Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 2 of 170
Found at i:374287 original size:18 final size:17
Alignment explanation
Indices: 374259--374293 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
374249 ATTATTAAGA
*
374259 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
374276 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
374294 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:374395 original size:59 final size:58
Alignment explanation
Indices: 374236--374412 Score: 150
Period size: 57 Copynumber: 3.0 Consensus size: 58
374226 GAATTTTTGT
*
374236 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATA-TATTTTAATTAAAATATA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATTATTTTAAGTAAAATATA
* * * * * * *
374293 TTTAATAATAATT-ATGT-TAAATTATATTTTA-TAGTATCATATATTATGATTTTAGT-AAATT
1 TATAAGAAT-ATTGAT-TATTAA-GA-ATTTTATTA-AAT--TATATTAT--TTTAAGTAAAATA
374354 TA
57 TA
*
374356 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATA-TATTTTAATTAAAATATA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATTATTTTAAGTAAAATATA
374413 ATTATGTTAA
Statistics
Matches: 90, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
56 5 0.06
57 18 0.20
58 10 0.11
59 12 0.13
61 12 0.13
62 10 0.11
63 18 0.20
64 5 0.06
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.49
Consensus pattern (58 bp):
TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATTATTTTAAGTAAAATATA
Found at i:374407 original size:18 final size:17
Alignment explanation
Indices: 374379--374427 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
374369 ATTATTAAGA
*
374379 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
374396 ATTTTAATTAAAATATA-
1 ATTTT-ATTAAAATATAT
* *
374413 ATTATGTTAAAATAT
1 ATTTTATTAAAATAT
374428 GATTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.32
17 9 0.32
18 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:379975 original size:18 final size:20
Alignment explanation
Indices: 379954--380015 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 20
379944 TTAAAAAAAG
379954 TATAAAT-TTTT-AAATTTT
1 TATAAATATTTTGAAATTTT
379972 TATAAATATTTTGAAA--TT
1 TATAAATATTTTGAAATTTT
*
379990 TAAAAATTATTTTG-AATTTT
1 TATAAA-TATTTTGAAATTTT
380010 T-TAAAT
1 TATAAAT
380016 TTATTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 17 0.46
19 14 0.38
20 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATAAATATTTTGAAATTTT
Found at i:379996 original size:28 final size:27
Alignment explanation
Indices: 379965--380018 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
379955 ATAAATTTTT
379965 AAATT-TTTATAAATATTTTGAAATTTAA
1 AAATTATTT-TAAAT-TTTTGAAATTTAA
* *
379993 AAATTATTTTGAATTTTTTAAATTTA
1 AAATTATTTTAAATTTTTGAAATTTA
380019 TTTTTGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 9 0.39
29 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
AAATTATTTTAAATTTTTGAAATTTAA
Found at i:380021 original size:20 final size:19
Alignment explanation
Indices: 379961--380032 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
379951 AAGTATAAAT
*
379961 TTTTAAATTTTTATAAA-TA
1 TTTTGAATTTTT-TAAATTA
* **
379980 TTTTGAAATTTAAAAATTA
1 TTTTGAATTTTTTAAATTA
379999 TTTTGAATTTTTTAAATTTA
1 TTTTGAATTTTTTAAA-TTA
*
380019 TTTTTGTATTTTTT
1 -TTTTGAATTTTTT
380033 TGTTGAGAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 3 0.07
19 24 0.57
20 3 0.07
21 12 0.29
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTGAATTTTTTAAATTA
Found at i:381918 original size:11 final size:12
Alignment explanation
Indices: 381892--381932 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
381882 AAAATATAAG
*
381892 TTTTTATGAATT
1 TTTTTATGAATA
381904 TTTTTAT-AATA
1 TTTTTATGAATA
381915 TTTTT-TGAATA
1 TTTTTATGAATA
381926 TTTTTAT
1 TTTTTAT
381933 ATTTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 1 0.04
11 17 0.65
12 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTTTATGAATA
Found at i:385402 original size:6 final size:6
Alignment explanation
Indices: 385391--385418 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
385381 GTGGCCCGGT
385391 AATTTA AATTTA AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
385419 CTTAATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:386382 original size:17 final size:18
Alignment explanation
Indices: 386345--386383 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
386335 TGTTTGATTC
**
386345 AATAAAATTATGATATTA
1 AATAAAATTATGATAGAA
386363 AATAAAATT-TGATAGAA
1 AATAAAATTATGATAGAA
386380 AATA
1 AATA
386384 TTAATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (18 bp):
AATAAAATTATGATAGAA
Found at i:401549 original size:7 final size:7
Alignment explanation
Indices: 401537--401565 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
401527 AGTGCGGTGA
401537 TTAAATT
1 TTAAATT
401544 TTAAATT
1 TTAAATT
401551 TTAAATT
1 TTAAATT
401558 TTAAATT
1 TTAAATT
401565 T
1 T
401566 ACAATGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTAAATT
Found at i:402062 original size:16 final size:16
Alignment explanation
Indices: 402041--402080 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
402031 CGTTTGGTTC
*
402041 GCTGTAATGGAATAGA
1 GCTGTAATGCAATAGA
402057 GCTGTAATGCAATAGA
1 GCTGTAATGCAATAGA
*
402073 ACTGTAAT
1 GCTGTAAT
402081 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (16 bp):
GCTGTAATGCAATAGA
Found at i:402400 original size:28 final size:28
Alignment explanation
Indices: 402363--402417 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
402353 AATTTACTAA
*
402363 AATAATAATATAT-AGTTAATAATAATTT
1 AATAAAAATATATAAGTTAATAA-AATTT
*
402391 AATAAAAATATATAATTTAATAAAATT
1 AATAAAAATATATAAGTTAATAAAATT
402418 CTTAATATAA
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:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AATAAAAATATATAAGTTAATAAAATTT
Found at i:402423 original size:17 final size:18
Alignment explanation
Indices: 402380--402415 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
402370 ATATATAGTT
402380 AATA-ATAATTTAATAAA
1 AATATATAATTTAATAAA
402397 AATATATAATTTAATAAA
1 AATATATAATTTAATAAA
402415 A
1 A
402416 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATATAATTTAATAAA
Found at i:405477 original size:15 final size:15
Alignment explanation
Indices: 405454--405484 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
405444 TGAAAATGAC
405454 CTAAAATTTGCAAAT
1 CTAAAATTTGCAAAT
*
405469 CTAACATTTGCAAAT
1 CTAAAATTTGCAAAT
405484 C
1 C
405485 AGCTGTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
CTAAAATTTGCAAAT
Found at i:406003 original size:23 final size:23
Alignment explanation
Indices: 405935--406003 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
405925 TTAATTTTAA
*
405935 ATTAA-ATAAAATTTTAAAATTT
1 ATTAATATAAAATTCTAAAATTT
405957 AATT-ATA-AAAATATCTAAAA--T
1 -ATTAATATAAAAT-TCTAAAATTT
*
405978 ATTAATATAAAATTGTAAAATTT
1 ATTAATATAAAATTCTAAAATTT
406001 ATT
1 ATT
406004 TTTCTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.08
21 10 0.26
22 11 0.29
23 14 0.37
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATTAATATAAAATTCTAAAATTT
Found at i:407731 original size:50 final size:50
Alignment explanation
Indices: 407615--407907 Score: 415
Period size: 50 Copynumber: 5.8 Consensus size: 50
407605 GATCATAACA
* * ** *
407615 TGCCAAAGCCATGTCCCAGACGTGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* ** *
407666 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
407716 TGCCAACGTCATGTCCCAGACATGGTCTTATATAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
407766 TGCCCATGCCATGTCCTAGACATGGTCTTACAAGGGACCTATCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
407816 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
407866 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
407908 TTACCCAAAT
Statistics
Matches: 211, Mismatches: 31, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
