Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 2 of 31
Found at i:362334 original size:14 final size:14
Alignment explanation
Indices: 362315--362342 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
362305 ATTTTTTAAT
362315 TTAATTAAAAATTA
1 TTAATTAAAAATTA
362329 TTAATTAAAAATTA
1 TTAATTAAAAATTA
362343 AATAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAAAATTA
Found at i:365076 original size:3 final size:3
Alignment explanation
Indices: 365068--365096 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
365058 CTAATTTAAA
365068 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
365097 CATCAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:365553 original size:2 final size:2
Alignment explanation
Indices: 365546--365596 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
365536 GGGAGGGAGG
* *
365546 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
365588 GA GA G- GA GA
1 GA GA GA GA GA
365597 CCATAGTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:371417 original size:22 final size:22
Alignment explanation
Indices: 371387--371440 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
371377 GAGAGGCATG
*
371387 ATGCTGGTAT-GTGGGTGCAGAA
1 ATGCAGGTATCGT-GGTGCAGAA
371409 ATGCAGGTATCGTGGTGCAGAA
1 ATGCAGGTATCGTGGTGCAGAA
* *
371431 ACGCAAGTAT
1 ATGCAGGTAT
371441 TATAGGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (22 bp):
ATGCAGGTATCGTGGTGCAGAA
Found at i:371452 original size:23 final size:22
Alignment explanation
Indices: 371400--371452 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
371390 CTGGTATGTG
* * *
371400 GGTGCAGAAATGCAGGTATCGT
1 GGTGCAGAAACGCAAGTATCAT
*
371422 GGTGCAGAAACGCAAGTATTAT
1 GGTGCAGAAACGCAAGTATCAT
371444 AGGTGCAGA
1 -GGTGCAGA
371453 GACAGCTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (22 bp):
GGTGCAGAAACGCAAGTATCAT
Found at i:372236 original size:2 final size:2
Alignment explanation
Indices: 372229--372265 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
372219 CTAAGAAAAC
*
372229 AT AT AT AT AT AT AT AT AT AT AT AT AGT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
372266 TGGTGCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:372529 original size:34 final size:34
Alignment explanation
Indices: 372491--372562 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
372481 TATTAACGTA
*
372491 TATTATATATATA-ATTAAAATTTTTATTA-GTATT
1 TATTATATATAGATATT--AATTTTTATTACGTATT
* *
372525 TATTATTTTTAGATATTAATTTTTATTACGTATT
1 TATTATATATAGATATTAATTTTTATTACGTATT
372559 TATT
1 TATT
372563 TATTGATAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 11 0.33
34 19 0.58
35 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (34 bp):
TATTATATATAGATATTAATTTTTATTACGTATT
Found at i:372558 original size:17 final size:16
Alignment explanation
Indices: 372509--372563 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
372499 ATATAATTAA
372509 AATTTTTATTAGTATT
1 AATTTTTATTAGTATT
*
372525 TATTATTT-TTAGATATT
1 AATT-TTTATTAG-TATT
372542 AATTTTTATTACGTATT
1 AATTTTTATTA-GTATT
*
372559 TATTT
1 AATTT
372564 ATTGATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 10 0.31
17 21 0.66
18 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (16 bp):
AATTTTTATTAGTATT
Found at i:372994 original size:104 final size:102
Alignment explanation
Indices: 372789--372997 Score: 321
Period size: 102 Copynumber: 2.0 Consensus size: 102
372779 ATAAATTATC
* *
372789 GTCTAGAGTCGTAAAGCGACGTACAAATGCTCTTTATATAAGATAATTTATTTTTTGCATTAATT
1 GTCTAGAGTCATAAAGCGACATACAAATGCTCTTTATATAAGATAATTTATTTTTTGCATTAATT
*
372854 ACTAAATTCGGGCACCAAAAGATTAGTCTCGAAATAG
66 ACTAAATTCGGGCACCAAAAGATTAGCCTCGAAATAG
* * *
372891 GTCTAGAGTCATAAAGCGGCATACGAATG-TCTTTTATATAGGATAATTCTATTTTTTGCATTAA
1 GTCTAGAGTCATAAAGCGACATACAAATGCTC-TTTATATAAGATAATT-TATTTTTTGCATTAA
*
372955 TTACGTAAATTCGGGCACCAAAAGATTGGCCTCGAAATAG
64 TTAC-TAAATTCGGGCACCAAAAGATTAGCCTCGAAATAG
372995 GTC
1 GTC
372998 GTCGTCTAGA
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
101 2 0.02
102 40 0.41
103 19 0.20
104 36 0.37
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (102 bp):
GTCTAGAGTCATAAAGCGACATACAAATGCTCTTTATATAAGATAATTTATTTTTTGCATTAATT
ACTAAATTCGGGCACCAAAAGATTAGCCTCGAAATAG
Found at i:375286 original size:3 final size:3
Alignment explanation
Indices: 375278--375333 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
375268 TTTAAATTGT
375278 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
375326 ATC ATA AT
1 ATA ATA AT
375334 CGAAAGAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:375666 original size:2 final size:2
Alignment explanation
Indices: 375659--375688 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
375649 GAATAATGTG
375659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375689 CACTGGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:376322 original size:13 final size:13
Alignment explanation
Indices: 376304--376329 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
376294 AAAAATATGC
376304 TTATTTTAAGTTA
1 TTATTTTAAGTTA
376317 TTATTTTAAGTTA
1 TTATTTTAAGTTA
376330 ATTTTAAATA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TTATTTTAAGTTA
Found at i:376391 original size:16 final size:15
Alignment explanation
Indices: 376370--376400 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
376360 CAACGGTTAA
376370 TTATTATTTTTTATTT
1 TTATTA-TTTTTATTT
376386 TTATTATTTTTATTT
1 TTATTATTTTTATTT
376401 AAAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTATTATTTTTATTT
Found at i:376410 original size:14 final size:16
Alignment explanation
Indices: 376390--376422 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
376380 TTATTTTTAT
*
376390 TATTTTTATT-TAAAA
1 TATTTTAATTATAAAA
376405 TATTTTAATTATAAAA
1 TATTTTAATTATAAAA
376421 TA
1 TA
376423 ATAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTAATTATAAAA
Found at i:376475 original size:16 final size:16
Alignment explanation
Indices: 376454--376485 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
376444 AAATTTTTTT
*
376454 AATTATTTTTAAATTA
1 AATTATTATTAAATTA
376470 AATTATTATTAAATTA
1 AATTATTATTAAATTA
376486 TATTTTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:376567 original size:14 final size:14
Alignment explanation
Indices: 376548--376612 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
376538 TATATTAACT
376548 TTAAAATTAATTTA
1 TTAAAATTAATTTA
*
376562 TTAAAA-TATTTTTA
1 TTAAAATTA-ATTTA
* *
376576 TTTAAATTAATTAA
1 TTAAAATTAATTTA
*
376590 TTAATATT-ATTTA
1 TTAAAATTAATTTA
*
376603 -AAAAATTAAT
1 TTAAAATTAAT
376613 GATAATGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
12 5 0.13
13 8 0.21
14 24 0.62
15 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAAATTAATTTA
Found at i:377039 original size:32 final size:33
Alignment explanation
Indices: 376976--377045 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
376966 AAAAAACTTA
*
376976 ATATATTTATTTAAATAAGAATATAATTTAATT
1 ATATATTTATTTAAATAAGAATATAAGTTAATT
* *
377009 ATATTTTTATTT-AATAATAAT-TAAAGTTAATT
1 ATATATTTATTTAAATAAGAATAT-AAGTTAATT
*
377041 TTATA
1 ATATA
377046 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 1 0.03
32 19 0.61
