34244688 TGAAAAAGAGGAAAAAAAAAT
1 TG-AAAA-A-GAAAAAGAAAT
*
34244709 TGAAAGAGAGAAAAG-AAT
1 TGAAAAAGA-AAAAGAAAT
* ***** *
34244727 CGAAAAAGATTGTTAAAA
1 TGAAAAAGAAAAAGAAAT
*
34244745 AGAAAAAGAAAAAGAAAT
1 TGAAAAAGAAAAAGAAAT
34244763 TGAAAAAGAAA
1 TGAAAAAGAAA
34244774 GTGAAAGTGA
Statistics
Matches: 61, Mismatches: 20, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
18 37 0.61
19 9 0.15
20 4 0.07
21 11 0.18
ACGTcount: A:0.67, C:0.01, G:0.20, T:0.12
Consensus pattern (18 bp):
TGAAAAAGAAAAAGAAAT
Found at i:34244778 original size:12 final size:12
Alignment explanation
Indices: 34244741--34244779 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34244731 AAAGATTGTT
*
34244741 AAAAAGAAAAAG
1 AAAAAGAAAATG
*
34244753 AAAAAGAAATTG
1 AAAAAGAAAATG
*
34244765 AAAAAGAAAGTG
1 AAAAAGAAAATG
34244777 AAA
1 AAA
34244780 GTGAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:34244779 original size:18 final size:20
Alignment explanation
Indices: 34244745--34244795 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
34244735 ATTGTTAAAA
*
34244745 AGAAAAAGAAAAAGAAA-T-
1 AGAAAAAGAAAGAGAAAGTG
* *
34244763 TGAAAAAGAAAGTGAAAGTG
1 AGAAAAAGAAAGAGAAAGTG
34244783 AGAAAAAGAAAGA
1 AGAAAAAGAAAGA
34244796 CAAAATTGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
AGAAAAAGAAAGAGAAAGTG
Found at i:34251336 original size:30 final size:30
Alignment explanation
Indices: 34251300--34251361 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
34251290 GCTAGGATTC
*
34251300 TTCAACTCTTTAACCGGTCATATTGAGAAG
1 TTCAACTCTTTAAACGGTCATATTGAGAAG
*
34251330 TTCAACTCTTTAAATGGTCATATTGAGAAG
1 TTCAACTCTTTAAACGGTCATATTGAGAAG
34251360 TT
1 TT
34251362 TAAAGTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (30 bp):
TTCAACTCTTTAAACGGTCATATTGAGAAG
Found at i:34252656 original size:14 final size:14
Alignment explanation
Indices: 34252639--34252678 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
34252629 CTTTATTAAT
*
34252639 ATATTTTATTTGGG
1 ATATTTTATTTAGG
34252653 ATATTTTATTTAGG
1 ATATTTTATTTAGG
34252667 ATATTTTATTTA
1 ATATTTTATTTA
34252679 TCTTTGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (14 bp):
ATATTTTATTTAGG
Found at i:34255873 original size:25 final size:25
Alignment explanation
Indices: 34255844--34255892 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
34255834 AAGGAGTCAA
34255844 CTTACCCTTTGGTATAATGTTTGAC
1 CTTACCCTTTGGTATAATGTTTGAC
34255869 CTTACCCTTTGGTATAATGTTTGA
1 CTTACCCTTTGGTATAATGTTTGA
34255893 ATCCCTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (25 bp):
CTTACCCTTTGGTATAATGTTTGAC
Found at i:34263224 original size:25 final size:25
Alignment explanation
Indices: 34263196--34263254 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
34263186 AGCTGTAAAC
* *
34263196 GGTAAGCTCCTCCGAGATGATTAAT
1 GGTAAGCTCCTCCAAGATGAATAAT
* *
34263221 GGTAAGCTCCTCTAAGCTGAATAAT
1 GGTAAGCTCCTCCAAGATGAATAAT
34263246 GGTAAGCTC
1 GGTAAGCTC
34263255 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCCTCCAAGATGAATAAT
Found at i:34263263 original size:25 final size:25
Alignment explanation
Indices: 34263217--34263291 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
34263207 CCGAGATGAT
* * *
34263217 TAATGGTAAGCTCCTCTAAGCTGAA
1 TAATGGTAAGCTCATATGAGCTGAA
*
34263242 TAATGGTAAGCTCATATGAGCTGAG
1 TAATGGTAAGCTCATATGAGCTGAA
*
34263267 T-ATCGGTAAGCTCATAAGAGCTGAA
1 TAAT-GGTAAGCTCATATGAGCTGAA
34263292 ATCAATAACC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 2 0.05
25 41 0.95
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (25 bp):
TAATGGTAAGCTCATATGAGCTGAA
Found at i:34265875 original size:27 final size:27
Alignment explanation
Indices: 34265845--34265947 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
34265835 TAAATGATCG
*
34265845 AAATACCCTCGAAGGGTAAAATTATCA
1 AAATACCCTCGAAGGGTAAAATTACCA
*
34265872 AAATACCCTCGAAGGGTAAATTTACCA
1 AAATACCCTCGAAGGGTAAAATTACCA
* * *
34265899 CAATACCCTCGATGGGTAAAATTACCG
1 AAATACCCTCGAAGGGTAAAATTACCA
*
34265926 AATTACCCTC-ATAGGGTAAAAT
1 AAATACCCTCGA-AGGGTAAAAT
34265948 GACTGTTATA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 1 0.02
27 65 0.98
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATTACCA
Found at i:34274194 original size:17 final size:18
Alignment explanation
Indices: 34274164--34274200 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
34274154 GCAACTAAAC
34274164 AAAACAAGGTTTTTC-TA
1 AAAACAAGGTTTTTCGTA
34274181 AAAACTAAGG-TTTTCGTA
1 AAAAC-AAGGTTTTTCGTA
34274199 AA
1 AA
34274201 TAGAAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
AAAACAAGGTTTTTCGTA
Found at i:34284560 original size:27 final size:25
Alignment explanation
Indices: 34284528--34284586 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 25
34284518 GTTAACACTT
34284528 TGAAATGACTATATGAATTGGTTATA
1 TGAAATGACTATATGAATT-GTTATA
* *
34284554 TGGAAATAATTATATGAATTGTTATA
1 T-GAAATGACTATATGAATTGTTATA
34284580 TGAAATG
1 TGAAATG
34284587 TTTACATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 8 0.28
27 16 0.55
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.39
Consensus pattern (25 bp):
TGAAATGACTATATGAATTGTTATA
Found at i:34284580 original size:12 final size:12
Alignment explanation
Indices: 34284537--34284588 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
34284527 TTGAAATGAC
34284537 TATATGAATTGGT
1 TATATGAATT-GT
**
34284550 TATATGGAAATAAT
1 TATAT-G-AATTGT
34284564 TATATGAATTGT
1 TATATGAATTGT
*
34284576 TATATGAAATGT
1 TATATGAATTGT
34284588 T
1 T
34284589 TACATGGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 16 0.50
13 6 0.19
14 7 0.22
15 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.44
Consensus pattern (12 bp):
TATATGAATTGT
Found at i:34289499 original size:27 final size:27
Alignment explanation
Indices: 34289469--34289522 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
34289459 TGTCATGTGA
*
34289469 AATTGAATGGCAAATTATTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
34289496 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
34289523 GGTTGTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:34311322 original size:13 final size:13
Alignment explanation
Indices: 34311304--34311333 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34311294 GTTAGCACTT
34311304 TGAAATGACTATA
1 TGAAATGACTATA
*
34311317 TGAAATGGCTATA
1 TGAAATGACTATA
34311330 TGAA
1 TGAA
34311334 TCAGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
TGAAATGACTATA
Found at i:34311342 original size:26 final size:25
Alignment explanation
Indices: 34311313--34311376 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
34311303 TTGAAATGAC
*
34311313 TATATGAAATGGCTATATGAA-TCAGT
1 TATATGAAATGACTATATGAAGT--GT
* *
34311339 TATATGGAAATAATTATATGAAGTGT
1 TATAT-GAAATGACTATATGAAGTGT
34311365 TATATGAAATGA
1 TATATGAAATGA
34311377 TTACATGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 6 0.19
26 12 0.38
27 13 0.41
28 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (25 bp):
TATATGAAATGACTATATGAAGTGT
Found at i:34314992 original size:27 final size:27
Alignment explanation
Indices: 34314962--34315019 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
34314952 TTCATCTCCT
*
34314962 AGGGGTA-TAAAGATCATTTTACCCTTA
1 AGGGGTATTAAAG-TAATTTTACCCTTA
* *
34314989 AGGGGTATTACAGTAATTTTACTCTTA
1 AGGGGTATTAAAGTAATTTTACCCTTA
34315016 AGGG
1 AGGG
34315020 TTTTTGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (27 bp):
AGGGGTATTAAAGTAATTTTACCCTTA
Found at i:34315097 original size:28 final size:27
Alignment explanation
Indices: 34314977--34315197 Score: 193
Period size: 27 Copynumber: 8.3 Consensus size: 27
34314967 TATAAAGATC
* *
34314977 ATTTTACCCTT-AAGGGGTATTAC-AGTA
1 ATTTTACCCTTCGA-GGGTATTTCGA-TA
* * * *
34315004 ATTTTACTCTT-AAGGGT-TTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
34315029 ATTTTACCCTTCGAGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
34315056 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
34315083 ATTTTTACCCTTCGAGGGTATTTCGGTA
1 A-TTTTACCCTTCGAGGGTATTTCGATA
* * *
34315111 ATTTAACCCTTTGAGGGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* * * *
34315138 ATTTTACCCTT-GGGGGTAATTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * * *
34315164 ATTTTACCCTTCGGGGGTAATTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
34315191 ATTTTAC
1 ATTTTAC
34315198 TTTTAGGGGG
Statistics
Matches: 168, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
25 14 0.08
26 29 0.17
27 99 0.59
28 26 0.15
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:34315100 original size:55 final size:55
Alignment explanation
Indices: 34314977--34315197 Score: 215
Period size: 55 Copynumber: 4.1 Consensus size: 55
34314967 TATAAAGATC
* * * * * *
34314977 ATTTTACCCTT-AAGGGGTATTACAGTAATTTTACTCTT-AAGGGT-TTTTG-GTA
1 ATTTTACCCTTCGA-GGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
* *
34315029 ATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCTTCGAGGGTATTTCGA-TA
1 ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
* * *
34315083 ATTTTTACCCTTCGAGGGTATTTCGGTAATTTAACCCTTTGAGGGTATTT-TAGTA
1 A-TTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
* * * * * *
34315138 ATTTTACCCTT-GGGGGTAATTCGGTCATTTTACCCTTCGGGGGTAATTCG-GTC