50 178 0.84
51 33 0.16
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:408280 original size:30 final size:29
Alignment explanation
Indices: 408245--408301 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
408235 CCTCGACTCT
*
408245 AACTTTTTCAAAATTACGATTTTGCCCCTA
1 AACTTTTGCAAAATTAC-ATTTTGCCCCTA
* *
408275 AACTTTTGCATAATTACATTTTTCCCC
1 AACTTTTGCAAAATTACATTTTGCCCC
408302 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (29 bp):
AACTTTTGCAAAATTACATTTTGCCCCTA
Found at i:410581 original size:56 final size:59
Alignment explanation
Indices: 410460--410583 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 59
410450 GTTTGACAAG
* **
410460 TACCAAATTGAACAAAAAAACAATTAGGTACCAAATTAGGGAAAAAATGTCAAGTTTGGA
1 TACCAAATTGAACAAAAAAACAATTAGGTACCAAATTA-GGAAAAAATATCAAGTTCAGA
* * * *
410520 TACCAACTTGGAC-AAAAAA-AATTAGGTACTAAATTA-GAAAAAATATCAAGTTCATA
1 TACCAAATTGAACAAAAAAACAATTAGGTACCAAATTAGGAAAAAATATCAAGTTCAGA
410576 TACCAAAT
1 TACCAAAT
410584 GTTATATTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 23 0.41
58 16 0.29
59 6 0.11
60 11 0.20
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (59 bp):
TACCAAATTGAACAAAAAAACAATTAGGTACCAAATTAGGAAAAAATATCAAGTTCAGA
Found at i:419064 original size:32 final size:32
Alignment explanation
Indices: 419028--419099 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
419018 GCTTTTTACA
*
419028 TGTTGCGACGAAATACGGTTCTTT-TCGTGACT
1 TGTTGCGACGAAATACGCTT-TTTCTCGTGACT
*
419060 TGTTGCGACGAAATATGCTTTTTCTCGTGACT
1 TGTTGCGACGAAATACGCTTTTTCTCGTGACT
419092 TGTTGCGA
1 TGTTGCGA
419100 AATGAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (32 bp):
TGTTGCGACGAAATACGCTTTTTCTCGTGACT
Found at i:421382 original size:8 final size:8
Alignment explanation
Indices: 421371--421400 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
421361 GAAGCAGAGG
421371 TTATCGAA
1 TTATCGAA
421379 TTATCGAA
1 TTATCGAA
421387 TTATCGAA
1 TTATCGAA
421395 TTATCG
1 TTATCG
421401 CTGCTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (8 bp):
TTATCGAA
Found at i:444491 original size:72 final size:72
Alignment explanation
Indices: 444406--444551 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 72
444396 CAAACTGCTC
* *
444406 CAAGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCTGGCTCAAGCTCAAGT
1 CAAGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGT
444471 AGGAATG
66 AGGAATG
* *
444478 CAAGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAATCAAGCTCAGCCTCAAGCTCAAGT
1 CAAGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGT
444543 AGGAATG
66 AGGAATG
444550 CA
1 CA
444552 TATGAAACAC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (72 bp):
CAAGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGT
AGGAATG
Found at i:449537 original size:12 final size:12
Alignment explanation
Indices: 449520--449554 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
449510 GACCCAACCC
449520 ATATTAATTTTT
1 ATATTAATTTTT
449532 ATATT-ATTTTT
1 ATATTAATTTTT
449543 ATA-TAATTTTT
1 ATATTAATTTTT
449554 A
1 A
449555 GATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 16 0.73
12 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:449712 original size:30 final size:30
Alignment explanation
Indices: 449678--449739 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
449668 CTTAACAAGT
449678 AAATGCCTCTAAAATAATAAAAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAATTAAC
* *
449708 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAATTAAC
449738 AA
1 AA
449740 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAAAAAAATTAAC
Found at i:457833 original size:24 final size:24
Alignment explanation
Indices: 457805--457856 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
457795 TTAGTAGGTC
* * *
457805 AAATAAATTGTGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
457829 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
457853 AAAT
1 AAAT
457857 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:464607 original size:19 final size:20
Alignment explanation
Indices: 464573--464614 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
464563 AATTTTTAAT
464573 TTTATTGTATATTATAATAA
1 TTTATTGTATATTATAATAA
* *
464593 TTTATTTTA-ATTATAATTA
1 TTTATTGTATATTATAATAA
464612 TTT
1 TTT
464615 GAATGTATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATTGTATATTATAATAA
Found at i:470739 original size:39 final size:39
Alignment explanation
Indices: 470680--470755 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
470670 TTCTTATATT
*
470680 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTTA
1 AAAATTCGAATCCAGCAGTCTTAAGTTTTAAGGTGTTTA
* **
470719 AAAATTCGAATCCAGTAGTCTTGTGTTTTAAGGTGTT
1 AAAATTCGAATCCAGCAGTCTTAAGTTTTAAGGTGTT
470756 CAAGAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (39 bp):
AAAATTCGAATCCAGCAGTCTTAAGTTTTAAGGTGTTTA
Found at i:473749 original size:22 final size:22
Alignment explanation
Indices: 473712--473778 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
473702 TTTTCCTTTC
473712 TTTATT-TATT-TCATTTACTTA
1 TTTATTATATTAT-ATTTACTTA
*
473733 TTTATTATATTATATTTA-TTT
1 TTTATTATATTATATTTACTTA
473754 TATTATTATATTATATATTTACTTA
1 T-TTATTATA-T-TATATTTACTTA
473779 AATATTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 9 0.24
22 17 0.45
23 2 0.05
24 8 0.21
25 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTATATTATATTTACTTA
Found at i:473750 original size:14 final size:14
Alignment explanation
Indices: 473731--473769 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
473721 TTCATTTACT
473731 TATTTATTATATTA
1 TATTTATTATATTA
*
473745 TATTTATTTTATTA
1 TATTTATTATATTA
*
473759 T-TATATTATAT
1 TATTTATTATAT
473770 ATTTACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTATTATATTA
Found at i:474774 original size:58 final size:58
Alignment explanation
Indices: 474624--474776 Score: 234
Period size: 58 Copynumber: 2.6 Consensus size: 58
474614 ATTCATCGGA
* * * *
474624 ATTAAACTCTAAACTTAACGCCAATTAACTTGAACTTACTAGCAATATCATTGACTCG
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
* * *
474682 ATTAAACTTTGAATTTAACGCCAATCAACTTGAATTTACCAGCAATATGATTGACTCG
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
*
474740 ATTAAACTCTGAACTTAATGCCAATCAACTTGAATTT
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTT
474777 TCCAATATCT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 85 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (58 bp):
ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
Found at i:476696 original size:4 final size:4
Alignment explanation
Indices: 476687--476724 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
476677 TAAAACTTCA
476687 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
476725 CCTGCAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:478896 original size:15 final size:16
Alignment explanation
Indices: 478865--478897 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
478855 TGTTATCAAC
*
478865 TAGTTAGACATAAATT
1 TAGTTAGACAAAAATT
478881 TAGTTAGA-AAAAATT
1 TAGTTAGACAAAAATT
478896 TA
1 TA
478898 AAATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (16 bp):
TAGTTAGACAAAAATT
Found at i:480356 original size:29 final size:29
Alignment explanation
Indices: 480304--480359 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
480294 TATAGAGACG
** * *
480304 GATTAATTTAGTCTTTTTATTATTAAATA
1 GATTAATTTAGTCACTGTAATATTAAATA
480333 GATTAATTTAGTCACTGTAATATTAAA
1 GATTAATTTAGTCACTGTAATATTAAA
480360 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (29 bp):
GATTAATTTAGTCACTGTAATATTAAATA
Found at i:485858 original size:21 final size:21
Alignment explanation
Indices: 485832--485872 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
485822 ATCTGCTCAA
* *
485832 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
485853 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
