Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008922.1 Hibiscus syriacus cultivar Beakdansim tig00112226_pilon, whole genome shotgun sequence
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: 568381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:255237 original size:3 final size:3
Alignment explanation
Indices: 255229--255253 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
255219 TCTTCAGGGA
255229 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
255254 AGGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:255462 original size:24 final size:24
Alignment explanation
Indices: 255428--255481 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
255418 CCATCACATC
255428 ATCAAAATCCGACTATTGACCAAG
1 ATCAAAATCCGACTATTGACCAAG
* **
255452 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGACTATTGACCAAG
255476 ATCAAA
1 ATCAAA
255482 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGACTATTGACCAAG
Found at i:255495 original size:24 final size:24
Alignment explanation
Indices: 255428--255495 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
255418 CCATCACATC
* * *
255428 ATCAAAATCCGACTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
255452 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
255476 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
255496 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:255628 original size:12 final size:12
Alignment explanation
Indices: 255607--255640 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
255597 GGTTGTGGGT
*
255607 TTTGAGATTGTG
1 TTTGATATTGTG
255619 TTTGATATTGTG
1 TTTGATATTGTG
*
255631 TTTGGTATTG
1 TTTGATATTG
255641 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:256490 original size:20 final size:20
Alignment explanation
Indices: 256399--256494 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
256389 TGTGAAATTA
*
256399 AATTCGCGTTGCGAATTTGG
1 AATTCGCGTTGCGAAATTGG
** * **
256419 AATATCGCAATGCG-ATTTAC
1 AAT-TCGCGTTGCGAAATTGG
256439 ATATTCGCGTTGCGAAATTGG
1 A-ATTCGCGTTGCGAAATTGG
* *
256460 AAAAT-GGGTTGCGAAATTGG
1 -AATTCGCGTTGCGAAATTGG
256480 AATTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
256495 TTTGTTGGTC
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.05
20 39 0.67
21 15 0.26
22 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:263361 original size:20 final size:20
Alignment explanation
Indices: 263336--263380 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
263326 ATCATATCAA
263336 ATCAAGTTAAATTAAAACAC
1 ATCAAGTTAAATTAAAACAC
263356 ATCAAGTTAAATTAAAACAC
1 ATCAAGTTAAATTAAAACAC
263376 ATCAA
1 ATCAA
263381 ATTCTGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (20 bp):
ATCAAGTTAAATTAAAACAC
Found at i:263916 original size:21 final size:22
Alignment explanation
Indices: 263890--263934 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
263880 ATAATTCTTA
263890 AAAATTAAAAATTTAAATA-TT
1 AAAATTAAAAATTTAAATACTT
* * *
263911 AAAATTGATAATTTAGATACTT
1 AAAATTAAAAATTTAAATACTT
263933 AA
1 AA
263935 CACGTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATTAAAAATTTAAATACTT
Found at i:272385 original size:59 final size:60
Alignment explanation
Indices: 272322--272461 Score: 183
Period size: 60 Copynumber: 2.4 Consensus size: 60
272312 ATTGGATATG
* * * * * * *
272322 CAAAAGTTTAGGGATTAATTTAGAATGATATTCATAG-TTTGGTATGAAATTAGAATGTT
1 CAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTTTGGGATGAAATCAAAATGTT
*
272381 CAAAAGTTTAAGGACTGATTTAGAATGAAAGTCATAGTTTTGGGATGAAATCAAAATGTT
1 CAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTTTGGGATGAAATCAAAATGTT
* *
272441 TAAAAGTTTAAAGACTAATTT
1 CAAAAGTTTAAGGACTAATTT
272462 GAAATGAGGG
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 32 0.46
60 37 0.54
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (60 bp):
CAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTTTGGGATGAAATCAAAATGTT
Found at i:272449 original size:60 final size:59
Alignment explanation
Indices: 272322--272483 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 59
272312 ATTGGATATG
* * * * * * *
272322 CAAAAGTTTAGGGATTAATTTAGAATGATATTCATAGTTTGGTATGAAATTAGAATGTT
1 CAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTTGGGATGAAATCAAAATGTT
*
272381 CAAAAGTTTAAGGACTGATTTAGAATGAAAGTCATAGTTTTGGGATGAAATCAAAATGTT
1 CAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAG-TTTGGGATGAAATCAAAATGTT
* * ** *
272441 TAAAAGTTTAAAGACTAATTT-GAAATGAGGGCCATAGTTTGGG
1 CAAAAGTTTAAGGACTAATTTAG-AATGAAAGTCATAGTTTGGG
272484 GACATACGAT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 39 0.45
60 48 0.55
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (59 bp):
CAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTTGGGATGAAATCAAAATGTT
Found at i:275716 original size:2 final size:2
Alignment explanation
Indices: 275709--275740 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
275699 TTCATGCTTA
275709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
275741 GCTCAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276038 original size:2 final size:2
Alignment explanation
Indices: 276031--276057 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
276021 GCTTGACTAT
276031 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
276058 GAGATTCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:285774 original size:21 final size:23
Alignment explanation
Indices: 285750--285805 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
285740 TTATGATTAG
*
285750 AAATATTGATTTTGAG-TT-ATT
1 AAATATTGATTTTAAGTTTCATT
*
285771 AAATATAGATTTTAAGTTTCATT
1 AAATATTGATTTTAAGTTTCATT
*
285794 AATTATT-ATTTT
1 AAATATTGATTTT
285806 TTGAAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.48
22 7 0.24
23 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.54
Consensus pattern (23 bp):
AAATATTGATTTTAAGTTTCATT
Found at i:287497 original size:15 final size:15
Alignment explanation
Indices: 287477--287533 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
287467 ATTAGATAAT
287477 AAATAAAAAATTTAA
1 AAATAAAAAATTTAA
*
287492 AAAT--AAAATATAA
1 AAATAAAAAATTTAA
*
287505 AATATAAAAAAATTAA
1 AA-ATAAAAAATTTAA
*
287521 AAATTAAAAATTT
1 AAATAAAAAATTT
287534 TATAGTGCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 10 0.29
14 2 0.06
15 13 0.38
16 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAAAATTTAA
Found at i:287506 original size:20 final size:20
Alignment explanation
Indices: 287477--287514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
287467 ATTAGATAAT
*
287477 AAATAAAAAATTTAAAAATA
1 AAATAAAAAATATAAAAATA
*
287497 AAATATAAAATATAAAAA
1 AAATAAAAAATATAAAAA
287515 AATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAAAAAATATAAAAATA
Found at i:288733 original size:18 final size:19
Alignment explanation
Indices: 288697--288733 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
288687 TACGGAATGT
288697 AAGATTATCAGTAGGAATAA
1 AAGATTATCAG-AGGAATAA
288717 AAGATTATCAG-GGAATA
1 AAGATTATCAGAGGAATA
288734 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGAGGAATAA
Found at i:288958 original size:37 final size:38
Alignment explanation
Indices: 288884--288959 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
288874 CTTAGAAACT
* * *
288884 ATTTATATATTTTCTTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTATTTTAAAAAAATTAAAATCATAAA
*
288922 ATTTATATAATTTATTTT-ACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTATTTTAAAAAAATT-AAAATCATAAA
288959 A
1 A
288960 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 13 0.39
38 20 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (38 bp):
ATTTATATAATTTATTTTAAAAAAATTAAAATCATAAA
Found at i:289768 original size:15 final size:14
Alignment explanation
Indices: 289748--289799 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
289738 TTTGGCTCTC
289748 TAATATTTTATATTT
1 TAATATTTTAT-TTT
289763 TAATA-TTTATTTCT
1 TAATATTTTATTT-T
* *
289777 AGAATATTCTATTTT
1 -TAATATTTTATTTT
289792 TAATATTT
1 TAATATTT
289800 AAATAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 10 0.33
16 6 0.20
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (14 bp):
TAATATTTTATTTT
Found at i:294039 original size:2 final size:2
Alignment explanation
Indices: 294034--294068 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
294024 ACACACACAC
294034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
294069 GGTGGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:295828 original size:31 final size:31
Alignment explanation
Indices: 295801--295861 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
295791 ATATATGGGT
*
295801 ACTTTCGTTTTCATTTAATTAAGATATGATA
1 ACTTTCGTTTTCATTTAACTAAGATATGATA
* *
295832 ACTTTTGTTTTCATTTAACTAAGATGTGAT
1 ACTTTCGTTTTCATTTAACTAAGATATGAT
295862 CACTATGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (31 bp):
ACTTTCGTTTTCATTTAACTAAGATATGATA
Found at i:296945 original size:20 final size:21
Alignment explanation
Indices: 296920--296965 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
296910 TGATAATTTT
* *
296920 AAAAATTTTATTTA-AAATTA
1 AAAAATTATATATATAAATTA
*
296940 AAAAATTATATATATATATTA
1 AAAAATTATATATATAAATTA
296961 AAAAA
