Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold291
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: 742724
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 5
Found at i:435565 original size:22 final size:22
Alignment explanation
Indices: 435539--435655 Score: 102
Period size: 22 Copynumber: 5.2 Consensus size: 22
435529 TGATGTATTT
435539 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTA
*
435561 GGTGATGTAT-TT-GGTGAAAATGTTA
1 GGTGA-GAATGTTAGGTG----TGTTA
*
435586 GGT--G--TGTTAGGTGATGTGTTT
1 GGTGAGAATGTTAGGT---GTGTTA
435607 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTA
435629 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTA
435651 GGTGA
1 GGTGA
435656 TGTATTTGGT
Statistics
Matches: 78, Mismatches: 3, Indels: 28
0.72 0.03 0.26
Matches are distributed among these distances:
20 1 0.01
21 13 0.17
22 43 0.55
23 4 0.05
25 17 0.22
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.38
Consensus pattern (22 bp):
GGTGAGAATGTTAGGTGTGTTA
Found at i:435656 original size:56 final size:56
Alignment explanation
Indices: 435573--435684 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
435563 TGATGTATTT
*
435573 GGTGAAAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAAAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
*
435629 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAAAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
435685 ACATGTATAT
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:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (56 bp):
GGTGAAAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
Found at i:440397 original size:34 final size:34
Alignment explanation
Indices: 440359--440528 Score: 331
Period size: 34 Copynumber: 5.0 Consensus size: 34
440349 CTTTGTTAAG
440359 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
440393 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
440427 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
440461 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
440495 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
440529 GAATGTTAGG
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 135 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:440412 original size:25 final size:25
Alignment explanation
Indices: 440383--440484 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
440373 ATGTTAGGTG
440383 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
* *
440408 TGTTAGGTG-TG--TTAGGTGATGTA
1 TGTTAGGTGATGTATTTGGTGA-GAA
*
440431 T-TT-GGTGA-GAATGTTAGGT--G--
1 TGTTAGGTGATGTAT-TT-GGTGAGAA
440451 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
440476 TGTTAGGTG
1 TGTTAGGTG
440485 TGTTAGGTGA
Statistics
Matches: 60, Mismatches: 4, Indels: 26
0.67 0.04 0.29
Matches are distributed among these distances:
20 1 0.02
21 10 0.17
22 17 0.28
23 8 0.13
24 3 0.05
25 21 0.35
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (25 bp):
TGTTAGGTGATGTATTTGGTGAGAA
Found at i:440535 original size:56 final size:56
Alignment explanation
Indices: 440468--440579 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
440458 TGATGTATTT
* **
440468 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGCTAGGTGATGCATTTGGTGAGAATGTTAGGTGTGTTA
440524 GGTGAGAATGTTAGGTGTGCTAGGTGATGCATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGCTAGGTGATGCATTTGGTGAGAATGTTAGGTGTGTTA
440580 ACATGTATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.38
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGCTAGGTGATGCATTTGGTGAGAATGTTAGGTGTGTTA
Found at i:440562 original size:68 final size:66
Alignment explanation
Indices: 440359--440579 Score: 309
Period size: 68 Copynumber: 3.4 Consensus size: 66
440349 CTTTGTTAAG
440359 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGT-AG-ATGTTAGGTGTGTTAGG
440424 TGA
64 TGA
440427 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGT-AG-ATGTTAGGTGTGTTAGG
440492 TGA
64 TGA
* *
440495 TGTGTTTGGTGAGAATGTTAGGTGTGTTA-G-G-TG-A----G-A-ATGTTAGGTGTGCTAGGTG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTAGATGTTAGGTGTGTTAGGTG
440550 A
66 A
*
440551 TGCATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTA
440580 ACATGTATAT
Statistics
Matches: 149, Mismatches: 4, Indels: 12
0.90 0.02 0.07
Matches are distributed among these distances:
56 46 0.31
58 1 0.01
60 1 0.01
64 1 0.01
65 2 0.01
66 1 0.01
67 1 0.01
68 96 0.64
ACGTcount: A:0.20, C:0.01, G:0.38, T:0.40
Consensus pattern (66 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTAGATGTTAGGTGTGTTAGGTG
A
Found at i:442483 original size:16 final size:16
Alignment explanation
Indices: 442464--442542 Score: 77
Period size: 16 Copynumber: 4.9 Consensus size: 16
442454 GTTCGAACTT
* *
442464 AAAAAATTTTAATCCA
1 AAAAAATTTAAATTCA
* *
442480 AAAATATTTAAATTTA
1 AAAAAATTTAAATTCA
* *
442496 AAATAATTTGAATTCA
1 AAAAAATTTAAATTCA
*
442512 AAATAAATTTAAATTTA
1 AAA-AAATTTAAATTCA
*
442529 AAATAATTTAAATT
1 AAAAAATTTAAATT
442543 TTAAAAATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 37 0.74
17 13 0.26
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (16 bp):
AAAAAATTTAAATTCA
Found at i:442527 original size:33 final size:32
Alignment explanation
Indices: 442462--442542 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 32
442452 TAGTTCGAAC
* * *
442462 TTAAAA-AATTTTAATCCAAAAATATTTAAAT
1 TTAAAATAATTTAAATTCAAAAAAATTTAAAT
*
442493 TTAAAATAATTTGAATTCAAAATAAATTTAAAT
1 TTAAAATAATTTAAATTCAAAA-AAATTTAAAT
442526 TTAAAATAATTTAAATT
1 TTAAAATAATTTAAATT
442543 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 6 0.14
32 13 0.30
33 25 0.57
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (32 bp):
TTAAAATAATTTAAATTCAAAAAAATTTAAAT
Found at i:442545 original size:17 final size:16
Alignment explanation
Indices: 442480--442548 Score: 95
Period size: 16 Copynumber: 4.2 Consensus size: 16
442470 TTTTAATCCA
442480 AAAAT-ATTTAAATTT
1 AAAATAATTTAAATTT
* *
442495 AAAATAATTTGAATTC
1 AAAATAATTTAAATTT
442511 AAAATAAATTTAAATTT
1 AAAAT-AATTTAAATTT
442528 AAAATAATTTAAATTTT
1 AAAATAATTTAAA-TTT
442545 AAAA
1 AAAA
442549 ATAACCTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.11
16 21 0.45
17 21 0.45
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:443062 original size:22 final size:26
Alignment explanation
Indices: 443036--443091 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 26
443026 GATTAATTTG
443036 ATTTAAATT-A-TTAAAATA-ATT-A
1 ATTTAAATTAATTTAAAATAGATTGA
* *
443058 ATTTAATTTAATTTAATATAGATTGA
1 ATTTAAATTAATTTAAAATAGATTGA
443084 ATTTAAAT
1 ATTTAAAT
443092 ACTTCACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 1 0.04
24 7 0.26
25 3 0.11
26 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
ATTTAAATTAATTTAAAATAGATTGA
Found at i:443272 original size:24 final size:25
Alignment explanation
Indices: 443219--443273 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
443209 ATTTAGATAT
443219 AAATATAAAAATATAATATTTTTAAA
1 AAAT-TAAAAATATAATATTTTTAAA
*
443245 AAATTAAACATAT-ATA-TTTTAAA
1 AAATTAAAAATATAATATTTTTAAA
443268 CAAATT
1 -AAATT
443274 TACTTGAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 7 0.26
24 8 0.30
25 8 0.30
26 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTAAAAATATAATATTTTTAAA
Found at i:443869 original size:2 final size:2
Alignment explanation
Indices: 443862--443886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
443852 GGTTTTCATT
443862 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
443887 GTATCAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:451548 original size:30 final size:30
Alignment explanation
Indices: 451512--451600 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 30
451502 ATATTTTTAC
451512 TACATTTAAATAAGTCCTTAACATTTAATT
1 TACATTTAAATAAGTCCTTAACATTTAATT
* * * * *
451542 TGCATTTAAATAAATCATTCACTTTTAATT
1 TACATTTAAATAAGTCCTTAACATTTAATT
* *** *
451572 TATACACAAATAAGCCCTTAACATTTAAT
1 TACATTTAAATAAGTCCTTAACATTTAAT
451601 ATATATTTCA
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.40
Consensus pattern (30 bp):
TACATTTAAATAAGTCCTTAACATTTAATT
Found at i:452018 original size:2 final size:2
Alignment explanation
Indices: 452011--452057 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
452001 GAAATTAAAA