485873 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:490061 original size:4 final size:4
Alignment explanation
Indices: 490052--490108 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
490042 TTAAAACTTC
490052 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
490100 ATGT ATGT A
1 ATGT ATGT A
490109 CCTGCAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:499933 original size:278 final size:282
Alignment explanation
Indices: 499129--499987 Score: 728
Period size: 278 Copynumber: 3.0 Consensus size: 282
499119 GGAATGTTGC
* * * *
499129 TTGAAAATGAAACCTAGCTTGTACTAAAGCTGCATGTAAATTTGA-ACTGGAGACTGGAACAAAA
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTT-ACACTGGAGAATGGAACAAAG
* * * ** * * *
499193 AATCATGCAAGTTATATAGTGGG-A-ATCATTTAACAGATTATGAAGCTTATATCTTCAATGAGT
65 AATCATGCAAGTTATATAATGGGAATATCATCTAA-TGATCGTGAAGCTTACATATTC--TGACT
** * * ***** * * *
499256 -TTTTTATTCATTAGTTACAGTGAAAGAGTCCCTCTTTCACTTCGATTTGTTCTTGCTGCACATT
127 GACTTT-TT-ATTAGTAACAGTGAAGGAGGGAAACTCTAACTTCAATTTGTTCTTGCTGCACATT
* * * ** ** **
499320 GGTTCTAGGCCTGCTTGTGTTCTTTCACTACAGTTTAGCTTCTTTCT-TTGTATT-AGCTAGAAT
190 GGTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCT-GTGT
** * * *
499383 -CT-AGTGAAA-TTGCATTTTGCCCATGGTGAAATGTT
254 GCTCA-T-AAACTAACA-CTTGCTC-T--TGCAA---T
* * *
499418 GCTTGAACATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACTCTGGAGAATGGAGCAAA
1 --TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACACTGGAGAATGGAACAAA
*
499483 GAATCATGCAAGTTATATAATGGGAAATATCATCTAATGGATCGTGAAGCTTACATCTTCTGACT
64 GAATCATGCAAGTTATATAATGGG-AATATCATCTAAT-GATCGTGAAGCTTACATATTCTGACT
** * * * *
499548 TTCTTTTTAATTAGTAACATTGGAGGAGGGACACTTTAACTTCAATTTGTTCTTGCTGCACATTG
127 GACTTTTT-ATTAGTAACAGTGAAGGAGGGAAACTCTAACTTCAATTTGTTCTTGCTGCACATTG
* * *
499613 GTTCTAGGTCTGCTTGTGTTCTTTCACTAGTGGTTAGCTTCTTTGTATTGGTTTCCCCTGTGTGC
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
499678 TCATAAACTAACACTTGCTCTTGCAAT
256 TCATAAACTAACACTTGCTCTTGCAAT
* * *
499705 TTGAAAATGAAACCTAGCTTGTACTAAAGCTGCATGGT-AATTTGCACTGGAGAATGGAACAAAG
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTGCAT-GTAAATTTACACTGGAGAATGGAACAAAG
*
499769 AATCATGCAAGTTATATAAT-GG-A-ATCATTTAAT-ATACTGTGAAGCTTACATATT-TGA-TG
65 AATCATGCAAGTTATATAATGGGAATATCATCTAATGAT-C-GTGAAGCTTACATATTCTGACTG
* * ** *
499828 AGTATTTT-TTAGTAACAGTGAAGGAGGGATAAC-CTCACTTGTATTTGTTCTTGTTGCACATTG
128 ACT-TTTTATTAGTAACAGTGAAGGAGGGA-AACTCTAACTTCAATTTGTTCTTGCTGCACATTG
** ** * * *
499891 GTTCTCTGCCTGCTTGTGTTCTTTTGCTACTGTTTAGCTTCTTTGTATTGGCTTCCCCTTTGTGT
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
* * *
499956 TCATAAACTGACACTTTCTCTTGTAAT
256 TCATAAACTAACACTTGCTCTTGCAAT
499983 TTGAA
1 TTGAA
499988 GATTAAGAGA
Statistics
Matches: 478, Mismatches: 74, Indels: 45
0.80 0.12 0.08
Matches are distributed among these distances:
278 128 0.27
279 6 0.01
280 8 0.02
281 24 0.05
282 1 0.00
284 2 0.00
285 75 0.16
286 2 0.00
287 1 0.00
290 5 0.01
291 77 0.16
292 94 0.20
293 20 0.04
294 34 0.07
295 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (282 bp):
TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACACTGGAGAATGGAACAAAGA
ATCATGCAAGTTATATAATGGGAATATCATCTAATGATCGTGAAGCTTACATATTCTGACTGACT
TTTTATTAGTAACAGTGAAGGAGGGAAACTCTAACTTCAATTTGTTCTTGCTGCACATTGGTTCT
AGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGCTCATA
AACTAACACTTGCTCTTGCAAT
Found at i:500056 original size:21 final size:22
Alignment explanation
Indices: 500013--500075 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
500003 AGAGAAGGCC
*
500013 AAGAAGGA-AAGGAAGAAAGAA
1 AAGAAGGAGAAGAAAGAAAGAA
500034 AAGAAGGAGAAGAAAG--AGAA
1 AAGAAGGAGAAGAAAGAAAGAA
500054 AA-AACGGGAGAAGAAAGAAAGA
1 AAGAA--GGAGAAGAAAGAAAGA
500076 GATAAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 19 0.53
22 6 0.17
23 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (22 bp):
AAGAAGGAGAAGAAAGAAAGAA
Found at i:502206 original size:125 final size:126
Alignment explanation
Indices: 501879--502229 Score: 492
Period size: 126 Copynumber: 2.8 Consensus size: 126
501869 ATTTCGAGTT
** *
501879 AACGTTTCTGATAAAATAATATAAAATCGCTTCTAGCAGGATGGTATTTGAGAAGAATTTGTGAA
1 AACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAA
*
501944 ATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAATTATTTTTTA
66 ATTGCGCCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAATTATTTTTTA
* * *
502005 AACGTTTCTAAGCAAATAGTATAAAATCGTTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAA
1 AACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAA
* **
502070 ATTGCGGCCTCGTCAG-CGCGCTTTTGCTACAGTAGGTCATCTAAGAAATAAATT-TTTTTT-
66 ATTGCGCCCTCGT-AGACGCGCTTTTGCTACAGTAGGTCATAGAAGAAAT-AATTATTTTTTA
* * * * *
502130 GATGTTTCTGAGCAAATAATATAAAATCGCTTATAACAGGATGCTATTTGAGAAGAATTTATGAA
1 AACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAA
* * * *
502195 ATTGCGCCCTCGTGGACGCGATTTTGTTATAGTAG
66 ATTGCGCCCTCGTAGACGCGCTTTTGCTACAGTAG
502230 CATGTTTGGG
Statistics
Matches: 199, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
124 1 0.01
125 85 0.43
126 108 0.54
127 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (126 bp):
AACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAA
ATTGCGCCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAATTATTTTTTA
Found at i:505345 original size:23 final size:23
Alignment explanation
Indices: 505319--505776 Score: 338
Period size: 23 Copynumber: 19.7 Consensus size: 23
505309 TATTACGTTA
505319 AGGTTAGGGTTTTTAATTGAATTAGGTT
1 AGGTTAGGGTTTTTAATT-AA--A--TT
*
505347 AGGGTTACGGTTTTTAATTAAATT
1 A-GGTTAGGGTTTTTAATTAAATT
*
505371 AGGTTAGAGTTTTTAAGTT-AA--
1 AGGTTAGGGTTTTTAA-TTAAATT
* *
505392 GGGTTTAGGATTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
* *
505416 AGGCTAGGATTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
* *
505439 ATGTTAGGGTCTTTAATT-AA--
1 AGGTTAGGGTTTTTAATTAAATT
*
505459 GGGTTTA-GGTTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
* *
505482 AAGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
505505 AGGTTAGGGTTTTTAATT-AA--
1 AGGTTAGGGTTTTTAATTAAATT
*
505525 GGGTTTAGGGTTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
* *
505549 AGGCTAGGATTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
505572 AGGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
* *
505595 AGGTTAGAGTTTTTAATTTAA--
1 AGGTTAGGGTTTTTAATTAAATT
*
505616 GGGTTTAGGGTTTTTAATTTAATTGAATT
1 AGG-TTAGGGTTTTTAA-TT-A---AATT
*
505645 AGGTTAGGGTTTTTAATTCAA--
1 AGGTTAGGGTTTTTAATTAAATT
* *
505666 GGGTTTAGGGTTTTAATTGAATTAGATT
1 AGG-TTAGGG-TTT--TT-AATTAAATT
505694 AGGGTTAGGGTTTTTAATT-AA--
1 A-GGTTAGGGTTTTTAATTAAATT
* * *
505715 GGGTTTCGGGCTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
***
505739 AGGTTAGGGTTTAGGATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
505762 AGGCTAGGGTTTTTA
1 AGGTTAGGGTTTTTA
505777 TTGCATGTCA
Statistics
Matches: 344, Mismatches: 51, Indels: 75
0.73 0.11 0.16
Matches are distributed among these distances:
20 15 0.04
21 41 0.12
22 41 0.12
23 173 0.50
24 15 0.04
25 4 0.01
26 6 0.02
27 7 0.02
28 22 0.06
29 20 0.06
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:505377 original size:29 final size:29
Alignment explanation
Indices: 505310--505377 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
505300 CAAATCTAAT
* * * *
505310 ATTACGTTAAGGTTAGGGTTTTTAATTGA
1 ATTAGGTTAGGGTTACGGTTTTTAATTAA
505339 ATTAGGTTAGGGTTACGGTTTTTAATTAA
1 ATTAGGTTAGGGTTACGGTTTTTAATTAA
505368 ATTAGGTTAG
1 ATTAGGTTAG
505378 AGTTTTTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (29 bp):
ATTAGGTTAGGGTTACGGTTTTTAATTAA
Found at i:505560 original size:133 final size:134
Alignment explanation
Indices: 505355--505690 Score: 439
Period size: 133 Copynumber: 2.5 Consensus size: 134
505345 TTAGGGTTAC
* *
505355 GGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGGTTTAGGATTTTTAATTAAATTAGGC