1 AAAAA
296966 AACACAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTATATATATAAATTA
Found at i:308658 original size:17 final size:18
Alignment explanation
Indices: 308636--308677 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
308626 ACTTAAAAAA
*
308636 TTAAAAAAATCAAATC-T
1 TTAAAAAAATCAAAACTT
*
308653 TTAAAAAAATTAAAACTT
1 TTAAAAAAATCAAAACTT
308671 TTAAAAA
1 TTAAAAA
308678 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAAATCAAAACTT
Found at i:319446 original size:18 final size:19
Alignment explanation
Indices: 319404--319443 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
319394 TTTGGTTCAC
319404 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
*
319424 GGAATGTAAGATTATCAGG
1 GGAATGTAAGATTACCAGG
319443 G
1 G
319444 AATATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:319711 original size:18 final size:18
Alignment explanation
Indices: 319688--319722 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
319678 TAATGAAAGG
319688 GTAAAATTTTATTTTAAT
1 GTAAAATTTTATTTTAAT
319706 GTAAAATTTTATTTTAA
1 GTAAAATTTTATTTTAA
319723 CCCTTGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
GTAAAATTTTATTTTAAT
Found at i:324183 original size:17 final size:17
Alignment explanation
Indices: 324154--324186 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
324144 AATTTTATTT
324154 ATATAAAATATAATATA
1 ATATAAAATATAATATA
324171 ATATGAAAA-ATAATAT
1 ATAT-AAAATATAATAT
324187 TGTGATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:325364 original size:60 final size:60
Alignment explanation
Indices: 325251--325366 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
325241 AATTATGATT
* * * * *
325251 ATAATTTTAAATTAGTCCTCAAACTCTTTAACATTTCAATTTCATCCCCAAACTATGACA
1 ATAATTCTAAATTAATCCCCAAACTCTTTAACATTCCAATTTCATACCCAAACTATGACA
* * * *
325311 ATAATTCTAAATTAATCCCCAAATTTTTTGAACATTCCAATTTTA-ACCTAAACTAT
1 ATAATTCTAAATTAATCCCCAAACTCTTT-AACATTCCAATTTCATACCCAAACTAT
325367 ATGTATATAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
60 33 0.72
61 13 0.28
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (60 bp):
ATAATTCTAAATTAATCCCCAAACTCTTTAACATTCCAATTTCATACCCAAACTATGACA
Found at i:325613 original size:60 final size:60
Alignment explanation
Indices: 325513--325628 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
325503 CAAAAGTCTG
* * *
325513 GGACCAATTTAGAAAGAGGTCATAGTTTAGGTTAAAAAATTAGAATGTTCCAAAATGTAA
1 GGACCAATTTAGAAAGAGGTCATAGTTTAGGTGAAAAAATTAGAATATTCAAAAATGTAA
* * ** *
325573 GGACTAATTTAGAATGAGAGTCATAGTTT-GGTGATGAAATTGGAATATTCAAAAAT
1 GGACCAATTTAGAAAGAG-GTCATAGTTTAGGTGAAAAAATTAGAATATTCAAAAAT
325629 TTTGGGACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 37 0.79
61 10 0.21
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (60 bp):
GGACCAATTTAGAAAGAGGTCATAGTTTAGGTGAAAAAATTAGAATATTCAAAAATGTAA
Found at i:327551 original size:14 final size:12
Alignment explanation
Indices: 327531--327569 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
327521 ATTTTTTATT
327531 TTTTTAAAAAAA
1 TTTTTAAAAAAA
327543 TATTATTAAAAAAA
1 T-TT-TTAAAAAAA
*
327557 TTTTAAAAAAAA
1 TTTTTAAAAAAA
327569 T
1 T
327570 CTGAACGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
14 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTTTAAAAAAA
Found at i:327679 original size:17 final size:15
Alignment explanation
Indices: 327648--327681 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
327638 TTAAACATTT
327648 ATTTTGACAAAAAAA
1 ATTTTGACAAAAAAA
327663 ATTTTAGACATAAAAAA
1 ATTTT-GACA-AAAAAA
327680 AT
1 AT
327682 AATTTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (15 bp):
ATTTTGACAAAAAAA
Found at i:328937 original size:69 final size:69
Alignment explanation
Indices: 328826--328963 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
328816 GAAAACCCAA
*
328826 TTGATCTCGTGGAGGAGATGAAATGTCCCAATCTAAAAGATACACAATATTTATAAATATATGTT
1 TTGATCTCATGGAGGAGATGAAATGTCCCAATCTAAAAGATACACAATATTTATAAATATATGTT
328891 TAGG
66 TAGG
328895 TTGATCTCATGGAGGAGACT-AAATGTCCCAATCTAAAAGATACACAATATTTATAAATATATGT
1 TTGATCTCATGGAGGAGA-TGAAATGTCCCAATCTAAAAGATACACAATATTTATAAATATATGT
328959 TTAGG
65 TTAGG
328964 GATGATTTTC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 66 0.99
70 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (69 bp):
TTGATCTCATGGAGGAGATGAAATGTCCCAATCTAAAAGATACACAATATTTATAAATATATGTT
TAGG
Found at i:329844 original size:13 final size:13
Alignment explanation
Indices: 329826--329851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329816 TCGTATTCTC
329826 TTAAAATTTTATA
1 TTAAAATTTTATA
329839 TTAAAATTTTATA
1 TTAAAATTTTATA
329852 AATTCGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAAATTTTATA
Found at i:331881 original size:6 final size:6
Alignment explanation
Indices: 331870--331897 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
331860 GTTATCACTT
331870 ATCTCC ATCTCC ATCTCC ATCTCC ATCT
1 ATCTCC ATCTCC ATCTCC ATCTCC ATCT
331898 GAATCAGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (6 bp):
ATCTCC
Found at i:333835 original size:29 final size:29
Alignment explanation
Indices: 333801--333857 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
333791 CCAGTAAACC
*
333801 TAGATAATCAGTTTGAAGCTCAAATCAAA
1 TAGATAATCAGTTTCAAGCTCAAATCAAA
333830 TAGATAATCAGTTTCAAGCTCAAATCAA
1 TAGATAATCAGTTTCAAGCTCAAATCAA
333858 GTATAGATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (29 bp):
TAGATAATCAGTTTCAAGCTCAAATCAAA
Found at i:333870 original size:29 final size:28
Alignment explanation
Indices: 333809--333870 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
333799 CCTAGATAAT
* *
333809 CAGTTTGAAGCTCAAATCAAATAGATAAT
1 CAGTTTCAAGCTCAAATCAAATAGAT-AG
333838 CAGTTTCAAGCTCAAATCAAGTATAGAT-G
1 CAGTTTCAAGCTCAAATCAA--ATAGATAG
333867 CAGT
1 CAGT
333871 AGCAGTGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 23 0.79
31 6 0.21
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (28 bp):
CAGTTTCAAGCTCAAATCAAATAGATAG
Found at i:338093 original size:2 final size:2
Alignment explanation
Indices: 338086--338134 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
338076 TTCCTTTCCT
338086 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
338128 TC TC TC T
1 TC TC TC T
338135 ATTATCCTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:343000 original size:2 final size:2
Alignment explanation
Indices: 342993--343022 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
342983 AATTATCATC
*
342993 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
343023 TGGGTAGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:362382 original size:10 final size:10
Alignment explanation
Indices: 362354--362383 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
362344 TTTAAAATAT
362354 TATTTTTTTA
1 TATTTTTTTA
362364 T-TTTTTTTA
1 TATTTTTTTA
362373 TATTTTTTTA
1 TATTTTTTTA
362383 T
1 T
362384 TAAACTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:364681 original size:121 final size:120
Alignment explanation
Indices: 364488--364728 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 120
364478 GAAAGATATT
* * *
364488 AGTTTACATGACGACCAGCATTCATTAAACTTTAAGGAATCACGTCGATTTGCCTAAAAATCCAG
1 AGTTTACACGACGACCAGCATTCATTAAACTATAAGGAATCACATCGATTTGCCTAAAAATCCAG
364553 AGCTTTGTACAAATATAGAATGTAAGAAACAGCAAGAGAGCAGAACACAGAAAAA
66 AGCTTTGTACAAATATAGAATGTAAGAAACAGCAAGAGAGCAGAACACAGAAAAA
* **
364608 AGTTTACACGGCGACCAGCATTTGTTAAACTGATAAGGAATCACATCGATTTGCCTAAAAATCCA
1 AGTTTACACGACGACCAGCATTCATTAAACT-ATAAGGAATCACATCGATTTGCCTAAAAATCCA
364673 GAGCTTTGTACAAATATAGAATGTAAGAAACAGCAAGAGAGCAGAACACAGAAAAA
65 GAGCTTTGTACAAATATAGAATGTAAGAAACAGCAAGAGAGCAGAACACAGAAAAA
364729 CTAATGCAAA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
120 27 0.24
121 87 0.76
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.21
Consensus pattern (120 bp):
AGTTTACACGACGACCAGCATTCATTAAACTATAAGGAATCACATCGATTTGCCTAAAAATCCAG
AGCTTTGTACAAATATAGAATGTAAGAAACAGCAAGAGAGCAGAACACAGAAAAA
Found at i:373343 original size:4 final size:4
Alignment explanation
Indices: 373336--373374 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
373326 TAAATATATA
373336 TATG TATG TATG TATG TATG TATG TATG TATG TAT- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
373375 ATATAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:378870 original size:3 final size:3
Alignment explanation
Indices: 378864--378996 Score: 203
Period size: 3 Copynumber: 43.7 Consensus size: 3
378854 TTTATCCATT
* **
378864 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA GCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
378912 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
378958 TTA TTA ATA TTA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
378997 TAATAAATAA
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 113 0.96
4 5 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:379480 original size:1 final size:1
Alignment explanation
Indices: 379437--379467 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
379427 GACAGAAACC
379437 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
379468 GAGAAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:379758 original size:13 final size:13