33 11 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
ATATATTTATTTAAATAAGAATATAAGTTAATT
Found at i:377762 original size:18 final size:18
Alignment explanation
Indices: 377735--377777 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
377725 AGCAACGATA
377735 ATAA-TAAAAATATATAT
1 ATAATTAAAAATATATAT
377752 ATAATTAAAAATATATAT
1 ATAATTAAAAATATATAT
*
377770 ATATTTAA
1 ATAATTAA
377778 TGTCAGTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATTAAAAATATATAT
Found at i:378088 original size:17 final size:18
Alignment explanation
Indices: 378063--378099 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
378053 TTTAAAAAAT
*
378063 ATTTATTAATAAAATTTA
1 ATTTATTAAAAAAATTTA
378081 ATTT-TTAAAAAAATTTA
1 ATTTATTAAAAAAATTTA
378098 AT
1 AT
378100 AATTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATTAAAAAAATTTA
Found at i:378659 original size:14 final size:13
Alignment explanation
Indices: 378619--378660 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
378609 TATAAAATAA
378619 AATTATAATAAAT
1 AATTATAATAAAT
*
378632 TATT-TAATTAAAT
1 AATTATAA-TAAAT
378645 AATTATAATACAAT
1 AATTATAATA-AAT
378659 AA
1 AA
378661 ATAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 13 0.54
14 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTATAATAAAT
Found at i:389723 original size:56 final size:54
Alignment explanation
Indices: 389632--389746 Score: 176
Period size: 56 Copynumber: 2.1 Consensus size: 54
389622 TTATATGTGC
* * *
389632 GTGCCCCATGAAATAGTTAAAACAAAGCCAAATAGATTATGCAGCACTTATTTGTA
1 GTGCTCCATGAAATAGTTAAAACAAAGACAAATAGATTATGCA--ACTTATTTATA
*
389688 GTGCTCCATGAAATAGTTAAAACAAAGACTAATAGATTATGCAACTTATTTATA
1 GTGCTCCATGAAATAGTTAAAACAAAGACAAATAGATTATGCAACTTATTTATA
389742 GTGCT
1 GTGCT
389747 GCATAAACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 15 0.27
56 40 0.73
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (54 bp):
GTGCTCCATGAAATAGTTAAAACAAAGACAAATAGATTATGCAACTTATTTATA
Found at i:392448 original size:13 final size:13
Alignment explanation
Indices: 392432--392456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
392422 TTTTTTCTCC
392432 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
392445 TTTTTTTTTTTG
1 TTTTTTTTTTTG
392457 GGGGGGGGGG
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:393816 original size:2 final size:2
Alignment explanation
Indices: 393809--393846 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
393799 AATTTCTAAG
393809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
393847 GTATTCATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:396065 original size:17 final size:16
Alignment explanation
Indices: 396039--396079 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
396029 TTTATTATTT
396039 ATAATTATTATATTAG
1 ATAATTATTATATTAG
*
396055 ATAAGTTATTATTTTAG
1 ATAA-TTATTATATTAG
396072 ATATATTA
1 ATA-ATTA
396080 AAATTCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 17 0.77
18 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
ATAATTATTATATTAG
Found at i:400788 original size:24 final size:24
Alignment explanation
Indices: 400756--400803 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
400746 TTCCATTGAT
400756 TAATCAGAGTACTTAAACAATGTA
1 TAATCAGAGTACTTAAACAATGTA
*
400780 TAATTAGAGTACTTAAACAATGTA
1 TAATCAGAGTACTTAAACAATGTA
400804 AACACATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
TAATCAGAGTACTTAAACAATGTA
Found at i:400992 original size:20 final size:21
Alignment explanation
Indices: 400952--400992 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
400942 TGGTTACATG
*
400952 TTTTAAAATATATATATATAA
1 TTTTAAAATATACATATATAA
*
400973 TTTTAAATTATACATA-ATAA
1 TTTTAAAATATACATATATAA
400993 CTAACGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAAATATACATATATAA
Found at i:402688 original size:2 final size:2
Alignment explanation
Indices: 402675--402712 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
402665 ATATGAATTA
*
402675 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402713 TTTGATGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:405775 original size:17 final size:19
Alignment explanation
Indices: 405740--405783 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
405730 TAAGATATTA
*
405740 ATATTTTATTAATTAAAAT
1 ATATTTTATAAATTAAAAT
405759 ATATTTTA-AAATT-AAAT
1 ATATTTTATAAATTAAAAT
405776 -TATTTTAT
1 ATATTTTAT
405784 TATATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 4 0.17
19 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTATAAATTAAAAT
Found at i:413908 original size:16 final size:16
Alignment explanation
Indices: 413882--413930 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
413872 TATTATTGTT
413882 ATTATTTTTAAATTTAA
1 ATTA-TTTTAAATTTAA
*
413899 ATTATTTTAAATATAA
1 ATTATTTTAAATTTAA
*
413915 ATTA-ATTAAATTTAA
1 ATTATTTTAAATTTAA
413930 A
1 A
413931 ATTTAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 10 0.34
16 15 0.52
17 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:413927 original size:22 final size:22
Alignment explanation
Indices: 413902--413948 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
413892 AATTTAAATT
*
413902 ATTTTAAATATAAATTAATTAA
1 ATTTAAAATATAAATTAATTAA
* *
413924 ATTTAAAATTTAAGTTAATTAA
1 ATTTAAAATATAAATTAATTAA
413946 ATT
1 ATT
413949 CAGTTAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTAAAATATAAATTAATTAA
Found at i:413946 original size:37 final size:37
Alignment explanation
Indices: 413885--413982 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 37
413875 TATTGTTATT
* * *
413885 ATTTTTAAATTTAAATTATTTTAAATATAAATTAATTAA
1 ATTTTAAAATTTAAATTA-ATTAAAT-TAAATTAATCAA
* * *
413924 A-TTTAAAATTTAAGTTAATTAAATTCAGTTAATCAA
1 ATTTTAAAATTTAAATTAATTAAATTAAATTAATCAA
**
413960 ATTTTATTATTTAAATTAATTAA
1 ATTTTAAAATTTAAATTAATTAA
413983 TTTCGAATCA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
36 10 0.20
37 24 0.49
38 14 0.29
39 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (37 bp):
ATTTTAAAATTTAAATTAATTAAATTAAATTAATCAA
Found at i:414099 original size:18 final size:18
Alignment explanation
Indices: 414049--414101 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
414039 CTAATATCAA
* *
414049 TTTAAATT-TAAATTATT
1 TTTAAATTATTAATTAAT
414066 TTTAAAATTATATTAATTAAT
1 TTT-AAA-T-TATTAATTAAT
414087 TTTAAATTATTAATT
1 TTTAAATTATTAATT
414102 TTTTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 11 0.37
19 2 0.07
20 4 0.13
21 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTATTAATTAAT
Found at i:415167 original size:3 final size:3
Alignment explanation
Indices: 415159--415213 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
415149 TACCATAAAT
* *
415159 ATA ATA ATA ATA ATA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
415207 ATA ATA A
1 ATA ATA A
415214 ATGCAATTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:417741 original size:2 final size:2
Alignment explanation
Indices: 417734--417764 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
417724 TTGATCTCAT
417734 TC TC 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 TC TC T
417765 ATATATATAT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:417769 original size:2 final size:2
Alignment explanation