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAATTAAATTAGGC
* * *
505420 TAGGATTTTTAATTAAATTATGTTAGGGTCTTTAATT-AA-GGGTTTAG-GTTTTTAATTAAATT
65 TAGGATTTTTAATTAAATTAGGCTAGGGTCTTTAATTAAATAGG-TTAGAGTTTTTAATTAAA--
505482 AAG-CTAG
127 AAGTCTAG
505489 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCT
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCT
* * **
505554 AGGATTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAAGGG
66 AGGATTTTTAATTAAATTAGGCTAGGGTCTTTAATTAAA-TAGGTTAGAGTTTTTAATTAAAAAG
*
505619 TTTAG
130 TCTAG
*
505624 GGTTTTTAATTTAATTGAATTAGGTTAGGGTTTTTAATTCAAGGGTTTAGGG-TTTTAATTGAAT
1 GGTTTTTAA-TT-A---AATTAGGTTAGGGTTTTTAATT-AAGGGTTTAGGGTTTTTAATTAAAT
505688 TAG
60 TAG
505691 ATTAGGGTTA
Statistics
Matches: 180, Mismatches: 11, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
133 65 0.36
134 34 0.19
135 16 0.09
136 16 0.09
137 1 0.01
140 36 0.20
141 12 0.07
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.47
Consensus pattern (134 bp):
GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCT
AGGATTTTTAATTAAATTAGGCTAGGGTCTTTAATTAAATAGGTTAGAGTTTTTAATTAAAAAGT
CTAG
Found at i:505571 original size:67 final size:67
Alignment explanation
Indices: 505357--505690 Score: 408
Period size: 67 Copynumber: 4.9 Consensus size: 67
505347 AGGGTTACGG
* *
505357 TTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGGTTTAGGATTTTTAATTAAATTAGGCTA
1 TTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAATTAAATTAGGCTA
505422 GGA
65 GGA
* * *
505425 TTTTTAATTAAATTATGTTAGGGTCTTTAATTAAGGGTTTA-GGTTTTTAATTAAATTAAGCTAG
1 TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAG
*
505489 GG
66 GA
505491 TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAG
1 TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAG
505556 GA
66 GA
* * * * *
505558 TTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGG-TTAGAGTTTTTAATTTAA--GGGT
1 TTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTAAATTAGG-
* *
505620 TTAGGG
62 CTAGGA
*
505626 TTTTTAATTTAATTGAATTAGGTTAGGGTTTTTAATTCAAGGGTTTAGGG-TTTTAATTGAATTA
1 TTTTTAA-TT-A---AATTAGGTTAGGGTTTTTAATT-AAGGGTTTAGGGTTTTTAATTAAATTA
505690 G
60 G
505691 ATTAGGGTTA
Statistics
Matches: 230, Mismatches: 23, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
66 61 0.27
67 67 0.29
68 40 0.17
69 18 0.08
70 3 0.01
71 12 0.05
72 5 0.02
73 24 0.10
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (67 bp):
TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAG
GA
Found at i:505645 original size:50 final size:49
Alignment explanation
Indices: 505493--505750 Score: 260
Period size: 50 Copynumber: 5.5 Consensus size: 49
505483 AGCTAGGGTT
505493 TTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAA
1 TTTAATT-AATTAGGTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA
* * * * *
505542 -TT-A--AATTAGGCTAGGATTTTTAATTAAATTAGG-CTAGGGTTTTTAA
1 TTTAATTAATTAGGTTAGGGTTTTTAATTTAA--GGGTTTAGGGTTTTTAA
*
505588 -TT-A--AATTAGGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAA
1 TTTAATTAATTAGGTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA
*
505633 TTTAATTGAATTAGGTTAGGGTTTTTAATTCAAGGGTTTAGGG-TTTTAA
1 TTTAATT-AATTAGGTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA
* * *
505682 TTGAATTAGATTAGGGTTAGGGTTTTTAA-TTAAGGGTTTCGGGCTTTTAA
1 TTTAATTA-ATTA-GGTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA
505732 -TT-A--AATTAGGTTAGGGTTT
1 TTTAATTAATTAGGTTAGGGTTT
505751 AGGATTAAAT
Statistics
Matches: 180, Mismatches: 17, Indels: 29
0.80 0.08 0.13
Matches are distributed among these distances:
44 31 0.17
45 19 0.11
46 39 0.22
47 4 0.02
48 4 0.02
49 29 0.16
50 54 0.30
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.47
Consensus pattern (49 bp):
TTTAATTAATTAGGTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA
Found at i:505649 original size:22 final size:22
Alignment explanation
Indices: 505579--505649 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
505569 ATTAGGCTAG
* *
505579 GGTTTTTAATTAAATT-AGGTTA
1 GGTTTTTAATTTAATTGA-ATTA
* **
505601 GAGTTTTTAATTTAA-GGGTTTA
1 G-GTTTTTAATTTAATTGAATTA
505623 GGGTTTTTAATTTAATTGAATTA
1 -GGTTTTTAATTTAATTGAATTA
505646 GGTT
1 GGTT
505650 AGGGTTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 21 0.55
23 17 0.45
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (22 bp):
GGTTTTTAATTTAATTGAATTA
Found at i:505695 original size:22 final size:22
Alignment explanation
Indices: 505633--505699 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
505623 GGGTTTTTAA
*
505633 TTTAATTGAATTAGGTTAGGGTT
1 TTTAATTGAATTAGATTAGGG-T
* ** *
505656 TTTAATTCAA-GGGTTTAGGGT
1 TTTAATTGAATTAGATTAGGGT
505677 TTTAATTGAATTAGATTAGGGT
1 TTTAATTGAATTAGATTAGGGT
505699 T
1 T
505700 AGGGTTTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 10 0.29
22 16 0.46
23 9 0.26
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.46
Consensus pattern (22 bp):
TTTAATTGAATTAGATTAGGGT
Found at i:505758 original size:44 final size:44
Alignment explanation
Indices: 505347--505750 Score: 374
Period size: 46 Copynumber: 8.8 Consensus size: 44
505337 GAATTAGGTT
* *
505347 AGGG-TTACGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTA
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTA
* * *
505391 AGGGTTTAGGATTTTTAATTAAATTAGGCTAGGATTTTTAATTAA
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-A
*** * *
505436 ATTATGTTAGGGTCTTTAATT-AA--GGGTTTA-GGTTTTTAATTA
1 AGGGT-TTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTA
*
505478 A--ATTAAGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
1 AGGGTT----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
* *
505524 AGGGTTTAGGGTTTTTAATTAAATTAGGCTAGGATTTTTAATTAA
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-A
* * *
505569 ATTAGG-CTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTA
1 A--GGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTA
505615 AGGGTTTAGGGTTTTTAATTTAATTGAATTAGGTTAGGGTTTTTAATTCA
1 AGGGTTTAGGGTTTTTAA-TT-A---AATTAGGTTAGGGTTTTTAATT-A
*
505665 AGGGTTTAGGGTTTTAATTGAATTAGATTAGGGTTAGGGTTTTTAATTA
1 AGGGTTTAGGG-TTT--TT-AATTAAATTA-GGTTAGGGTTTTTAATTA
* *
505714 AGGGTTTCGGGCTTTTAATTAAATTAGGTTAGGGTTT
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
505751 AGGATTAAAT
Statistics
Matches: 300, Mismatches: 30, Indels: 60
0.77 0.08 0.15
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
42 2 0.01
43 25 0.08
44 58 0.19
45 62 0.21
46 66 0.22
47 5 0.02
48 4 0.01
49 17 0.06
50 48 0.16
51 3 0.01
52 1 0.00
53 4 0.01
54 2 0.01
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (44 bp):
AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
Found at i:505878 original size:52 final size:53
Alignment explanation
Indices: 505808--505929 Score: 194
Period size: 53 Copynumber: 2.3 Consensus size: 53
505798 TTTATTACAT
505808 TAAATAATA-TCAAAATAACTCAAAAAATTTATA-TTTTTTACATAAAATAATA
1 TAAA-AATATTCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATA
* **
505860 TTAAAATATTCAAAATAACTCAAAATTTTTATATTTTTTTACATAAAATAATA
1 TAAAAATATTCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATA
505913 TAAAAATATTCAAAATA
1 TAAAAATATTCAAAATA
505930 TTTGTATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 4 0.06
52 25 0.39
53 35 0.55
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (53 bp):
TAAAAATATTCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATA
Found at i:505889 original size:43 final size:43
Alignment explanation
Indices: 505802--505890 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 43
505792 TTTTATTTTA
* * * * *
505802 TTACATTAAATAATATCAAAATAACTCAAAAAATTTATATTTT
1 TTACATAAAATAATATCAAAATAACTCAAAAAACTCAAAATTT
* *
505845 TTACATAAAATAATATTAAAAT-ATTCAAAATAACTCAAAATTT
1 TTACATAAAATAATATCAAAATAACTCAAAA-AACTCAAAATTT
505888 TTA
1 TTA
505891 TATTTTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 7 0.18
43 31 0.82
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (43 bp):