1 ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
34315191 ATTTTAC
1 ATTTTAC
34315198 TTTTAGGGGG
Statistics
Matches: 140, Mismatches: 22, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
52 30 0.21
53 45 0.32
54 18 0.13
55 47 0.34
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (55 bp):
ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
Found at i:34315206 original size:27 final size:27
Alignment explanation
Indices: 34314975--34315224 Score: 148
Period size: 27 Copynumber: 9.3 Consensus size: 27
34314965 GGTATAAAGA
* *
34314975 TCATTTTACCCTTAAGGGGT-ATTACAG
1 TCATTTTACCCTTAGGGGGTAATT-CGG
* * * * *
34315002 TAATTTTACTCTTA-AGGGT-TTTTGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
* * * * * *
34315027 TAATTTTACCCTTCGAGGGTATTTTGA
1 TCATTTTACCCTTAGGGGGTAATTCGG
* * * * *
34315054 TAATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTAGGGGGTAATTCGG
* * * *
34315081 TAATTTTTACCCTTCGAGGGTATTTCGG
1 TCA-TTTTACCCTTAGGGGGTAATTCGG
* * * * * **
34315109 TAATTTAACCCTTTGAGGGTATTTTAG
1 TCATTTTACCCTTAGGGGGTAATTCGG
*
34315136 TAATTTTACCCTT-GGGGGTAATTCGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
*
34315162 TCATTTTACCCTTCGGGGGTAATTCGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
** *
34315189 TCATTTTACTTTTAGGGGGTAATACGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
34315216 TCATTTTAC
1 TCATTTTAC
34315225 GCACGATTCG
Statistics
Matches: 194, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.07
26 32 0.16
27 123 0.63
28 26 0.13
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTAGGGGGTAATTCGG
Found at i:34330666 original size:20 final size:20
Alignment explanation
Indices: 34330643--34330685 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34330633 CCCCTGTATA
* *
34330643 CACTTCGGTGTCCCTATTCG
1 CACTACGGTGCCCCTATTCG
*
34330663 CACTACGGTGCCCCTATTTG
1 CACTACGGTGCCCCTATTCG
34330683 CAC
1 CAC
34330686 ATTTGTGCCC
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:0.14, C:0.37, G:0.19, T:0.30
Consensus pattern (20 bp):
CACTACGGTGCCCCTATTCG
Found at i:34352307 original size:20 final size:20
Alignment explanation
Indices: 34352284--34352327 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
34352274 AATTTTGATA
34352284 TTTTATTTCAATT-TTTTTAT
1 TTTTATTT-AATTATTTTTAT
*
34352304 TTTTCTTTAATTATTTTTAT
1 TTTTATTTAATTATTTTTAT
34352324 TTTT
1 TTTT
34352328 TATAACTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTAATTATTTTTAT
Found at i:34358091 original size:38 final size:38
Alignment explanation
Indices: 34358040--34358117 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
34358030 GAATTCTTCG
*
34358040 TAAGGCTTTTTGTGTACGTTTAGTTTATCATCTTTCCC
1 TAAGGCTTTTTGTGTACGTTCAGTTTATCATCTTTCCC
* *
34358078 TAAGGCTTTTTGTGTTCGTTCATTTTATCATCTTTCCC
1 TAAGGCTTTTTGTGTACGTTCAGTTTATCATCTTTCCC
34358116 TA
1 TA
34358118 TTGTGTTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.15, C:0.19, G:0.14, T:0.51
Consensus pattern (38 bp):
TAAGGCTTTTTGTGTACGTTCAGTTTATCATCTTTCCC
Found at i:34362420 original size:14 final size:13
Alignment explanation
Indices: 34362399--34362438 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
34362389 AGTATCTTAG
34362399 AAATTAAATTATA
1 AAATTAAATTATA
*
34362412 AATATTAAATTTTA
1 AA-ATTAAATTATA
*
34362426 AAATTAAAATATA
1 AAATTAAATTATA
34362439 TTAGAGGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAAATTATA
Found at i:34364174 original size:28 final size:28
Alignment explanation
Indices: 34364132--34364281 Score: 173
Period size: 28 Copynumber: 5.4 Consensus size: 28
34364122 AAACAGCATG
* *
34364132 CAGTAACAGTCTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
34364160 CAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
* *
34364188 GAGTAAC-A-GATGGGACTTAGCCCAATA
1 CAGTAACAATG-TGGGCCTTAGCCCAATA
* * *
34364215 CAG-AATTAGTGTGGGCCTTAGCCCAGTA
1 CAGTAA-CAATGTGGGCCTTAGCCCAATA
*
34364243 CAG-AATCAGTGTGGGCCTTAGCCCAATA
1 CAGTAA-CAATGTGGGCCTTAGCCCAATA
34364271 CAGTAACAATG
1 CAGTAACAATG
34364282 CAGTGCAATA
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
26 3 0.03
27 19 0.18
28 80 0.76
29 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:34364228 original size:55 final size:56
Alignment explanation
Indices: 34364132--34364281 Score: 198
Period size: 55 Copynumber: 2.7 Consensus size: 56
34364122 AAACAGCATG
*
34364132 CAGTAACAGTCTGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCCCAATA
* * * * *
34364188 GAGTAACAG-ATGGGACTTAGCCCAATACAG-AATTAGTGTGGGCCTTAGCCCAGTA
1 CAGTAACAGTATGGGCCTTAGCCCAATACAGTAA-CAATGTGGGCCTTAGCCCAATA
*
34364243 CAG-AATCAGTGTGGGCCTTAGCCCAATACAGTAACAATG
1 CAGTAA-CAGTATGGGCCTTAGCCCAATACAGTAACAATG
34364282 CAGTGCAATA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.05
55 43 0.54
56 30 0.38
57 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (56 bp):
CAGTAACAGTATGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:34364677 original size:27 final size:26
Alignment explanation
Indices: 34364647--34364869 Score: 248
Period size: 27 Copynumber: 8.2 Consensus size: 26
34364637 GGTATAAAAA
* *
34364647 TCATTTTACCTTATGGGGTTATTTTGG
1 TCATTTTACCCTATGGGG-TATTTCGG
*
34364674 TCATTTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATG-GGGTATTTCGG
*
34364701 TCATTTTACCCTATTAGGGGTATTTTGG
1 TCATTTTACCCTA-T-GGGGTATTTCGG
* *
34364729 TTATTCTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
34364756 TCATTCTACCCTATGAGGGTATTTTGG
1 TCATTTTACCCTATG-GGGTATTTCGG
* **
34364783 TCATTTTACACTATGGGGGTATTTCAA
1 TCATTTTACCCTAT-GGGGTATTTCGG
34364810 TCATTTTACCCTATGGAGGTATTTCGG
1 TCATTTTACCCTATGG-GGTATTTCGG
* *
34364837 TCATTTTACCTTATGGGGGTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
34364864 TCATTT
1 TCATTT
34364870 ATCGACCTCT
Statistics
Matches: 168, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.02
27 137 0.82
28 27 0.16
29 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (26 bp):
TCATTTTACCCTATGGGGTATTTCGG
Found at i:34364742 original size:55 final size:53
Alignment explanation
Indices: 34364646--34364869 Score: 313
Period size: 54 Copynumber: 4.1 Consensus size: 53
34364636 GGGTATAAAA
* *
34364646 ATCATTTTACCTTATGGGGTTATTTTGGTCATTTTACCCTATGAGGGTATTTCG
1 ATCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCCTATGGGGGTATTTCG
* *
34364700 ATCATTTTACCCTATTAGGGGTATTTTGGTTATTCTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTA-T-GGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
* * * *
34364755 GTCATTCTACCCTATGAGGGTATTTTGGTCATTTTACACTATGGGGGTATTTCA
1 ATCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
* *
34364809 ATCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGGGGGTATTTCG
1 ATCATTTTACCCTATGG-GGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
34364863 ATCATTT
1 ATCATTT
34364870 ATCGACCTCT
Statistics
Matches: 150, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 100 0.67
55 44 0.29
56 4 0.03
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (53 bp):
ATCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
Found at i:34377921 original size:12 final size:12
Alignment explanation
Indices: 34377904--34377945 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
34377894 ATCCCAATAT
34377904 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
34377916 TCTCTCC-AAATA
1 TCTCTCCTCAA-A
*
34377928 TCCCTCCTCAAA
1 TCTCTCCTCAAA
34377940 TCTCTC
1 TCTCTC
34377946 TATGACCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:34380009 original size:18 final size:18
Alignment explanation
Indices: 34379983--34380022 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34379973 GACAGATGTT
* * *
34379983 CAAATATAGGAGTTTGGA
1 CAAAGATAGGAGATAGGA
34380001 CAAAGATAGGAGATAGGA
1 CAAAGATAGGAGATAGGA
34380019 CAAA
1 CAAA
34380023 AGCACACATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.17
Consensus pattern (18 bp):
CAAAGATAGGAGATAGGA
Found at i:34382101 original size:21 final size:22
Alignment explanation
Indices: 34382072--34382112 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
34382062 AATTATATTT
**
34382072 TTAATAGAATTATAAAAAATAA
1 TTAATAGAAAAATAAAAAATAA
34382094 TTAA-AGAAAAATAAAAAAT
1 TTAATAGAAAAATAAAAAAT
34382113 TTGACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (22 bp):
TTAATAGAAAAATAAAAAATAA
Found at i:34384144 original size:27 final size:27
Alignment explanation
Indices: 34384113--34384290 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34384103 TAAATTGTAC
34384113 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
34384140 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34384166 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
34384194 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
34384222 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34384249 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
34384276 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34384291 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:34384227 original size:82 final size:81
Alignment explanation
Indices: 34384114--34384269 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34384104 AAATTGTACA
* *
34384114 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34384178 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