452011 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
452053 AG AG A
1 AG AG A
452058 TATTAAAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:452123 original size:34 final size:34
Alignment explanation
Indices: 452080--452148 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
452070 TGGTCTTTTC
452080 GTTCATTCTTTGGCTAATAGTGGTGCCGATGGGT
1 GTTCATTCTTTGGCTAATAGTGGTGCCGATGGGT
*
452114 GTTCATTCTTTGGCTAGTAGTGGTGCCGATGGGT
1 GTTCATTCTTTGGCTAATAGTGGTGCCGATGGGT
452148 G
1 G
452149 CCGATGGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.13, C:0.14, G:0.35, T:0.38
Consensus pattern (34 bp):
GTTCATTCTTTGGCTAATAGTGGTGCCGATGGGT
Found at i:452602 original size:18 final size:18
Alignment explanation
Indices: 452562--452615 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
452552 CTGTGTTTAT
**
452562 TTTATATTTTATATTTTA
1 TTTATATTTTATATCATA
* *
452580 ATTATTTTTTATATCATA
1 TTTATATTTTATATCATA
*
452598 TTTATATTGTATAATCAT
1 TTTATATTTTAT-ATCAT
452616 GCTGCATTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATATTTTATATCATA
Found at i:455132 original size:3 final size:3
Alignment explanation
Indices: 455124--455158 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
455114 TGAAAATGCA
455124 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
455159 ATTTATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:456443 original size:73 final size:73
Alignment explanation
Indices: 456351--456497 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
456341 ATCTCAAATT
*
456351 ACATGTTTTAGGAATAAAGTTTAAAGGAATTCTAGTTTGGGAAATAAGATTGCAAACAA-TCTTA
1 ACATGTTTTAGGAATAAAGTTTAAAAGAATTCTAGTTTGGGAAATAAGATTGCAAACAACT-TTA
456415 GTCTAGGAA
65 GTCTAGGAA
456424 ACATGTTTTAGGAATAAAGTTTAAAAGAATTCTAGTTTGGGAAATAAGATTGCAAACAACTTTAG
1 ACATGTTTTAGGAATAAAGTTTAAAAGAATTCTAGTTTGGGAAATAAGATTGCAAACAACTTTAG
*
456489 TGTAGGAA
66 TCTAGGAA
456497 A
1 A
456498 AAAAACTCTA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 70 0.99
74 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (73 bp):
ACATGTTTTAGGAATAAAGTTTAAAAGAATTCTAGTTTGGGAAATAAGATTGCAAACAACTTTAG
TCTAGGAA
Found at i:458789 original size:2 final size:2
Alignment explanation
Indices: 458784--458814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
458774 ATTTTTCTTT
458784 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
458815 TTTTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:458851 original size:2 final size:2
Alignment explanation
Indices: 458844--458868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
458834 TGTTTCTTAG
458844 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 A
458869 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:458873 original size:2 final size:2
Alignment explanation
Indices: 458868--458902 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
458858 ATATATATAT
458868 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
458903 TTTATTCTTT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:460344 original size:31 final size:31
Alignment explanation
Indices: 460309--460367 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
460299 ATTATTTTTT
*
460309 TAATTTATAATTAATCTTCTTTTCTATTTGA
1 TAATTTATAACTAATCTTCTTTTCTATTTGA
*
460340 TAATTTCTAACTAATCTTCTTTTCTATT
1 TAATTTATAACTAATCTTCTTTTCTATT
460368 GTTTTTAATT
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:0.27, C:0.14, G:0.02, T:0.58
Consensus pattern (31 bp):
TAATTTATAACTAATCTTCTTTTCTATTTGA
Found at i:461303 original size:34 final size:34
Alignment explanation
Indices: 461234--461451 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 34
461224 GAATATAGTA
* * *
461234 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
461267 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
461301 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
461334 ATTGTTGATTAAATTGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
461368 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
461402 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
461436 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
461452 TGGTTTTTAC
Statistics
Matches: 161, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
33 41 0.25
34 120 0.75
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:461342 original size:67 final size:66
Alignment explanation
Indices: 461234--461453 Score: 296
Period size: 67 Copynumber: 3.3 Consensus size: 66
461224 GAATATAGTA
* * *
461234 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTG
461299 CC
65 CC
* ** * * * *
461301 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATTGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG
461366 CC
65 CC
* *
461368 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
461433 GCC
64 GCC
461436 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
461454 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (66 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGC
C
Found at i:461408 original size:101 final size:102
Alignment explanation
Indices: 461234--461449 Score: 337
Period size: 101 Copynumber: 2.1 Consensus size: 102
461224 GAATATAGTA
** * *
461234 ATTGTTGATTAAA-TGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGATTAAATTGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
*
461298 GCCATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
66 ACCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
*
461334 ATTGTTGATTAAATTGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATTGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
* * *
461399 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
66 ACCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
461436 ATTGTTGATTAAAT
1 ATTGTTGATTAAAT
461450 GGTGGTTTTT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
100 13 0.12
101 62 0.59
102 30 0.29
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41
Consensus pattern (102 bp):
ATTGTTGATTAAATTGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
ACCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
Found at i:461794 original size:19 final size:19
Alignment explanation
Indices: 461757--461803 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
461747 TTGGTTGTCG
**
461757 AGGTACTGTTCACGTATAC
1 AGGTACTGTTCACACATAC
*
461776 AGGTACTGTTCATACATAC
1 AGGTACTGTTCACACATAC
*
461795 AGTTACTGT
1 AGGTACTGT
461804 GCACGTGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (19 bp):
AGGTACTGTTCACACATAC
Found at i:465936 original size:34 final size:34
Alignment explanation
Indices: 465867--466084 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
465857 AAGTGGGAGA
* * *
465867 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
465900 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
465934 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
465967 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
466001 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
466035 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
466069 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
466085 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:466050 original size:68 final size:67
Alignment explanation
Indices: 465867--466086 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
465857 AAGTGGGAGA
* * * * *
465867 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
465932 CC
66 CC
* ** * *
465934 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
465999 CC
66 CC
* * *
466001 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
466066 GCC
65 GCC
466069 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
466087 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:467499 original size:31 final size:32
Alignment explanation
Indices: 467464--467530 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
467454 TGGATGAACC
**
467464 TTCTAATTAATGCTGTTTTCTATTTTTT-AAT
1 TTCTAATTAATGCTCCTTTCTATTTTTTAAAT
* *
467495 TTCTAATTAATGTTCCTTTCTTTTTTTTAAAT
1 TTCTAATTAATGCTCCTTTCTATTTTTTAAAT
467527 TTCT
1 TTCT
467531 TTGGCTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.63
Consensus pattern (32 bp):
TTCTAATTAATGCTCCTTTCTATTTTTTAAAT
Found at i:476152 original size:30 final size:30
Alignment explanation
Indices: 476116--476176 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