TTACATAAAATAATATCAAAATAACTCAAAAAACTCAAAATTT
Found at i:506998 original size:7 final size:7
Alignment explanation
Indices: 506988--507012 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
506978 ATACATACAT
506988 AATACTA
1 AATACTA
506995 AATACTA
1 AATACTA
507002 AATACTA
1 AATACTA
507009 AATA
1 AATA
507013 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:508267 original size:22 final size:22
Alignment explanation
Indices: 508242--508315 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
508232 AAATATAGAT
*
508242 TTGAAAGAATTTTGGAAGGAAA
1 TTGAAAGAATTTTGAAAGGAAA
*
508264 TTGAGAGAATTTTGAAAGGAAA
1 TTGAAAGAATTTTGAAAGGAAA
* *
508286 TTGAGAGGAA--TTGAGAGGAAA
1 TTGA-AAGAATTTTGAAAGGAAA
508307 TATGAAAGA
1 T-TGAAAGA
508316 GGATTTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.32
22 27 0.61
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (22 bp):
TTGAAAGAATTTTGAAAGGAAA
Found at i:508270 original size:51 final size:51
Alignment explanation
Indices: 508155--508270 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
508145 TATTTTAAAA
* * * * *
508155 AAGGAAATTGAGAAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAGGAAATTAAAATTAAATATAGATTTGAAAGAATTTTGG
508206 AAGGAAATTGAGAGGAAATTAAAATTAAATATAGATTTGAAAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTAAAATTAAATATAGATTTGAAAGAATTTTGG
508257 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
508271 AATTTTGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTAAAATTAAATATAGATTTGAAAGAATTTTGG
Found at i:511290 original size:102 final size:103
Alignment explanation
Indices: 511109--511303 Score: 293
Period size: 102 Copynumber: 1.9 Consensus size: 103
511099 TAGCCTAAGA
* *
511109 CCCCTCTATCCGGTAGCTACATTGGACTTAAATAAACCCGAAGTTTAGCCAAATTAGACCCTTAC
1 CCCCTCTATCCGGTAGCTACATTGAACTTAAATAAACCCGAAGTTTAGCCAAATTAGACCCTTAA
**
511174 GAAAGCAAACTCTCCTAGTGGTATTTTCAATCCAGACT
66 GAAAGCAAACTCTCCTACCGGTATTTTCAATCCAGACT
* * * * *
511212 CCCC-CTATCTGGTAGCTACGTTGAACTTAACTAAACCCGGAGTTTAGCCGAATTAGACCCTTAA
1 CCCCTCTATCCGGTAGCTACATTGAACTTAAATAAACCCGAAGTTTAGCCAAATTAGACCCTTAA
*
511276 GAAAGCAAGCTCTCCTACCGGTATTTTC
66 GAAAGCAAACTCTCCTACCGGTATTTTC
511304 TCCACTCCTA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 78 0.95
103 4 0.05
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (103 bp):
CCCCTCTATCCGGTAGCTACATTGAACTTAAATAAACCCGAAGTTTAGCCAAATTAGACCCTTAA
GAAAGCAAACTCTCCTACCGGTATTTTCAATCCAGACT
Found at i:514496 original size:19 final size:19
Alignment explanation
Indices: 514472--514510 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
514462 AGAGACCCCA
514472 CTATATAAGGATAAATGGT
1 CTATATAAGGATAAATGGT
514491 CTATATAAGGATAAATGGT
1 CTATATAAGGATAAATGGT
514510 C
1 C
514511 CATTATCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (19 bp):
CTATATAAGGATAAATGGT
Found at i:517096 original size:30 final size:30
Alignment explanation
Indices: 517049--517126 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
517039 AAACCGTATA
*
517049 AATTAAATTGTAATTTTTATAATTTTTAAAAG
1 AATTAAATT-AAATTTTTA-AATTTTTAAAAG
* *
517081 -ATTAAATTAAATTTTTAATTTTTTAAATG
1 AATTAAATTAAATTTTTAAATTTTTAAAAG
*
517110 AATTAAACTACAATTTT
1 AATTAAATTA-AATTTT
517127 ACTTTTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.25
30 16 0.40
31 14 0.35
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (30 bp):
AATTAAATTAAATTTTTAAATTTTTAAAAG
Found at i:518486 original size:18 final size:18
Alignment explanation
Indices: 518463--518499 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
518453 AAAACGGGCT
518463 TAACTTGACTTGATTTCA
1 TAACTTGACTTGATTTCA
518481 TAACTTGACTTGATTTCA
1 TAACTTGACTTGATTTCA
518499 T
1 T
518500 TTACATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (18 bp):
TAACTTGACTTGATTTCA
Found at i:519083 original size:10 final size:10
Alignment explanation
Indices: 519070--519095 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
519060 ATAAAATTAA
519070 ATAATTTTTT
1 ATAATTTTTT
519080 ATAATTTTTT
1 ATAATTTTTT
519090 ATAATT
1 ATAATT
519096 AAATAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:520727 original size:31 final size:32
Alignment explanation
Indices: 520691--520761 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
520681 TTATAAAATT
520691 GTCACTAAACTATTTGAAAGTTTTCA-TTTAA
1 GTCACTAAACTATTTGAAAGTTTTCATTTTAA
* *
520722 GTCACTGAACTATTTGAAAGTTTTTATTTTTAA
1 GTCACTAAACTATTTGAAAGTTTTCA-TTTTAA
520755 GTCACTA
1 GTCACTA
520762 GGTTGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 24 0.69
33 11 0.31
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (32 bp):
GTCACTAAACTATTTGAAAGTTTTCATTTTAA
Found at i:522574 original size:4 final size:4
Alignment explanation
Indices: 522567--522600 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
522557 AGGCAGGAAG
522567 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
522601 GGTCATGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:534467 original size:146 final size:145
Alignment explanation
Indices: 534238--534595 Score: 542
Period size: 146 Copynumber: 2.5 Consensus size: 145
534228 GGGACTAATT
* * * *
534238 CCAAAATTAGAGCATAATAGAAGGG-CCAAAATCAGAATTTGA-CCCT-GATTTTAACCATGGAT
1 CCAAATTTA-AGCATAACAG-AGGGACCAAAATCAGAATTTGACCCCTAG-TTTCAGCCATGGAT
* *
534300 GAGCAAACTACTATTTGATTGGAATTCTAACGATATTTTGATTAACTAAAGGAAAAGAATCATGC
63 GAGCAAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGC
534365 CAAATTATAAACACAACC
128 CAAATTATAAACACAACC
*
534383 CCAAATTTAAGCATAACAGAGGGAACAAAATCAGAATTTGACCCGCTAGTTTCAGCCATGGATGA
1 CCAAATTTAAGCATAACAGAGGGACCAAAATCAGAATTTGACCC-CTAGTTTCAGCCATGGATGA
*
534448 GTAAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCA
65 GCAAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCA
* *
534513 AATTTTAAGCACAACC
130 AATTATAAACACAACC
* *
534529 CCAAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCCTCTAGTTTCAGCCATGGATGA
1 CCAAATTTAAGCATAACAGAGGGACCAAAATCAGAATTTGACCC-CTAGTTTCAGCCATGGATGA
534594 GC
65 GC
534596 TGAGAAAAAG
Statistics
Matches: 194, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
143 4 0.02
144 25 0.13
145 10 0.05
146 154 0.79
147 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (145 bp):
CCAAATTTAAGCATAACAGAGGGACCAAAATCAGAATTTGACCCCTAGTTTCAGCCATGGATGAG
CAAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAA
ATTATAAACACAACC
Found at i:541500 original size:20 final size:20
Alignment explanation
Indices: 541475--541515 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
541465 TTCGTGTTAC
541475 TTGTTCAAGTCATTTCAAGT
1 TTGTTCAAGTCATTTCAAGT
541495 TTGTTCAAGTCATTTCAAGT
1 TTGTTCAAGTCATTTCAAGT
541515 T
1 T
541516 CAAGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGTTCAAGTCATTTCAAGT
Found at i:541518 original size:16 final size:17
Alignment explanation
Indices: 541476--541520 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
541466 TCGTGTTACT
541476 TGTTCAAGTCATTTCAA
1 TGTTCAAGTCATTTCAA
541493 GTTTGTTCAAGTCATTTCAA
1 ---TGTTCAAGTCATTTCAA
541513 -GTTCAAGT
1 TGTTCAAGT
541521 TTTTTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.32
20 17 0.68
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (17 bp):
TGTTCAAGTCATTTCAA
Found at i:541724 original size:29 final size:29
Alignment explanation
Indices: 541682--541740 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
541672 GGGTTAAAAT
541682 TGAAAACTATACATATATGGTCTCCATGG
1 TGAAAACTATACATATATGGTCTCCATGG
541711 TGAAAACTATACATATATGGTCTCCATGG
1 TGAAAACTATACATATATGGTCTCCATGG
541740 T
1 T
541741 ACATGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (29 bp):
TGAAAACTATACATATATGGTCTCCATGG
Found at i:544930 original size:17 final size:17
Alignment explanation
Indices: 544905--544963 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
544895 CCCATTATCC
*
544905 AAAACAAAAGGAAAAAAA
1 AAAAGAAAA-GAAAAAAA
544923 AAAA-AAAAGAAAAGAAA
1 AAAAGAAAAGAAAA-AAA