34384195 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34384260 TGCGAGTTGA
65 TGCGAATTGA
34384270 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34384281 original size:82 final size:81
Alignment explanation
Indices: 34384110--34384290 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
34384100 GATTAAATTG
* *
34384110 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
34384175 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
34384191 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
34384255 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
34384273 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
34384291 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:34394562 original size:30 final size:31
Alignment explanation
Indices: 34394523--34394582 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
34394513 GGAGATGGGA
*
34394523 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
* **
34394554 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAA
34394583 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
Found at i:34394810 original size:9 final size:9
Alignment explanation
Indices: 34394796--34394832 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
34394786 TATAGTTTGA
34394796 TATTCGAAT
1 TATTCGAAT
34394805 TATTCGAAT
1 TATTCGAAT
*
34394814 TATTCGAGT
1 TATTCGAAT
34394823 TATTCGAAT
1 TATTCGAAT
34394832 T
1 T
34394833 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:34399143 original size:27 final size:27
Alignment explanation
Indices: 34399110--34399224 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 27
34399100 CGAAAAGGTT
34399110 GTAAAATTACTAAAATACCCTTAAAGG
1 GTAAAATTACTAAAATACCCTTAAAGG
* * * *
34399137 GTAAAATTACAAAAATACCCCTGATGG
1 GTAAAATTACTAAAATACCCTTAAAGG
* * * *
34399164 GTAAGATTACTGAAATACCCTCACTA-G
1 GTAAAATTACTAAAATACCCTTA-AAGG
* * *
34399191 GTAAAATTACTGAAATGCCCTTATAGG
1 GTAAAATTACTAAAATACCCTTAAAGG
34399218 GTAAAAT
1 GTAAAAT
34399225 GATCGTAATG
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 2 0.03
27 69 0.97
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (27 bp):
GTAAAATTACTAAAATACCCTTAAAGG
Found at i:34399245 original size:27 final size:27
Alignment explanation
Indices: 34399215--34399280 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
34399205 ATGCCCTTAT
* *
34399215 AGGGTAAAATGATCGTAATGCCTCTGG
1 AGGGTAAAATGATCGTAATGCCCCTGA
* * *
34399242 AGGGTAAATTAACCGTAATGCCCCTGA
1 AGGGTAAAATGATCGTAATGCCCCTGA
34399269 AGGGT-AAATGAT
1 AGGGTAAAATGAT
34399281 TGATTTTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (27 bp):
AGGGTAAAATGATCGTAATGCCCCTGA
Found at i:34399444 original size:27 final size:27
Alignment explanation
Indices: 34399401--34399466 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
34399391 GGAAGTACTA
* *
34399401 TACTGGTGGTTTTGCCACA-ATCACTGT
1 TACTGGTGGCTTGGCCACATAT-ACTGT
34399428 TACTGGTGGCTTGGCCACATATACTGT
1 TACTGGTGGCTTGGCCACATATACTGT
*
34399455 TACTGGTAGCTT
1 TACTGGTGGCTT
34399467 TATTGCGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (27 bp):
TACTGGTGGCTTGGCCACATATACTGT
Found at i:34399501 original size:26 final size:26
Alignment explanation
Indices: 34399448--34399501 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
34399438 TTGGCCACAT
* *
34399448 ATACTGTTACTGGTAGCTTTATTGCG
1 ATACTGTTACTGGCAGCTTTATTACG
** *
34399474 ATACTGTTGTTGGCAGCTTTGTTACG
1 ATACTGTTACTGGCAGCTTTATTACG
34399500 AT
1 AT
34399502 GCTACTGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTATTACG
Found at i:34399627 original size:22 final size:22
Alignment explanation
Indices: 34399602--34399665 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
34399592 ATTACTGAAC
*
34399602 TTATGGCTCGTAGCCATTCTAT
1 TTATGGCTCATAGCCATTCTAT
* * * * *
34399624 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTCATAGCCATTCTAT
* *
34399646 TTACGGCTCTTAGCCATTCT
1 TTATGGCTCATAGCCATTCT
34399666 GGTTACTGGC
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (22 bp):
TTATGGCTCATAGCCATTCTAT
Found at i:34402737 original size:12 final size:13
Alignment explanation
Indices: 34402705--34402747 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
34402695 AATTAGAGAT
*
34402705 AAAAATAATTATCA
1 AAAAAT-ATTAACA
34402719 GAAAAATATTAA-A
1 -AAAAATATTAACA
34402732 AAAAATATTAACA
1 AAAAATATTAACA
34402745 AAA
1 AAA
34402748 GATGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 11 0.42
13 5 0.19
14 4 0.15
15 6 0.23
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAAATATTAACA
Found at i:34423394 original size:41 final size:41
Alignment explanation
Indices: 34423340--34423615 Score: 329
Period size: 41 Copynumber: 6.8 Consensus size: 41
34423330 CATTAGTGGA
* * * * * *
34423340 ATTTTTCCTATAAATGCCGCAAAAGGTAAAGCAATAGTGGT
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* * * *
34423381 ATATTGCCCATAAACACCGCAAAAGGTAAAGCAATAGCGGT
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
*
34423422 ATTTTGCCCATAAATGCCACAAAAGGTAAAGCAATAGCGGC
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* *
34423463 ATTTTGCCCATAAATGCCACAAAAGGTAAAGCAATAGCGGT
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* * * ***
34423504 GTTTTTCCCATACACGCTGTAAAAGGT-AAGCAATAGCGGC
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* *
34423544 ATTTTTCCCATAAACGCCACAAAAGGTAAAGCAATAGTGGC
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* * *
34423585 GTTTTTCCCATAAACGCCATAAAAGGTAAAG
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAG
34423616 TTGTTGAATA
Statistics
Matches: 206, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 34 0.17
41 172 0.83
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (41 bp):
ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
Found at i:34423569 original size:81 final size:82
Alignment explanation
Indices: 34423341--34423615 Score: 363
Period size: 82 Copynumber: 3.4 Consensus size: 82
34423331 ATTAGTGGAA
* * ** * * * * *
34423341 TTTTTCCTATAAATGCCGCAAAAGGTAAAGCAATAGTGGTATATTGCCCATAAACACCGCAAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
*
34423406 GTAAAGCAATAGCGGTA
66 GTAAAGCAATAGCGGTG
* * * *
34423423 TTTTGCCCATAAATGCCACAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAATGCCACAAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
34423488 GTAAAGCAATAGCGGTG
66 GTAAAGCAATAGCGGTG
* ** *
34423505 TTTTTCCCATACACGCTGTAAAAGGT-AAGCAATAGCGGCATTTTTCCCATAAACGCCACAAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
* *
34423569 GTAAAGCAATAGTGGCG
66 GTAAAGCAATAGCGGTG
34423586 TTTTTCCCATAAACGCCATAAAAGGTAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAG
34423616 TTGTTGAATA
Statistics
Matches: 169, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
81 74 0.44
82 95 0.56
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (82 bp):
TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
GTAAAGCAATAGCGGTG
Found at i:34426385 original size:21 final size:22
Alignment explanation
Indices: 34426356--34426402 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
34426346 CAGAAGGAGT
*
34426356 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
34426378 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
34426399 GAGT
1 GAGT
34426403 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:34430843 original size:25 final size:25
Alignment explanation
Indices: 34430757--34430840 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
34430747 CAGCTCTTAT
* * *
34430757 GAGCTTACCATTACTCAACTCGTAT
1 GAGCTTACCATTATTCAACTCGAAG
**
34430782 GAGCTTACCATTATTCCTCTCGAAG
1 GAGCTTACCATTATTCAACTCGAAG
*
34430807 GAGCTTACCGTTATTCAACTC-AGAG
1 GAGCTTACCATTATTCAACTCGA-AG
34430832 GAGCTTACC
1 GAGCTTACC
34430841 GTTTACAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
24 1 0.02
25 49 0.98
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (25 bp):
GAGCTTACCATTATTCAACTCGAAG
Found at i:34430859 original size:24 final size:25
Alignment explanation
Indices: 34430805--34430852 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
34430795 TTCCTCTCGA
*
34430805 AGGAGCTTACCGTTATTCAACTCAG
1 AGGAGCTTACCGTTATACAACTCAG
*
34430830 AGGAGCTTACCGTT-TACAGCTCA
1 AGGAGCTTACCGTTATACAACTCA
34430853 TATGAGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (25 bp):
AGGAGCTTACCGTTATACAACTCAG
Found at i:34440766 original size:27 final size:27
Alignment explanation
Indices: 34440727--34440802 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
34440717 GAAAAGAAAT
34440727 TAAAAAAA-TGAAGTATTTAAGAATAA
1 TAAAAAAATTGAAGTATTTAAGAATAA
*
34440753 TAAAAAAATTGAAGTATTTAAAAATAA
1 TAAAAAAATTGAAGTATTTAAGAATAA
34440780 TAAAAAAATTGAAGTATTTAAGA
1 TAAAAAAATTGAAGTATTTAAGA
34440803 CCATGGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 8 0.17
27 39 0.83
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (27 bp):
TAAAAAAATTGAAGTATTTAAGAATAA
Found at i:34440978 original size:101 final size:101
Alignment explanation
Indices: 34440798--34441010 Score: 309
Period size: 101 Copynumber: 2.1 Consensus size: 101
34440788 TTGAAGTATT
* * * *
34440798 TAAGACCATGGTTGGACCATGGCAGTGTATATATGTAAGACCATTGCTGGGTTATGGCATTTTGA
1 TAAGACCATGGTTAGACCATGGCAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
* *
34440863 TGGTAAGACCATAACTGAGTTATAACACTATGGACG