476106 GGTAAAATGC
476116 ATAGTTTCATTTGTTCATTCTTTTACTAGT
1 ATAGTTTCATTTGTTCATTCTTTTACTAGT
*
476146 ATAGTTTCATTTGTTCATTCTTTTCCTAGT
1 ATAGTTTCATTTGTTCATTCTTTTACTAGT
476176 A
1 A
476177 ATGCTGCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (30 bp):
ATAGTTTCATTTGTTCATTCTTTTACTAGT
Found at i:477908 original size:19 final size:17
Alignment explanation
Indices: 477875--477918 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
477865 ACTTAAACAC
477875 AAAATGAAAAAAATAATTA
1 AAAAT-AAAAAAAT-ATTA
*
477894 AAACATAAAACAATATTA
1 AAA-ATAAAAAAATATTA
477912 AAAATAA
1 AAAATAA
477919 CATAAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 10 0.43
20 2 0.09
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAATAAAAAAATATTA
Found at i:478085 original size:16 final size:16
Alignment explanation
Indices: 478061--478107 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
478051 AATACAAAAA
*
478061 TCTTTTTTTCTTTCCT
1 TCTTCTTTTCTTTCCT
478077 TCTTCTTTTCTTT-CT
1 TCTTCTTTTCTTTCCT
* *
478092 TTTTCTTTTTTTTCCT
1 TCTTCTTTTCTTTCCT
478108 CTTTCCCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTCTTTTCTTTCCT
Found at i:478112 original size:16 final size:16
Alignment explanation
Indices: 478061--478112 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
478051 AATACAAAAA
478061 TCTTT-TTTTCTTTCC
1 TCTTTCTTTTCTTTCC
478076 T-TCTTCTTTTCTTT-C
1 TCT-TTCTTTTCTTTCC
* *
478091 TTTTTCTTTTTTTTCC
1 TCTTTCTTTTCTTTCC
478107 TCTTTC
1 TCTTTC
478113 CCTTTGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 1 0.03
15 15 0.48
16 15 0.48
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTTTCTTTTCTTTCC
Found at i:478644 original size:9 final size:9
Alignment explanation
Indices: 478610--478644 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
478600 GTTCAAAAGC
478610 TTTTTAATA
1 TTTTTAATA
*
478619 -TTTTAATT
1 TTTTTAATA
478627 TTTTTAATA
1 TTTTTAATA
478636 TTTTTAATA
1 TTTTTAATA
478645 GAAAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTAATA
Found at i:478670 original size:21 final size:20
Alignment explanation
Indices: 478641--478683 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
478631 TAATATTTTT
*
478641 AATAGAAAACAAAATCAAAAA
1 AATAAAAAACAAAAT-AAAAA
* *
478662 AATAAAAAATAAACTAAAAA
1 AATAAAAAACAAAATAAAAA
478682 AA
1 AA
478684 GGTTAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (20 bp):
AATAAAAAACAAAATAAAAA
Found at i:479384 original size:22 final size:24
Alignment explanation
Indices: 479346--479398 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
479336 TTTTTTGATG
*
479346 TATTTATAATTATTTTTTATATTA
1 TATTTATAATTATTTTTCATATTA
*
479370 TATTT-TAATTA-TTTTCGTATTA
1 TATTTATAATTATTTTTCATATTA
479392 TATTTAT
1 TATTTAT
479399 GTTATGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 14 0.54
23 7 0.27
24 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTATAATTATTTTTCATATTA
Found at i:490226 original size:2 final size:2
Alignment explanation
Indices: 490219--490254 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
490209 GAAGTCGAGA
490219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
490255 GTATGTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:491671 original size:3 final size:3
Alignment explanation
Indices: 491663--491687 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
491653 AGGGCAACGA
491663 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
491688 CTCTGGTTTA
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:498356 original size:19 final size:19
Alignment explanation
Indices: 498332--498370 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
498322 TAAATTTAAA
*
498332 ATATGCTTAGTACATCAAT
1 ATATGCTTAGTAAATCAAT
498351 ATATGCTTAGTAAATCAAT
1 ATATGCTTAGTAAATCAAT
498370 A
1 A
498371 AGACATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (19 bp):
ATATGCTTAGTAAATCAAT
Found at i:501125 original size:18 final size:18
Alignment explanation
Indices: 501102--501163 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
501092 CATGTTCTTG
501102 GCAGAATTTCGTAAGAGA
1 GCAGAATTTCGTAAGAGA
***
501120 GCAGAATTT--TAATCTTA
1 GCAGAATTTCGTAA-GAGA
*
501137 GCAGAATTTCGTTAGAGA
1 GCAGAATTTCGTAAGAGA
*
501155 ACAGAATTT
1 GCAGAATTT
501164 TAAAGCTTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
16 3 0.09
17 10 0.30
18 18 0.55
19 2 0.06
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (18 bp):
GCAGAATTTCGTAAGAGA
Found at i:501148 original size:35 final size:35
Alignment explanation
Indices: 501097--501166 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
501087 ATTACCATGT
* *
501097 TCTTGGCAGAATTTCGTAAGAGAGCAGAATTTTAA
1 TCTTAGCAGAATTTCGTAAGAGAACAGAATTTTAA
*
501132 TCTTAGCAGAATTTCGTTAGAGAACAGAATTTTAA
1 TCTTAGCAGAATTTCGTAAGAGAACAGAATTTTAA
501167 AGCTTGTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (35 bp):
TCTTAGCAGAATTTCGTAAGAGAACAGAATTTTAA
Found at i:503949 original size:11 final size:11
Alignment explanation
Indices: 503861--503952 Score: 66
Period size: 11 Copynumber: 8.5 Consensus size: 11
503851 ATAATTTATA
*
503861 TTATATAAAAT
1 TTATATAATAT
503872 TTA-A-AATAT
1 TTATATAATAT
*
503881 TTATAAAATAT
1 TTATATAATAT
* *
503892 TTTTATAATTTT
1 TTATATAA-TAT
*
503904 TTATATTATAT
1 TTATATAATAT
* *
503915 TATATTTAAAAT
1 T-TATATAATAT
*
503927 TTATAT--TTT
1 TTATATAATAT
503936 TTATATAATAT
1 TTATATAATAT
503947 TTATAT
1 TTATAT
503953 TATGTAATAT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
9 14 0.23
10 2 0.03
11 29 0.48
12 16 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTATATAATAT
Found at i:503955 original size:16 final size:16
Alignment explanation
Indices: 503903--503963 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
503893 TTTATAATTT
*
503903 TTTATATTATATTATA
1 TTTATATTATATAATA
* *
503919 TTTA-A-AAT-TTATA
1 TTTATATTATATAATA
503932 TTT-T-TTATATAATA
1 TTTATATTATATAATA
*
503946 TTTATATTATGTAATA
1 TTTATATTATATAATA
503962 TT
1 TT
503964 ATTTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 10 0.28
14 9 0.25
15 2 0.06
16 15 0.42
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTATATTATATAATA
Found at i:504137 original size:22 final size:22
Alignment explanation
Indices: 504097--504162 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
504087 ATATATAAAG
* *
504097 TAATAAAAATTAAAATATTTTTA
1 TAAT-AAAATTTAATTATTTTTA
*
504120 T-ATAAATATTTATTTA-TTTTA
1 TAATAAA-ATTTAATTATTTTTA
504141 TAATAAAATTTAATT-TTTTTA
1 TAATAAAATTTAATTATTTTTA
504162 T
1 T
504163 TTATTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
21 22 0.61
22 13 0.36
23 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAAATTTAATTATTTTTA
Found at i:504539 original size:48 final size:47
Alignment explanation
Indices: 504436--504539 Score: 108
Period size: 48 Copynumber: 2.2 Consensus size: 47
504426 AATTTAAATT
*
504436 ATTATTTAATAATAAAAATATTTTTAAAATTTAATTAAAATATATAAAA
1 ATTA-TTAATAATAAAAATATTTTTAAAATTT-ATTAAAATATAAAAAA
*
504485 A-TATTAAT-ATAAAAATAAATTTTTAATATTT-TT-AAATAATAAAATAA
1 ATTATTAATAATAAAAAT--ATTTTTAAAATTTATTAAAAT-ATAAAA-AA
504532 ATTATTAA
1 ATTATTAA
504540 ATTGATTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
45 4 0.08
46 15 0.31
47 8 0.17
48 20 0.42
49 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (47 bp):
ATTATTAATAATAAAAATATTTTTAAAATTTATTAAAATATAAAAAA
Found at i:505535 original size:24 final size:23
Alignment explanation
Indices: 505508--505572 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
505498 AAGACAAGAA
505508 AAAATAAAATCAAAAGGAAATAGT
1 AAAATAAAA-CAAAAGGAAATAGT
**
505532 AAAATAAAACATAAAAAACAATAGT
1 AAAATAAAACA-AAAGGA-AATAGT
505557 -AAATAAAA-AAAAGGAA
1 AAAATAAAACAAAAGGAA
505573 TAGATCAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.03
22 4 0.11
23 3 0.09
24 21 0.60
25 6 0.17
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (23 bp):
AAAATAAAACAAAAGGAAATAGT
Found at i:505680 original size:37 final size:36
Alignment explanation
Indices: 505608--505684 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
505598 TAAATTTAAA
* * **
505608 TTATATATTTTATTAAAAATTTATTTATATTTATAT
1 TTATATATTTTATTAAAAATTTAATTAAAAATATAT
505644 TTATATATTTTA-TAATTAAATTTAATTAAAAATATAT
1 TTATATATTTTATTAA--AAATTTAATTAAAAATATAT
505681 TTAT
1 TTAT
505685 TTTAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 3 0.09