Alignment explanation
Indices: 379740--379768 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
379730 ACCACCGTTA
379740 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
379753 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
379766 CGG
1 CGG
379769 AATACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:391729 original size:5 final size:5
Alignment explanation
Indices: 391719--391771 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
391709 GCTTGAAGAA
*
391719 AAAAG AAAAG AAAAAG AAAAG -AAAG AAGA- AAAAG AAAAAG AAAAG AAAA-
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG
391768 AAAA
1 AAAA
391772 AATAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
4 11 0.26
5 21 0.50
6 10 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:391733 original size:6 final size:6
Alignment explanation
Indices: 391718--391801 Score: 86
Period size: 6 Copynumber: 14.0 Consensus size: 6
391708 TGCTTGAAGA
391718 AAAAAG -AAAAG AAAAAG -AAAAG AAAGAAG AAAAAG AAAAAG -AAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG
* *
391764 AAAAA- AAAAAT AAATATAG AAAAGG AAAAAAG AAAAAG
1 AAAAAG AAAAAG AAA-A-AG AAAAAG -AAAAAG AAAAAG
391802 GAGGGTCAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
5 20 0.30
6 30 0.45
7 13 0.19
8 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:391748 original size:30 final size:29
Alignment explanation
Indices: 391713--391800 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 29
391703 TATTATGCTT
391713 GAAGAAAAAAGAAAAGAAAAAGAAAAGAAA
1 GAAGAAAAAAGAAAAGAAAAAGAAAA-AAA
391743 GAAG-AAAAAGAAAA-AGAAAAGAAAAAAA
1 GAAGAAAAAAGAAAAGA-AAAAGAAAAAAA
* * *
391771 AAATAAATATAGAAAAGGAAAAAAGAAAAA
1 GAAGAAA-AAAGAAAA-G-AAAAAGAAAAA
391801 GGAGGGTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
28 6 0.12
29 21 0.43
30 11 0.22
32 10 0.20
33 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (29 bp):
GAAGAAAAAAGAAAAGAAAAAGAAAAAAA
Found at i:391756 original size:24 final size:24
Alignment explanation
Indices: 391714--391801 Score: 110
Period size: 24 Copynumber: 3.7 Consensus size: 24
391704 ATTATGCTTG
391714 AAGAAAAAAG-AAAAGAAAAAGAA
1 AAGAAAAAAGAAAAAGAAAAAGAA
*
391737 AAGAAAGAAGAAAAAGAAAAAGAA
1 AAGAAAAAAGAAAAAGAAAAAGAA
*
391761 AAGAAAAAA-AAAATA-AATATAGAA
1 AAGAAAAAAGAAAA-AGAA-AAAGAA
391785 AAGGAAAAAAGAAAAAG
1 AA-GAAAAAAGAAAAAG
391802 GAGGGTCAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
23 15 0.27
24 29 0.52
25 8 0.14
26 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAGAAAAAGAAAAAGAA
Found at i:391757 original size:35 final size:37
Alignment explanation
Indices: 391720--391799 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
391710 CTTGAAGAAA
*
391720 AAAGAAAAGAAAAAGAAAAGAAAGA-AGAAAAAG-AA
1 AAAGAAAAGAAAAAAAAAAGAAAGATAGAAAAAGAAA
* * *
391755 AAAGAAAAGAAAAAAAAAATAAATATAGAAAAGGAAA
1 AAAGAAAAGAAAAAAAAAAGAAAGATAGAAAAAGAAA
391792 AAAGAAAA
1 AAAGAAAA
391800 AGGAGGGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 22 0.56
36 7 0.18
37 10 0.26
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (37 bp):
AAAGAAAAGAAAAAAAAAAGAAAGATAGAAAAAGAAA
Found at i:392819 original size:52 final size:51
Alignment explanation
Indices: 392741--393139 Score: 674
Period size: 52 Copynumber: 7.7 Consensus size: 51
392731 TATGTGCTCA
*
392741 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-AAAAC
*
392793 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAAAC
*
392844 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAAAC
* *
392895 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-AAAAC
*
392947 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAAAC
392998 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAA-A-AAC
*
393050 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAAAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG-GAAAAAC
*
393102 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
393140 CGAAGAAGTG
Statistics
Matches: 332, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
50 3 0.01
51 147 0.44
52 179 0.54
53 1 0.00
54 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (51 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAAAC
Found at i:392948 original size:103 final size:103
Alignment explanation
Indices: 392741--393139 Score: 701
Period size: 103 Copynumber: 3.9 Consensus size: 103
392731 TATGTGCTCA
* *
392741 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AAAACATAGCATCTTCTG
* *
392806 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AAAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
392844 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGG
*
392909 AAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
392947 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGG
*
393012 AAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
393050 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAAAAAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-AGAAAAACATAGCATCTTCTG
*
393115 GAAGTGTTCTTTGAGTTATTTGATC
65 GAAGTGTTCTTTGAGTTATCTGATC
393140 CGAAGAAGTG
Statistics
Matches: 285, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
102 48 0.17
103 193 0.68
104 44 0.15
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (103 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:393021 original size:154 final size:155
Alignment explanation
Indices: 392741--393139 Score: 730
Period size: 154 Copynumber: 2.6 Consensus size: 155
392731 TATGTGCTCA
392741 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
392806 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGGAAGTGTTCTTTGA
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGGAAGTGTTCTTTGA
392871 GTTATCTGATCTGGTTAGAA-A-AAC
131 GTTATCTGATCTGGTT-GAACAGAAC
*
392895 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
392960 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGGAAGTGTTCTTTGA
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGGAAGTGTTCTTTGA
393025 GTTATCTGATCTGGTTGAACAGAAC
131 GTTATCTGATCTGGTTGAACAGAAC
* * *
393050 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAAAAAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
*
393115 GAAGTGTTCTTTGAGTTATTTGATC
66 GAAGTGTTCTTTGAGTTATCTGATC
393140 CGAAGAAGTG
Statistics
Matches: 237, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
153 3 0.01
154 146 0.62
155 88 0.37
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (155 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAAAACATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGGTTGAACAGAAC
Found at i:394159 original size:113 final size:113
Alignment explanation
Indices: 393696--394378 Score: 1015
Period size: 113 Copynumber: 5.9 Consensus size: 113
393686 CAAAGATTCA
* * * *
393696 AATTCATCACTTGATGGATCATCATTACCAGAGAAGGTCCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
393761 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
393809 AATTCATCACTTGATGGATCAACATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATCT
393874 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
393927 AATTCATCACTTGATGGATCAACATTTCCAGAGGAAGAGTTCATAATGAGAGGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATCT
*
393992 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * * *
394045 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
394110 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * * *
394158 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
394223 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * ** *
394271 AATTCATCATTTGATGAATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAG
*
394336 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
394379 GTTTGATATC
Statistics
Matches: 534, Mismatches: 30, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
113 228 0.43
114 67 0.13
115 16 0.03
116 17 0.03
117 4 0.01
118 202 0.38
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:394683 original size:3 final size:3
Alignment explanation
Indices: 394677--394794 Score: 173
Period size: 3 Copynumber: 38.7 Consensus size: 3
394667 TTTATCCATT
* **
394677 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA GCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
394725 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
394771 TTA TATA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TT
394795 TAATAAATAA
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
3 98 0.95
4 5 0.05
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:395275 original size:1 final size:1
Alignment explanation
Indices: 395235--395259 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
395225 GACAGAAACC
395235 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
395260 CAGAGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:395551 original size:13 final size:13
Alignment explanation
Indices: 395533--395561 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
395523 ACCACCGTTA
395533 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
395546 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
395559 CGG
1 CGG
395562 AATACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:400678 original size:2 final size:2