66 TGGTAAGACCATAACTGAGTTATAACACTATGAACA
* * *
34440899 TAAGACAATGGTTAGACCATGGTAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TAAGACCATGGTTAGACCATGGCAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
* * **
34440964 TGGTAAGACTATAACTGGGTTATGGCACTATGAACA
66 TGGTAAGACCATAACTGAGTTATAACACTATGAACA
34441000 TAAGACCATGG
1 TAAGACCATGG
34441011 CAAGGCTATG
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTAGACCATGGCAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
TGGTAAGACCATAACTGAGTTATAACACTATGAACA
Found at i:34442256 original size:49 final size:49
Alignment explanation
Indices: 34442184--34442282 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
34442174 CCGCAGAAAC
34442184 ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
1 ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
*
34442233 ATAGTCATTTTCCGAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
1 ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
34442282 A
1 A
34442283 ATTAAAAGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
Found at i:34445931 original size:31 final size:32
Alignment explanation
Indices: 34445882--34445944 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
34445872 ATGAGATAGC
34445882 AAAAAGAAAGATTAAAAATTACCCACTTCCAA
1 AAAAAGAAAGATTAAAAATTACCCACTTCCAA
34445914 AAAAAGAAAGATT-AAAATTACCCACTTCCAA
1 AAAAAGAAAGATTAAAAATTACCCACTTCCAA
34445945 CATGAAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (32 bp):
AAAAAGAAAGATTAAAAATTACCCACTTCCAA
Found at i:34450717 original size:15 final size:15
Alignment explanation
Indices: 34450697--34450726 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34450687 AAAAAAAAGA
34450697 AAAATAAACAATAAT
1 AAAATAAACAATAAT
34450712 AAAATAAACAATAAT
1 AAAATAAACAATAAT
34450727 TAAAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAAACAATAAT
Found at i:34452258 original size:24 final size:24
Alignment explanation
Indices: 34452210--34452256 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
34452200 ACTGGTCATA
*
34452210 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
34452234 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
34452257 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:34452888 original size:27 final size:27
Alignment explanation
Indices: 34452858--34453185 Score: 404
Period size: 27 Copynumber: 12.1 Consensus size: 27
34452848 TTACACTTTT
* * *
34452858 ATGACCGATATGCCCCCATAGGATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
34452885 ATGACTGAAATACCCTCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
34452912 ATGACTGAAATACCCCCATATGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
34452939 ATAACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
34452966 ATGACCGAAATACCTCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** * *
34452993 ATGACTAAAATACCCCTAGAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
34453020 ATAACCGAAATACCCCCATAGCGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** *
34453047 ATGACTAAAATACTCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* **
34453074 ATGACCAAAATACCCCCATAATGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
34453101 ATGATCGAAATAGCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
34453128 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
34453155 ATGACCGAAATGCCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
34453182 ATGA
1 ATGA
34453186 GTGTTATACC
Statistics
Matches: 258, Mismatches: 43, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 258 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:34453463 original size:18 final size:18
Alignment explanation
Indices: 34453437--34453482 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
34453427 ACTAGCAGTT
*
34453437 GTGCTGCAATATTGTTTA
1 GTGCCGCAATATTGTTTA
34453455 GTGCCGCAATATTGTTTA
1 GTGCCGCAATATTGTTTA
*
34453473 GTGTCGCAAT
1 GTGCCGCAAT
34453483 CGGTGCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (18 bp):
GTGCCGCAATATTGTTTA
Found at i:34455453 original size:24 final size:24
Alignment explanation
Indices: 34455405--34455451 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
34455395 ACAAGTAATA
*
34455405 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
34455429 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
34455452 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:34455895 original size:21 final size:21
Alignment explanation
Indices: 34455869--34455910 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
34455859 GTGGGCCACG
*
34455869 TTGGGCCGAAATGGGTCGTGT
1 TTGGGCCGAAATGGGCCGTGT
34455890 TTGGGCCGAAATGGGCCGTGT
1 TTGGGCCGAAATGGGCCGTGT
34455911 AGGCTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.43, T:0.26
Consensus pattern (21 bp):
TTGGGCCGAAATGGGCCGTGT
Found at i:34456638 original size:24 final size:26
Alignment explanation
Indices: 34456580--34456638 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
34456570 TATTCCTTAT
34456580 TTTAGTTA-CTCAACTGTATATATTTA
1 TTTA-TTAGCTCAACTGTATATATTTA
**
34456606 TTT-CGAGCTCAACT-TATATA-TTA
1 TTTATTAGCTCAACTGTATATATTTA
34456629 TTTATTAGCT
1 TTTATTAGCT
34456639 TACACATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
23 6 0.22
24 11 0.41
25 7 0.26
26 3 0.11
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (26 bp):
TTTATTAGCTCAACTGTATATATTTA
Found at i:34463939 original size:19 final size:19
Alignment explanation
Indices: 34463915--34463963 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
34463905 TGGTCTATGT
*
34463915 AGGGTCCAATTTTTGACCC
1 AGGGTCCAATTTTTGACCA
34463934 AGGGTCCAATTTTTGACCA
1 AGGGTCCAATTTTTGACCA
*
34463953 AGGGCCCAATT
1 AGGGTCCAATT
34463964 ACAAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (19 bp):
AGGGTCCAATTTTTGACCA
Found at i:34465107 original size:3 final size:3
Alignment explanation
Indices: 34465099--34465143 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
34465089 GTGCTATCAT
** * *
34465099 TTA TTA TTA TTA TTA TTA TTA TTA GCA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34465144 AATACTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:34489323 original size:27 final size:27
Alignment explanation
Indices: 34489293--34489470 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34489283 ATATTGAGTC
* * * *
34489293 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
34489320 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34489347 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
34489375 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
34489402 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
34489429 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34489456 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34489471 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:34489432 original size:82 final size:81
Alignment explanation
Indices: 34489314--34489469 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34489304 TGCTATATAA
* *
34489314 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
34489379 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
34489396 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
34489460 CACTTAGTGC
65 CACTTAGTGC
34489470 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:34499444 original size:27 final size:27
Alignment explanation
Indices: 34499413--34499503 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
34499403 TATTACGAGA
*
34499413 GTAAAACAATAAGTATTTTTATGGTTT
1 GTAAAATAATAAGTATTTTTATGGTTT
** * *
34499440 GTAAAATAATGAACAATTATATTACGAG--A
1 GTAAAATAAT-AAGTATT-T-TTATG-GTTT
34499469 GTAAAATAATAAGTATTTTTATGGTTT
1 GTAAAATAATAAGTATTTTTATGGTTT
34499496 GTAAAATA
1 GTAAAATA
34499504 TTGAAATAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 18 0.37
28 10 0.20
29 11 0.22
30 4 0.08
31 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.38
Consensus pattern (27 bp):
GTAAAATAATAAGTATTTTTATGGTTT
Found at i:34499462 original size:56 final size:56
Alignment explanation
Indices: 34499397--34499508 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
34499387 TACTTTAAGT
34499397 CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
1 CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
* *
34499453 CAATTATATTACGAGAGTAAAATAATAAGTATTTTTATGGTTTGTAAAATATTGAA
1 CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
34499509 ATAAAATATC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (56 bp):
CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
Found at i:34519386 original size:20 final size:20
Alignment explanation
Indices: 34519361--34519400 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34519351 AGCTGGGAGA
34519361 TAGCTTCCCATAGATGATTT
1 TAGCTTCCCATAGATGATTT
34519381 TAGCTTCCCATAGATGATTT
1 TAGCTTCCCATAGATGATTT
34519401 CATTCCCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
TAGCTTCCCATAGATGATTT
Found at i:34520441 original size:26 final size:28
Alignment explanation
Indices: 34520411--34520480 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
34520401 AGTAAACACA
* *
34520411 AAACATAGATAG-TTC-ACTGAGACAGT
1 AAACATAGATAGAGTCTACCGAGACAGT
* *
34520437 AAACACAAATAGAGTCTACCGAGACAGT
1 AAACATAGATAGAGTCTACCGAGACAGT
34520465 AAACATAGGATA-AGTC