36 12 0.34
37 20 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
TTATATATTTTATTAAAAATTTAATTAAAAATATAT
Found at i:505705 original size:19 final size:21
Alignment explanation
Indices: 505664--505714 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
505654 TATAATTAAA
505664 TTTAATTAAAAATATATTTAT
1 TTTAATTAAAAATATATTTAT
*
505685 TTTAATTTAAAAT-TA-TTAT
1 TTTAATTAAAAATATATTTAT
*
505704 TTTAAATAAAA
1 TTTAATTAAAA
505715 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATTAAAAATATATTTAT
Found at i:507489 original size:13 final size:13
Alignment explanation
Indices: 507473--507497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507463 TATTCGACAT
507473 ATATTTTAAACAC
1 ATATTTTAAACAC
507486 ATATTTTAAACA
1 ATATTTTAAACA
507498 TAAATATAAA
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:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTTTAAACAC
Found at i:509194 original size:5 final size:5
Alignment explanation
Indices: 509184--509253 Score: 58
Period size: 5 Copynumber: 14.4 Consensus size: 5
509174 TGTAGTAAAA
* * *
509184 TATAT TATAT TA-AT TATAT T-TAAA TATAA AATAT TATAT T-TAT TATAT
1 TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT
*
509232 TATAT AATTAT TATAT T-TAT TA
1 TATAT TA-TAT TATAT TATAT TA
509254 AACGTTTCGT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 13 0.25
5 35 0.66
6 5 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:509217 original size:24 final size:24
Alignment explanation
Indices: 509181--509252 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
509171 AAATGTAGTA
**
509181 AAATATATTATATTA-ATTATATTT
1 AAATATAAAATATTATATT-TATTT
509205 AAATATAAAATATTATATTTA-TT
1 AAATATAAAATATTATATTTATTT
* *
509228 ATATTATATAATTATTATATTTATT
1 A-AATATA-AAATATTATATTTATT
509253 AAACGTTTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.08
24 20 0.50
25 16 0.40
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AAATATAAAATATTATATTTATTT
Found at i:509252 original size:29 final size:29
Alignment explanation
Indices: 509182--509253 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
509172 AATGTAGTAA
509182 AATATATTATATTAATTATATTTAAATAT
1 AATATATTATATTAATTATATTTAAATAT
* *
509211 AAAATATTATATTTATTATA-TT--ATAT
1 AATATATTATATTAATTATATTTAAATAT
*
509237 AAT-TATTATATTTATTA
1 AATATATTATATTAATTA
509254 AACGTTTCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.35
26 6 0.15
28 2 0.05
29 18 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
AATATATTATATTAATTATATTTAAATAT
Found at i:510006 original size:19 final size:19
Alignment explanation
Indices: 509984--510026 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
509974 ATTTAGTCTA
509984 TTTTT-TAAATAAGCTTAAT
1 TTTTTGTAAATAAG-TTAAT
**
510003 TTTTTGTATCTAAGTTAAT
1 TTTTTGTAAATAAGTTAAT
510022 TTTTT
1 TTTTT
510027 AGGCCTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTGTAAATAAGTTAAT
Found at i:510147 original size:13 final size:14
Alignment explanation
Indices: 510129--510159 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
510119 CGTGTTAAAA
510129 AAAATT-ATATTTT
1 AAAATTAATATTTT
510142 AAAATTAATATTTT
1 AAAATTAATATTTT
510156 AAAA
1 AAAA
510160 GATAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATTAATATTTT
Found at i:510939 original size:18 final size:20
Alignment explanation
Indices: 510918--510956 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
510908 AATATTTATT
510918 TAAATTT-AAA-TTAAAAAA
1 TAAATTTAAAATTTAAAAAA
510936 TAAATTTAAAATTTAAAAAA
1 TAAATTTAAAATTTAAAAAA
510956 T
1 T
510957 TTATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATTTAAAATTTAAAAAA
Found at i:510993 original size:17 final size:16
Alignment explanation
Indices: 510953--510998 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
510943 AAAATTTAAA
510953 AAATTTATATTAATTAT
1 AAATTTAT-TTAATTAT
*
510970 AAA-TTATTTGATTATT
1 AAATTTATTTAATTA-T
510986 AAATTTATTTAAT
1 AAATTTATTTAAT
510999 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AAATTTATTTAATTAT
Found at i:511782 original size:22 final size:22
Alignment explanation
Indices: 511754--511817 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 22
511744 AATTAATTTG
**
511754 ATTTAATTTAATTTAAATTATT
1 ATTTAATTTAATTTAAAAAATT
511776 ATTTAA--TAA-TTAAAAAATT
1 ATTTAATTTAATTTAAAAAATT
*
511795 ATTTAAATTTAATAATAAAAAAT
1 ATTT-AATTTAAT-TTAAAAAAT
511818 ATAATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 12 0.35
20 5 0.15
22 9 0.26
24 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATTTAATTTAAAAAATT
Found at i:511829 original size:25 final size:26
Alignment explanation
Indices: 511775--511829 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
511765 TTTAAATTAT
*
511775 TATTTAATAATTAAAAAATTATTTAA
1 TATTTAATAATTAAAAAATTATATAA
511801 -ATTTAATAA-TAAAAAA-TATAATAA
1 TATTTAATAATTAAAAAATTAT-ATAA
511825 TATTT
1 TATTT
511830 TTTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.12
24 10 0.38
25 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TATTTAATAATTAAAAAATTATATAA
Found at i:511836 original size:18 final size:18
Alignment explanation
Indices: 511815--511859 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
511805 AATAATAAAA
*
511815 AATATAATAATATTTTTT
1 AATATAATAATATTATTT
**
511833 AATATTTTAATATTATTT
1 AATATAATAATATTATTT
511851 AA-ATAATAA
1 AATATAATAA
511860 AATTCATTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATAATAATATTATTT
Found at i:512611 original size:21 final size:20
Alignment explanation
Indices: 512575--512617 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
512565 TTCATTTTTT
512575 AAAAATTTTTTATATATTTA
1 AAAAATTTTTTATATATTTA
512595 AAAAATTATATTT-TATATTTA
1 AAAAATT-T-TTTATATATTTA
512616 AA
1 AA
512618 TTTGAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 11 0.52
22 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAAATTTTTTATATATTTA
Found at i:514589 original size:30 final size:31
Alignment explanation
Indices: 514528--514607 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
514518 CAAATTGATA
*
514528 TAAAAATTTATATTATTATTTAAAATAATAT
1 TAAAAATTTAAATTATTATTTAAAATAATAT
* *
514559 TAAAAATTTAAATTATT-TTTATATTAATAT
1 TAAAAATTTAAATTATTATTTAAAATAATAT
*
514589 T-AATATATT-AATTATTATT
1 TAAAAAT-TTAAATTATTATT
514608 GTTCAGTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 11 0.26
30 16 0.37
31 16 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TAAAAATTTAAATTATTATTTAAAATAATAT
Found at i:516643 original size:38 final size:38
Alignment explanation
Indices: 516542--516643 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 38
516532 GTACAATTAA
* * *
516542 AAAAATTACTATTCTT-AATTAGTAGCACAATTCGAAAC
1 AAAAATTACTATT-TTAAACTAGTGGCACAATTCAAAAC
* * *
516580 AAAAATTA-T-TTCTAAACCAGTGGCACAATTCAAAAT
1 AAAAATTACTATTTTAAACTAGTGGCACAATTCAAAAC
516616 AAAAATTACTATTTTAAACTAGTGGCAC
1 AAAAATTACTATTTTAAACTAGTGGCAC
516644 GTTGAAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 1 0.02
36 27 0.51
37 2 0.04
38 23 0.43
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (38 bp):
AAAAATTACTATTTTAAACTAGTGGCACAATTCAAAAC
Found at i:516743 original size:5 final size:5
Alignment explanation
Indices: 516733--516767 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
516723 TCATATTAGG
*
516733 AAACA AAACA AAACA AAACA AAATA AAACA AAACA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA
516768 TGTTTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.80, C:0.17, G:0.00, T:0.03
Consensus pattern (5 bp):
AAACA
Found at i:519200 original size:27 final size:26
Alignment explanation
Indices: 519155--519217 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
519145 ATATACATTA
*
519155 AAAAATATAATAAATTATTTAAAGT-TT
1 AAAAAT-TAATAAAATA-TTAAAGTATT
*
519182 AAAAATTAATAAAAATATTAAATTATT
1 AAAAATTAAT-AAAATATTAAAGTATT
519209 AAAAATTAA
1 AAAAATTAA
519218 ATTTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAAATTAATAAAATATTAAAGTATT
Found at i:519218 original size:15 final size:15
Alignment explanation
Indices: 519184--519260 Score: 77
Period size: 15 Copynumber: 5.1 Consensus size: 15
519174 TAAAGTTTAA
*
519184 AAATTAATAAAAATATT
1 AAATTATTAAAAA-A-T
*
519201 AAATTATTAAAAATT
1 AAATTATTAAAAAAT
519216 AAATT-TTAAAAAAT
1 AAATTATTAAAAAAT
* *
519230 ATATTTTTAAAAAAT
1 AAATTATTAAAAAAT