*
544940 AAAAGAAATGAAAACATAA
1 AAAAGAAAAGAAAA-A-AA
544959 AAAAG
1 AAAAG
544964 TAACATCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 5 0.14
17 11 0.31
18 13 0.36
19 7 0.19
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAGAAAAAAA
Found at i:544952 original size:13 final size:13
Alignment explanation
Indices: 544916--544953 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
544906 AAACAAAAGG
544916 AAAA-AAAA-AAA
1 AAAAGAAAAGAAA
544927 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
*
544940 AAAAGAAATGAAA
1 AAAAGAAAAGAAA
544953 A
1 A
544954 CATAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 4 0.17
12 4 0.17
13 16 0.67
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:545871 original size:66 final size:65
Alignment explanation
Indices: 545763--545933 Score: 207
Period size: 66 Copynumber: 2.6 Consensus size: 65
545753 AGGAGGAGAA
* * **
545763 GGATCTGAGTAACCGTTATGGCCGCTAACGGAATATTCAAAAGACGGTGCCGTTGGCGCAAAAGA
1 GGATCTGAGTAACCGTTATGG-TGCTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGA
545828 C
65 C
* * *
545829 GGATCTGAGTAACCGTTATGGTGACTGACGGAATATTGAAAAGACTCAGCCGTTGGTGCAAAAGA
1 GGATCTGAGTAACCGTTATGGTG-CTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGA
545894 C
65 C
* *** *
545895 GGAGCTGAGTGGTCGTTACGGTGTCTAACGGAATATTGA
1 GGATCTGAGTAACCGTTATGGTG-CTAACGGAATATTGA
545934 GGATAGTCCG
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 1 0.01
66 89 0.99
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (65 bp):
GGATCTGAGTAACCGTTATGGTGCTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGAC
Found at i:549063 original size:29 final size:29
Alignment explanation
Indices: 549020--549075 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
549010 GTTGAGATTT
*
549020 TGTCAATTTAGTCCTTATACTAATAAATG
1 TGTCAATTTAATCCTTATACTAATAAATG
*
549049 TGTCAATTTAATCCTTATACTATTAAA
1 TGTCAATTTAATCCTTATACTAATAAA
549076 AGAAATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (29 bp):
TGTCAATTTAATCCTTATACTAATAAATG
Found at i:549382 original size:20 final size:20
Alignment explanation
Indices: 549359--549398 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
549349 AAAAAATTCC
549359 AAAAAT-TTCTAAAGAAATAA
1 AAAAATATT-TAAAGAAATAA
*
549379 AAAAATATTTAAATAAATAA
1 AAAAATATTTAAAGAAATAA
549399 TAATGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAAATATTTAAAGAAATAA
Found at i:562517 original size:170 final size:170
Alignment explanation
Indices: 562300--562691 Score: 538
Period size: 174 Copynumber: 2.3 Consensus size: 170
562290 AGACAAAATG
562300 GCCATTCGAGTCATGTTTTCCATCACCAAATGCCATCATGTCACAATAAGGACTAGTTCTAGCAA
1 GCCATTCGAGT-ATGTTTTCCATCACCAAATGCCATCATGTCACAAT-AGGACTAGTTCTAGCAA
* * *
562365 AGTAAACAATAAGGTA-A-GTCAGGTCAAGATCCTTATCTTTGCAATAAAGGAGAGAAATGTTGA
64 AGTAAACAATAAGGTAGATGTCAGGTCAAGATCCATATCTTTGCAAGAAAGGAGAGAAATGTAGA
*
562428 CAAAATATGTCTTCATTAGATGCTAC-AAGGATAATAAGACCA
129 CAAAATATGTCTTCATGAGATGCTACAAAGG-TAATAAGACCA
* * * *
562470 GCCATTCGAGTGATGTTTTTCATCACCAAATGCCATCACGTCACAATAGGCCTAGTTCTAGCTAA
1 GCCATTCGAGT-ATGTTTTCCATCACCAAATGCCATCATGTCACAATAGGACTAGTTCTAGCAAA
562535 GTAAACAATAAGGTACGGTATGTCAGGTCAAGATCCATATCTTTGCAAGAAAGGAGAGAAATGTA
65 GTAAACAATAAGGTA--G-ATGTCAGGTCAAGATCCATATCTTTGCAAGAAAGGAGAGAAATGTA
* * **
562600 GACAAAATATGTCTTCATGATATGGTACAAAGGTAATAAGACTG
127 GACAAAATATGTCTTCATGAGATGCTACAAAGGTAATAAGACCA
* * * *
562644 GCCATTCTAGTATCGTTTGCCACCACCAAAATGCCATCATGCCACAAT
1 GCCATTCGAGTAT-GTTTTCCATCACC-AAATGCCATCATGTCACAAT
562692 TGCCCAAGTA
Statistics
Matches: 195, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
169 31 0.16
170 44 0.23
173 3 0.02
174 95 0.49
175 22 0.11
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (170 bp):
GCCATTCGAGTATGTTTTCCATCACCAAATGCCATCATGTCACAATAGGACTAGTTCTAGCAAAG
TAAACAATAAGGTAGATGTCAGGTCAAGATCCATATCTTTGCAAGAAAGGAGAGAAATGTAGACA
AAATATGTCTTCATGAGATGCTACAAAGGTAATAAGACCA
Found at i:568963 original size:164 final size:164
Alignment explanation
Indices: 568502--569117 Score: 810
Period size: 164 Copynumber: 3.7 Consensus size: 164
568492 ATGCAATTCT
* * * *
568502 TTACATTTATT-AGTGAGTACTCGAAACTTGTCCATCAAATGAGTATGACAGAGACTTTAGCTCC
1 TTACATTTATTGA-TGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCC
* * *
568566 AGTATCATGTGGCCTTAGGCTCAAAACTTCTGTCCTTACGTCAACTTATGTCTAAGTTATATGTA
65 GGTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTATATGTA
*
568631 TATGCAACTTTTTCTAATGTGTAA-AGTTGATTTTC
130 TATGCAACTTTTTCTAATGTGTAACA-CTGATTTTC
* * *
568666 TTACATTTATTGATGAATACTCGAAACATGTCGGTTACATGAGCATGACAGAG-CTTTAGCTCCG
1 TTACATTTATTGATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCCG
*
568730 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTTTATGTAT
66 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTATATGTAT
**
568795 ATGCAACTCGTTCTAATGTGTAACACTGATTTTC
131 ATGCAACTTTTTCTAATGTGTAACACTGATTTTC
* * *
568829 TTACATTTATTGACGAGTACTTGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGTTCCG
1 TTACATTTATTGATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCCG
* *
568894 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTTAAGGTATGTCTAAGTTATATGTAT
66 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTATATGTAT
*
568959 ATGCAACTTTTTCTAATGTGTAACGCTGATTTTC
131 ATGCAACTTTTTCTAATGTGTAACACTGATTTTC
* * * * * *
568993 CTACCTTTATTAAAGAGTACTCGAAACTTGCCCGTCCGTTGCATGAGAATGGA-AGAGACTTTAG
1 TTACATTTATTGATGAGTACTCGAAACTT----GTCCGTTACATGAGCAT-GACAGAGACTTTAG
* * * * * * * * *
569057 CTCCGGCATCTTGCCGTCC-TAGACTCAAAACTTACGTCCTTACATCAACATACGTCTAAGT
61 CTCCGGTATCATG-TGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGT
569118 CGTCAACGTT
Statistics
Matches: 398, Mismatches: 45, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
163 149 0.37
164 172 0.43
165 1 0.00
168 71 0.18
169 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (164 bp):
TTACATTTATTGATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCCG
GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTATATGTAT
ATGCAACTTTTTCTAATGTGTAACACTGATTTTC
Found at i:573745 original size:34 final size:33
Alignment explanation
Indices: 573705--573795 Score: 87
Period size: 37 Copynumber: 2.7 Consensus size: 33
573695 AATTTGGCAA
* *
573705 AATTAAACTTATTATATAATTTTTTAATTTTTTT
1 AATTAAACTTATTATAT-ATTTTTTAATTTCTAT
* *
573739 AATTAAAAAATTATTATAATTATTTTTTTATTTCTAT
1 AATT--AAACTTATTAT-A-TATTTTTTAATTTCTAT
573776 AA--AAACTTATTATATATTTT
1 AATTAAACTTATTATATATTTT
573796 AATTTTATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
31 6 0.12
32 1 0.02
33 10 0.21
34 4 0.08
36 10 0.21
37 16 0.33
38 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (33 bp):
AATTAAACTTATTATATATTTTTTAATTTCTAT
Found at i:579777 original size:47 final size:46
Alignment explanation
Indices: 579714--579807 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 46
579704 GTCACCAAAC
**
579714 TATGAAAAGTTACAAAAT-AGTCATTCAACTATTTAATTTTGTCTTT
1 TATGAAAAGTTACAAAATGA-TCACCCAACTATTTAATTTTGTCTTT
579760 TATGAAAAGGTTACAAAATGATCACCCAACTATTTAATTTTGTCTTT
1 TATGAAAA-GTTACAAAATGATCACCCAACTATTTAATTTTGTCTTT
579807 T
1 T
579808 CTAGTCACGT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 8 0.18
47 35 0.80
48 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (46 bp):
TATGAAAAGTTACAAAATGATCACCCAACTATTTAATTTTGTCTTT
Found at i:580124 original size:19 final size:19
Alignment explanation
Indices: 580100--580136 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
580090 TTAATTTCAC
580100 AAAAAAAAA-CAAAATTACA
1 AAAAAAAAATC-AAATTACA
580119 AAAAAAAAATCAAATTAC
1 AAAAAAAAATCAAATTAC
580137 TCAATGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAAAAATCAAATTACA
Found at i:580777 original size:198 final size:198
Alignment explanation
Indices: 580437--580837 Score: 721
Period size: 198 Copynumber: 2.0 Consensus size: 198
580427 TACACTTTTT
*
580437 TTTTATATTTAAACGATTAAATCCATTTTGATCCCTAAACTTGATAAATATAAAAATGGGTAAGC