1 AAACATA-GATAGAGTC
34520481 CGATGGGATG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 10 0.29
27 2 0.06
28 20 0.57
29 3 0.09
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (28 bp):
AAACATAGATAGAGTCTACCGAGACAGT
Found at i:34523993 original size:19 final size:19
Alignment explanation
Indices: 34523944--34523993 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
34523934 CTTATAGAGT
* *
34523944 TTCAATTTTTTTATATTAT
1 TTCAATTTTTATATATTAA
*
34523963 TTTAATAGTTTTATATATTAA
1 TTCAAT--TTTTATATATTAA
34523984 TTCAATTTTT
1 TTCAATTTTT
34523994 TATTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.36
21 16 0.64
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTCAATTTTTATATATTAA
Found at i:34524935 original size:2 final size:2
Alignment explanation
Indices: 34524928--34524986 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
34524918 CCTACAATAA
* *
34524928 AC AC AC AC AC AC AC AT AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34524970 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
34524987 TAATAACATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:34527418 original size:73 final size:73
Alignment explanation
Indices: 34527341--34527477 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
34527331 GCCAAGCTAT
* * * * *
34527341 TTGATGTGTTGACATAAAGGTTTAGCCCAGACGGGTAA-CTTGACATGATTGTATGTTCAGCTTG
1 TTGATGTATCGACATAAAGGTTTAGCCCAGACAGGTAATCTT-ACATGATTATATGATCAGCTTG
34527405 AACGAGGAA
65 AACGAGGAA
**
34527414 TTGATGTATCGGTATAAAGGTTTAGCCCAGACAGGTAATCTTACATGATTATATGATCAGCTTG
1 TTGATGTATCGACATAAAGGTTTAGCCCAGACAGGTAATCTTACATGATTATATGATCAGCTTG
34527478 GACAAACCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 53 0.95
74 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (73 bp):
TTGATGTATCGACATAAAGGTTTAGCCCAGACAGGTAATCTTACATGATTATATGATCAGCTTGA
ACGAGGAA
Found at i:34529718 original size:17 final size:17
Alignment explanation
Indices: 34529666--34529729 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 17
34529656 AACAATTTAA
34529666 TTTTTTTCTTTTATGTTT-
1 TTTTTTTC-TTTAT-TTTC
* *
34529684 TTTTTTCACTTTCCTTTTC
1 TTTTTT-TCTTT-ATTTTC
34529703 TTTTTTTCTTTATTTTC
1 TTTTTTTCTTTATTTTC
*
34529720 -TATTTTCTTT
1 TTTTTTTCTTT
34529730 TACTTCTCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 9 0.24
17 5 0.13
18 16 0.42
19 8 0.21
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTTATTTTC
Found at i:34532193 original size:21 final size:18
Alignment explanation
Indices: 34532159--34532212 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
34532149 ACACCACATA
34532159 GTGGATAAAACCACTCATCGTT
1 GTGGAT-AAACCACTCA---TT
*
34532181 GTGGATGAACCACTCATT
1 GTGGATAAACCACTCATT
34532199 GTGGATAAACCACT
1 GTGGATAAACCACT
34532213 AGTAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 15 0.50
21 9 0.30
22 6 0.20
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (18 bp):
GTGGATAAACCACTCATT
Found at i:34532495 original size:34 final size:35
Alignment explanation
Indices: 34532438--34532533 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 35
34532428 ATCATTTAAT
* * *
34532438 TATGCTTTTAACAGAAC-AGTACAGTAGC-AATCAA
1 TATGCTTATAACAGATCAACTACAGTAGCAAAT-AA
* *
34532472 TATGCTTATAATAGTTCAA-TACAGTAGCAAATAA
1 TATGCTTATAACAGATCAACTACAGTAGCAAATAA
34532506 TATGCTTATAACAGATCAACT-CAGTAGC
1 TATGCTTATAACAGATCAACTACAGTAGC
34532534 CAAAAGTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 48 0.91
35 5 0.09
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (35 bp):
TATGCTTATAACAGATCAACTACAGTAGCAAATAA
Found at i:34532838 original size:27 final size:27
Alignment explanation
Indices: 34532789--34532883 Score: 99
Period size: 27 Copynumber: 3.6 Consensus size: 27
34532779 GGTAAAACTA
34532789 TAAAATCT--AAAA-AAGGGAAAATTG
1 TAAAATCTGAAAAATAAGGGAAAATTG
*
34532813 TAAAATTTGAAAAATAAGGGAAAATTAG
1 TAAAATCTGAAAAATAAGGGAAAATT-G
* ***
34532841 -AAAATCTAAAAAATAAGGGTAAAACCA
1 TAAAATCTGAAAAATAAGGG-AAAATTG
34532868 TAAAATCTGAAAAATA
1 TAAAATCTGAAAAATA
34532884 GGAGACGCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 7 0.12
26 4 0.07
27 28 0.48
28 19 0.33
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (27 bp):
TAAAATCTGAAAAATAAGGGAAAATTG
Found at i:34538598 original size:44 final size:44
Alignment explanation
Indices: 34538540--34538626 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
34538530 TGAACTAAAA
* * * *
34538540 TAGAAGTTGTGATAATTATACATTTAAAAATAACTATAATTTAG
1 TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTAG
34538584 TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTA
1 TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTA
34538627 AAATACAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.38
Consensus pattern (44 bp):
TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTAG
Found at i:34539802 original size:8 final size:8
Alignment explanation
Indices: 34539789--34539815 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
34539779 CAAGTTCGAG
34539789 TATTTTAA
1 TATTTTAA
34539797 TATTTTAA
1 TATTTTAA
34539805 TATTTTAA
1 TATTTTAA
34539813 TAT
1 TAT
34539816 AAGATGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:34540026 original size:31 final size:31
Alignment explanation
Indices: 34539991--34540049 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
34539981 CATTAATTTT
*
34539991 GTTCAATTATAAACATGAAAA-TTTGATTATA
1 GTTCAAATATAAACAT-AAAATTTTGATTATA
*
34540022 GTTCAAATGTAAACATAAAATTTTGATT
1 GTTCAAATATAAACATAAAATTTTGATT
34540050 TTAATTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (31 bp):
GTTCAAATATAAACATAAAATTTTGATTATA
Found at i:34551315 original size:18 final size:18
Alignment explanation
Indices: 34551281--34551315 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34551271 AATAAATGGA
*
34551281 AGGGCAAGAACATGAGGC
1 AGGGCAAGAACAGGAGGC
*
34551299 AGGGCAAGAGCAGGAGG
1 AGGGCAAGAACAGGAGG
34551316 AGTGATGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.46, T:0.03
Consensus pattern (18 bp):
AGGGCAAGAACAGGAGGC
Found at i:34555804 original size:13 final size:13
Alignment explanation
Indices: 34555786--34555810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34555776 ATTTACAAGA
34555786 TTACATAATCAAT
1 TTACATAATCAAT
34555799 TTACATAATCAA
1 TTACATAATCAA
34555811 ATTCAATCTA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:34556712 original size:215 final size:215
Alignment explanation
Indices: 34556334--34556762 Score: 777
Period size: 215 Copynumber: 2.0 Consensus size: 215
34556324 TCCTTTCTTC
*
34556334 AAAACTTTAAAAGGGCCTCTACATTCTTGTCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
1 AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
* * *
34556399 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTGTCCAACTTACATTACCACTTTCTT
66 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
* *
34556464 GGAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATTCGATGTGTTAATAGAAGTGA
131 GAAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATCCGATGTGTTAATAGAAGTGA
34556529 GCCTAATTGATCCTAGCTTA
196 GCCTAATTGATCCTAGCTTA
34556549 AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
1 AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
34556614 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
66 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
* *
34556679 GAAGTTTGATGCACAACCCACCTCTCTCATAGGTGGTAGCTCCTCCGATGTGTTAATAGAAGTGA
131 GAAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATCCGATGTGTTAATAGAAGTGA
*
34556744 GCCTCATTGATCCTAGCTT
196 GCCTAATTGATCCTAGCTT
34556763 CAAAGTTTGT
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
215 205 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (215 bp):
AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
GAAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATCCGATGTGTTAATAGAAGTGA
GCCTAATTGATCCTAGCTTA
Found at i:34565747 original size:12 final size:10
Alignment explanation
Indices: 34565717--34565759 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
34565707 AATATGAACA
*
34565717 TGATGAATTT
1 TGATTAATTT
*
34565727 TAATTAATTT
1 TGATTAATTT
34565737 TGTAGTTAATTT
1 TG-A-TTAATTT
34565749 TGATTAATTT
1 TGATTAATTT
34565759 T
1 T
34565760 TACTATTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 17 0.61
11 2 0.07
12 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (10 bp):
TGATTAATTT
Found at i:34569629 original size:39 final size:40
Alignment explanation
Indices: 34569584--34569715 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
34569574 GCTCCTCGTT
* * *
34569584 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
34569624 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
34569663 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
34569703 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
34569716 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 34 0.43
40 46 0.57
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:34569777 original size:41 final size:41
Alignment explanation
Indices: 34569700--34569777 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
34569690 TTAGTATCTC
* * *
34569700 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
34569741 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