519245 AAATTA-TAAAATAAT
1 AAATTATTAAAA-AAT
519260 A
1 A
519261 CATATAAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
14 17 0.33
15 23 0.44
17 12 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTATTAAAAAAT
Found at i:519234 original size:34 final size:35
Alignment explanation
Indices: 519151--519234 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
519141 TAATATATAC
* **
519151 ATTAAAAAATATAATAAATTATTTAAAGTTTAAAA
1 ATTAAAAAATATATTAAATTATTTAAAAATTAAAA
*
519186 ATTAATAAAA-ATATTAAATTA-TTAAAAATTAAAT
1 ATTAA-AAAATATATTAAATTATTTAAAAATTAAAA
*
519220 TTTAAAAAATATATT
1 ATTAAAAAATATATT
519235 TTTAAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
33 4 0.10
34 19 0.45
35 15 0.36
36 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (35 bp):
ATTAAAAAATATATTAAATTATTTAAAAATTAAAA
Found at i:519279 original size:31 final size:32
Alignment explanation
Indices: 519241--519320 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
519231 TATTTTTAAA
*
519241 AAATAAATTATAAAATA-ATACATATAAATCT
1 AAATAAATTATAAAATATATACATATAAATAT
* * **
519272 AAATAAATT-TAAATTATTTATTTATAAATAT
1 AAATAAATTATAAAATATATACATATAAATAT
519303 AAATAAATATAATAAAAT
1 AAATAAAT-T-ATAAAAT
519321 TAAATTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 6 0.15
31 27 0.69
32 1 0.03
34 5 0.13
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
AAATAAATTATAAAATATATACATATAAATAT
Found at i:520012 original size:18 final size:18
Alignment explanation
Indices: 519991--520133 Score: 71
Period size: 18 Copynumber: 7.7 Consensus size: 18
519981 TTATTACATG
* *
519991 TTATATTTATCTTTTATA
1 TTATATTTATATTTAATA
*
520009 TTATAATTATATTTAATA
1 TTATATTTATATTTAATA
* * *
520027 TAATATATAAATTTTAATA
1 TTATATTTATA-TTTAATA
* *
520046 -TATTATATAAAATTTAAAATA
1 TTA-TAT-TTATATTT--AATA
520067 TTTATATATTATA-TTAATA
1 -TTATAT-TTATATTTAATA
* *
520086 TTATTTTTATATTT-TTA
1 TTATATTTATATTTAATA
520103 -TATA-TTATATTTTAATTA
1 TTATATTTATA-TTTAA-TA
520121 TTTATATTTATAT
1 -TTATATTTATAT
520134 ATATTTAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
15 5 0.05
16 6 0.06
17 7 0.07
18 32 0.34
19 17 0.18
20 8 0.08
21 11 0.12
22 7 0.07
23 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATTTATATTTAATA
Found at i:520067 original size:19 final size:19
Alignment explanation
Indices: 520005--520074 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
519995 ATTTATCTTT
* *
520005 TATATTATAATTATATTTAA
1 TATATTAT-ATAAAATTTAA
* *
520025 TATAATATATAAATTTTAA
1 TATATTATATAAAATTTAA
520044 TATATTATATAAAATTTAA
1 TATATTATATAAAATTTAA
*
520063 AATATTTATATA
1 TATA-TTATATA
520075 TTATATTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 28 0.67
20 14 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATTATATAAAATTTAA
Found at i:520103 original size:32 final size:30
Alignment explanation
Indices: 520067--520138 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 30
520057 ATTTAAAATA
*
520067 TTTATATATTATA-TTAATATTATTTTTATATT
1 TTTATATATTATATTTTA-ATTA--TTTATATT
520099 TTTATATATTATATTTTAATTATTTATATT
1 TTTATATATTATATTTTAATTATTTATATT
*
520129 TATATATATT
1 TTTATATATT
520139 TAAAATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 17 0.46
32 17 0.46
33 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTATATATTATATTTTAATTATTTATATT
Found at i:520125 original size:30 final size:31
Alignment explanation
Indices: 519969--520138 Score: 100
Period size: 32 Copynumber: 5.4 Consensus size: 31
519959 TTTTTTTAAG
* * *
519969 TTTTATATATAATTATTACATGTTATATTTATCT
1 TTTTATATATTA-TATTA-ATATTAT-TTTATAT
* * *
520003 TTTATATTATAATTATATTTAATATAATATATAAAT
1 TTT-TA-TAT-ATTATA-TTAATATTAT-TTTATAT
* * *
520039 TTTAATATATTATA-TAA-A--ATTTAAAAT
1 TTTTATATATTATATTAATATTATTTTATAT
*
520066 ATTTATATATTATATTAATATTATTTTTATAT
1 TTTTATATATTATATTAATATTA-TTTTATAT
*
520098 TTTTATATATTATATT-TTAATTA-TTTATAT
1 TTTTATATATTATATTAAT-ATTATTTTATAT
*
520128 TTATATATATT
1 TTTTATATATT
520139 TAAAATTATT
Statistics
Matches: 110, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
27 17 0.15
28 5 0.05
29 1 0.01
30 18 0.16
31 5 0.05
32 25 0.23
33 6 0.05
34 6 0.05
35 3 0.03
36 18 0.16
37 6 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (31 bp):
TTTTATATATTATATTAATATTATTTTATAT
Found at i:520285 original size:19 final size:18
Alignment explanation
Indices: 520261--520309 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
520251 TTTGACACAT
520261 TATTATATTTTCATATTA
1 TATTATATTTTCATATTA
* *
520279 GTATTATTTTTTTCATGTTA
1 -TATTA-TATTTTCATATTA
520299 TATTATATTTT
1 TATTATATTTT
520310 AGTTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 10 0.38
20 11 0.42
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (18 bp):
TATTATATTTTCATATTA
Found at i:521403 original size:19 final size:20
Alignment explanation
Indices: 521353--521407 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 20
521343 GTAATAATTT
521353 TTATAATTTTTTAAATATCGA
1 TTAT-ATTTTTTAAATATCGA
521374 TCATAATATTTTTTAAATAT-GA
1 T--T-ATATTTTTTAAATATCGA
521396 TTATATTTTTTA
1 TTATATTTTTTA
521408 TATTAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 10 0.32
20 1 0.03
21 1 0.03
22 3 0.10
23 14 0.45
24 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
TTATATTTTTTAAATATCGA
Found at i:523106 original size:18 final size:18
Alignment explanation
Indices: 523083--523132 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
523073 GATCTTATTA
523083 ATTAAATTTAC-TTAAATT
1 ATTAAATTT-CTTTAAATT
*
523101 ATTAAAGTTCTTTAAATT
1 ATTAAATTTCTTTAAATT
*
523119 ATTTAATTT-TTTAA
1 ATTAAATTTCTTTAA
523133 GTAAGTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTTCTTTAAATT
Found at i:523546 original size:3 final size:3
Alignment explanation
Indices: 523538--523587 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
523528 CTCCATTTAA
*
523538 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
523586 AA
1 AA
523588 ATTTAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:523874 original size:26 final size:27
Alignment explanation
Indices: 523845--523917 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
523835 AAATATTTTT
*
523845 ATTTTATTTTATTTTATAATAATATGA
1 ATTTTATTTTATTTTATAATAATATTA
* * *
523872 TTTTTA-TGT-TTTTATTAATTATATTA
1 ATTTTATTTTATTTTA-TAATAATATTA
*
523898 ATTTTA-TTTAATTTATAATA
1 ATTTTATTTTATTTTATAATA
523918 TTAAACTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
25 5 0.14
26 22 0.61
27 9 0.25
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (27 bp):
ATTTTATTTTATTTTATAATAATATTA
Found at i:524118 original size:36 final size:38
Alignment explanation
Indices: 524061--524133 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 38
524051 GAACCAATAA
524061 TTAAATAATATGTCCTTAAAAAA-ATAA-GAAATATAG
1 TTAAATAATATGTCCTTAAAAAACATAATGAAATATAG
*
524097 TTAAAT-AT-TGTCCTTAAAAAAAACATAATTAAATATA
1 TTAAATAATATGTCCTT--AAAAAACATAATGAAATATA
524134 TTGTTCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 7 0.22
35 2 0.06
36 12 0.38
37 4 0.12
38 7 0.22
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (38 bp):
TTAAATAATATGTCCTTAAAAAACATAATGAAATATAG
Found at i:524414 original size:18 final size:18
Alignment explanation
Indices: 524369--524414 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
524359 TAATGCATGA
524369 TGATATTGATTTATCGTAT
1 TGATA-TGATTTATCGTAT
* *
524388 TAATTTGATTTATCGTAT
1 TGATATGATTTATCGTAT
524406 TGATATGAT
1 TGATATGAT
524415 ATGTTCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (18 bp):
TGATATGATTTATCGTAT
Found at i:524801 original size:21 final size:20
Alignment explanation
Indices: 524767--524809 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
524757 ATTATGTCTT
*
524767 AATTATTTTAAAATTAAGTTA
1 AATTATTTTAAAA-TAAGATA
524788 AATTAATTTT-AAATAAGATA
1 AATT-ATTTTAAAATAAGATA
524808 AA
1 AA
524810 ATTTTCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AATTATTTTAAAATAAGATA
Found at i:525826 original size:20 final size:20
Alignment explanation
Indices: 525812--525863 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
525802 GAAGTGGGAG
525812 TTTTTTAAAATAAGTGGATA
1 TTTTTTAAAATAAGTGGATA
* **
525832 TTTTTTAAAA-AAATTAATA
1 TTTTTTAAAATAAGTGGATA
*
525851 TTTTTTAATATAA
1 TTTTTTAAAATAA
525864 AAATACGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTTTAAAATAAGTGGATA
Found at i:531099 original size:12 final size:11