Indices: 417764--417804 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
417754 TCTCTCTCTC
* *
417764 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TT TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
417805 ACTAGCCCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:418961 original size:16 final size:16
Alignment explanation
Indices: 418931--418960 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
418921 TTGGGCGATG
418931 CTTTTTTTTTCTTTTC
1 CTTTTTTTTTCTTTTC
418947 CTTTTTTTTT-TTTT
1 CTTTTTTTTTCTTTT
418961 TTATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
CTTTTTTTTTCTTTTC
Found at i:420872 original size:19 final size:19
Alignment explanation
Indices: 420850--420894 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
420840 TTAATTTAAT
420850 TTAAAATAATAT-TTTTATA
1 TTAAAATAATATATTTT-TA
420869 TTAAAATAATATATTTTTA
1 TTAAAATAATATATTTTTA
*
420888 TTTAAAT
1 TTAAAAT
420895 TTAATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAATAATATATTTTTA
Found at i:420892 original size:20 final size:18
Alignment explanation
Indices: 420823--420893 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 18
420813 GTAATTAATT
*
420823 TAAT-TTTTTATTTTAAA
1 TAATATTTTTATTTAAAA
* *
420840 T--TAATTTAATTTAAAA
1 TAATATTTTTATTTAAAA
420856 TAATATTTTTATATTAAAA
1 TAATATTTTTAT-TTAAAA
420875 TAATATATTTTTATTTAAA
1 T-A-ATATTTTTATTTAAA
420894 TTTAATTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.02
16 11 0.26
17 1 0.02
18 7 0.16
19 7 0.16
20 6 0.14
21 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATTTTTATTTAAAA
Found at i:420899 original size:21 final size:21
Alignment explanation
Indices: 420850--420893 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
420840 TTAATTTAAT
420850 TTAAAAT-A-ATATTTTTATA
1 TTAAAATAATATATTTTTATA
420869 TTAAAATAATATATTTTTAT-
1 TTAAAATAATATATTTTTATA
420889 TTAAA
1 TTAAA
420894 TTTAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAAATAATATATTTTTATA
Found at i:424309 original size:3 final size:3
Alignment explanation
Indices: 424301--424336 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
424291 ATACACTGAA
424301 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
424337 CTATTAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:424435 original size:2 final size:2
Alignment explanation
Indices: 424428--424471 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
424418 TCATCGAGTA
424428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
424470 AT
1 AT
424472 TCATACTCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:425342 original size:16 final size:16
Alignment explanation
Indices: 425323--425374 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
425313 CCTGAATCTG
425323 AAATGATCTAAACCCA
1 AAATGATCTAAACCCA
*
425339 AAATGACCTAAACCCA
1 AAATGATCTAAACCCA
* * *
425355 AAATAATCCAAACCCG
1 AAATGATCTAAACCCA
425371 AAAT
1 AAAT
425375 AACCCAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.52, C:0.27, G:0.06, T:0.15
Consensus pattern (16 bp):
AAATGATCTAAACCCA
Found at i:425375 original size:16 final size:16
Alignment explanation
Indices: 425332--425382 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
425322 GAAATGATCT
* *
425332 AAACCCAAAATGACCT
1 AAACCCAAAATAACCC
*
425348 AAACCCAAAATAATCC
1 AAACCCAAAATAACCC
*
425364 AAACCCGAAATAACCC
1 AAACCCAAAATAACCC
425380 AAA
1 AAA
425383 TAATTAACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.55, C:0.31, G:0.04, T:0.10
Consensus pattern (16 bp):
AAACCCAAAATAACCC
Found at i:429209 original size:27 final size:27
Alignment explanation
Indices: 429179--429230 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
429169 AATTCATTTT
*
429179 TTTTAACTGATAA-ATATATTTATTTAA
1 TTTTAA-TGATAATATATATTAATTTAA
*
429206 TTTTAATTATAATATATATTAATTT
1 TTTTAATGATAATATATATTAATTT
429231 TAAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTAATGATAATATATATTAATTTAA
Found at i:432545 original size:17 final size:17
Alignment explanation
Indices: 432501--432550 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
432491 CGTATTATAT
*
432501 TATTTAGATTT-TAATA
1 TATTTATATTTATAATA
*
432517 TATTTAATTATTTATATTA
1 TATTT-A-TATTTATAATA
432536 TATTTATATTTATAA
1 TATTTATATTTATAA
432551 AATTCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 5 0.18
19 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTTATATTTATAATA
Found at i:433214 original size:2 final size:2
Alignment explanation
Indices: 433207--433239 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
433197 AAACCTATTA
433207 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 A
433240 CGTATGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:434454 original size:3 final size:3
Alignment explanation
Indices: 434446--434475 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
434436 AATTGTTTTT
434446 TAA TAA TAA TAA TAA TAA TAA TAA TGAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA
434476 CTGTTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:436648 original size:2 final size:2
Alignment explanation
Indices: 436643--436677 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
436633 AGGCACACAC
436643 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
436678 CACACGCCCA
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:437633 original size:27 final size:27
Alignment explanation
Indices: 437603--437675 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
437593 AAAGTTATCT
*
437603 TTTGTATTTGTCAAAAATGATAGTTCA
1 TTTGTGTTTGTCAAAAATGATAGTTCA
* * *
437630 TTTGTGTTTATAAAAAATGATAGTTCC
1 TTTGTGTTTGTCAAAAATGATAGTTCA
*
437657 TTTTTGTTTGTCAAAAATG
1 TTTGTGTTTGTCAAAAATG
437676 GTAGCTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (27 bp):
TTTGTGTTTGTCAAAAATGATAGTTCA
Found at i:439132 original size:27 final size:27
Alignment explanation
Indices: 439101--439191 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
439091 TTTGTGTTTG
439101 TCAAAAATGGTGATTCTTTTATATTTA
1 TCAAAAATGGTGATTCTTTTATATTTA
* * * *
439128 TCAAAAATGGTGGTTCCTTTATGTTTG
1 TCAAAAATGGTGATTCTTTTATATTTA
* * * *
439155 TAAAAAATTGTG--GCTTAT-TATTTA
1 TCAAAAATGGTGATTCTTTTATATTTA
*
439179 TCAAAATTGGTGA
1 TCAAAAATGGTGA
439192 CTAATTTTTG
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
24 13 0.27
25 3 0.06
27 33 0.67
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (27 bp):
TCAAAAATGGTGATTCTTTTATATTTA
Found at i:452490 original size:28 final size:27
Alignment explanation
Indices: 452459--452525 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
452449 ACGAACATTA
*
452459 AAATTTAAATTATAAATTTATTAAATAT
1 AAATTTAAATTATAAATTCATTAAAT-T
*
452487 AAA-TTAATTATATAAATTCATTAAATT
1 AAATTTAAAT-TATAAATTCATTAAATT
452514 AAATTTTAAATT
1 AAA-TTTAAATT
452526 TAACTAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 9 0.27
28 19 0.58
29 5 0.15
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTTAAATTATAAATTCATTAAATT
Found at i:452934 original size:15 final size:15
Alignment explanation
Indices: 452916--452989 Score: 71
Period size: 15 Copynumber: 5.0 Consensus size: 15
452906 TGTACAAATA
452916 TTTTGACATAAGTAC
1 TTTTGACATAAGTAC
**
452931 TTTTGATTTAAGTAC
1 TTTTGACATAAGTAC
*
452946 TTTCGACAT-AGATA-