34569778 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:34575424 original size:23 final size:23
Alignment explanation
Indices: 34575397--34575518 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
34575387 AGTGTTATTG
34575397 ATCAGTGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
* *
34575419 ATTCAGTGGTAGCTACGGTTACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
34575443 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
34575466 TTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
34575489 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
34575512 ATCAGTG
1 ATCAGTG
34575519 TGGCACTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 84 0.98
24 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:34575464 original size:46 final size:46
Alignment explanation
Indices: 34575397--34575518 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
34575387 AGTGTTATTG
**
34575397 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
* *
34575443 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
34575489 ATCAGTGGTAGCTTCGGCTAC-ATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACAAT-TCAGTG
34575519 TGGCACTCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.01
46 69 0.99
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
Found at i:34575835 original size:104 final size:104
Alignment explanation
Indices: 34575655--34575862 Score: 407
Period size: 104 Copynumber: 2.0 Consensus size: 104
34575645 AATTGAATTG
34575655 AATAGTGATCGAAAGTGAAAAAGTGAAATTATGAAATAGTAGAATTAGCAACAAAATAGTTTTGG
1 AATAGTGATCGAAAGTGAAAAAGTGAAATTATGAAATAGTAGAATTAGCAACAAAATAGTTTTGG
34575720 ACAGAAACAGTTGTGTGACTTTGAAAAATCACCAAAAAT
66 ACAGAAACAGTTGTGTGACTTTGAAAAATCACCAAAAAT
34575759 AATAGTGATCGAAAGTGAAAAAGTGAAATTATGAAATAGTAGAATTAGCAACAAAATAGTTTTGG
1 AATAGTGATCGAAAGTGAAAAAGTGAAATTATGAAATAGTAGAATTAGCAACAAAATAGTTTTGG
*
34575824 ACAGAAACAGTTGTGTGACTTTGAAAAATCACCATAAAT
66 ACAGAAACAGTTGTGTGACTTTGAAAAATCACCAAAAAT
34575863 CGTATGAATC
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (104 bp):
AATAGTGATCGAAAGTGAAAAAGTGAAATTATGAAATAGTAGAATTAGCAACAAAATAGTTTTGG
ACAGAAACAGTTGTGTGACTTTGAAAAATCACCAAAAAT
Found at i:34582928 original size:8 final size:8
Alignment explanation
Indices: 34582892--34582941 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
34582882 ACCCGACTAT
34582892 TTCTTTTC
1 TTCTTTTC
*
34582900 CT-TTTTC
1 TTCTTTTC
*
34582907 TT-TCTTC
1 TTCTTTTC
34582914 TTCTTTTC
1 TTCTTTTC
*
34582922 TTATTTTC
1 TTCTTTTC
34582930 TTCTTTT-
1 TTCTTTTC
34582937 TTCTT
1 TTCTT
34582942 CTTTATCTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
7 17 0.49
8 18 0.51
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:34584062 original size:22 final size:22
Alignment explanation
Indices: 34584014--34584066 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
34584004 AGTATTCTTG
34584014 TATATT-TTTTTCTAATTTTCC
1 TATATTCTTTTTCTAATTTTCC
*
34584035 T-T-TTCTTTTTCT-ATTATTCT
1 TATATTCTTTTTCTAATT-TTCC
34584055 TATATTCTTTTT
1 TATATTCTTTTT
34584067 TCTTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 2 0.07
22 8 0.30
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (22 bp):
TATATTCTTTTTCTAATTTTCC
Found at i:34589514 original size:31 final size:29
Alignment explanation
Indices: 34589435--34589516 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 29
34589425 GGTTTGCTGC
*
34589435 TGTTGGGTCTGATAGGTT-GGTCTACTGT
1 TGTTGGGTCTGATGGGTTGGGTCTACTGT
*
34589463 TGTTGGG-CTGACTGGATTGGGCTACTACTGT
1 TGTTGGGTCTGA-TGGGTTGGG-T-CTACTGT
*
34589494 TGTTGGGTCTGTTGGGTTGGGTC
1 TGTTGGGTCTGATGGGTTGGGTC
34589517 GCTTTTGGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
27 4 0.09
28 11 0.24
29 3 0.07
30 2 0.04
31 22 0.49
32 3 0.07
ACGTcount: A:0.09, C:0.12, G:0.39, T:0.40
Consensus pattern (29 bp):
TGTTGGGTCTGATGGGTTGGGTCTACTGT
Found at i:34589595 original size:10 final size:10
Alignment explanation
Indices: 34589577--34589636 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
34589567 CGATTATTTC
*
34589577 TCTTCCTTTT
1 TCTTTCTTTT
34589587 TCTTTCTTTTT
1 TCTTTC-TTTT
34589598 TCTTTCTTCTT
1 TCTTTCTT-TT
*
34589609 T-TTTTTATTT
1 TCTTTCT-TTT
*
34589619 TCTTCCTTTT
1 TCTTTCTTTT
34589629 TC-TTCTTT
1 TCTTTCTTT
34589637 ATCTCTTTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 5 0.12
10 19 0.46
11 17 0.41
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (10 bp):
TCTTTCTTTT
Found at i:34589599 original size:11 final size:11
Alignment explanation
Indices: 34589573--34589629 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
34589563 GACCCGATTA
*
34589573 TTTCTCTTCCTT
1 TTTCT-TTCTTT
34589585 TTTCTTTCTTT
1 TTTCTTTCTTT
34589596 TTTCTTTCTTCT
1 TTTCTTTCTT-T
*
34589608 TTT-TTT-TAT
1 TTTCTTTCTTT
*
34589617 TTTCTTCCTTT
1 TTTCTTTCTTT
34589628 TT
1 TT
34589630 CTTCTTTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 4 0.11
10 3 0.08
11 22 0.58
12 9 0.24
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:34589613 original size:17 final size:17
Alignment explanation
Indices: 34589582--34589636 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
34589572 ATTTCTCTTC
34589582 CTTT-TTCTTTCTTTTTT
1 CTTTCTTCTTT-TTTTTT
34589599 CTTTCTTCTTTTTTTTAT
1 CTTTCTTCTTTTTTTT-T
* *
34589617 -TTTCTTCCTTTTTCTT
1 CTTTCTTCTTTTTTTTT
34589633 CTTT
1 CTTT
34589637 ATCTCTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 1 0.03
17 25 0.76
18 7 0.21
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
CTTTCTTCTTTTTTTTT
Found at i:34589613 original size:27 final size:27
Alignment explanation
Indices: 34589583--34589636 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
34589573 TTTCTCTTCC
**
34589583 TTTTT-CTTTCTTTTTTCTTTCTTCTTT
1 TTTTTACTTTCTTCCTT-TTTCTTCTTT
*
34589610 TTTTTATTTTCTTCCTTTTTCTTCTTT
1 TTTTTACTTTCTTCCTTTTTCTTCTTT
34589637 ATCTCTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTACTTTCTTCCTTTTTCTTCTTT
Found at i:34589619 original size:21 final size:22
Alignment explanation
Indices: 34589570--34589632 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
34589560 TCGGACCCGA
34589570 TTATTTCTCTTCCTTTTTCTTTC
1 TTATTT-TCTTCCTTTTTCTTTC
*
34589593 TT-TTTTCTTTCTTCTTT-TTT-
1 TTATTTTCTTCCTT-TTTCTTTC
34589613 TTATTTTCTTCCTTTTTCTT
1 TTATTTTCTTCCTTTTTCTT
34589633 CTTTATCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 5 0.14
21 22 0.63
22 6 0.17
23 2 0.06
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTTTCTTCCTTTTTCTTTC
Found at i:34589631 original size:24 final size:24
Alignment explanation
Indices: 34589577--34589632 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
34589567 CGATTATTTC
*
34589577 TCTTCCTTTTTCTTTCTTTTTTCTT
1 TCTT-CTTTTTCTTTATTTTTTCTT
34589602 TCTTCTTTTT-TTTATTTTCTTCCTT
1 TCTTCTTTTTCTTTATTTT-TT-CTT
34589627 T-TTCTT
1 TCTTCTT
34589633 CTTTATCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 7 0.25
24 13 0.46
25 8 0.29
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TCTTCTTTTTCTTTATTTTTTCTT
Found at i:34590686 original size:30 final size:30
Alignment explanation
Indices: 34590623--34590725 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
34590613 CAAAGCTCCA
*
34590623 AGGGCTAAAATGTAATTTTAGAAAAAAA-G
1 AGGGCCAAAATGTAATTTTAGAAAAAAATG
34590652 -GGGCCAAAATGT-ATTTTCAGAAAAAAATG
1 AGGGCCAAAATGTAATTTT-AGAAAAAAATG
*
34590681 AGGGCCAAAATGTAATTTTAG-AAAAATTG
1 AGGGCCAAAATGTAATTTTAGAAAAAAATG
34590710 AGGGGCCAAAATGTAA
1 A-GGGCCAAAATGTAA
34590726 ATAGTATTCT
Statistics
Matches: 67, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
27 5 0.07
28 20 0.30
29 9 0.13
30 28 0.42
31 5 0.07
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.23
Consensus pattern (30 bp):
AGGGCCAAAATGTAATTTTAGAAAAAAATG
Found at i:34591363 original size:40 final size:40
Alignment explanation
Indices: 34591331--34591768 Score: 473
Period size: 40 Copynumber: 10.9 Consensus size: 40
34591321 CACACCAGAT
* * * * *
34591331 AAAAGCTCGTAACAGCTAATCCAACCGAAACACGCCGAGC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * * * *
34591371 AAAAGCTCATAAGAGCTGATCTAATCAAAACATGCCAAAT
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * *
34591411 AGAAGCTTATAAGAGCTGATCCAACCGAAACATGCCAAAC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * * *
34591451 AAAAGCTCATAAGAGCTGATCCACCCAAAACATGCGAAAC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
*
34591491 AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* *
34591531 AGAAGCTCATAAGAGCTGATCCACCCGAAACACGCCAAAC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* *
34591571 AAAAGCTCATAAGAGCTGATCCAACCAAAACACACCAAAC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * * * * *
34591611 AAAAGCTCATTAGAACTGGTCC-ACCTAAAACACGCTAGAC
1 AAAAGCTCATAAGAGCTGATCCAACC-GAAACACGCCAAAC
* * * * * *
34591651 AGATGCTCATAAGAGTTGATCCAACCGAAACACACAAAAT
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * ** *
34591691 AGAAGCTCGTAAGATTTGATTCAACCGAAACACGCCAAAC
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * * *
34591731 AGAAGCTCATAAGAGCTGGTCCAACCAAAACACACCAA
1 AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAA
34591769 CTACAGAGTA
Statistics
Matches: 334, Mismatches: 62, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
39 3 0.01
40 328 0.98
41 3 0.01