Alignment explanation
Indices: 531082--531126 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
531072 AAATGTTAAA
531082 AAAAAAACTTAT
1 AAAAAAA-TTAT
*
531094 AAAAAAATTTT
1 AAAAAAATTAT
531105 AAAAAAATTTAT
1 AAAAAAA-TTAT
*
531117 AATAAAATTA
1 AAAAAAATTA
531127 AATATACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 13 0.45
12 16 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:531116 original size:23 final size:23
Alignment explanation
Indices: 531082--531125 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
531072 AAATGTTAAA
531082 AAAAAAACTTATAAAAAAATTTT
1 AAAAAAACTTATAAAAAAATTTT
* *
531105 AAAAAAATTTATAATAAAATT
1 AAAAAAACTTATAAAAAAATT
531126 AAATATACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAAAACTTATAAAAAAATTTT
Found at i:532268 original size:17 final size:18
Alignment explanation
Indices: 532246--532284 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
532236 CAAATTTGAA
*
532246 TAAATT-AATTTTAATTT
1 TAAATTAAATTTAAATTT
532263 TAAATTAAATTTAAATTT
1 TAAATTAAATTTAAATTT
532281 TAAA
1 TAAA
532285 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATTAAATTTAAATTT
Found at i:533905 original size:20 final size:21
Alignment explanation
Indices: 533867--533905 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
533857 AGCAAATATG
* *
533867 AAAAATGATTAATAGTATTAA
1 AAAAATCATTAATAATATTAA
533888 AAAAATCATTAA-AATATT
1 AAAAATCATTAATAATATT
533906 GATGTAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAATCATTAATAATATTAA
Found at i:534085 original size:29 final size:31
Alignment explanation
Indices: 534051--534117 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
534041 ATTTCAAAAG
534051 TATAAAGA-TTAAAATACTT-AATT-TAATAA
1 TATAAA-ATTTAAAATACTTCAATTATAATAA
**
534080 TATAAAATTTAAAATACTTCTTTTATAATAA
1 TATAAAATTTAAAATACTTCAATTATAATAA
534111 TATAAAA
1 TATAAAA
534118 AATCCTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 1 0.03
29 17 0.52
30 2 0.06
31 13 0.39
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TATAAAATTTAAAATACTTCAATTATAATAA
Found at i:535280 original size:16 final size:16
Alignment explanation
Indices: 535259--535311 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
535249 ATTCATAATT
* *
535259 AAATAATTTAAATTAA
1 AAATAATTAAAATTTA
*
535275 AAATAAATAAAATTTA
1 AAATAATTAAAATTTA
*
535291 AAATAATTCAAATTTA
1 AAATAATTAAAATTTA
535307 AAATA
1 AAATA
535312 TAAATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATTAAAATTTA
Found at i:535708 original size:23 final size:23
Alignment explanation
Indices: 535665--535718 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
535655 TTTTAATAAA
*
535665 ATATATATTATATTCACATGCAC
1 ATATATATTATATTCAAATGCAC
*
535688 ATATATATATATATT-AAATGCAT
1 ATATATAT-TATATTCAAATGCAC
*
535711 ATAAATAT
1 ATATATAT
535719 GTTTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (23 bp):
ATATATATTATATTCAAATGCAC
Found at i:537314 original size:19 final size:19
Alignment explanation
Indices: 537290--537341 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
537280 TGTCGGACAC
* *
537290 ATACCCGTATCTGACACTT
1 ATACCCGAATCCGACACTT
*
537309 ATACCCAAATCCGACACTT
1 ATACCCGAATCCGACACTT
*
537328 ATACCCGGATCCGA
1 ATACCCGAATCCGA
537342 GTAAACATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.23
Consensus pattern (19 bp):
ATACCCGAATCCGACACTT
Found at i:541586 original size:81 final size:82
Alignment explanation
Indices: 541488--541641 Score: 265
Period size: 81 Copynumber: 1.9 Consensus size: 82
541478 AAGTGTACCA
* *
541488 AGTATTCATCTGTATGAATACAGAAAAAGCACCAACCCAAAATCAATGCAACTTC-TTTAGTTTC
1 AGTATTCATCTGTATGAATAAAGAAAAAGCACCAACCCAAAATCAATACAACTTCTTTTAGTTTC
541552 TATGTTTTTCTACAATG
66 TATGTTTTTCTACAATG
* *
541569 AGTATTCATCTGTATGAATAAAGAAAAAGCACCAACCTAAGATCAATACAACTTCTTTTAGTTTC
1 AGTATTCATCTGTATGAATAAAGAAAAAGCACCAACCCAAAATCAATACAACTTCTTTTAGTTTC
541634 TATGTTTT
66 TATGTTTT
541642 CCGACGATGT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
81 51 0.75
82 17 0.25
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (82 bp):
AGTATTCATCTGTATGAATAAAGAAAAAGCACCAACCCAAAATCAATACAACTTCTTTTAGTTTC
TATGTTTTTCTACAATG
Found at i:544164 original size:32 final size:34
Alignment explanation
Indices: 544128--544192 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
544118 TTTATTTATA
* *
544128 TTAAAGAGTTTTATTTAATTT-AA-ATTAAAAAT
1 TTAAAAAGTTTTATATAATTTAAAGATTAAAAAT
*
544160 TTAAAAATTTTTATATAATTTAAAGATTAAAAA
1 TTAAAAAGTTTTATATAATTTAAAGATTAAAAA
544193 GTTATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 18 0.64
33 2 0.07
34 8 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (34 bp):
TTAAAAAGTTTTATATAATTTAAAGATTAAAAAT
Found at i:544225 original size:57 final size:58
Alignment explanation
Indices: 544138--544290 Score: 167
Period size: 57 Copynumber: 2.7 Consensus size: 58
544128 TTAAAGAGTT
* *
544138 TTATTT-AATTTAAATTAAAAATTTAAAAATTTTTATATAAT-T-TAAAGAT-TAAAAA
1 TTATTTAAATATAAATTAAAAATTTAAAAATTTTTATATAATATATAAAAATAT-AAAA
*
544193 GTTATTTAAATATAAATTAAAAATTAAAAAATTTATT-TA-AATATAATAAAAATATAAAA
1 -TTATTTAAATATAAATTAAAAATTTAAAAATTT-TTATATAATAT-ATAAAAATATAAAA
* * *
544252 TTATTTAAATAAAAAAT-AAAATTTAAAAGTTTTTATATA
1 TTATTTAAATATAAATTAAAAATTTAAAAATTTTTATATA
544291 GTCATTTTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 14
0.80 0.07 0.14
Matches are distributed among these distances:
56 11 0.13
57 42 0.51
58 18 0.22
59 10 0.12
60 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (58 bp):
TTATTTAAATATAAATTAAAAATTTAAAAATTTTTATATAATATATAAAAATATAAAA
Found at i:544262 original size:27 final size:31
Alignment explanation
Indices: 544138--544279 Score: 133
Period size: 27 Copynumber: 4.9 Consensus size: 31
544128 TTAAAGAGTT
* *
544138 TTATTT-AATTTAAATTAAAAATTTAAAAA-
1 TTATTTAAATATAAATTAAAAATTAAAAAAG
* *
544167 TT-TTT--ATATAATTTAAAGATT-AAAAAG
1 TTATTTAAATATAAATTAAAAATTAAAAAAG
*
544194 TTATTTAAATATAAATTAAAAATTAAAAAAT
1 TTATTTAAATATAAATTAAAAATTAAAAAAG
*
544225 TTATTTAAATAT-AA-TAAAAA-TATAAAA-
1 TTATTTAAATATAAATTAAAAATTAAAAAAG
* * *
544252 TTATTTAAATAAAAAATAAAATTTAAAA
1 TTATTTAAATATAAATTAAAAATTAAAA
544280 GTTTTTATAT
Statistics
Matches: 95, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
26 5 0.05
27 26 0.27
28 14 0.15
29 13 0.14
30 20 0.21
31 17 0.18
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TTATTTAAATATAAATTAAAAATTAAAAAAG
Found at i:544433 original size:11 final size:11
Alignment explanation
Indices: 544417--544441 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
544407 TTTGATTTAT
544417 TATTTAAAATA
1 TATTTAAAATA
544428 TATTTAAAATA
1 TATTTAAAATA
544439 TAT
1 TAT
544442 AATTATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTTAAAATA
Found at i:544460 original size:32 final size:27
Alignment explanation
Indices: 544440--544516 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 27
544430 TTTAAAATAT
544440 ATAATTATATGATATAAATATAATAAAAA
1 ATAATTA-AT-ATATAAATATAATAAAAA
*
544469 ATAATTAATATAT-AATATAAT-ATAA
1 ATAATTAATATATAAATATAATAAAAA
* *
544494 AT-ATGAA-ATAAAAATATAATAAA
1 ATAATTAATATATAAATATAATAAA
544517 CATCTTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 3 0.07
24 12 0.29
25 6 0.14
26 8 0.19
27 4 0.10
28 2 0.05
29 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (27 bp):
ATAATTAATATATAAATATAATAAAAA
Found at i:544493 original size:21 final size:22
Alignment explanation
Indices: 544435--544493 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
544425 ATATATTTAA
*
544435 AATATATAAT-T-ATATGATAT
1 AATATATAATATAATATAATAT
* *
544455 AA-ATATAATAAAAAATAAT-T
1 AATATATAATATAATATAATAT
544475 AATATATAATATAATATAA
1 AATATATAATATAATATAA
544494 ATATGAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.23
20 5 0.16
21 19 0.61
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATATATAATATAATATAATAT
Found at i:544515 original size:11 final size:11
Alignment explanation
Indices: 544422--544516 Score: 57
Period size: 11 Copynumber: 8.2 Consensus size: 11
544412 TTTATTATTT
* *
544422 AAAATATATTT
1 AAAATATAATA
544433 AAAATAT-ATA
1 AAAATATAATA
** *
544443 ATTATATGATA
1 AAAATATAATA
*
544454 TAAATATAATAA
1 AAAATATAAT-A
544466 AAAATAATTAATA
1 AAAAT-A-TAATA
*
544479 TATAATATAATA
1 -AAAATATAATA
*
544491 TAAATATGAAATA
1 AAAATAT--AATA
544504 AAAATATAATA
1 AAAATATAATA