Alignment explanation
Indices: 400671--400697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
400661 TTTTATTAGT
400671 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
400698 CCTATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:402937 original size:15 final size:15
Alignment explanation
Indices: 402917--402945 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
402907 TCATAAACCC
402917 TAAACCCTAATCATA
1 TAAACCCTAATCATA
402932 TAAACCCTAATCAT
1 TAAACCCTAATCAT
402946 CAAATCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAACCCTAATCATA
Found at i:406011 original size:14 final size:14
Alignment explanation
Indices: 405992--406021 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
405982 GTAAAAACGA
*
405992 AACAAATGTCTTTC
1 AACAAATGTATTTC
406006 AACAAATGTATTTC
1 AACAAATGTATTTC
406020 AA
1 AA
406022 ACTATCGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AACAAATGTATTTC
Found at i:408869 original size:18 final size:18
Alignment explanation
Indices: 408846--408890 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
408836 AACTTTGGTA
408846 AATTAATTTGTATCATAC
1 AATTAATTTGTATCATAC
408864 AATTAATTTGTATCATAC
1 AATTAATTTGTATCATAC
408882 AATTAATTT
1 AATTAATTT
408891 CCAACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (18 bp):
AATTAATTTGTATCATAC
Found at i:410569 original size:60 final size:60
Alignment explanation
Indices: 410496--410642 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 60
410486 ATAAAAGGGT
* * * *
410496 AAAG-TACATAAATGGTCCCCCAACTATAGAATACTACTTTCTTAAGTCCATCGACTATTA
1 AAAGTTACA-AAATGGTCACCCGACTATAGAATACTACTTTCTCAAATCCATCGACTATTA
* * ** * ** * * *
410556 AAAGTTATAAAATGATCATTCGACTATATAATGTTGCTTTGTCAAATCCCTCGACTATTA
1 AAAGTTACAAAATGGTCACCCGACTATAGAATACTACTTTCTCAAATCCATCGACTATTA
410616 AAAGTTACAAAATGGTCACCCGACTAT
1 AAAGTTACAAAATGGTCACCCGACTAT
410643 TCATTATGTT
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
60 65 0.96
61 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCACCCGACTATAGAATACTACTTTCTCAAATCCATCGACTATTA
Found at i:411768 original size:19 final size:20
Alignment explanation
Indices: 411732--411774 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
411722 AATGTTAGGT
411732 TTTTTTATAAACATAATAATA
1 TTTTTTATAAACATAATAA-A
411753 TTTTTTATAAA-A-AATAAA
1 TTTTTTATAAACATAATAAA
411771 TTTT
1 TTTT
411775 AAAATTACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 1 0.05
21 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTTATAAACATAATAAA
Found at i:419594 original size:19 final size:18
Alignment explanation
Indices: 419566--419622 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
419556 ATATTTGAAC
419566 TAAATTTAAAATATATAT
1 TAAATTTAAAATATATAT
* *
419584 TATACTTTAAAAT-TAAAAT
1 TA-AATTTAAAATAT-ATAT
419603 TAAATATTAAAATATATAT
1 TAAAT-TTAAAATATATAT
419622 T
1 T
419623 TATTCTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 5 0.16
19 25 0.81
20 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTAAAATATATAT
Found at i:433361 original size:14 final size:14
Alignment explanation
Indices: 433328--433369 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
433318 TGAGTTATCA
433328 TCTTTC-TTCTTCTT
1 TCTTTCATTCTT-TT
*
433342 TTTTTCATTCTTTT
1 TCTTTCATTCTTTT
433356 TCTTTCATT-TTTT
1 TCTTTCATTCTTTT
433369 T
1 T
433370 GCTCTGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 15 0.60
15 5 0.20
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (14 bp):
TCTTTCATTCTTTT
Found at i:433759 original size:18 final size:16
Alignment explanation
Indices: 433725--433786 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
433715 ATCCATGCAT
*
433725 TTAGTTCATCGAATAAAA
1 TTAGTTCAT-TAAT-AAA
433743 TTAGTTCATTAATTAAA
1 TTAGTTCATTAA-TAAA
* *
433760 CTAGTTCATTCATCAAA
1 TTAGTTCATTAAT-AAA
*
433777 CTAGTTCATT
1 TTAGTTCATT
433787 TATTGAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 28 0.72
18 10 0.26
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (16 bp):
TTAGTTCATTAATAAA
Found at i:433766 original size:17 final size:17
Alignment explanation
Indices: 433744--433796 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
433734 CGAATAAAAT
433744 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
433761 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
433778 TAGTTCATTTATTGAAC
1 TAGTTCATTAATTAAAC
433795 TA
1 TA
433797 ACTTTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:434967 original size:23 final size:23
Alignment explanation
Indices: 434890--434953 Score: 128
Period size: 23 Copynumber: 2.8 Consensus size: 23
434880 TATAATTTCC
434890 ATTACTTTCATATACATACTTCT
1 ATTACTTTCATATACATACTTCT
434913 ATTACTTTCATATACATACTTCT
1 ATTACTTTCATATACATACTTCT
434936 ATTACTTTCATATACATA
1 ATTACTTTCATATACATA
434954 GATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTACTTTCATATACATACTTCT
Found at i:435159 original size:10 final size:10
Alignment explanation
Indices: 435144--435169 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
435134 CCGGGTTAGT
435144 AAAAAAATTA
1 AAAAAAATTA
435154 AAAAAAATTA
1 AAAAAAATTA
435164 AAAAAA
1 AAAAAA
435170 GAAAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:436665 original size:14 final size:15
Alignment explanation
Indices: 436646--436675 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
436636 TAACCTGAAA
436646 AACAAAAT-AATAAT
1 AACAAAATAAATAAT
436660 AACAAAATAAATAAT
1 AACAAAATAAATAAT
436675 A
1 A
436676 CTAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AACAAAATAAATAAT
Found at i:440116 original size:28 final size:27
Alignment explanation
Indices: 440084--440152 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 27
440074 TAAGTTTGTA
440084 AAGAGAAAA-AAAACCTATCAT-AAGTATG
1 AAGAGAAAATAAAA-CT-TC-TGAAGTATG
*
440112 AAGAGAAAATCAAACTTCTGAAGTATG
1 AAGAGAAAATAAAACTTCTGAAGTATG
440139 AAGAGAAAATAAAA
1 AAGAGAAAATAAAA
440153 AACAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 22 0.59
28 11 0.30
29 3 0.08
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.17
Consensus pattern (27 bp):
AAGAGAAAATAAAACTTCTGAAGTATG
Found at i:440541 original size:3 final size:3
Alignment explanation
Indices: 440533--440607 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
440523 CCATATTGAT
*
440533 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
440581 TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
440608 AATATATTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:450210 original size:21 final size:20
Alignment explanation
Indices: 450169--450210 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
450159 AAGATATCTT
* *
450169 TGCCTGGTTTTATCAAGATA
1 TGCCTGGTTTAAGCAAGATA
450189 TGCCTGGTTTAAGCACAGATA
1 TGCCTGGTTTAAGCA-AGATA
450210 T
1 T
450211 AGTGATACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (20 bp):
TGCCTGGTTTAAGCAAGATA
Found at i:453350 original size:17 final size:17
Alignment explanation
Indices: 453328--453399 Score: 103
Period size: 17 Copynumber: 4.3 Consensus size: 17
453318 TTATGCTTGA
453328 AAAAAAAAGAGAAAAAG
1 AAAAAAAAGAGAAAAAG
*
453345 AAAAAAAATAGAAAAAG
1 AAAAAAAAGAGAAAAAG
453362 AAAAAAAAAGAGAAAAA-
1 -AAAAAAAAGAGAAAAAG
*
453379 AGAAAAAAG-GAAAAAG
1 AAAAAAAAGAGAAAAAG
453395 AAAAA
1 AAAAA
453400 GGGGGGTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
15 6 0.12
16 12 0.24
17 16 0.33
18 15 0.31
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAAG
Found at i:453357 original size:11 final size:10
Alignment explanation
Indices: 453328--453386 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 10
453318 TTATGCTTGA
453328 AAAAAAAAGAG
1 AAAAAAAA-AG
*
453339 AAAAAGAAAAA
1 AAAAA-AAAAG
453350 AAATAGAAAAAG
1 AAA-A-AAAAAG
453362 AAAAAAAAAG
1 AAAAAAAAAG
*
453372 -AGAAAAAAG
1 AAAAAAAAAG
453381 AAAAAA
1 AAAAAA
453387 GGAAAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 8 0.20
10 10 0.25
11 10 0.25
12 11 0.28
13 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:453369 original size:27 final size:27
Alignment explanation
Indices: 453339--453398 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
453329 AAAAAAAGAG
*
453339 AAAAAGAAAAAAAATAGAAAAA-GAAAA
1 AAAAAGAAAAAAAAGA-AAAAAGGAAAA
*
453366 AAAAAGAGAAAAAAGAAAAAAGGAAAA
1 AAAAAGAAAAAAAAGAAAAAAGGAAAA
453393 AGAAAA
1 A-AAAA
453399 AGGGGGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 20 0.69
28 4 0.14
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (27 bp):
AAAAAGAAAAAAAAGAAAAAAGGAAAA
Found at i:453372 original size:35 final size:33
Alignment explanation
Indices: 453326--453399 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 33
453316 TATTATGCTT
453326 GAAAAAAAAAGAGAAAAAGAAAAAAAATAGAAAAA
1 GAAAAAAAAAGAGAAAAA-AAAAAAAA-AGAAAAA
* *
453361 GAAAAAAAAAGAGAAAAAAGAAAAAAGGAAAAA
1 GAAAAAAAAAGAGAAAAAAAAAAAAAAGAAAAA
453394 GAAAAA
1 GAAAAA
453400 GGGGGGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 12 0.32
34 7 0.19
35 18 0.49
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (33 bp):
GAAAAAAAAAGAGAAAAAAAAAAAAAAGAAAAA
Found at i:453385 original size:33 final size:35
Alignment explanation
Indices: 453326--453399 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 35
453316 TATTATGCTT
453326 GAAAAAAAAAGAGAAAAAGAAAAAAAATA-GAAAAA