1 TTTTGACATAAG-TAC
*
452960 TTTTGACATAAATAC
1 TTTTGACATAAGTAC
**
452975 TTTCAACATAAGTAC
1 TTTTGACATAAGTAC
452990 ATTAACACAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 12 0.26
15 34 0.74
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (15 bp):
TTTTGACATAAGTAC
Found at i:455046 original size:95 final size:96
Alignment explanation
Indices: 454878--455062 Score: 327
Period size: 95 Copynumber: 1.9 Consensus size: 96
454868 GTTTTTGATT
*
454878 AGATAAGCATAAACGGATTTGACTCAACATTCAACCGAGTCATCTGGAATGAATATTAAGGGCTG
1 AGATAAGCATAAACGGATTTGACTCAACATTCAACCGAGTCATCTGGAATGAATATGAAGGGCTG
*
454943 TGAAAGGATTCGAT-GGGAAAAAAATTCCAA
66 TGAAAGGATTCAATGGGGAAAAAAATTCCAA
* *
454973 AGATGAGCATAAACGGATTTGACTCAACATTCAACCGAGTCATCTGGAATGAATATGAAGGGTTG
1 AGATAAGCATAAACGGATTTGACTCAACATTCAACCGAGTCATCTGGAATGAATATGAAGGGCTG
455038 TGAAAGGATTCAATGGGGAAAAAAA
66 TGAAAGGATTCAATGGGGAAAAAAA
455063 AAAATTCCAA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
95 75 0.88
96 10 0.12
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (96 bp):
AGATAAGCATAAACGGATTTGACTCAACATTCAACCGAGTCATCTGGAATGAATATGAAGGGCTG
TGAAAGGATTCAATGGGGAAAAAAATTCCAA
Found at i:456697 original size:2 final size:2
Alignment explanation
Indices: 456692--456728 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
456682 ACACAAAATC
*
456692 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
456729 GAAAACCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 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):
GA
Found at i:461055 original size:15 final size:15
Alignment explanation
Indices: 461020--461061 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
461010 ATATTTTATT
*
461020 TATTTTTAATTA-AT
1 TATTTTTAATTATAA
*
461034 TAATTTTAATTATAA
1 TATTTTTAATTATAA
*
461049 TATTTTTTATTAT
1 TATTTTTAATTAT
461062 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTAATTATAA
Found at i:465982 original size:2 final size:2
Alignment explanation
Indices: 465975--465999 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
465965 CTATTCTGCT
465975 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 T
466000 TCGTTCCTGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:466705 original size:14 final size:14
Alignment explanation
Indices: 466675--466716 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
466665 TATTTTATTT
466675 AATAA-TAT-TAAA
1 AATAATTATATAAA
*
466687 TATAATTATATAAA
1 AATAATTATATAAA
466701 AATAATTATAATAAA
1 AATAATTAT-ATAAA
466716 A
1 A
466717 TTTAACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 3 0.12
14 12 0.48
15 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATTATATAAA
Found at i:466792 original size:26 final size:26
Alignment explanation
Indices: 466712--466811 Score: 102
Period size: 25 Copynumber: 3.9 Consensus size: 26
466702 ATAATTATAA
* *
466712 TAAAATTTAACATAAATAT-ACATATTT
1 TAAAATTT-ATATAAATATAAAATA-TT
466739 TAAAATTTATAT-AATATTAAAATA-T
1 TAAAATTTATATAAATA-TAAAATATT
466764 TAAAATTTATATAAATATAAAATATT
1 TAAAATTTATATAAATATAAAATATT
* *
466790 TAAAATATA-ATATA-ATAAAATA
1 TAAAATTTATATAAATATAAAATA
466812 AAATCTACAA
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
24 8 0.12
25 28 0.43
26 17 0.26
27 12 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAAATTTATATAAATATAAAATATT
Found at i:477510 original size:97 final size:97
Alignment explanation
Indices: 477403--477598 Score: 392
Period size: 97 Copynumber: 2.0 Consensus size: 97
477393 AGAAAGATTC
477403 AAGTGTGTGAATAATTAAAAGATAAATAAGAACCACCACATGGACAGGCATATTAGAATGAACTT
1 AAGTGTGTGAATAATTAAAAGATAAATAAGAACCACCACATGGACAGGCATATTAGAATGAACTT
477468 TTGCAAACAGCATCAAGTTAAAAGACGGTATT
66 TTGCAAACAGCATCAAGTTAAAAGACGGTATT
477500 AAGTGTGTGAATAATTAAAAGATAAATAAGAACCACCACATGGACAGGCATATTAGAATGAACTT
1 AAGTGTGTGAATAATTAAAAGATAAATAAGAACCACCACATGGACAGGCATATTAGAATGAACTT
477565 TTGCAAACAGCATCAAGTTAAAAGACGGTATT
66 TTGCAAACAGCATCAAGTTAAAAGACGGTATT
477597 AA
1 AA
477599 TCTCGCTTTA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.23
Consensus pattern (97 bp):
AAGTGTGTGAATAATTAAAAGATAAATAAGAACCACCACATGGACAGGCATATTAGAATGAACTT
TTGCAAACAGCATCAAGTTAAAAGACGGTATT
Found at i:484347 original size:39 final size:39
Alignment explanation
Indices: 484261--484358 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
484251 TTGAGTGACT
* * *
484261 GACT-GAAGTCCGTTGCTATTGTTGGGCTACTTGTTGAA
1 GACTGGAAGTCCATTGCTATTGTCGGGCTAATTGTTGAA
*
484299 GACTTGAAGTCCATTGCTATTGTCGGGCTAATTGTTGAA
1 GACTGGAAGTCCATTGCTATTGTCGGGCTAATTGTTGAA
*
484338 -ACCTGGAAGTCCATTGTTATT
1 GA-CTGGAAGTCCATTGCTATT
484359 ACTGGGCTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
38 5 0.09
39 48 0.91
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (39 bp):
GACTGGAAGTCCATTGCTATTGTCGGGCTAATTGTTGAA
Found at i:484366 original size:39 final size:38
Alignment explanation
Indices: 484261--484369 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 38
484251 TTGAGTGACT
* * *
484261 GACT-GAAGTCCGTTGCTATTGTTGGGCTACTTGTTGAA
1 GACTGGAAGTCCATTGCTATT-CTGGGCTAATTGTTGAA
* *
484299 GACTTGAAGTCCATTGCTATTGTCGGGCTAATTGTTGAA
1 GACTGGAAGTCCATTGCTATTCT-GGGCTAATTGTTGAA
*
484338 -ACCTGGAAGTCCATTGTTATTACTGGGCTAAT
1 GA-CTGGAAGTCCATTGCTATT-CTGGGCTAAT
484370 CTAACCAGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
38 6 0.10
39 54 0.89
40 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.36
Consensus pattern (38 bp):
GACTGGAAGTCCATTGCTATTCTGGGCTAATTGTTGAA
Found at i:488763 original size:15 final size:16
Alignment explanation
Indices: 488742--488779 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
488732 TAATTATATG
488742 ATTTTATTATTTTTAT
1 ATTTTATTATTTTTAT
488758 -TTTTATTATTTTTAT
1 ATTTTATTATTTTTAT
488773 ATTTTAT
1 ATTTTAT
488780 AAAAGGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTATTATTTTTAT
Found at i:512927 original size:22 final size:21
Alignment explanation
Indices: 512885--512927 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
512875 TTAACCCAAA
* * *
512885 AAAAATTATAATTTTAGAATT
1 AAAAATAATAATATTAAAATT
512906 AAAAATAATAAATATTAAAATT
1 AAAAATAAT-AATATTAAAATT
512928 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAATAATAATATTAAAATT
Found at i:512971 original size:13 final size:12
Alignment explanation
Indices: 512935--512973 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
512925 ATTTTTAAAT
512935 TTATTAAAA-AA
1 TTATTAAAATAA
512946 TTATTAAAATAA
1 TTATTAAAATAA
*
512958 TTATATAAATTAA
1 TTAT-TAAAATAA
512971 TTA
1 TTA
512974 AATTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.36
12 6 0.24
13 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATTAAAATAA
Found at i:513962 original size:22 final size:22
Alignment explanation
Indices: 513943--513994 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
513933 TAGATTTATG
513943 TCATTTAAATTTAATATTTAAA
1 TCATTTAAATTTAATATTTAAA
*
513965 TTATTTAAATTTAAT-TTTAAA
1 TCATTTAAATTTAATATTTAAA
*
513986 T-TTTTAAAT
1 TCATTTAAAT
513995 AAAATCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 7 0.25
21 7 0.25
22 14 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TCATTTAAATTTAATATTTAAA
Found at i:514738 original size:22 final size:22
Alignment explanation