544515 AA
1 AA
544517 CATCTTTCAA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
10 6 0.09
11 27 0.42
12 10 0.16
13 13 0.20
14 8 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAATATAATA
Found at i:544679 original size:2 final size:2
Alignment explanation
Indices: 544672--544700 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
544662 GCTATTTGTC
544672 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
544701 GCAATCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:550229 original size:20 final size:21
Alignment explanation
Indices: 550190--550229 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
550180 ACTAAAATTG
*
550190 TTTTTTCTTTTCTGGTTTTTT
1 TTTTTTCTTTTCTAGTTTTTT
*
550211 TTTTTTTTTTTCTAGTTTT
1 TTTTTTCTTTTCTAGTTTT
550230 ACATCTGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.82
Consensus pattern (21 bp):
TTTTTTCTTTTCTAGTTTTTT
Found at i:551387 original size:12 final size:12
Alignment explanation
Indices: 551370--551394 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
551360 GTTTCCTATA
551370 TATTTATAACTC
1 TATTTATAACTC
551382 TATTTATAACTC
1 TATTTATAACTC
551394 T
1 T
551395 TCTTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTATAACTC
Found at i:559477 original size:2 final size:2
Alignment explanation
Indices: 559472--559506 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
559462 ATTTTAAGCT
559472 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
559507 GCGCTTGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:561254 original size:209 final size:210
Alignment explanation
Indices: 560889--562158 Score: 1146
Period size: 209 Copynumber: 6.1 Consensus size: 210
560879 TCTTACTAAG
* * *** * * ** *
560889 CAAGCTTGTTGCTTCTGCACA-TCAGCCTGAATCATATAATCCATGAATTAAACACCTGTAGGTG
1 CAAGCTTGTTGCTTCTGCCCATTTA-CCTGAATTGCACAATCCATGTATTAAACAGATATAGGTG
* * * * ** ** *
560953 ACAACGTCTGGTTTTAAATCTCTCTGAATCAACAATTTGAACA-AGGTAATGACTTCTTCAGTCT
65 ACAATGTCAGGCTTTAGATCTCTCTGAATCATTAATTCCAACATA-GTAATGGCTTCTTCAGTCT
** * * * * *
561017 TCAATTCCTTGCACAAAGCATTGATTAAAGAGTTGAAAGCTACCACATCAGGCTGGACTCCTTCA
129 TCTTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAAGTTACCACATTAGGATGGACTCCTTCA
561082 TTCATCATTCTATTGAA
194 TTCATCATTCTATTGAA
** * * * * *
561099 CAAGCTTGTTGCTTCTTTCCATTGAGCTGAATTG-AGCAATCCATTTATTAAAGAGATGTAGGTG
1 CAAGCTTGTTGCTTCTGCCCATTTACCTGAATTGCA-CAATCCATGTATTAAACAGATATAGGTG
* ** * * *
561163 A-AATATTGGGCTTTAGATCTCTCTGAATCATTAGTTCCAACATGGTAATGGCTTCTTC-GTACC
65 ACAATGTCAGGCTTTAGATCTCTCTGAATCATTAATTCCAACATAGTAATGGCTTCTTCAGT-CT
* * * *
561226 TCTTTTCCTTGCATAAAACATGGATTAAAGAATTGAAAGTTACTACATTAGGATGAACTCCTTCA
129 TCTTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAAGTTACCACATTAGGATGGACTCCTTCA
**
561291 TTCATCATTCTACAGAA
194 TTCATCATTCTATTGAA
* ** *
561308 CAAGTTTATCGCATCTGCCCACTGCCCATTTACCTGAATTGCACAATCCATGAATTAAACA-AGT
1 CAAG-CT-T-G--T-TG-CTTCTGCCCATTTACCTGAATTGCACAATCCATGTATTAAACAGA-T
* * * *
561372 GTAGGTGACAATGTCA-GCTTTTAGATCTCTCTGAATCATTACTTCCGACATGGTAATGGCTTCT
58 ATAGGTGACAATGTCAGGC-TTTAGATCTCTCTGAATCATTAATTCCAACATAGTAATGGCTTCT
* * * * * **
561436 TCAGTCCTCTTTTCGTTGCATAAAGCATTGAGTAAAGAACTGAAAGTTACCACATCAGGAAAGAC
122 TCAGTCTTCTTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAAGTTACCACATTAGGATGGAC
*
561501 TCCTTCATTCAGCATTCTATTGAA
187 TCCTTCATTCATCATTCTATTGAA
* * * * * * * **
561525 CTAGCTTGTCGGTTCTGCCCGTTTAGCTGAATTGCAAAATCCATGTATCAAACAGCCATAGGTGA
1 CAAGCTTGTTGCTTCTGCCCATTTACCTGAATTGCACAATCCATGTATTAAACAGATATAGGTGA
* * * * * * * *
561590 CAACGTCAGGTTTTAGATCTCCCTGAATCATCAATTTCAACAAAGCAATGGCTTCTGCAGTCTTC
66 CAATGTCAGGCTTTAGATCTCTCTGAATCATTAATTCCAACATAGTAATGGCTTCTTCAGTCTTC
* *** *
561655 TTTTCCTTGCATAAAGCACTGATTAAAGAATT-AAAGGTTGTTACATTAGGATGAACTCCTTCAT
131 TTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAA-GTTACCACATTAGGATGGACTCCTTCAT
561719 TCATCATTCTATT-AA
195 TCATCATTCTATTGAA
* * *
561734 GCAAGCTT-TTCACTTCT-TCCATTGACCTGAATTGCACAATCCATGTATTAAACAGATATAGGT
1 -CAAGCTTGTT-GCTTCTGCCCATTTACCTGAATTGCACAATCCATGTATTAAACAGATATAGGT
**** * * * * *
561797 GATGGCGTCAGG-TTTTGTATCTCTCTGAATCATCAATTTCAACAAAGTAATGGCTTCTTCTGT-
64 GACAATGTCAGGCTTTAG-ATCTCTCTGAATCATTAATTCCAACATAGTAATGGCTTCTTCAGTC
* * * * * * * *
561860 TTCCTTTCCTTGCACAAAGTACTGATCAAACAAAT-AAATGTTACTACATTAGGATGGACTCCTT
128 TTCTTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAA-GTTACCACATTAGGATGGACTCCTT
* *
561924 CATTCATTATTCTATTGAG
192 CATTCATCATTCTATTGAA
* * *
561943 CAAGCTTCTCGCTTCTGCCCATTTACCTGAATTG--C-A--CA---A-TAAACAGTTATAGGTGA
1 CAAGCTTGTTGCTTCTGCCCATTTACCTGAATTGCACAATCCATGTATTAAACAGATATAGGTGA
* * *
561999 CAATGTCAGGTTTTAGATCTCTCTGAATCATTGATTCCAACATATTAATGGCTTCTTCAGTCTTC
66 CAATGTCAGGCTTTAGATCTCTCTGAATCATTAATTCCAACATAGTAATGGCTTCTTCAGTCTTC
* * *
562064 TTTTCCTTGCATAAAGCATTGATTAAAGAATTCAGAGTTACCACATTAGGATGGACTTCTTCATT
131 TTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAAGTTACCACATTAGGATGGACTCCTTCATT
* * * *
562129 CACCACTCTACTAAA
196 CATCATTCTATTGAA
*
562144 CAAGCTCGTTGCTTC
1 CAAGCTTGTTGCTTC
562159 CATTGCCCAG
Statistics
Matches: 859, Mismatches: 173, Indels: 65
0.78 0.16 0.06
Matches are distributed among these distances:
200 61 0.07
201 81 0.09
202 2 0.00
204 2 0.00
206 1 0.00
207 1 0.00
208 87 0.10
209 229 0.27
210 212 0.25
211 5 0.01
212 2 0.00
214 2 0.00
215 4 0.00
216 44 0.05
217 124 0.14
218 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (210 bp):
CAAGCTTGTTGCTTCTGCCCATTTACCTGAATTGCACAATCCATGTATTAAACAGATATAGGTGA
CAATGTCAGGCTTTAGATCTCTCTGAATCATTAATTCCAACATAGTAATGGCTTCTTCAGTCTTC
TTTTCCTTGCATAAAGCATTGATTAAAGAATTGAAAGTTACCACATTAGGATGGACTCCTTCATT
CATCATTCTATTGAA
Found at i:563528 original size:159 final size:159
Alignment explanation
Indices: 563236--563553 Score: 557
Period size: 159 Copynumber: 2.0 Consensus size: 159
563226 ATTGTGGGCA
* *
563236 GCTCAGAAAAGGAAAAAGAGAAGAAATTACCAGGTGAAGGAGGAATAAGACCAGGAATTGTTGAG
1 GCTCAGAAAAGGAAAAAGAGAAGAAATTACCAGGTGAAGGACGAATAAAACCAGGAATTGTTGAG
*
563301 GTTATTCTCTTCATCTTGATCACTGACTTCGTTTCAGCCAATGTCGAGGAATACGTTCTTCACAC
66 GTTATTCTCTTCATCTTGATCACTGACTTCGTTTCAGCCAATGTCGAGGAATACGCTCTTCACAC
563366 TCATTGCCCCAGGACAC-TCAGTGGAAGTT
131 TCATTGCCCCAGGAC-CGTCAGTGGAAGTT
563395 GCTCAGAAAAGGAAAAAGAGAAGAAATTACCAGGTGAAGGACGAATAAAACCAGGAATTGTTGAG
1 GCTCAGAAAAGGAAAAAGAGAAGAAATTACCAGGTGAAGGACGAATAAAACCAGGAATTGTTGAG
* * *
563460 GTTATTCTCTTCATCTTGATCACTGTCTTCGTTTCAGCCAGTGTCGAGGAATACGCTCTTCACGC
66 GTTATTCTCTTCATCTTGATCACTGACTTCGTTTCAGCCAATGTCGAGGAATACGCTCTTCACAC
*
563525 TCATTGCCCCAGGACCGTCGGTGGAAGTT
131 TCATTGCCCCAGGACCGTCAGTGGAAGTT
563554 AAGATCCGGG
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
158 1 0.01
159 150 0.99
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (159 bp):
GCTCAGAAAAGGAAAAAGAGAAGAAATTACCAGGTGAAGGACGAATAAAACCAGGAATTGTTGAG
GTTATTCTCTTCATCTTGATCACTGACTTCGTTTCAGCCAATGTCGAGGAATACGCTCTTCACAC
TCATTGCCCCAGGACCGTCAGTGGAAGTT
Found at i:564506 original size:19 final size:19
Alignment explanation
Indices: 564464--564506 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
564454 TAAATATTTA
564464 AAATAT-TATTTTTATATT
1 AAATATATATTTTTATATT
564482 -AATATATA-TTTTATGATT
1 AAATATATATTTTTAT-ATT
564500 AAATATA
1 AAATATA
564507 AATGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.50
18 5 0.23
19 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AAATATATATTTTTATATT
Found at i:564751 original size:20 final size:20
Alignment explanation
Indices: 564728--564791 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
564718 TTTAAAATTG
*
564728 TATATATTTATATAAATTTT
1 TATATATTTATATATATTTT
*
564748 TATATA-TTA-ATATATTTA
1 TATATATTTATATATATTTT
564766 TATCATATTTATAT-TATTTT
1 TAT-ATATTTATATATATTTT
564786 TATATA
1 TATATA
564792 ATATTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 10 0.26
19 9 0.24
20 17 0.45
21 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATATTTATATATATTTT
Found at i:564775 original size:11 final size:10
Alignment explanation
Indices: 564728--564797 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 10
564718 TTTAAAATTG
564728 TATATATTTA
1 TATATATTTA
* *
564738 TATAAATTTT
1 TATATATTTA
564748 TATATA-TTA
1 TATATATTTA
564757 -ATATATTTA
1 TATATATTTA
564766 TATCATATTTA
1 TAT-ATATTTA
*
564777 TATTATTTTTA
1 TA-TATATTTA
564788 TATAATATTT
1 TAT-ATATTT