1 GAAAAAAAAAGAGAAAAAGAAAAAAAA-AGGAAAAA
*
453361 GAAAAAAAAAGAG-AAAA-AAGAAAAAAGGAAAAA
1 GAAAAAAAAAGAGAAAAAGAAAAAAAAAGGAAAAA
453394 GAAAAA
1 GAAAAA
453400 GGGGGGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 1 0.03
33 19 0.51
34 4 0.11
35 13 0.35
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (35 bp):
GAAAAAAAAAGAGAAAAAGAAAAAAAAAGGAAAAA
Found at i:453738 original size:16 final size:16
Alignment explanation
Indices: 453712--453756 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
453702 TTTGAATACA
*
453712 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
453729 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
453744 ATTCAATTTATTT
1 ATTCAATTTATTT
453757 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:454692 original size:83 final size:83
Alignment explanation
Indices: 454544--455585 Score: 1859
Period size: 83 Copynumber: 12.7 Consensus size: 83
454534 GAATAAATGC
*
454544 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
454609 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
454627 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
454692 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
454710 AATGTGCTCATAGC-TCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
454774 CATTGAA-TTGGAAGATG
66 CATTGAATTTGGAAGATG
454791 AATGTGCTCATAGCA---TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
454853 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
454871 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
454936 CATTGAATTTAGAAGATG
66 CATTGAATTTGGAAGATG
* *
454954 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455019 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
455037 AATGT--TCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGG-TTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455099 CA-TGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
455116 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455181 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* * *
455199 AATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455264 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
455282 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455347 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
455365 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455430 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
455448 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
455513 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
455531 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTAATCTGGTTTGG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
455586 TAGGAACTAC
Statistics
Matches: 921, Mismatches: 29, Indels: 18
0.95 0.03 0.02
Matches are distributed among these distances:
79 74 0.08
80 39 0.04
81 107 0.12
82 72 0.08
83 629 0.68
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
CATTGAATTTGGAAGATG
Found at i:455475 original size:494 final size:491
Alignment explanation
Indices: 454544--455582 Score: 1875
Period size: 494 Copynumber: 2.1 Consensus size: 491
454534 GAATAAATGC
454544 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGT-CTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGG-TTGGCAGAACCAAT
*
454609 CATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
64 CATTGAATTTGGAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
454674 TGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCTCTTCTGGAAGTGTT
129 TGGTTTGGCAAAACCAATCATTGAATTTGGAAGATGAATGTGCTAATAGCTCTTCTGGAAGTGTT
454739 CTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTGGAAGATGAATGTGCTCATAG
194 CTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTGGAAGATGAATGTGCTCATAG
454804 CATCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGA
259 CATCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGA
* *
454869 TGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCA
324 TGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCA
454934 ATCATTGAATTTAGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
389 ATCATTGAATTTAGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
454999 TCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATG
454 TCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATG
455037 AATGT-TCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGCAGAACCAATCA
1 AATGTCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGCAGAACCAATCA
*
455101 -TGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
66 TTGAATTTGGAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
455165 GTTTGGCAAAACCAATCATTGAATTTGGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTC
131 GTTTGGCAAAACCAATCATTGAATTTGGAAGATGAATGTGCTAATAGC-TCTTCTGGAAGTGTTC
455230 TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAG
195 TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA-TTGGAAGATGAATGTGCTCATAG
455295 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGA
259 CA---TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGA
*
455360 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
321 AGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
*
455425 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
386 CCAATCATTGAATTTAGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
455490 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATG
451 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATG
* * *
455531 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTAATCTGGTT
1 AATGT-CTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTT
455583 TGGTAGGAAC
Statistics
Matches: 526, Mismatches: 13, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
489 106 0.20
490 73 0.14
491 68 0.13
493 5 0.01
494 232 0.44
496 42 0.08
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (491 bp):
AATGTCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGCAGAACCAATCA
TTGAATTTGGAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTTGGCAAAACCAATCATTGAATTTGGAAGATGAATGTGCTAATAGCTCTTCTGGAAGTGTTCT
TTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTGGAAGATGAATGTGCTCATAGCA
TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATG
AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAAT
CATTGAATTTAGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGCAGAACCAATCATTGAATTTGGAAGATG
Found at i:456439 original size:113 final size:113
Alignment explanation
Indices: 456252--456706 Score: 829
Period size: 113 Copynumber: 4.0 Consensus size: 113
456242 TGGATTGACA
456252 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
456317 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
456365 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
456430 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATAGATCAGCC
66 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
*
456478 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
456543 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
66 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
*
456591 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
456656 AGAACTTGTTCAACTTTTTACCTGAATTCATCAATTGATGGATCAACC
66 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
456704 TTT
1 TTT
456707 TGCTCAAATC
Statistics
Matches: 331, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 331 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
Found at i:457070 original size:3 final size:3
Alignment explanation
Indices: 457062--457136 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
457052 CCATATTGAT
*
457062 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
457110 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
457137 AATATATTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:460463 original size:15 final size:15
Alignment explanation
Indices: 460443--460618 Score: 228
Period size: 15 Copynumber: 11.3 Consensus size: 15
460433 TAATAAGGTT
460443 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
460458 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
460473 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
460488 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
460503 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
460518 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
460533 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
460548 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* * *
460563 AATTAGTATAAAATATGGA
1 ATTTA-TTTTAAA-AT--A
460582 TTTATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
460600 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
460614 ATTTA
1 ATTTA
460619 CTAGTATGGA
Statistics
Matches: 142, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
14 14 0.10
15 108 0.76
16 5 0.04
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 5 0.04
22 4 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:460479 original size:30 final size:30
Alignment explanation
Indices: 460443--460618 Score: 255
Period size: 30 Copynumber: 5.7 Consensus size: 30
460433 TAATAAGGTT
*
460443 ATTTATTTTAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
460473 ATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