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (40 bp):
AAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
Found at i:34597125 original size:13 final size:13
Alignment explanation
Indices: 34597074--34597126 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
34597064 AGTTCTTCAT
*
34597074 TGCTTTTGAAAAG
1 TGCTTTTCAAAAG
* ** *
34597087 TGCTGTGGAAAAA
1 TGCTTTTCAAAAG
34597100 TGCTTTTCAAAAG
1 TGCTTTTCAAAAG
34597113 TGCTTTTCAAAAG
1 TGCTTTTCAAAAG
34597126 T
1 T
34597127 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (13 bp):
TGCTTTTCAAAAG
Found at i:34599332 original size:27 final size:27
Alignment explanation
Indices: 34599278--34599491 Score: 281
Period size: 27 Copynumber: 8.0 Consensus size: 27
34599268 GGGTATAATA
34599278 GTCATTTTACCCTAT-G-GGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
34599304 GTCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
34599331 GTCA-TTTACCCTTTCAAGGGTATTTTG
1 GTCATTTTACCC-TTCGAGGGTATTTCG
* * *
34599358 GTTATTTTACCCTTTGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
34599385 ATCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
34599412 ATCATTTTACCCTTCAAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
34599439 GTCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
34599466 TTCATTTTACCCTTCGAGGGTATTTC
1 GTCATTTTACCCTTCGAGGGTATTTC
34599492 AGTTATTTGC
Statistics
Matches: 169, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
25 1 0.01
26 21 0.12
27 140 0.83
28 7 0.04
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:34608595 original size:19 final size:19
Alignment explanation
Indices: 34608567--34608622 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
34608557 CGGGTTTATT
*
34608567 CACTTCGTGTGCTAGTATG
1 CACTTTGTGTGCTAGTATG
*
34608586 CACTTTGTGTG-TCAATATG
1 CACTTTGTGTGCT-AGTATG
* *
34608605 CACTATATGTGCTAGTAT
1 CACTTTGTGTGCTAGTAT
34608623 ATTTGCTCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (19 bp):
CACTTTGTGTGCTAGTATG
Found at i:34608663 original size:43 final size:43
Alignment explanation
Indices: 34608602--34608690 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
34608592 GTGTGTCAAT
* *
34608602 ATGCACTATATGTGCTAGTATATTTGCTCCGGTTAGTCTGATG
1 ATGCACTATATGTGCTAGTATACTTGCTCCGGTTAGTCTAATG
* * *
34608645 ATGCACTATGTGTGCTAGTGTACTTGCTCCGGTTTGTCTAATG
1 ATGCACTATATGTGCTAGTATACTTGCTCCGGTTAGTCTAATG
34608688 ATG
1 ATG
34608691 TAATAGCCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (43 bp):
ATGCACTATATGTGCTAGTATACTTGCTCCGGTTAGTCTAATG
Found at i:34624238 original size:20 final size:18
Alignment explanation
Indices: 34624195--34624256 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 18
34624185 AATATTCTAG
34624195 ATATCAAAAT-AAAACAA
1 ATATCAAAATAAAAACAA
34624212 A-AT-AAAATAAAAAGTCAA
1 ATATCAAAATAAAAA--CAA
34624230 ATATCAAAATAGAAAAACAA
1 ATATCAAAAT--AAAAACAA
34624250 ATATCAA
1 ATATCAA
34624257 TAGTATAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.13
16 6 0.16
17 1 0.03
18 4 0.11
19 2 0.05
20 15 0.39
22 5 0.13
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (18 bp):
ATATCAAAATAAAAACAA
Found at i:34626531 original size:42 final size:43
Alignment explanation
Indices: 34626443--34626566 Score: 187
Period size: 42 Copynumber: 2.9 Consensus size: 43
34626433 GCGTTTACAG
* * * *
34626443 AAAAAATGCCGCTAAAGGTCATGTTTTTTAACGGCGCTTCGAA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGAA
*
34626486 AAAAAACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTCG-A
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGAA
*
34626528 AAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
34626567 AAAAAATCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 38 0.51
43 36 0.49
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGAA
Found at i:34626610 original size:63 final size:63
Alignment explanation
Indices: 34626510--34626632 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
34626500 AAGATCATGT
*
34626510 TCTTTAGCGGCGCTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAAAAA
1 TCTTTAGCGGCACTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAAAAA
* *
34626573 TCTTTAGCGGCACTTTC-AAAAAAACGCCGCTAGAGATCATGTTCTTTAGCGGCGCTTAAA
1 TCTTTAGCGGCAC-TTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAA
34626633 GAAAAACGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 53 0.95
64 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (63 bp):
TCTTTAGCGGCACTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAAAAA
Found at i:34626638 original size:42 final size:41
Alignment explanation
Indices: 34626573--34626713 Score: 183
Period size: 42 Copynumber: 3.4 Consensus size: 41
34626563 GCTTAAAAAA
* * *
34626573 TCTTTAGCGGCACTTTCAAAAAAACGCCGCTAGAGATCATGT
1 TCTTTAGCGGCGC-TTAAAAAAAACGCCGCTAAAGATCATGT
*
34626615 TCTTTAGCGGCGCTTAAAGAAAAACGCCGCTAAAGATCATAT
1 TCTTTAGCGGCGCTTAAA-AAAAACGCCGCTAAAGATCATGT
** * *
34626657 TCTTTAGCGGCGCTTGGTAAAAAACGCCTCTATAGATCATGT
1 TCTTTAGCGGCGCTT-AAAAAAAACGCCGCTAAAGATCATGT
34626699 TCTTTAGCGGCGCTT
1 TCTTTAGCGGCGCTT
34626714 TCATCACAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 4 0.05
42 83 0.94
43 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGATCATGT
Found at i:34626710 original size:147 final size:147
Alignment explanation
Indices: 34626443--34626713 Score: 409
Period size: 147 Copynumber: 1.8 Consensus size: 147
34626433 GCGTTTACAG
* * * *
34626443 AAAAAATGCCGCTAAAGGTCATGTTTTTTAACGGCGCTTCGAAAAAAAACGTCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTC-AAAAAAAACGCCGCTAAAGATCAT
*
34626508 GTTCTTTAGCGGCGCTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAAAAA
65 ATTCTTTAGCGGCGCTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAAAAA
34626573 TCTTTAGCGGCACTTTCA
130 TCTTTAGCGGCACTTTCA
* *
34626591 AAAAAACGCCGCTAGAGATCATGTTCTTTAGCGGCGCTT-AAAGAAAAACGCCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTCAAA-AAAAACGCCGCTAAAGATCAT
* * * * *
34626655 ATTCTTTAGCGGCGCTTGGTAAAAAACGCCTCTATAGATCATGTTCTTTAGCGGCGCTT
65 ATTCTTTAGCGGCGCTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTT
34626714 TCATCACAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
146 3 0.03
147 73 0.66
148 34 0.31
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (147 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTCAAAAAAAACGCCGCTAAAGATCATA
TTCTTTAGCGGCGCTTCGAAAAAAACGCCGCTAAAGATCATGATCTTTAGCGGCGCTTAAAAAAT
CTTTAGCGGCACTTTCA
Found at i:34626768 original size:43 final size:42
Alignment explanation
Indices: 34626573--34626772 Score: 152
Period size: 42 Copynumber: 4.7 Consensus size: 42
34626563 GCTTAAAAAA
* ** * * * *
34626573 TCTTTAGCGGCACTTTCAAAAAAACGCCGCTAGAGATCATGT
1 TCTTTAGCGGCGCTTTGTAAAAAACGCCACAAAAGATAATGT
** * * * *
34626615 TCTTTAGCGGCGC-TTAAAGAAAAACGCCGCTAAAGATCATAT
1 TCTTTAGCGGCGCTTTGTA-AAAAACGCCACAAAAGATAATGT
* * * * *
34626657 TCTTTAGCGGCGCTTGGTAAAAAACGCCTCTATAGATCATGT
1 TCTTTAGCGGCGCTTTGTAAAAAACGCCACAAAAGATAATGT
* * *
34626699 TCTTTAGCGGCGCTTTCATCACAAACGCCACGAAAAG-TAATGT
1 TCTTTAGCGGCGCTTT-GTAAAAAACGCCAC-AAAAGATAATGT
*
34626742 TCTTTAGTGGCGCTATTGTAAAAAACGCCAC
1 TCTTTAGCGGCGCT-TTGTAAAAAACGCCAC
34626773 TAATTTTGGG
Statistics
Matches: 131, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
41 4 0.03
42 81 0.62
43 41 0.31
44 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTTGTAAAAAACGCCACAAAAGATAATGT
Found at i:34627182 original size:21 final size:21
Alignment explanation
Indices: 34627158--34627227 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
34627148 GCTTCTCTCG
* *
34627158 CTGCTTCTCGCCCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
34627179 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
34627200 CTACTTCCCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
34627221 TTGCTTC
1 CTGCTTC
34627228 CCTCATTGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.06, C:0.43, G:0.17, T:0.34
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:34627228 original size:21 final size:21
Alignment explanation
Indices: 34627170--34627231 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
34627160 GCTTCTCGCC
*
34627170 CTGCAGCCTCTGCTTCTCTCG
1 CTGCAGCCTCTGCTTCCCTCG
* *
34627191 CTGTAGCCTCTACTTCCCTCG
1 CTGCAGCCTCTGCTTCCCTCG
*
34627212 CTGCAGCCTTTGCTTCCCTC
1 CTGCAGCCTCTGCTTCCCTC
34627232 ATTGCCACCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.06, C:0.44, G:0.16, T:0.34
Consensus pattern (21 bp):
CTGCAGCCTCTGCTTCCCTCG
Found at i:34629745 original size:9 final size:9
Alignment explanation
Indices: 34629728--34630053 Score: 272
Period size: 9 Copynumber: 37.3 Consensus size: 9
34629718 TCATAGATAA
*
34629728 GTAAATTAT
1 GTAAGTTAT
34629737 GTAAGTTAT
1 GTAAGTTAT
*
34629746 GTACGTGTA-
1 GTAAGT-TAT
34629755 -TAAGTTAT
1 GTAAGTTAT
34629763 GTAAGTTAT
1 GTAAGTTAT
*
34629772 GT-A-TTAA
1 GTAAGTTAT
*
34629779 GTAAGCTAT
1 GTAAGTTAT
*
34629788 GTAAGTTGT
1 GTAAGTTAT
34629797 GT-A-TTAT
1 GTAAGTTAT
34629804 GTAAGTTAT
1 GTAAGTTAT
34629813 GTAAGTTAT
1 GTAAGTTAT
** *
34629822 CAAAGTAAT
1 GTAAGTTAT
*
34629831 GTATGTTAT
1 GTAAGTTAT
34629840 GTAAG-T-T
1 GTAAGTTAT
34629847 GTAAGTTAT
1 GTAAGTTAT
*
34629856 -TATGTATTAT
1 GTAAG--TTAT
34629866 GTAAGTTAT
1 GTAAGTTAT
34629875 GTAAGTTAT
1 GTAAGTTAT
34629884 GTAAGTTAAAT
1 GTAAGTT--AT
34629895 GT-A-TTAT