1 TTTTATACTTAAACGATTAAATCCATTTTGATCCCTAAACTTGATAAATATAAAAATGGGTAAGC
580502 TACAAAAAGTTACTTTTATTTGCCTCAAATTACATTTTAGTCACTTACGTTATCGTTTTGTTACG
66 TACAAAAAGTTACTTTTATTTGCCTCAAATTACATTTTAGTCACTTACGTTATCGTTTTGTTACG
** * *
580567 AAGTGGTCACTCTACCGTTAAACTCCGTTACCTTCCTAGCGGCAATCCTACGTGTCAGTCTAAAT
131 AAGTAATCACTCTACCGTTAAACTCCGTTACCTCCCTAGCGGCAATCCTACGTGGCAGTCTAAAT
580632 GGG
196 GGG
580635 TTTTATACTTAAACGATTAAATCCATTTTGATCCCTAAACTTGATAAATATAAAAATGGGTAAGC
1 TTTTATACTTAAACGATTAAATCCATTTTGATCCCTAAACTTGATAAATATAAAAATGGGTAAGC
* * *
580700 TACAAAAAGTTACTTTTGTTTGTCTCAGATTACATTTTAGTCACTTACGTTATCGTTTTGTTACG
66 TACAAAAAGTTACTTTTATTTGCCTCAAATTACATTTTAGTCACTTACGTTATCGTTTTGTTACG
*
580765 AAGTAATCACTCTACTGTTAAACTCCGTTACCTCCCTAGCGGCAATCCTACGTGGCAGTCTAAAT
131 AAGTAATCACTCTACCGTTAAACTCCGTTACCTCCCTAGCGGCAATCCTACGTGGCAGTCTAAAT
580830 GGG
196 GGG
580833 TTTTA
1 TTTTA
580838 AATGTCAACT
Statistics
Matches: 194, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 194 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (198 bp):
TTTTATACTTAAACGATTAAATCCATTTTGATCCCTAAACTTGATAAATATAAAAATGGGTAAGC
TACAAAAAGTTACTTTTATTTGCCTCAAATTACATTTTAGTCACTTACGTTATCGTTTTGTTACG
AAGTAATCACTCTACCGTTAAACTCCGTTACCTCCCTAGCGGCAATCCTACGTGGCAGTCTAAAT
GGG
Found at i:585273 original size:7 final size:7
Alignment explanation
Indices: 585261--585312 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
585251 AAACTTTCAA
585261 TAAATAT
1 TAAATAT
585268 TAAATATAT
1 T-AA-ATAT
585277 TAAATAT
1 TAAATAT
585284 TAAATAT
1 TAAATAT
*
585291 TAAAATAA
1 T-AAATAT
585299 TATAATA-
1 TA-AATAT
585306 TAAATAT
1 TAAATAT
585313 ATTTTTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 4 0.10
7 16 0.41
8 14 0.36
9 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATAT
Found at i:585291 original size:23 final size:22
Alignment explanation
Indices: 585260--585312 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
585250 AAAACTTTCA
*
585260 ATAAATATTAAATATATTA-AAT
1 ATAAATATTAAA-ATAATATAAT
585282 ATTAAATATTAAAATAATATAAT
1 A-TAAATATTAAAATAATATAAT
585305 ATAAATAT
1 ATAAATAT
585313 ATTTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATATTAAAATAATATAAT
Found at i:587705 original size:21 final size:20
Alignment explanation
Indices: 587675--587714 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
587665 AAATGAATAG
*
587675 TCGAAAAAATTAAACAAAAA
1 TCGAAAAAATCAAACAAAAA
*
587695 TCGAGAAAAATCGAACAAAA
1 TCGA-AAAAATCAAACAAAA
587715 TTAGTCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (20 bp):
TCGAAAAAATCAAACAAAAA
Found at i:590159 original size:17 final size:17
Alignment explanation
Indices: 590137--590180 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
590127 TCCGAACATA
*
590137 TATTTGTAATTACATTG
1 TATTTGTAATTACATTC
*
590154 TATTTGTGAA-TATATTC
1 TATTTGT-AATTACATTC
590171 TATTTGTAAT
1 TATTTGTAAT
590181 AATAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (17 bp):
TATTTGTAATTACATTC
Found at i:591902 original size:15 final size:15
Alignment explanation
Indices: 591864--591905 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
591854 AGTTTACATT
591864 TTTAAATTTGAA-TTA
1 TTTAAATTT-AATTTA
**
591879 TTTTGATTTAATTTA
1 TTTAAATTTAATTTA
591894 TTTAAATTTAAT
1 TTTAAATTTAAT
591906 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTAAATTTAATTTA
Found at i:593178 original size:16 final size:17
Alignment explanation
Indices: 593137--593178 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
593127 TTTTTCTTTA
593137 AAATTTAAAAAATAAAT
1 AAATTTAAAAAATAAAT
*
593154 -AA-TTATAAAATAAAAT
1 AAATTTAAAAAAT-AAAT
593170 AAATTTAAA
1 AAATTTAAA
593179 TTTAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 2 0.10
18 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTTAAAAAATAAAT
Found at i:594002 original size:13 final size:13
Alignment explanation
Indices: 593984--594011 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
593974 AAACATTATC
593984 TTATTTTATTTTA
1 TTATTTTATTTTA
593997 TTATTTTATTTTA
1 TTATTTTATTTTA
594010 TT
1 TT
594012 TTTCTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:594005 original size:18 final size:18
Alignment explanation
Indices: 593978--594013 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
593968 ACAAAAAAAC
593978 ATTATCTTATTTTATTTT
1 ATTATCTTATTTTATTTT
*
593996 ATTATTTTATTTTATTTT
1 ATTATCTTATTTTATTTT
594014 TCTACCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTATCTTATTTTATTTT
Found at i:594939 original size:11 final size:11
Alignment explanation
Indices: 594919--594948 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
594909 ACAACAGCAA
594919 CAAAATAATAG
1 CAAAATAATAG
*
594930 CAATATAATAG
1 CAAAATAATAG
594941 CAAAATAA
1 CAAAATAA
594949 CAATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:596134 original size:37 final size:40
Alignment explanation
Indices: 596078--596177 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 40
596068 AAGTAATAAT
* *
596078 TTGACACCTAGTGTCTCATCG-GTTAAACCG-A-AGTAAA
1 TTGACACCCAGTGTCTCATCGAATTAAACCGAAGAGTAAA
* * **
596115 TTGACACCCAATGTGTCATCGAATTAATTCGAAGTAGTAAA
1 TTGACACCCAGTGTCTCATCGAATTAAACCGAAG-AGTAAA
596156 TTGACACCCAGTGTCTCATCGA
1 TTGACACCCAGTGTCTCATCGA
596178 CTCGAAGTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 18 0.35
38 6 0.12
39 1 0.02
41 26 0.51
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (40 bp):
TTGACACCCAGTGTCTCATCGAATTAAACCGAAGAGTAAA
Found at i:597107 original size:5 final size:5
Alignment explanation
Indices: 597097--597140 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
597087 TTCTGTTTAT
597097 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
597141 TACTTAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:602782 original size:4 final size:4
Alignment explanation
Indices: 602773--602835 Score: 99
Period size: 4 Copynumber: 15.8 Consensus size: 4
602763 TGTCATGTCA
* * *
602773 TATG TATG TATG TATG CATG CATG CATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
602821 TATG TATG TATG TAT
1 TATG TATG TATG TAT
602836 TAGAATTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:603169 original size:244 final size:244
Alignment explanation
Indices: 602733--603188 Score: 549
Period size: 244 Copynumber: 1.9 Consensus size: 244
602723 GGTAACGTAT
* *
602733 GTATGTGAACTACCAAATGCTGAAGTTCAATGTCATGTCATATGTATGTATGTATGCATGCATGC
1 GTATATGAACTACCAAATGCTGAAGTTAAATGTCATGTCATATGTATGTATGTATGCATGCATGC
* *
602798 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATTAGAATTAGATATAGTTGTATTGAATG
66 ATGTATGCATGTATGTATGTATGTATGTATGTATGCATTAGAATTAGATATAGTTGTATTGAATG
* ** * *
602863 CAAGCAGTTTACATGGTTATTAACAGAAAAAATCGTGTTCGGGTTCGGAATGTCTTGTAATTTGT
131 CAAGCAGTTTACATGGCTATTAACAGAAAAAATCGTGTTCAAGTTCGCAATGTCTGGTAATTTGT
602928 TTCATGTTTTGAGCATTCGGCGCATATGTATGAGTTAAAACGTTTAAAA
196 TTCATGTTTTGAGCATTCGGCGCATATGTATGAGTTAAAACGTTTAAAA
* * **
602977 GTATATGAACTACCAAATTCTGAAGTTAAATGTGCA-GTCATTCATGTATGTATGTATGTATGTG
1 GTATATGAACTACCAAATGCTGAAGTTAAATGT-CATGTCA-T-ATGTATGTATGTATGCATGCA
** * *
603041 TGTTTGTATGCATGT-T-TAT-TGATGCT-TGTCTG-ATGCATTCGGAAGTTAGATATCA-TTGT
63 TGCATGTATGCATGTATGTATGT-ATG-TATGTATGTATGCATT-AGAA-TTAGATAT-AGTTGT
* *
603100 ATTG-ATGCTAGCAGTTTAC-TCGGCTATTAACA-AGAATAATCGTGTTCAAGTTC-CAA-GCTG
123 ATTGAATGCAAGCAGTTTACAT-GGCTATTAACAGA-AAAAATCGTGTTCAAGTTCGCAATG-T-
603160 CTGGTAATTTGTTTCATGTTTTGAGCATT
184 CTGGTAATTTGTTTCATGTTTTGAGCATT
603189 ATGAATGCTT
Statistics
Matches: 181, Mismatches: 19, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
242 1 0.01
243 12 0.07
244 116 0.64
245 21 0.12
246 31 0.17
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (244 bp):
GTATATGAACTACCAAATGCTGAAGTTAAATGTCATGTCATATGTATGTATGTATGCATGCATGC
ATGTATGCATGTATGTATGTATGTATGTATGTATGCATTAGAATTAGATATAGTTGTATTGAATG
CAAGCAGTTTACATGGCTATTAACAGAAAAAATCGTGTTCAAGTTCGCAATGTCTGGTAATTTGT
TTCATGTTTTGAGCATTCGGCGCATATGTATGAGTTAAAACGTTTAAAA