460503 ATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
460533 ATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
* *
460563 AATTAGTATAAAATATGGATTTATTTATTTTAAAATA
1 ATTTATTAT-AAA-AT--A---ATTTATTTTAAAATA
460600 ATTTATT-TAAAATAATTTA
1 ATTTATTATAAAATAATTTA
460619 CTAGTATGGA
Statistics
Matches: 134, Mismatches: 5, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.04
30 96 0.72
31 3 0.02
32 3 0.02
34 3 0.02
35 3 0.02
36 1 0.01
37 20 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTATTATAAAATAATTTATTTTAAAATA
Found at i:460610 original size:14 final size:15
Alignment explanation
Indices: 460585--460618 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
460575 ATATGGATTT
460585 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
460600 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
460614 ATTTA
1 ATTTA
460619 CTAGTATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:460639 original size:22 final size:21
Alignment explanation
Indices: 460623--460667 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
460613 AATTTACTAG
460623 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTA-TTTAAAA
*
460645 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
460666 TA
1 TA
460668 ATATATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:460667 original size:54 final size:54
Alignment explanation
Indices: 460600--461263 Score: 526
Period size: 54 Copynumber: 12.1 Consensus size: 54
460590 TTTTAAAATA
* *
460600 ATTTATTTAAAATAATTTACTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
460654 ATTTATTTTAAATAATATATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
460708 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *
460762 ATTTATTATT--GTAGTTGTA-TGGT-TTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTG
** ** * *
460820 ATTTATTTTAAA-ATATGGATT-G-ATTTATT--TTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTGATTT--AT--TTTA-AAATATGGATTG
* ** * ** * * * *
460875 ATTTATTTTAAA-ATATTGATT-G-ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
** ** * ** * * *
460929 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
*
460983 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
**
461037 ATTTA--TT--AT--TGGAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
*
461095 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
461149 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
461203 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
461257 ATTTATT
1 ATTTATT
461264 ATTGTAGTTG
Statistics
Matches: 532, Mismatches: 41, Indels: 74
0.82 0.06 0.11
Matches are distributed among these distances:
48 20 0.04
49 4 0.01
50 4 0.01
52 10 0.02
53 11 0.02
54 331 0.62
55 68 0.13
56 6 0.01
57 7 0.01
58 36 0.07
59 3 0.01
60 4 0.01
62 4 0.01
63 4 0.01
64 20 0.04
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:460686 original size:32 final size:32
Alignment explanation
Indices: 460645--460751 Score: 135
Period size: 32 Copynumber: 3.7 Consensus size: 32
460635 TATTTTAAAA
460645 TATGGATTGATTTATTTTAAATAATATATTAG
1 TATGGATTGATTTATTTTAAATAATATATTAG
460677 TATGGATTGATTTA-TTT---T-A-A-A--A-
1 TATGGATTGATTTATTTTAAATAATATATTAG
*
460699 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATATATTAG
460731 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
460752 ATATGGATTG
Statistics
Matches: 64, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 2 0.03
27 2 0.03
28 1 0.02
29 1 0.02
31 4 0.06
32 35 0.55
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATATATTAG
Found at i:460705 original size:22 final size:22
Alignment explanation
Indices: 460677--460719 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
460667 AATATATTAG
460677 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
460699 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
460720 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:460821 original size:32 final size:32
Alignment explanation
Indices: 460778--461246 Score: 381
Period size: 32 Copynumber: 15.7 Consensus size: 32
460768 TATTGTAGTT
*
460778 GTATGGTTTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
460810 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
460833 -TATGGATTGATTTATTTTTAAATAATTTATTA
1 GTATGGATTGATTTA-TTTTAAATAATTTATTA
460865 GTATGGATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
460890 -T-T-GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
460919 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
460942 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
460973 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
461005 GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTA
1 GTATGGATTGATTTATTTT--AA-AT--A---ATTTATTA
*
461045 TTGGAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
1 --GTA------TGGATTGATTTATTTTAAATAATTTATTA
*
461085 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
461117 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
461140 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
461171 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
461194 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
461225 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
461247 ATATAGATTG
Statistics
Matches: 361, Mismatches: 9, Indels: 134
0.72 0.02 0.27
Matches are distributed among these distances:
22 68 0.19
23 14 0.04
24 5 0.01
25 8 0.02
26 10 0.03
27 3 0.01
28 13 0.04
29 7 0.02
30 3 0.01
31 16 0.04
32 155 0.43
33 14 0.04
34 2 0.01
35 2 0.01
37 1 0.00
38 2 0.01
40 16 0.04
42 2 0.01
43 1 0.00
45 2 0.01
46 2 0.01
48 15 0.04
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:460836 original size:22 final size:22
Alignment explanation
Indices: 460811--460856 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
460801 AATTTATTAG
460811 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
460833 TATGGATTGATTTATTTTTAAA
1 TATGGATTGATTTATTTTAAAA
460855 TA
1 TA
460857 ATTTATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:460945 original size:22 final size:22
Alignment explanation
Indices: 460920--460962 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
460910 AATTTATTAG
460920 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
460942 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
460963 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:461082 original size:14 final size:14
Alignment explanation
Indices: 461063--461115 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
461053 GTATGGATTG
461063 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
461077 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
461095 ATTTATTTTAAATA
1 ATTTATTTTAAATA
461109 ATTTATT
1 ATTTATT
461116 AGTATGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:461100 original size:18 final size:18
Alignment explanation
Indices: 461077--461133 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
461067 ATTTTAAATA
461077 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
461095 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
461109 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
461127 ATTTATT
1 ATTTATT
461134 TTAAAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 2 0.06
17 1 0.03
18 17 0.55
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:461143 original size:22 final size:22
Alignment explanation
Indices: 461118--461160 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
461108 AATTTATTAG
461118 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
461140 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
461161 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:461197 original size:22 final size:22
Alignment explanation
Indices: 461172--461214 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
461162 AATTTATTAG
461172 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
461194 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
461215 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:461255 original size:22 final size:23
Alignment explanation
Indices: 461230--461345 Score: 83
Period size: 22 Copynumber: 4.7 Consensus size: 23
461220 TATTAGTATG
461230 GATTGATTTATTTTAAAATATA-
1 GATTGATTTATTTTAAAATATAT
* ** *
461252 GATTGATTTATTATTGTAGTTGTAT
1 GATTGATTTATT-TT-AAAATATAT
461277 GAATTGATTTATTTTAAATAATTTATTAT
1 G-ATTGATTTATTTT-AA-AA--TA-TAT
*
461306 GGATTGATTTATTTTAAAATAT-G
1 -GATTGATTTATTTTAAAATATAT
*
461329 GATTAATTTATTTTAAA
1 GATTGATTTATTTTAAA
461346 TAATTTATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
22 28 0.38
23 2 0.03
24 5 0.07
25 6 0.08
26 11 0.15
27 2 0.03
28 3 0.04
29 16 0.22
30 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (23 bp):
GATTGATTTATTTTAAAATATAT
Found at i:461314 original size:77 final size:79
Alignment explanation
Indices: 461194--461340 Score: 244
Period size: 77 Copynumber: 1.9 Consensus size: 79
461184 TATTTTAAAA
* *
461194 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTA-TATGGATTGATTTATTTTAAAATATAGATTAAT
461259 TTATTATTGTAGTTG
65 TTATTATTGTAGTTG
*
461274 TATGAATTGATTTATTTTAAATAATTTA-T-TATGGATTGATTTATTTTAAAATATGGATTAATT
1 TATGAATTGATTTATTTTAAATAATTTATTATATGGATTGATTTATTTTAAAATATAGATTAATT
461337 TATT
66 TATT