Indices: 514713--514754 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
514703 TAGTATTTGA
*
514713 ATAATTAATTTAA-AAAATTAAT
1 ATAA-TAATATAACAAAATTAAT
514735 ATAATAATATAACAAAATTA
1 ATAATAATATAACAAAATTA
514755 TAAATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATAATATAACAAAATTAAT
Found at i:515172 original size:20 final size:22
Alignment explanation
Indices: 515132--515179 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
515122 TTTAAAAATA
515132 AAATTATATTTAATATAAATTT
1 AAATTATATTTAATATAAATTT
*
515154 AAATTATA-TTAA-GTAAATTT
1 AAATTATATTTAATATAAATTT
*
515174 GAATTA
1 AAATTA
515180 AGATCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
22 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
AAATTATATTTAATATAAATTT
Found at i:518733 original size:19 final size:18
Alignment explanation
Indices: 518713--518770 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
518703 GTTACTACAT
*
518713 ATATTATAAAATTTAT-A
1 ATATTATAAAATATATAA
*
518730 ATA-TAAAAAATAATATAA
1 ATATTATAAAAT-ATATAA
518748 ATATTATTAAAATATATAA
1 ATATTA-TAAAATATATAA
518767 ATAT
1 ATAT
518771 GAGAGCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
18 4 0.12
19 12 0.35
20 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATTATAAAATATATAA
Found at i:518859 original size:24 final size:23
Alignment explanation
Indices: 518815--518859 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
518805 TTATTATTTT
* *
518815 TTTAAAAAATTATATTTATTAAA
1 TTTAAAAAATTATAATAATTAAA
518838 TTTAAAAATATTATAATAATTA
1 TTTAAAAA-ATTATAATAATTA
518860 TATAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAAAATTATAATAATTAAA
Found at i:529994 original size:43 final size:43
Alignment explanation
Indices: 529933--530018 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
529923 GCCTGTTCCA
529933 AGATCTTCATTTTGAAGATTTGGTTCAAGAAATGCTGACAATG
1 AGATCTTCATTTTGAAGATTTGGTTCAAGAAATGCTGACAATG
529976 AGATCTTCATTTTGAAGATTTGGTTCAAGAAATGCTGACAATG
1 AGATCTTCATTTTGAAGATTTGGTTCAAGAAATGCTGACAATG
530019 CAGCTTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (43 bp):
AGATCTTCATTTTGAAGATTTGGTTCAAGAAATGCTGACAATG
Found at i:533657 original size:3 final size:3
Alignment explanation
Indices: 533649--533707 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
533639 AAACACCAAT
533649 AAG AAG AAG AAG AAG AAG AAG AAG 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
*
533697 AAG GAG AAG AA
1 AAG AAG AAG AA
533708 AACCGAAGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:536669 original size:2 final size:2
Alignment explanation
Indices: 536662--536690 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
536652 ATCCTCAAAC
536662 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 A
536691 AGTGAAAGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:537004 original size:2 final size:2
Alignment explanation
Indices: 536999--537028 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
536989 GAAAAAAGAA
536999 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
537029 TTAGGGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:539442 original size:37 final size:37
Alignment explanation
Indices: 539369--539460 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
539359 TTAAAAAACG
*
539369 AAATCAATTAAGATAATG--AT---AAAAAAAAAAAG
1 AAATCAATTAAGATAATGATATGCAAAAAAAAAAAAA
*
539401 AAATCAATTAGGATAATGATATGCAAAAAAAAAAAAA
1 AAATCAATTAAGATAATGATATGCAAAAAAAAAAAAA
539438 AAATCAATTAAGATAATGATATG
1 AAATCAATTAAGATAATGATATG
539461 TAAGTTATCG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
32 17 0.33
34 2 0.04
37 33 0.63
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (37 bp):
AAATCAATTAAGATAATGATATGCAAAAAAAAAAAAA
Found at i:541559 original size:2 final size:2
Alignment explanation
Indices: 541552--541578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
541542 TTTAATCATC
541552 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 A
541579 GCATGGAAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:542904 original size:16 final size:16
Alignment explanation
Indices: 542885--542918 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
542875 ATTTTAATAT
542885 AATTTATATTT-ATTTA
1 AATTTA-ATTTAATTTA
542901 AATTTAATTTAATTTA
1 AATTTAATTTAATTTA
542917 AA
1 AA
542919 ACATGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTAATTTAATTTA
Found at i:543113 original size:21 final size:22
Alignment explanation
Indices: 543071--543124 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
543061 ATACTTTTTA
*
543071 ATATTTATATTTTAAAATTATAT
1 ATATTTAT-TTTTAAAACTATAT
*
543094 ATATTTATTTTT-ATACTATAT
1 ATATTTATTTTTAAAACTATAT
*
543115 AAATTATATT
1 ATATT-TATT
543125 GTGTATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.41
22 8 0.30
23 8 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTATTTTTAAAACTATAT
Found at i:543731 original size:2 final size:2
Alignment explanation
Indices: 543724--543750 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
543714 AACTGTAAAG
543724 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
543751 TTTCTCCTTG
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:546923 original size:2 final size:2
Alignment explanation
Indices: 546918--546942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
546908 ATATATATAT
546918 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 A
546943 TAAGCCCATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:551362 original size:3 final size:3
Alignment explanation
Indices: 551354--551393 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
551344 ATACTATTGC
551354 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
551394 AATTCTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:557260 original size:2 final size:2
Alignment explanation
Indices: 557253--557284 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
557243 ATATTCTTTG
557253 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
557285 GAATTTTAAA
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:559015 original size:2 final size:2
Alignment explanation
Indices: 559008--559040 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
558998 TATTTTGGTA
559008 TC TC TC 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 TC TC TC T
559041 AAGAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:562916 original size:2 final size:2
Alignment explanation
Indices: 562911--562941 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
562901 TGTGTGTGTG
*
562911 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
562942 CGCTGTCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:562955 original size:3 final size:3
Alignment explanation
Indices: 562947--562978 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
562937 TATATCGCTG
562947 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
562979 GTTATTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:566675 original size:14 final size:15
Alignment explanation
Indices: 566647--566675 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
566637 AGCAAGCAAA
566647 CACATGATCGGCATG
1 CACATGATCGGCATG
566662 CACATGAT-GGCATG
1 CACATGATCGGCATG
566676 ACAAACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (15 bp):
CACATGATCGGCATG