1 GTAAGTTAT
*
34629902 GTAGGTTAT
1 GTAAGTTAT
*
34629911 GTAAGTTGT
1 GTAAGTTAT
*
34629920 GTAAGATAT
1 GTAAGTTAT
* *
34629929 TTAGGTTAT
1 GTAAGTTAT
*
34629938 GTAAGTTTT
1 GTAAGTTAT
34629947 GT-A-TTAT
1 GTAAGTTAT
34629954 GTAAGTTAT
1 GTAAGTTAT
34629963 GTAAGTTAT
1 GTAAGTTAT
34629972 GTAAGTTAAAT
1 GTAAGTT--AT
34629983 GT-A-TTAT
1 GTAAGTTAT
*
34629990 GTAGGTTAT
1 GTAAGTTAT
*
34629999 GTAAGTTGT
1 GTAAGTTAT
*
34630008 GTAAGATAT
1 GTAAGTTAT
* *
34630017 TTAAGTTAC
1 GTAAGTTAT
*
34630026 GTAAGTTTT
1 GTAAGTTAT
34630035 GT-A-TTAT
1 GTAAGTTAT
34630042 GTAAGTTAT
1 GTAAGTTAT
34630051 GTA
1 GTA
34630054 TGCTATGTAT
Statistics
Matches: 250, Mismatches: 43, Indels: 48
0.73 0.13 0.14
Matches are distributed among these distances:
7 36 0.14
8 17 0.07
9 178 0.71
10 8 0.03
11 11 0.04
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:34629799 original size:25 final size:25
Alignment explanation
Indices: 34629725--34630073 Score: 174
Period size: 25 Copynumber: 13.4 Consensus size: 25
34629715 TAATCATAGA
*
34629725 TAAGTAAATTATGTAAGTTATGTACGT
1 TAAGTAAGTTATGTAAGTTATGTA--T
34629752 GT-A-TAAGTTATGTAAGTTATGTAT
1 -TAAGTAAGTTATGTAAGTTATGTAT
* *
34629776 TAAGTAAGCTATGTAAGTTGTGTAT
1 TAAGTAAGTTATGTAAGTTATGTAT
* ** *
34629801 TATGTAAGTTATGTAAGTTATCAAAG
1 TAAGTAAGTTATGTAAGTTAT-GTAT
* *
34629827 TAATGTATGTTATGTAAGTTGTAAGTTAT
1 TAA-GTAAGTTATGTAAG-T-TATG-TAT
*
34629856 TATGT-A-TTATGTAAGTTATGTAAGT
1 TAAGTAAGTTATGTAAGTTATGT-A-T
*
34629881 TATGTAAGTTAAATGT-A-TTATGTAGGT
1 TAAGTAAGTT--ATGTAAGTTATGTA--T
* * * *
34629908 TATGTAAGTTGTGTAAGATATTTAGGT
1 TAAGTAAGTTATGTAAGTTATGTA--T
* *
34629935 TATGTAAGTTTTGT-A-TTATGTAAGT
1 TAAGTAAGTTATGTAAGTTATGT-A-T
*
34629960 TATGTAAGTTATGTAAGTTAAATGTAT
1 TAAGTAAGTTATGTAAGTT--ATGTAT
* * * *
34629987 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TAAGTAAGTTATGTAAGTTATGT-A-T
** * *
34630014 TATTTAAGTTACGTAAGTTTTGTAT
1 TAAGTAAGTTATGTAAGTTATGTAT
* * *
34630039 TATGTAAGTTATGTATGCTATGTAT
1 TAAGTAAGTTATGTAAGTTATGTAT
*
34630064 TACGTAAGTT
1 TAAGTAAGTT
34630074 GTTATTTTTA
Statistics
Matches: 259, Mismatches: 39, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.01
24 6 0.02
25 98 0.38
26 39 0.15
27 95 0.37
28 6 0.02
29 13 0.05
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (25 bp):
TAAGTAAGTTATGTAAGTTATGTAT
Found at i:34629962 original size:88 final size:88
Alignment explanation
Indices: 34629733--34630062 Score: 377
Period size: 88 Copynumber: 3.8 Consensus size: 88
34629723 GATAAGTAAA
* * * * * * * * *
34629733 TTATGTAAGTTATGTACG-TGTATAAGTTATGTAAGTTATGTATTAAGTAAGCTATGTAAGTTGT
1 TTATGTAAGTTGTGTAAGATATTTAAGTTACGTAAGTTTTGTATTATGTAAGTTATGTAAGTTAT
*
34629797 GT-A-TT--ATGTAAGTTATGTAAG
66 GTAAGTTAAATGT-A-TTATGTAGG
** ** * * *
34629818 TTATCAAAGTAATGTATGTTATGTAAGTT--GTAAGTTATTATGTATTATGTAAGTTATGTAAGT
1 TTATGTAAGTTGTGTAAGATATTTAAGTTACGTAAG-T-TT-TGTATTATGTAAGTTATGTAAGT
34629881 TATGTAAGTTAAATGTATTATGTAGG
63 TATGTAAGTTAAATGTATTATGTAGG
* *
34629907 TTATGTAAGTTGTGTAAGATATTTAGGTTATGTAAGTTTTGTATTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTGTGTAAGATATTTAAGTTACGTAAGTTTTGTATTATGTAAGTTATGTAAGTTAT
34629972 GTAAGTTAAATGTATTATGTAGG
66 GTAAGTTAAATGTATTATGTAGG
* *
34629995 TTATGTAAGTTGTGTAAGATATTTAAGTTACGTAAGTTTTGTATTATGTAAGTTATGTATGCTAT
1 TTATGTAAGTTGTGTAAGATATTTAAGTTACGTAAGTTTTGTATTATGTAAGTTATGTAAGTTAT
34630060 GTA
66 GTA
34630063 TTACGTAAGT
Statistics
Matches: 212, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
84 5 0.02
85 15 0.07
86 9 0.04
87 25 0.12
88 114 0.54
89 33 0.16
90 2 0.01
91 9 0.04
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.45
Consensus pattern (88 bp):
TTATGTAAGTTGTGTAAGATATTTAAGTTACGTAAGTTTTGTATTATGTAAGTTATGTAAGTTAT
GTAAGTTAAATGTATTATGTAGG
Found at i:34630209 original size:23 final size:23
Alignment explanation
Indices: 34630183--34630226 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
34630173 AAAAAATTAT
*
34630183 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
34630206 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
34630227 TACATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:34631295 original size:18 final size:18
Alignment explanation
Indices: 34631272--34631309 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
34631262 TTTCTTCAAA
34631272 AATATTAACACTGCAAGT
1 AATATTAACACTGCAAGT
34631290 AATATTAACACTGCAAGT
1 AATATTAACACTGCAAGT
34631308 AA
1 AA
34631310 CTAACAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (18 bp):
AATATTAACACTGCAAGT
Found at i:34632649 original size:365 final size:365
Alignment explanation
Indices: 34631974--34632683 Score: 1206
Period size: 365 Copynumber: 1.9 Consensus size: 365
34631964 TCGACATTTG
*
34631974 CGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGTGCCATTTCATAAA
1 CGGCATTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGTGCCATTTCATAAA
* *
34632039 AATATAAGGAAACATTCTGGCGTTTTCCCAAACACGCCACAATTAATATATTATCGAACCGGCGT
66 AATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCGC
** * *
34632104 CGTTTTCAGTAAATTTTATACATCCTTGCGGCATTTTTAATAAAACGCCACTAAAAGATTCCATC
131 CGTTTTCAAAAAATTTTATACATCCTTGCGACATTTATAATAAAACGCCACTAAAAGATTCCATC
*
34632169 CTTCAACTGAAACGGTGCCGTTTTCGCAAAGTTCAAATATTATTTACGCCGTTTTTAGGAAAAAC
196 CTTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTACGCCGTTTTTAGGAAAAAC
* *
34632234 GCCACAACTAAAATTTATTCCCTAAGCCGAAACGACACCGTATCGGTAAATGCAATAAATATTTG
261 GCCACAACTAAAACTTATTCCCTAAGCCGAAACAACACCGTATCGGTAAATGCAATAAATATTTG
34632299 TGGCATTTTTTATCAAAACGTAGGTAATGTCTACCTTTTA
326 TGGCATTTTTTATCAAAACGTAGGTAATGTCTACCTTTTA
*
34632339 CGGCATTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGTGCCATTTTATAAA
1 CGGCATTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGTGCCATTTCATAAA
34632404 AATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCGC
66 AATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCGC
* * *
34632469 CGTTTTCAAAAAATTTTATACATCCTTGCGACGTTTATAATAAAATGCCACTAAAATATTCCATC
131 CGTTTTCAAAAAATTTTATACATCCTTGCGACATTTATAATAAAACGCCACTAAAAGATTCCATC
* * * * *
34632534 CTTCAACTGAAACGGCGCTGTTTTGGCAAAGTTTAAATATTATTTACGGC-TCTTTTCGGAAAAA
196 CTTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTACGCCGT-TTTTAGGAAAAA
* *
34632598 CGCCACAACTAAAACTTATTCCCTAAGCCGAAACAACGCCGTATCGGTAAATGCAATAAATTTTT
260 CGCCACAACTAAAACTTATTCCCTAAGCCGAAACAACACCGTATCGGTAAATGCAATAAATATTT
*
34632663 GTGGCGTTTTTTATCAAAACG
325 GTGGCATTTTTTATCAAAACG
34632684 CCGCAAAATC
Statistics
Matches: 322, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
364 1 0.00
365 321 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (365 bp):
CGGCATTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGTGCCATTTCATAAA
AATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCGC
CGTTTTCAAAAAATTTTATACATCCTTGCGACATTTATAATAAAACGCCACTAAAAGATTCCATC
CTTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTACGCCGTTTTTAGGAAAAAC
GCCACAACTAAAACTTATTCCCTAAGCCGAAACAACACCGTATCGGTAAATGCAATAAATATTTG
TGGCATTTTTTATCAAAACGTAGGTAATGTCTACCTTTTA
Found at i:34632711 original size:4 final size:4
Alignment explanation
Indices: 34632702--34632731 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
34632692 TCTTACATAT
34632702 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
34632732 GTATCATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:34632768 original size:24 final size:23
Alignment explanation
Indices: 34632741--34632821 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 23
34632731 TGTATCATTC
34632741 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTAT-T
*
34632765 ATTTAAACAATTAATTACCTAAAAATT
1 ATTTAAATAATTAATTACCT----ATT
34632792 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTA-TT
34632817 ATTTA
1 ATTTA
34632822 TTTGCTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
24 25 0.51
25 2 0.04
27 1 0.02
28 21 0.43
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAAATAATTAATTACCTATT
Found at i:34632824 original size:28 final size:26
Alignment explanation
Indices: 34632741--34632824 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 26
34632731 TGTATCATTC
*
34632741 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
34632765 ATTTAAACAATTAATTACCTAAAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
34632793 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
34632821 ATTT
1 ATTT
34632825 GCTTATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 18 0.38
26 1 0.02
28 28 0.60
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:34633277 original size:14 final size:14
Alignment explanation
Indices: 34633258--34633297 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34633248 GATCCTAAAT
*
34633258 CCCTAACCCTTAAC
1 CCCTAAACCTTAAC
* *
34633272 CCCTAATCCATAAC
1 CCCTAAACCTTAAC
34633286 CCCTAAACCTTA
1 CCCTAAACCTTA
34633298 TTTAATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:34633558 original size:20 final size:21
Alignment explanation
Indices: 34633533--34633576 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34633523 ATCTTAAATT
*
34633533 AACCATATATA-TATACCCTA
1 AACCATATATATTAAACCCTA
*
34633553 AACCATATTTATTAAACCCTA
1 AACCATATATATTAAACCCTA
34633574 AAC
1 AAC
34633577 TATAATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (21 bp):
AACCATATATATTAAACCCTA
Done.