564798 TAATTATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 5 0.10
9 5 0.10
10 16 0.33
11 22 0.45
12 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATTTA
Found at i:564790 original size:22 final size:22
Alignment explanation
Indices: 564749--564806 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
564739 ATAAATTTTT
* * *
564749 ATATATTAA-TATATTTATATC
1 ATATTTTAATTATTTTTATATA
564770 ATA-TTTATATTATTTTTATATA
1 ATATTTTA-ATTATTTTTATATA
564792 ATATTTTAATTATTT
1 ATATTTTAATTATTT
564807 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 20 0.65
23 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTAATTATTTTTATATA
Found at i:564790 original size:28 final size:28
Alignment explanation
Indices: 564729--564783 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
564719 TTAAAATTGT
*
564729 ATATATTTATATAAATTTTTATATATTA
1 ATATATTTATATAAATTTATATATATTA
*
564757 ATATATTTATATCATATTTATAT-TATT
1 ATATATTTATAT-AAATTTATATATATT
564784 TTTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATATTTATATAAATTTATATATATTA
Found at i:565062 original size:11 final size:11
Alignment explanation
Indices: 565032--565108 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
565022 ATTTTAAGTA
*
565032 TTTATATCATCT
1 TTTATATTAT-T
565044 TATTATATTATT
1 T-TTATATTATT
565056 TTTATATTA--
1 TTTATATTATT
*
565065 --TATAATA-T
1 TTTATATTATT
565073 TTTATATTATAT
1 TTTATATTAT-T
565085 TTTA-ATTA-T
1 TTTATATTATT
*
565094 TTTATAATATT
1 TTTATATTATT
565105 TTTA
1 TTTA
565109 GTATGTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
7 6 0.11
9 5 0.09
10 9 0.17
11 17 0.32
12 8 0.15
13 8 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATATTATT
Found at i:565077 original size:17 final size:16
Alignment explanation
Indices: 565044--565084 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
565034 TATATCATCT
*
565044 TATTATATTATTTTTA
1 TATTATATAATTTTTA
565060 TATTATATAATATTTTA
1 TATTATATAAT-TTTTA
565077 TATTATAT
1 TATTATAT
565085 TTTAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATATAATTTTTA
Found at i:565079 original size:12 final size:11
Alignment explanation
Indices: 565058--565106 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
565048 ATATTATTTT
*
565058 TATATTATATA
1 TATATTTTATA
565069 -ATATTTTATA
1 TATATTTTATA
565079 TTATATTTTA-A
1 -TATATTTTATA
565090 T-TATTTTATA
1 TATATTTTATA
565100 -ATATTTT
1 TATATTTT
565107 TAGTATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
9 7 0.21
10 17 0.52
11 1 0.03
12 8 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTTATA
Found at i:565084 original size:33 final size:33
Alignment explanation
Indices: 565044--565123 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 33
565034 TATATCATCT
565044 TATTATATTATTTTTATATTATATAATA-TTTTA-
1 TATTATATTATTTTTAT-TT-TATAATATTTTTAG
*
565077 TATTATATT-TTAATTATTTTATAATATTTTTAG
1 TATTATATTATT-TTTATTTTATAATATTTTTAG
565110 TATGTA-ATTATTTT
1 TAT-TATATTATTTT
565124 GAGTCTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
31 7 0.17
32 9 0.22
33 20 0.50
34 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (33 bp):
TATTATATTATTTTTATTTTATAATATTTTTAG
Found at i:565103 original size:31 final size:30
Alignment explanation
Indices: 565022--565106 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
565012 TATTAAATAA
* *
565022 ATTTTAAGTATTTATATCATCTTATTATATTAT
1 ATTTTAA-TATTT-TATAATATT-TTATATTAT
*
565055 -TTTT-ATATTATATAATATTTTATATTAT
1 ATTTTAATATTTTATAATATTTTATATTAT
565083 ATTTTAATTATTTTATAATATTTT
1 ATTTTAA-TATTTTATAATATTTT
565107 TAGTATGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 9 0.20
29 11 0.24
30 5 0.11
31 16 0.36
32 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (30 bp):
ATTTTAATATTTTATAATATTTTATATTAT
Found at i:565384 original size:19 final size:18
Alignment explanation
Indices: 565357--565401 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
565347 ATTTAAATAA
*
565357 AAATATATTATTTTAATTT
1 AAAT-TATTATTTTAAATT
565376 ATAATTATTATTTTAAATT
1 A-AATTATTATTTTAAATT
565395 AAATTAT
1 AAATTAT
565402 ATTAAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 15 0.62
20 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTATTATTTTAAATT
Found at i:569429 original size:38 final size:38
Alignment explanation
Indices: 569373--569445 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
569363 GATGCATGTT
* *
569373 TGTGTCATGATTCGAGACTCAAACTTTAAACTTGTGAA
1 TGTGTCATGAGTCAAGACTCAAACTTTAAACTTGTGAA
* *
569411 TGTGTCATGAGTCAAGACTTAAATTTTAAACTTGT
1 TGTGTCATGAGTCAAGACTCAAACTTTAAACTTGT
569446 ATAATTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (38 bp):
TGTGTCATGAGTCAAGACTCAAACTTTAAACTTGTGAA
Found at i:572101 original size:16 final size:16
Alignment explanation
Indices: 572070--572130 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
572060 AATTAAAATA
*
572070 AAAATTTTTTTAATTAT
1 AAAA-TTTTATAATTAT
* *
572087 AAACTTTTATCATTA-
1 AAAATTTTATAATTAT
*
572102 AAAATTTTATAAATAT
1 AAAATTTTATAATTAT
572118 AAAATTTTA-AATT
1 AAAATTTTATAATT
572131 TTTATCATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 15 0.42
16 18 0.50
17 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATTTTATAATTAT
Found at i:572664 original size:19 final size:19
Alignment explanation
Indices: 572640--572689 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
572630 TAATTTATTA
572640 TTATATATTTTTAAAATAT
1 TTATATATTTTTAAAATAT
** **
572659 TTATATATTCATATTATAT
1 TTATATATTTTTAAAATAT
572678 TTATAT-TTTTTA
1 TTATATATTTTTA
572690 TGTTTTATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATATTTTTAAAATAT
Found at i:572708 original size:32 final size:32
Alignment explanation
Indices: 572669--572741 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
572659 TTATATATTC
572669 ATATTATATTTATATTTT-TTATGTTTTATTAT
1 ATATTATATTTATATTTTATTAT-TTTTATTAT
* *
572701 ATTTTATA-TTATATTTTAATTATTTTTATTTT
1 ATATTATATTTATATTTT-ATTATTTTTATTAT
572733 ATATTATAT
1 ATATTATAT
572742 CAAGTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 9 0.26
32 22 0.63
33 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (32 bp):
ATATTATATTTATATTTTATTATTTTTATTAT
Found at i:572710 original size:37 final size:40
Alignment explanation
Indices: 572659--572741 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 40
572649 TTTAAAATAT
572659 TTATATATTCATATTATA-TTT-A-TATTTTTTATGTTT-TA
1 TTATATATTCATATTATATTTTAATTA-TTTTTAT-TTTATA
*
572697 TTATAT-TTTATATTATATTTTAATTATTTTTATTTTATA
1 TTATATATTCATATTATATTTTAATTATTTTTATTTTATA
572736 TTATAT
1 TTATAT
572742 CAAGTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
37 10 0.25
38 12 0.30
39 16 0.40
40 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (40 bp):
TTATATATTCATATTATATTTTAATTATTTTTATTTTATA
Found at i:572712 original size:22 final size:22
Alignment explanation
Indices: 572634--572737 Score: 74
Period size: 22 Copynumber: 4.8 Consensus size: 22
572624 AATTAATAAT
*
572634 TTATTATTATA-TAT-TTTTAAA
1 TTATTTTTATATTATATTTT-AA
* * * *
572655 ATATTTATATATTCATATTATAT
1 TTATTTTTATATT-ATATTTTAA
* *
572678 TTATATTT-T-TTATGTTTT-A
1 TTATTTTTATATTATATTTTAA
572697 TTATATTTTATATTATATTTTAA
1 TTAT-TTTTATATTATATTTTAA
*
572720 TTATTTTTATTTTATATT
1 TTATTTTTATATTATATT
572738 ATATCAAGTT
Statistics
Matches: 62, Mismatches: 14, Indels: 13
0.70 0.16 0.15
Matches are distributed among these distances:
19 4 0.06
20 8 0.13
21 11 0.18
22 23 0.37
23 13 0.21
24 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
TTATTTTTATATTATATTTTAA
Found at i:573535 original size:16 final size:17
Alignment explanation
Indices: 573503--573641 Score: 83
Period size: 16 Copynumber: 7.9 Consensus size: 17
573493 ATGATTATAT
*
573503 TAATATAATATATATAAAG
1 TAATATAA-A-ATATAAAA
573522 TAAT-TAAAATATAAAA
1 TAATATAAAATATAAAA
573538 TAATATAAAATAT-AAA
1 TAATATAAAATATAAAA
* *
573554 T--TTTAATATATTAAAA
1 TAATATAAAATA-TAAAA
*
573570 TTAATAT-AAATATTAAA
1 -TAATATAAAATATAAAA
* *
573587 TATTTTAAATATTATTATAATA
1 TAATATAAA-A-TA-TA-AA-A
573609 TAATA-AAATATATAAAAA
1 TAATATAAA-ATAT-AAAA
573627 TAATATAAAATATAA
1 TAATATAAAATATAA
573642 GTGGTTATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
14 7 0.07
15 1 0.01
16 22 0.23
17 18 0.19
18 18 0.19
19 14 0.15
20 4 0.04
21 7 0.07
22 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TAATATAAAATATAAAA
Done.