Found at i:567238 original size:2 final size:2
Alignment explanation
Indices: 567231--567264 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
567221 TAACAGCATT
567231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
567265 ACCAACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:568213 original size:19 final size:19
Alignment explanation
Indices: 568189--568247 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
568179 GATAATGCTA
568189 AAATATAATTTAAATATAT
1 AAATATAATTTAAATATAT
*
568208 AAATAT-A-TTAAA-ATTT
1 AAATATAATTTAAATATAT
*
568224 AAATAAAATTTTAAATATA-
1 AAATATAA-TTTAAATATAT
568243 AAATA
1 AAATA
568248 ATATGATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 1 0.03
19 16 0.48
20 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATAATTTAAATATAT
Found at i:568275 original size:20 final size:20
Alignment explanation
Indices: 568236--568283 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
568226 ATAAAATTTT
*
568236 AAATATAAAATAATATGATA
1 AAATATAAAATAATAAGATA
568256 AAATAGTAAAATAA-AAGAT-
1 AAATA-TAAAATAATAAGATA
568275 AAATATAAA
1 AAATATAAA
568284 TAAACCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 5 0.19
20 9 0.35
21 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
AAATATAAAATAATAAGATA
Found at i:568434 original size:5 final size:5
Alignment explanation
Indices: 568424--568448 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
568414 CTAAAGAGCC
568424 ACAGG ACAGG ACAGG ACAGG ACAGG
1 ACAGG ACAGG ACAGG ACAGG ACAGG
568449 GCAGCTCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
ACAGG
Found at i:576356 original size:118 final size:118
Alignment explanation
Indices: 576148--576386 Score: 433
Period size: 118 Copynumber: 2.0 Consensus size: 118
576138 TATTGAAATA
* *
576148 TAGAAATTACTACTTGAACGAGGAAAGCATACCCTTAATTAGCAAGGCCCTTTATTGACATAGCA
1 TAGAAATTACTACTTGAACAAGGAAAGCATACCCTTAATTAGCAAGGCCCTTTATTGACACAGCA
576213 CCAGGAAGGCAGGAACTAAAACGGAGACAAACTTCTGTTATTCAACGGATACG
66 CCAGGAAGGCAGGAACTAAAACGGAGACAAACTTCTGTTATTCAACGGATACG
* *
576266 TAGAAATTACTACTTGAATAAGGAAAGCATACCCTTAATTAGTAAGGCCCTTTATTGACACAGCA
1 TAGAAATTACTACTTGAACAAGGAAAGCATACCCTTAATTAGCAAGGCCCTTTATTGACACAGCA
*
576331 CCAGGAAGGCAGGAACTAAAACGGAGATAAACTTCTGTTATTCAACGGATACG
66 CCAGGAAGGCAGGAACTAAAACGGAGACAAACTTCTGTTATTCAACGGATACG
576384 TAG
1 TAG
576387 GAGCCGTCGG
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (118 bp):
TAGAAATTACTACTTGAACAAGGAAAGCATACCCTTAATTAGCAAGGCCCTTTATTGACACAGCA
CCAGGAAGGCAGGAACTAAAACGGAGACAAACTTCTGTTATTCAACGGATACG
Found at i:578561 original size:2 final size:2
Alignment explanation
Indices: 578554--578591 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
578544 ATGAATATCA
578554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
578592 CCTCTAAGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:580004 original size:3 final size:3
Alignment explanation
Indices: 579998--580037 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
579988 CGGTCAAACG
579998 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
580038 AGGGTTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:587761 original size:16 final size:16
Alignment explanation
Indices: 587740--587785 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
587730 TATCGAATAT
587740 AAATATATTTAAATTC
1 AAATATATTTAAATTC
* * *
587756 AAATATATTTGATTTT
1 AAATATATTTAAATTC
587772 ATAATATATTTAAA
1 A-AATATATTTAAA
587786 AAATTATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AAATATATTTAAATTC
Found at i:587795 original size:14 final size:14
Alignment explanation
Indices: 587776--587815 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
587766 GATTTTATAA
587776 TATATTTAAAAAAT
1 TATATTTAAAAAAT
* * *
587790 TATATTTATATATT
1 TATATTTAAAAAAT
587804 TATATTTAAAAA
1 TATATTTAAAAA
587816 TATATCAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTTAAAAAAT
Found at i:587801 original size:39 final size:39
Alignment explanation
Indices: 587758--587834 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
587748 TTAAATTCAA
* *
587758 ATATATTTGAT-TTTATAATATATTTAAAAAATTA-TATTT
1 ATATATTT-ATATTTA-AAAATATATAAAAAATTAGTATTT
*
587797 ATATATTTATATTTAAAAATATATCAAAAATTAGTATT
1 ATATATTTATATTTAAAAATATATAAAAAATTAGTATT
587835 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (39 bp):
ATATATTTATATTTAAAAATATATAAAAAATTAGTATTT
Found at i:589480 original size:33 final size:36
Alignment explanation
Indices: 589430--589505 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 36
589420 CAGTACTGAA
* *
589430 TAAAATTTTTTAAAATTACGAT-TAA-ATTT-AATT
1 TAAATTTTTTTAAAATTAAGATATAATATTTAAATT
* *
589463 TAAATTTTTTTATAATTAATATATAATATTTAAATT
1 TAAATTTTTTTAAAATTAAGATATAATATTTAAATT
589499 TAAATTT
1 TAAATTT
589506 AATATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 18 0.50
34 3 0.08
35 4 0.11
36 11 0.31
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
TAAATTTTTTTAAAATTAAGATATAATATTTAAATT
Found at i:600692 original size:282 final size:279
Alignment explanation
Indices: 600190--600739 Score: 745
Period size: 282 Copynumber: 2.0 Consensus size: 279
600180 CTAGAATGCA
* * **
600190 TTGATGATAAGCAAGAGCATAAAGCCATGGTAGGCTGACATTCAATTTTTTTTTTTTTTTTTGGG
1 TTGATGATAAGCAAGAGCATAAAGCCATGGTAGGCTGACACTCAATTTTTTGTAGTTTTTTTGGG
* ***
600255 AAAAATTGCCTTTGGTGGAAAGAAAATTTTCACTTTCATTTTTTAATCTTTGCTAAGATGGATTT
66 AAAAATTGCCTTTGGTGCAAAGAAAATTTTCACTTTCATTTTTTAATCTTCAATAAGATGGATTT
* * * *
600320 CTTTCCCTGGATTGTCAGGTAAGAAGTTCTGAAGCAGATGCTAGTTCTCCAAGCATTTGTGTTTC
131 CTTTCCATGGATGGGCAGGTAAGAAGTCCTGAA-CAGATGCTAGTTCTCCAAGCATTTGTGTTTC
* * *
600385 AAATTATAACTGTCAGAGTTGTCAGGTACATG-TAACCAATTTCTTAGATCAGGATTGTCAGATA
195 AAATTACAACTGTCAGAGTTGTCAGGTACA-GCAAACCAATTTCTTAAATCAGGATTGTCAGATA
600449 ATGTACATGTTTAACATGCCT
259 ATGTACATGTTTAACATGCCT
*
600470 TTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTCAAAATTTTCTCTGGTAGTTTTT
1 TTGATGATAAGCAAGAGCATAAAGCCATGGTAGGCTGACACTC--AATTTT-T-T-GTAGTTTTT
* * *
600535 TT-GG-AGAATTGCCTTTGGTTCAAAGAAAA-TTTCTTCTTTCA-TTTTTAATCTTCAATAAGAT
61 TTGGGAAAAATTGCCTTTGGTGCAAAGAAAATTTTC-ACTTTCATTTTTTAATCTTCAATAAGAT
* *
600596 GGATTTGTTTCCATGGATGGGCAGGTGAGAAGTCCTG-A-AGATGCTAGTTCTCCAAGCATTTGT
125 GGATTTCTTTCCATGGATGGGCAGGTAAGAAGTCCTGAACAGATGCTAGTTCTCCAAGCATTTGT
600659 GTTTCAAATGATGACAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAAATCAGGATTG
190 GTTTCAAAT--T-ACAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAAATCAGGATTG
* *
600724 TCAGATTATTTACATG
252 TCAGATAATGTACATG
600740 CCACGCTTAT
Statistics
Matches: 237, Mismatches: 23, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
279 34 0.14
280 41 0.17
281 3 0.01
282 119 0.50
283 29 0.12
284 3 0.01
285 8 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (279 bp):
TTGATGATAAGCAAGAGCATAAAGCCATGGTAGGCTGACACTCAATTTTTTGTAGTTTTTTTGGG
AAAAATTGCCTTTGGTGCAAAGAAAATTTTCACTTTCATTTTTTAATCTTCAATAAGATGGATTT
CTTTCCATGGATGGGCAGGTAAGAAGTCCTGAACAGATGCTAGTTCTCCAAGCATTTGTGTTTCA
AATTACAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAAATCAGGATTGTCAGATAAT
GTACATGTTTAACATGCCT
Found at i:601608 original size:394 final size:390
Alignment explanation
Indices: 600462--601652 Score: 1530
Period size: 407 Copynumber: 3.0 Consensus size: 390