461341 TTAAATAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
77 36 0.56
79 1 0.02
80 27 0.42
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (79 bp):
TATGAATTGATTTATTTTAAATAATTTATTATATGGATTGATTTATTTTAAAATATAGATTAATT
TATTATTGTAGTTG
Found at i:461427 original size:31 final size:31
Alignment explanation
Indices: 461370--461428 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
461360 AGTTGTATGG
**
461370 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
461401 ATTATTTAAATTTCAGTATTACAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
461429 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:465584 original size:19 final size:19
Alignment explanation
Indices: 465543--465599 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
465533 ACTAGCCAAG
*
465543 AGTATCGATACTCCTATAAA
1 AGTATCGATACT-TTATAAA
* *
465563 AGTTTCGATACTTTATATA
1 AGTATCGATACTTTATAAA
*
465582 AGTACCGATACTTT-TAAA
1 AGTATCGATACTTTATAAA
465600 CATTCTGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 3 0.10
19 17 0.55
20 11 0.35
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
AGTATCGATACTTTATAAA
Found at i:469718 original size:23 final size:23
Alignment explanation
Indices: 469685--469770 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
469675 AGAAATTGCA
469685 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* * *
469708 CCGAAGGGCCACATAGTATTGTC
1 CCGAAGGACCACATAGAAATGTC
* *
469731 CCGAAGGACCGCGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
*
469754 CCGAAGGACCACGTAGA
1 CCGAAGGACCACATAGA
469771 TTTATCCTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 1 0.02
23 53 0.98
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:469788 original size:46 final size:46
Alignment explanation
Indices: 469698--469794 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 46
469688 AAGTGCCACA
* * *
469698 TAGAAATGTCCCGAAGGGCCACATAGTATTGTCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGTATTATCCCGAAGAACCGCG
* *
469744 TAGAAATGTCCCGAAGGACCACGTAG-ATTTATCCTGAAGAACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGTA-TTATCCCGAAGAACCGCG
*
469790 CAGAA
1 TAGAA
469795 CCCTCAACTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
45 1 0.02
46 43 0.98
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGTATTATCCCGAAGAACCGCG
Found at i:470523 original size:20 final size:20
Alignment explanation
Indices: 470476--470525 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
470466 TCGATACCCA
*
470476 TGGTATCAATGCTACTCCCT
1 TGGTATCGATGCTACTCCCT
470496 TGGTATCGATGCTACT-CCT
1 TGGTATCGATGCTACTCCCT
470515 TCGGTATCGAT
1 T-GGTATCGAT
470526 ACTGATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (20 bp):
TGGTATCGATGCTACTCCCT
Found at i:471001 original size:16 final size:18
Alignment explanation
Indices: 470980--471012 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
470970 TCATAACTTG
470980 TAATTCT-TTT-AGTTTC
1 TAATTCTCTTTAAGTTTC
470996 TAATTCTCTTTAAGTTT
1 TAATTCTCTTTAAGTTT
471013 TCTCAAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (18 bp):
TAATTCTCTTTAAGTTTC
Found at i:472899 original size:15 final size:15
Alignment explanation
Indices: 472879--472908 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
472869 AATATTCGAC
472879 TTCAAACAATTGCAT
1 TTCAAACAATTGCAT
*
472894 TTCAAACAGTTGCAT
1 TTCAAACAATTGCAT
472909 CTAAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (15 bp):
TTCAAACAATTGCAT
Found at i:478875 original size:22 final size:23
Alignment explanation
Indices: 478850--478896 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
478840 TAATCGCGAG
478850 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
478872 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
478895 TT
1 TT
478897 ATTTAAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:483025 original size:3 final size:3
Alignment explanation
Indices: 483017--483051 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
483007 AACCCAATTC
483017 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
483052 ATTTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:483042 original size:14 final size:14
Alignment explanation
Indices: 483017--483054 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
483007 AACCCAATTC
483017 TATTATTATTATTAT
1 TATTA-TATTATTAT
483032 TATTATATTATTAT
1 TATTATATTATTAT
483046 TATTATATT
1 TATTATATT
483055 TTAAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:485502 original size:2 final size:2
Alignment explanation
Indices: 485495--485520 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
485485 TGTGTTTTGA
485495 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
485521 GATGTTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:509911 original size:30 final size:29
Alignment explanation
Indices: 509854--509911 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
509844 AAATTTTATT
* * * *
509854 TTTATCTTCTAAAATTTTATAATTTTAAA
1 TTTATCTCCTAAAATGTTAAAAGTTTAAA
509883 TTTATCTCCTTAAAATGTTAAAAGTTTAA
1 TTTATCTCC-TAAAATGTTAAAAGTTTAA
509912 GTTCATCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (29 bp):
TTTATCTCCTAAAATGTTAAAAGTTTAAA
Found at i:511077 original size:38 final size:38
Alignment explanation
Indices: 511035--511108 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
511025 AGAGTGTTAC
* *
511035 TTTGTTGAGTCTCTTGACTATTGAAAGTTATAAAATGG
1 TTTGTTGAGTCCCTTGACTATTGAAAGTTACAAAATGG
*
511073 TTTGTTGAGTCCCTTGTCTATTGAAAGTTACAAAAT
1 TTTGTTGAGTCCCTTGACTATTGAAAGTTACAAAAT
511109 AGTCACCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (38 bp):
TTTGTTGAGTCCCTTGACTATTGAAAGTTACAAAATGG
Found at i:513041 original size:31 final size:31
Alignment explanation
Indices: 512998--513088 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 31
512988 ATTACTGAGC
512998 TCGACTCGAAAACTTTGAAATGAAGCTCGAT
1 TCGACTCGAAAACTTTGAAATGAAGCTCGAT
* *
513029 TCGATTCGAAAACTTTGAAATTAAGCTCGAT
1 TCGACTCGAAAACTTTGAAATGAAGCTCGAT
*
513060 TCGAACTCG-AAA-TTCTGAACTGAAGCTCG
1 TCG-ACTCGAAAACTT-TGAAATGAAGCTCG
513089 TGAGCAGCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
30 2 0.04
31 47 0.89
32 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
TCGACTCGAAAACTTTGAAATGAAGCTCGAT
Found at i:523542 original size:130 final size:130
Alignment explanation
Indices: 523309--523957 Score: 1289
Period size: 130 Copynumber: 5.0 Consensus size: 130
523299 ATAGTCAGGT
523309 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
1 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
523374 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
66 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
523439 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
1 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
523504 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
66 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
523569 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
1 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
523634 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
66 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
*
523699 GACCATTTTATAACTTTTAATAATTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
1 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
523764 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
66 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
523829 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
1 GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
523894 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTG
66 TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTG
523958 TGTGCTTTAC
Statistics
Matches: 517, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 517 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (130 bp):
GACCATTTTATAACTTTTAATAGTTGAGAGACTCAACGAAGCAACACTCTATAGTTAGGGGATCA
TTTTGTAACTTTTAATAGTCGATGGACTTAATAAAGCAGTACCCTATAACTGGGAGACCATTTGA
Found at i:528099 original size:19 final size:19
Alignment explanation
Indices: 528072--528109 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
528062 AATAATAATA
*
528072 TAAATAATAATTTAAAAAT
1 TAAAAAATAATTTAAAAAT
528091 TAAAAAATAATTTAAAAAT
1 TAAAAAATAATTTAAAAAT
528110 ATAACGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAAATAATTTAAAAAT
Found at i:528755 original size:15 final size:15
Alignment explanation
Indices: 528720--528760 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
528710 GCAGAGTGAC
*
528720 GGGGAAGAGAGGGGA
1 GGGGAAGAGAGGGAA
**
528735 TAGGAAGAGAGGGAA
1 GGGGAAGAGAGGGAA
528750 GGGGAAGAGAG
1 GGGGAAGAGAG
528761 AGAATTAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (15 bp):
GGGGAAGAGAGGGAA
Found at i:529199 original size:23 final size:24
Alignment explanation
Indices: 529173--529217 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
529163 TAATTTATTA
529173 TTGTCTCC-TAAAATATTATAAAT
1 TTGTCTCCATAAAATATTATAAAT
* * *
529196 TTGTTTCCATAGAATGTTATAA
1 TTGTCTCCATAAAATATTATAA
529218 GTTCACCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (24 bp):
TTGTCTCCATAAAATATTATAAAT
Found at i:537273 original size:3 final size:3
Alignment explanation
Indices: 537255--537332 Score: 86