600452 TACATGTTTA
* *
600462 ACATGCCTTTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTCAAAATTTTCTCTGG
1 ACATGCCATTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTC--AATTTT-TCTAG
* ** *
600527 TAGTTTTTTTGGAG-AATTGCCTTTGGTTCAAAGAAAA-TTTCTTCTTTCA-TTTTTAATCTTCA
63 TAGTTTTTTTGGAGAAATTGCCTTTGATGGAAAGAAAATTTTC-CCTTTCATTTTTTAATCTTCA
* * * *
600589 ATAAGATGGATTTGTTTCCATGGATGGGCAGGTGAGAAGTCCTGAAGATGCTAGTTCTCCAAGCA
127 GTAAGATGG-TTTGTTTCCATGGATGGTCAGGTAAGAAGTTCTGAAGATGCTAGTTCTCCAAGCA
*
600654 TTTGTGTTTCAAATGATGACAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAAATCAG
191 TTTGTGTTTCAAATGATGATAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAAATCAG
* * * * * *
600719 GATTGTCAGATTATTTACATGCCACGCTTATTGGAACGGATTTGACAGAAATATCATATGCTGTC
256 GATTGTCAGATTATATACATGCCACGCATATCGGAATGGCTTTGACA-AAA-A--A-AT--TGTA
** * *
600784 TACTGTCTAAATTAGATACATGAAACCTTTCCTGGGACTGGAAATATTCATGAGGATTCAGGTGA
314 TGGTGTCTAAATTAGATACATGAAAGCTTTCCTGGGACTGGAAATATTCATGAGGATTCAAGTGA
*
600849 GGCAGATTATAT
379 GTCAGATTATAT
* * *
600861 ACAGGCAATTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTGAATTTTTTTCTTTT
1 ACATGCCATTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTCAA--TTTTTC----
** ** * * * *
600926 TTTTTTTTTTTTTTGGGAGAAATTGCATTTGGTTGGAAGGAAAATTTTCCTTTTCATTTTTTAAT
60 -TAGTAGTTTTTTT-GGAGAAATTGCCTTT-GATGGAAAGAAAATTTTCCCTTTCATTTTTTAAT
* * * ** *
600991 CTACTGTAAGAAGGGTTTGTTTCCATGGATGGTCAGGTAAGTTGTTCTGAAGATGCTAGTTCTAC
122 CTTCAGTAAG-ATGGTTTGTTTCCATGGATGGTCAGGTAAGAAGTTCTGAAGATGCTAGTTCTCC
* *
601056 AAGCATTTGTGCTTCAAATGATGATAACTGTCAGAGTTGTCAGGTACAGCAAACTAATTTCTTAA
186 AAGCATTTGTGTTTCAAATGATGATAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAA
* * * *
601121 ATCAGGATTGTCAGATTAAATACATGCAATGCATATCGGAATGGCTTTGACAGAAAAATTGTATG
251 ATCAGGATTGTCAGATTATATACATGCCACGCATATCGGAATGGCTTTGACAAAAAAATTGTATG
*
601186 GTGTCTAAATTAGATACATGAAAGCTTTCCCGGGACTGGAAATATTCATGAGGATTCAAGTGAGT
316 GTGTCTAAATTAGATACATGAAAGCTTTCCTGGGACTGGAAATATTCATGAGGATTCAAGTGAGT
601251 CTA-ATTATAT
381 C-AGATTATAT
*
601261 ACATGCCATTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGCCACTCAATTTTTCTAGTAG
1 ACATGCCATTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTCAATTTTTCTAGTAG
* *
601326 GTTTTTTGGAGAAATTGCCTTTGATGGAAAGAAAATTTTCCCTTTCATTTTTTAATCTTCCGTAA
66 TTTTTTTGGAGAAATTGCCTTTGATGGAAAGAAAATTTTCCCTTTCATTTTTTAATCTTCAGTAA
* * *
601391 GATGGTTTGTTTCCCTGGATGGTCAGGTAAGAAGTTCAGAAGTGGACGCTAGTTCTCCAAGCATT
131 GATGGTTTGTTTCCATGGATGGTCAGGTAAGAAGTTCTGAA---GATGCTAGTTCTCCAAGCATT
* * * *
601456 TGTGTTTCAAATGATGATAACTGTCAGAGTTGTCACGTACAGGTATCACCAA-TTCTTAAATCAA
193 TGTGTTTCAAATGATGATAACTGTCAGAGTTGTCAGGTACA-GCA-AACCAATTTCTTAAATCAG
* *
601520 GATTGTCAGATTATATACATGCCACGCATATCAGAATGGCTTTGACACAAAAATTGTATGGTGTC
256 GATTGTCAGATTATATACATGCCACGCATATCGGAATGGCTTTGACAAAAAAATTGTATGGTGTC
* * *
601585 TAAATTAGATAGAAGAAAGCTTTCCTGGGACTGGAAATATTC-TCGAGCATTCAAGTGAGTCAGA
321 TAAATTAGATACATGAAAGCTTTCCTGGGACTGGAAATATTCAT-GAGGATTCAAGTGAGTCAGA
601649 TTAT
385 TTAT
601653 GCGGTTGTTG
Statistics
Matches: 690, Mismatches: 81, Indels: 47
0.84 0.10 0.06
Matches are distributed among these distances:
390 35 0.05
391 39 0.06
392 14 0.02
393 68 0.10
394 133 0.19
395 4 0.01
397 2 0.00
398 8 0.01
399 51 0.07
400 121 0.18
401 1 0.00
402 2 0.00
403 10 0.01
404 4 0.01
405 10 0.01
406 16 0.02
407 169 0.24
408 3 0.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (390 bp):
ACATGCCATTGATGATAAGCAAGAGCATGAAGCCATGGTAGGCTGACACTCAATTTTTCTAGTAG
TTTTTTTGGAGAAATTGCCTTTGATGGAAAGAAAATTTTCCCTTTCATTTTTTAATCTTCAGTAA
GATGGTTTGTTTCCATGGATGGTCAGGTAAGAAGTTCTGAAGATGCTAGTTCTCCAAGCATTTGT
GTTTCAAATGATGATAACTGTCAGAGTTGTCAGGTACAGCAAACCAATTTCTTAAATCAGGATTG
TCAGATTATATACATGCCACGCATATCGGAATGGCTTTGACAAAAAAATTGTATGGTGTCTAAAT
TAGATACATGAAAGCTTTCCTGGGACTGGAAATATTCATGAGGATTCAAGTGAGTCAGATTATAT
Found at i:603146 original size:22 final size:20
Alignment explanation
Indices: 603111--603155 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
603101 AAATTTTATG
603111 TAAATTTAATTAAAAAAATA
1 TAAATTTAATTAAAAAAATA
*
603131 TAAATGTTAATATAAAATAATA
1 TAAAT-TTAAT-TAAAAAAATA
603153 TAA
1 TAA
603156 TAAGCTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAATTTAATTAAAAAAATA
Found at i:627973 original size:24 final size:24
Alignment explanation
Indices: 627941--628017 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 24
627931 AATTTTTTAA
627941 ATATATATTTTAATATATTTAAAG
1 ATATATATTTTAATATATTTAAAG
* *
627965 ATTTATATTTTTATATTTATATTTAAAT
1 ATATATA-TTTTA-A--TATATTTAAAG
*
627993 ATATATTATGTTAATAT-TTTAAAG
1 ATATA-TATTTTAATATATTTAAAG
628017 A
1 A
628018 AATGAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
24 13 0.30
25 8 0.19
26 1 0.02
27 1 0.02
28 18 0.42
29 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
ATATATATTTTAATATATTTAAAG
Found at i:629280 original size:2 final size:2
Alignment explanation
Indices: 629267--629298 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
629257 AAAGAAATCT
629267 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
629299 TTACGGTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:630883 original size:34 final size:34
Alignment explanation
Indices: 630815--630894 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
630805 CTAATATTTG
* *
630815 TTAATTAAATGAATGATTTGGTAATTTGTAATTA
1 TTAATTAAATGAATGATTTGATAATTTATAATTA
* *
630849 TTAATTAAATGAATGATTTGATAGTTTATCATTA
1 TTAATTAAATGAATGATTTGATAATTTATAATTA
* *
630883 TTGACTAAATGA
1 TTAATTAAATGA
630895 CTAAAAGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.45
Consensus pattern (34 bp):
TTAATTAAATGAATGATTTGATAATTTATAATTA
Found at i:635033 original size:25 final size:28
Alignment explanation
Indices: 634990--635040 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
634980 TTATATTTAA
*
634990 ATATATTTTAAACACAATATT-AAATTC
1 ATATATTTTAAACAAAATATTCAAATTC
635017 ATATA-TTTAAA-AAAATATTCAAAT
1 ATATATTTTAAACAAAATATTCAAAT
635041 AACATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 10 0.45
27 5 0.23
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATATTTTAAACAAAATATTCAAATTC
Found at i:635046 original size:27 final size:25
Alignment explanation
Indices: 634990--635054 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
634980 TTATATTTAA
* *
634990 ATATATTTTAAACACAATATTAAATTC
1 ATATA-TTTAAA-AAAATATTAAATAC
635017 ATATATTTAAAAAAATATTCAAATAAC
1 ATATATTTAAAAAAATATT-AAAT-AC
*
635044 ATA-AATTAAAA
1 ATATATTTAAAA
635055 CAAACCTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 7 0.21
26 17 0.52
27 9 0.27
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
ATATATTTAAAAAAATATTAAATAC
Found at i:637939 original size:21 final size:19
Alignment explanation
Indices: 637915--637956 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
637905 TGCATATCAC
*
637915 TTATAATTTTTTACTATAATA
1 TTATAATTATTTA--ATAATA
637936 TTATAATTATTTAATAATA
1 TTATAATTATTTAATAATA
637955 TT
1 TT
637957 TAAAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAATTATTTAATAATA
Found at i:640258 original size:15 final size:16
Alignment explanation
Indices: 640238--640276 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
640228 TAAAATATAC
640238 TTAAAATTA-TTAAAT
1 TTAAAATTATTTAAAT
*
640253 TTAAAATAATTTAAAT
1 TTAAAATTATTTAAAT
*
640269 TTATAATT
1 TTAAAATT
640277 TAATTGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAAATTATTTAAAT
Found at i:640268 original size:16 final size:15
Alignment explanation
Indices: 640238--640327 Score: 52
Period size: 16 Copynumber: 6.3 Consensus size: 15
640228 TAAAATATAC
*
640238 TTAAAATTATTAAAT
1 TTAAAATAATTAAAT
640253 TTAAAATAATTTAAAT
1 TTAAAATAA-TTAAAT
*
640269 TT---ATAATTTAAT
1 TTAAAATAATTAAAT
* *
640281 TGAATA-AATTAAAT
1 TTAAAATAATTAAAT
640295 TTAAGTAA-AATT---T
1 TTAA--AATAATTAAAT
640308 TTAAAAATAATTAAAT
1 TT-AAAATAATTAAAT
640324 TTAA
1 TTAA
640328 TCTAGTTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
12 8 0.14
13 11 0.19
14 12 0.21
15 11 0.19
16 16 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TTAAAATAATTAAAT
Found at i:642101 original size:2 final size:2
Alignment explanation
Indices: 642094--642120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
642084 GTCCATCCTT
642094 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
642121 GTGAGTGTGT
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:649100 original size:51 final size:52
Alignment explanation
Indices: 649008--649106 Score: 141
Period size: 51 Copynumber: 1.9 Consensus size: 52
648998 CGATTTGTAA
* *
649008 TTAAATTTGTTTATAAATTATATTTTAATTTAAAAAAATTTAAAATTTTTAG
1 TTAAATTTGTTTATAAATTATATTTAAATTAAAAAAAATTTAAAATTTTTAG
649060 TTAAA-TT-TTTATTAAATTA-ATTTAAATTAAAAAAATATTTAAAATTT
1 TTAAATTTGTTTA-TAAATTATATTTAAATTAAAAAAA-ATTTAAAATTT
649107 AATTCATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
50 18 0.42
51 20 0.47
52 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (52 bp):
TTAAATTTGTTTATAAATTATATTTAAATTAAAAAAAATTTAAAATTTTTAG
Found at i:649446 original size:20 final size:21
Alignment explanation
Indices: 649400--649448 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
649390 AATTATTATT
*
649400 ATTATTATATAAATATGTAAAA
1 ATTATT-TATAAATATATAAAA
*
649422 TTTATTTATAAAT-TATAAAA
1 ATTATTTATAAATATATAAAA
649442 ATTATTT
1 ATTATTT
649449 TTATGAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.50
21 7 0.29
22 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTATTTATAAATATATAAAA
Found at i:649457 original size:22 final size:21
Alignment explanation
Indices: 649401--649459 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
649391 ATTATTATTA
*
649401 TTATTATATAAA-TATGTAAAAT
1 TTATT-TATAAATTAT-AAAAAT
649423 TTATTTATAAATTATAAAAAT
1 TTATTTATAAATTATAAAAAT
* *
649444 TATTTTTATGAATTAT
1 T-TATTTATAAATTAT
649460 GATTAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TTATTTATAAATTATAAAAAT
Found at i:653115 original size:39 final size:39
Alignment explanation
Indices: 653066--653149 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
653056 GAACTATGTT
* * *
653066 TTACAAACTTGTACATGTTGTTTAATTGATGCATGTTAA
1 TTACGAACTTGTACATGTTATTTAATCGATGCATGTTAA
* *
653105 TTACGAACTTGTGCATGTTATTTAATCGATGTATGTTAA
1 TTACGAACTTGTACATGTTATTTAATCGATGCATGTTAA
653144 TTACGA
1 TTACGA
653150 TCAAGCAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (39 bp):
TTACGAACTTGTACATGTTATTTAATCGATGCATGTTAA
Found at i:655253 original size:48 final size:48
Alignment explanation
Indices: 655182--655277 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
655172 ATGCAGAAAA
*
655182 AGAAATACTATGAGTTAAGGAAATGAAAATCGAAGTCTATTTGAGCAC
1 AGAAATACAATGAGTTAAGGAAATGAAAATCGAAGTCTATTTGAGCAC
655230 AGAAATACAATGAGTTAAGGAAATGAAAATCGAAGTCTATTTGAGCAC
1 AGAAATACAATGAGTTAAGGAAATGAAAATCGAAGTCTATTTGAGCAC
655278 TAATCGTAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (48 bp):
AGAAATACAATGAGTTAAGGAAATGAAAATCGAAGTCTATTTGAGCAC
Found at i:658077 original size:6 final size:6
Alignment explanation
Indices: 658066--658092 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
658056 AAACCACCGC
658066 CATTGG CATTGG CATTGG CATTGG CAT
1 CATTGG CATTGG CATTGG CATTGG CAT
658093 GGGAATGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (6 bp):
CATTGG
Found at i:659086 original size:3 final size:3
Alignment explanation
Indices: 659038--659072 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
659028 TTCCCCCCAA
659038 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
659073 AATCCAAAAT
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:660335 original size:19 final size:19
Alignment explanation
Indices: 660277--660341 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
660267 AAGAGATATA
* *
660277 ATTATATTATTTAATTTATT
1 ATTATAATA-TTAATTTAAT
**
660297 AATTAT-ATAAAAATTATAAT
1 -ATTATAATATTAATT-TAAT
660317 ATTATAATATTAATTTAAT
1 ATTATAATATTAATTTAAT
*
660336 TTTATA
1 ATTATA
660342 TTAATATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 18 0.51
20 12 0.34
21 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTATAATATTAATTTAAT
Found at i:660947 original size:26 final size:24
Alignment explanation
Indices: 660885--660951 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 24
660875 TAGACACTCG
*
660885 ATTATATTAAATATGATAAAAAATA
1 ATTATA-TAAATATGATAAAAAAAA
* *
660910 ATTATA-ATATATTATAATAAAAAA
1 ATTATATAAATATGATAA-AAAAAA
660934 ATTCATATAAATATGATA
1 ATT-ATATAAATATGATA
660952 TAATTATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 9 0.26
26 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (24 bp):
ATTATATAAATATGATAAAAAAAA
Found at i:660991 original size:34 final size:33
Alignment explanation
Indices: 660944--661030 Score: 94
Period size: 32 Copynumber: 2.7 Consensus size: 33
660934 ATTCATATAA
*
660944 ATATGATAT-AATTATATAATTATTTTAAAAGTT
1 ATAT-ATATAAATTATATAATTATATTAAAAGTT
* *
660977 ATTTAATATAAATTAT-TAATT-TATTAAAATTT
1 ATAT-ATATAAATTATATAATTATATTAAAAGTT
661009 ATATATATAAA--ATATAATTATA
1 ATATATATAAATTATATAATTATA
661031 ATATAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.04
30 5 0.11
31 9 0.20
32 12 0.26
33 12 0.26
34 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (33 bp):
ATATATATAAATTATATAATTATATTAAAAGTT
Found at i:661029 original size:29 final size:30
Alignment explanation
Indices: 660957--661054 Score: 76
Period size: 32 Copynumber: 3.2 Consensus size: 30
660947 TGATATAATT
*
660957 ATATAATTATTTTAAAAGTTATTTAATATAAA
1 ATATAATTA--TTAAAAGTTATATAATATAAA
* *
660989 TTATTAATTTATTAAAATTTATAT-ATATAAA
1 ATA-TAA-TTATTAAAAGTTATATAATATAAA
* * *
661020 ATATAATTA-TAATA-TAATAAAATATATAA
1 ATATAATTATTAAAAGTTATATAATATA-AA
661049 ATATAA
1 ATATAA
661055 GAATTATGGA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.07
28 9 0.16
29 11 0.20
30 3 0.05
31 9 0.16
32 13 0.24
33 3 0.05
34 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
ATATAATTATTAAAAGTTATATAATATAAA
Found at i:661053 original size:36 final size:38
Alignment explanation
Indices: 660981--661054 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 38
660971 AAAGTTATTT
* * * *
660981 AATATAAATTATTAATTTATTAAAATTTATATATATAA
1 AATATAAATTATTAATATAATAAAATATATAAATATAA
661019 AATAT-AATTA-TAATATAATAAAATATATAAATATAA
1 AATATAAATTATTAATATAATAAAATATATAAATATAA
661055 GAATTATGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 22 0.69
37 5 0.16
38 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (38 bp):
AATATAAATTATTAATATAATAAAATATATAAATATAA
Done.