Period size: 3 Copynumber: 26.3 Consensus size: 3
537245 CGAGAGTGTG
* *
537255 GGA GGG GGA AGA GGA GGA GGA GGA GGA GGA GGA GGA GGA -GA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
* * * * *
537302 GGA GAA GAA GGA GGA GAA GAA GGA GAA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
537333 AAGAAGAAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:537337 original size:9 final size:9
Alignment explanation
Indices: 537307--537659 Score: 271
Period size: 9 Copynumber: 39.6 Consensus size: 9
537297 GAGGAGGAGA
*
537307 AGAAGGAGG
1 AGAAGAAGG
537316 AGAAGAAGG
1 AGAAGAAGG
* *
537325 AGAAGGAGA
1 AGAAGAAGG
*
537334 AGAAGAAGA
1 AGAAGAAGG
537343 AGAAGAAGG
1 AGAAGAAGG
* *
537352 AGAAAAAGA
1 AGAAGAAGG
*
537361 AGAAGAATG
1 AGAAGAAGG
537370 AGAAG-A--
1 AGAAGAAGG
537376 AGAAGAAGG
1 AGAAGAAGG
537385 AG-A-AAGG
1 AGAAGAAGG
*
537392 AGAAGGAGG
1 AGAAGAAGG
537401 AGAAGAAGG
1 AGAAGAAGG
*
537410 AGGAGAAGG
1 AGAAGAAGG
537419 A-AGAGAAGG
1 AGA-AGAAGG
*
537428 AGAAGAAGA
1 AGAAGAAGG
*
537437 AGAAGAAGA
1 AGAAGAAGG
*
537446 AGAAGAAGA
1 AGAAGAAGG
*
537455 AGAAGAAGT
1 AGAAGAAGG
537464 AGAAGAAGG
1 AGAAGAAGG
**
537473 AGAAGGAGAAA
1 AGAA-GA-AGG
*
537484 AAAAGAAGG
1 AGAAGAAGG
537493 AGAAGAA-G
1 AGAAGAAGG
537501 -G-AGAAGG
1 AGAAGAAGG
537508 AGAAGAAGG
1 AGAAGAAGG
537517 AGAAAGAGGAGG
1 AG-AAGA--AGG
*
537529 AGGAGAAGG
1 AGAAGAAGG
*
537538 AGAAGAAGA
1 AGAAGAAGG
*
537547 AGGAGAA-G
1 AGAAGAAGG
537555 -G-AGAAGG
1 AGAAGAAGG
* *
537562 AGAAGGATG
1 AGAAGAAGG
*
537571 AGAATAAGG
1 AGAAGAAGG
537580 AGAAGAAGCAG
1 AGAAGAAG--G
* *
537591 AAGCAGAAGC
1 -AGAAGAAGG
537601 AGAAGAAGG
1 AGAAGAAGG
* *
537610 AGAAGCAGA
1 AGAAGAAGG
*
537619 AGCAGAAGG
1 AGAAGAAGG
537628 AGAAGAAGG
1 AGAAGAAGG
*
537637 AGAAGAAGA
1 AGAAGAAGG
* *
537646 AGGAGAAGA
1 AGAAGAAGG
537655 AGAAG
1 AGAAG
537660 CTGCCACATC
Statistics
Matches: 276, Mismatches: 47, Indels: 42
0.76 0.13 0.12
Matches are distributed among these distances:
6 13 0.05
7 11 0.04
8 6 0.02
9 217 0.79
10 9 0.03
11 8 0.03
12 12 0.04
ACGTcount: A:0.56, C:0.01, G:0.41, T:0.01
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:537393 original size:7 final size:6
Alignment explanation
Indices: 537266--537659 Score: 200
Period size: 6 Copynumber: 65.3 Consensus size: 6
537256 GAGGGGGAAG
* * * * * * *
537266 AGGAGG AGGAGG AGGAGG AGGAGG AGGAGA GGAGGAGG AGAAGA AGGAGG
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA --AGGAGA AGGAGA AGGAGA
* * ** *
537316 AGAAGA AGGAGA AGGAGA AGAAGAAGA AGAAGA AGGAGA AAAAGA AGAAGA
1 AGGAGA AGGAGA AGGAGA AG--G-AGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * * *
537367 ATGAGAAGA AGAAGA AGGAGAA AGGAGA AGGAGG AGAAGA AGGAGG AGAAGGA
1 A-G-G-AGA AGGAGA AGGAG-A AGGAGA AGGAGA AGGAGA AGGAGA AGGA-GA
* * * * *
537420 A-GAGA AGGAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGTAGAAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AG--G-AGA
* * * * *
537470 AGGAGA AGGAGA A-AAAA AGAAGG AGAAGA AGGAGA AGGAG- A--AGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* *
537514 AGGAGA A--AG- AGGAGG AGGAGA AGGAGA AGAAGA AGGAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * * * * * * *
537559 AGGAGA AGGATG- AGAATA AGGAGA AGAAGC AGAAGC AGAAGC AGAAGA
1 AGGAGA AGGA-GA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * *
537607 AGGAGA AGCAGA AGCAGA AGGAG- A--AGA AGGAGA AGAAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
*
537652 AGAAGA AG
1 AGGAGA AG
537660 CTGCCACATC
Statistics
Matches: 313, Mismatches: 49, Indels: 52
0.76 0.12 0.13
Matches are distributed among these distances:
3 5 0.02
4 4 0.01
5 10 0.03
6 262 0.84
7 11 0.04
8 7 0.02
9 14 0.04
ACGTcount: A:0.54, C:0.01, G:0.44, T:0.01
Consensus pattern (6 bp):
AGGAGA
Found at i:537903 original size:3 final size:3
Alignment explanation
Indices: 537895--538278 Score: 354
Period size: 3 Copynumber: 130.0 Consensus size: 3
537885 ATATTTTATT
* * *
537895 AAG AAG AAG GAG AAG -AG GAG AAG GAG AAG AAG AAG -AG AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * * *
537940 AAG GAG GAG AAG AGAG GAG AAG GAG GAG AAG AAG GAG AAG -AG GAG
1 AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
537985 AA- AGAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
538030 AAG AAG -AG AAG AAG AAT AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
*
538078 AAG AAG AAG -AG AAG AAG GAG AA- AAG -AG AAG AAG AA- AGAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG
* * *
538120 -AG AAG AAG AAG AAG AAT AGG AAG AAAG AA- AAG CAAG GAG AAG AATG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG -AAG AAG AAG AA-G
* *
538166 -AG AAG CAG AAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
538213 GAG GAG AAG AATG -AG AAG GAG AATG -AG AA- AGAG AA- AGAG AATG
1 AAG AAG AAG AA-G AAG AAG AAG AA-G AAG AAG A-AG AAG A-AG AA-G
538256 -AG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG
538279 CTACCACATC
Statistics
Matches: 319, Mismatches: 32, Indels: 60
0.78 0.08 0.15
Matches are distributed among these distances:
2 28 0.09
3 272 0.85
4 19 0.06
ACGTcount: A:0.60, C:0.01, G:0.38, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:548797 original size:29 final size:29
Alignment explanation
Indices: 548763--548831 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
548753 TTTATGTTAA
* *
548763 AGGGGACGAATTTGAACTTTTAAAATTTT
1 AGGGGACGAACTTGAACTTATAAAATTTT
* *
548792 TGGGGATGAACTTGAACTTATAAAATTTT
1 AGGGGACGAACTTGAACTTATAAAATTTT
*
548821 AGGGGATGAAC
1 AGGGGACGAAC
548832 ACAAATTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (29 bp):
AGGGGACGAACTTGAACTTATAAAATTTT
Found at i:551203 original size:179 final size:180
Alignment explanation
Indices: 550861--551227 Score: 603
Period size: 179 Copynumber: 2.0 Consensus size: 180
550851 TTCGAGTCGA
* *
550861 GTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACTGGACCAACCCGAAAATATATATAATTCAAG
1 GTCGGGTCGAGTTCGGATTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATTCAA-
550926 TCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTATTATTTCCGGTCGGGTCG
65 --GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTATTATTTCCGGTCGGGTCG
* *
550991 GATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTTGG
128 GATTTCTAATTCATATATTCGGGTCGAGTCGGATGAAACTTTATTTTGTTCGG
* *
551044 GTCGGGTCGGGTTCGGATTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTC-A-
1 GTCGGGTCGAGTTCGGATTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATTCAAG
* * *
551107 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCGGGTCGGGTCGGA
66 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTT-TTATTATTTCCGGTCGGGTCGGA
551172 TTTCTAATTCATATATTCGGGTCGAGTCGGATGAAACTTTATTTTGTTCGG
130 TTTCTAATTCATATATTCGGGTCGAGTCGGATGAAACTTTATTTTGTTCGG
551223 GTCGG
1 GTCGG
551228 TTTTTTTAAG
Statistics
Matches: 174, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
178 39 0.22
179 76 0.44
182 1 0.01
183 58 0.33
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (180 bp):
GTCGGGTCGAGTTCGGATTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATTCAAG
GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTATTATTTCCGGTCGGGTCGGAT
TTCTAATTCATATATTCGGGTCGAGTCGGATGAAACTTTATTTTGTTCGG
Found at i:551419 original size:216 final size:216
Alignment explanation
Indices: 551043--551540 Score: 636
Period size: 216 Copynumber: 2.3 Consensus size: 216
551033 ATTTTGTTTG
*
551043 GGTCGGGTCGGGTTCGGATTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAA-TTCA
1 GGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTTCA
*
551107 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCGGGTCGGGTCGGA
66 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCAGGTCGGGTCGGA
* ** *
551172 TTTCTAATTCATATATTCGGGTCGAGTCGGA-TG-AAACT-T-TATTTTGTTCGGGTC-GGTTTT
131 -TTCAAATTCATATATTCGGGTCGAGTCGGATTGTAAACTGTATATTCGGGTCGGGTCGGGTTTT
*
551232 TTTAAGTGTGATATTCGGGTC-
195 TTTAAGTGTGATATTCGAGTCA
* *
551253 GAGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAAGCAGACCGACCCGAAAATATATATAATTCG
1 G-GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATT--
* *
551318 GGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAATTAATTTT-TTATTATTTCAGGTCGG
63 --TCAGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAAT-ATTTTATTATTATTTCAGGTCGG
* * * * * * *
551382 GTCGGA-TGAAACTTTATTTTGTTCGGGTCGGGTCGGATTTGTTAAGTGTGATATTCGGGTCGGG
125 GTCGGATTCAAA-TTCA-TATATTCGGGTCGAGTCGGA-TTGTAAACTGT-ATATTCGGGTCGGG
551446 TCGGGTTTTTTTAAGTGTGATATTCGAGTCA
186 TCGGGTTTTTTTAAGTGTGATATTCGAGTCA
** *
551477 GGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACTAACCCGAAAAAAATATATAATTT
1 GGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCG-AAAATATATATAATTT
551541 TACCTTATAT
Statistics
Matches: 247, Mismatches: 23, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
210 1 0.00
211 56 0.23
212 1 0.00
214 3 0.01
215 3 0.01
216 76 0.31
217 5 0.02
218 2 0.01
219 3 0.01
220 2 0.01
222 12 0.05
223 68 0.28
224 15 0.06
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (216 bp):
GGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTTCA
GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCAGGTCGGGTCGGA
TTCAAATTCATATATTCGGGTCGAGTCGGATTGTAAACTGTATATTCGGGTCGGGTCGGGTTTTT
TTAAGTGTGATATTCGAGTCA
Done.