Found at i:617671 original size:21 final size:19
Alignment explanation
Indices: 617629--617685 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
617619 TTATTATCCT
617629 GAACCCTAA-CCTAGAACTC
1 GAACCCTAACCCT-GAACTC
617648 GAACCCTAGACCCTGAACCTC
1 GAACCCTA-ACCCTGAA-CTC
*
617669 GAACCCCAAACCCTGAA
1 GAA-CCCTAACCCTGAA
617686 TCCCAAACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 4 0.12
21 17 0.52
22 4 0.12
ACGTcount: A:0.35, C:0.40, G:0.12, T:0.12
Consensus pattern (19 bp):
GAACCCTAACCCTGAACTC
Found at i:643556 original size:22 final size:21
Alignment explanation
Indices: 643521--643562 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
643511 TTATTTTCTA
*
643521 TTTTAAATATAAAATATTTAT
1 TTTTAAATATAAAAAATTTAT
*
643542 TTTTACATCATAAAAAATTTA
1 TTTTAAAT-ATAAAAAATTTA
643563 AATTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTAAATATAAAAAATTTAT
Found at i:646809 original size:7 final size:7
Alignment explanation
Indices: 646797--646821 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
646787 TATATTTTTA
646797 TTTTATT
1 TTTTATT
646804 TTTTATT
1 TTTTATT
646811 TTTTATT
1 TTTTATT
646818 TTTT
1 TTTT
646822 GAAAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:661272 original size:3 final size:3
Alignment explanation
Indices: 661266--661291 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
661256 GGCAACGACA
661266 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
661292 GGAGAACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:662900 original size:137 final size:140
Alignment explanation
Indices: 662644--663122 Score: 586
Period size: 137 Copynumber: 3.4 Consensus size: 140
662634 CTCTAGCAGA
* * * * * * *
662644 AAGGGCGCAAAGCCAAGCTAAAACCCTTAAATTATCTTGCACTCGAAAGAGGTTTTTTGTATGTG
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-AAGAGTTTTTTTGTGTGTG
* * * * * *
662709 TCTCTTATTCGAAAGGGTTCAAGACATTTTTGTAGTAGAGCTAAATTCACTAGGCAATGGCAAAA
65 TCTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACAA
662774 CTAGTGTTGTT
130 CTAGTGTTGTT
* * *
662785 AAAGGTGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-A-A-TTTTTTTGTGTGTCT
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAGAGTTTTTTTGTGTGTGT
*
662847 CTCTCATTTGAAAGGGTTCGAGATATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACAAC
66 CTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACAAC
* *
662912 TGGTGTTGAT
131 TAGTGTTGTT
* * *
662922 AAGGGAGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGGATTTCTTTCTTGTGT
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-AA-GAGTT-TTT-TTGTGT
* * * * *
662987 GTGTTTCTCACTTGAAAGGGTTCGGGACATTTTTGTACTAAAGCTAAATTCATTAGGCAATGTCA
62 GTGTCTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCA
663052 CAACTAGTGTTGTT
127 CAACTAGTGTTGTT
* ** * * *
663066 AAGGGCGCAAAGCCGGGCTAGAACCCTTATATTGTTTTGCATTTGAAAGGGTTTTTT
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-AAGAGTTTTTT
663123 CTTTTTATGT
Statistics
Matches: 293, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
137 119 0.41
138 1 0.00
139 2 0.01
141 41 0.14
142 5 0.02
143 6 0.02
144 119 0.41
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (140 bp):
AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAGAGTTTTTTTGTGTGTGT
CTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACAAC
TAGTGTTGTT
Found at i:663044 original size:144 final size:143
Alignment explanation
Indices: 662644--663125 Score: 554
Period size: 144 Copynumber: 3.4 Consensus size: 143
662634 CTCTAGCAGA
* * * * * * * *
662644 AAGGGCGCAAAGCCAAGCTAAAACCCTTAA-ATTATCTTGCACTCGAAAGAGGTTTTTT-GTATG
1 AAGGGAGCAAAGCCGAGCTAGAACCC-TAATATTGTCTTGCATTCGAAAG-GATTTTTTCTTGTG
* * * *
662707 TGTCTCT-T-A-TTCGAAAGGGTTCAAGACATTTTTGTAGTAGAGCTAAATTCACTAGGCAATGG
64 TGTCTCTCTCACTT-GAAAGGGTTCGAGACATTTTTGTACTAAAGCTAAATTCACTAGGCAATGT
* *
662769 CAAAACTAGTGTTGTT
128 CACAACTAGTGTTGAT
* * * *
662785 AAAGGTGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG--A--A-TTTTT-TTGTGTG
1 AAGGGAGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGGATTTTTTCTTGTGTG
* * *
662844 TCTCTCTCATTTGAAAGGGTTCGAGATATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCAC
66 TCTCTCTCACTTGAAAGGGTTCGAGACATTTTTGTACTAAAGCTAAATTCACTAGGCAATGTCAC
*
662909 AACTGGTGTTGAT
131 AACTAGTGTTGAT
662922 AAGGGAGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGGATTTCTTTCTTGTGT
1 AAGGGAGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGGATTT-TTTCTTGTGT
* * * *
662987 GTGTTTCTCACTTGAAAGGGTTCGGGACATTTTTGTACTAAAGCTAAATTCATTAGGCAATGTCA
65 GTCTCTCTCACTTGAAAGGGTTCGAGACATTTTTGTACTAAAGCTAAATTCACTAGGCAATGTCA
*
663052 CAACTAGTGTTGTT
130 CAACTAGTGTTGAT
* * * * * *
663066 AAGGGCGCAAAGCCGGGCTAGAACCCTTATATTGTTTTGCATTTGAAAGGGTTTTTTCTT
1 AAGGGAGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGGATTTTTTCTT
663126 TTTATGTGTG
Statistics
Matches: 295, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
135 15 0.05
136 1 0.00
137 101 0.34
138 2 0.01
139 2 0.01
140 2 0.01
141 37 0.13
142 2 0.01
143 9 0.03
144 124 0.42
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (143 bp):
AAGGGAGCAAAGCCGAGCTAGAACCCTAATATTGTCTTGCATTCGAAAGGATTTTTTCTTGTGTG
TCTCTCTCACTTGAAAGGGTTCGAGACATTTTTGTACTAAAGCTAAATTCACTAGGCAATGTCAC
AACTAGTGTTGAT
Found at i:664963 original size:26 final size:26
Alignment explanation
Indices: 664919--664992 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
664909 AAAAGGTAAA
* * *
664919 TGTATGTATGTATGTATGTGTGTGTG
1 TGTATGCATGCATGCATGTGTGTGTG
* *
664945 TTTATGCATGCATGCATGTATGTGTG
1 TGTATGCATGCATGCATGTGTGTGTG
* *
664971 TGTATGTATGCATGCGTGTGTG
1 TGTATGCATGCATGCATGTGTG
664993 CTTTGGAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.16, C:0.07, G:0.32, T:0.45
Consensus pattern (26 bp):
TGTATGCATGCATGCATGTGTGTGTG
Found at i:666722 original size:13 final size:13
Alignment explanation
Indices: 666704--666731 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
666694 GTGTAGTCTT
666704 CAACCGGATTCAC
1 CAACCGGATTCAC
666717 CAACCGGATTCAC
1 CAACCGGATTCAC
666730 CA
1 CA
666732 GCCCAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.39, G:0.14, T:0.14
Consensus pattern (13 bp):
CAACCGGATTCAC
Found at i:667153 original size:31 final size:31
Alignment explanation
Indices: 667118--667176 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
667108 TAACATTATT
*
667118 CATTTGTTAATATGTATTAAAAATTAAATTA
1 CATTTGTTAATATGTATTAAAAAATAAATTA
* * * *
667149 CATTTTTTATTTTTTATTAAAAAATAAA
1 CATTTGTTAATATGTATTAAAAAATAAA
667177 CAAATTAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
CATTTGTTAATATGTATTAAAAAATAAATTA
Found at i:671360 original size:10 final size:10
Alignment explanation
Indices: 671345--671378 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
671335 TTGAATTAGG
671345 TTTTTTAATT
1 TTTTTTAATT
671355 TTTTTTAATT
1 TTTTTTAATT
**
671365 TTTAATAATT
1 TTTTTTAATT
671375 TTTT
1 TTTT
671379 AATCAAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:671368 original size:17 final size:18
Alignment explanation
Indices: 671346--671381 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
671336 TGAATTAGGT
*
671346 TTTTTAAT-TTTTTTTAA
1 TTTTTAATAATTTTTTAA
671363 TTTTTAATAATTTTTTAA
1 TTTTTAATAATTTTTTAA
671381 T
1 T
671382 CAAATTGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAATAATTTTTTAA
Found at i:673020 original size:127 final size:125
Alignment explanation
Indices: 672777--673013 Score: 275
Period size: 127 Copynumber: 1.9 Consensus size: 125
672767 AACGGTTAAC
* *
672777 GATAGTTTAGGGATGTATTTAGAATGATTTAAAGTTTATGGAACAATTTAGAATGAGAGCCATAG
1 GATAGTTTAGGGATGTAATTAGAATGATTTAAAGTTTAGGGAACAATTTAGAAT-AGAGCCATAG
* * * ** * *
672842 TTTGAGGATGTTTTGTGCAATTAACTCTTAAATTAATGATTTAGTAATGAAATAACCTTATT
65 TTTGAGGACGTTTAGTGCAATTAACACTTAAATTAACCA-TAAGAAATGAAATAACCTTATT
* * *
672904 GATAGTTTCA-GGATGTAATTAGAATGTTTTAAAAGTTT-GGGACCAATTTAGAAT-GAGTCATA
1 GATAGTTT-AGGGATGTAATTAGAATGATTT-AAAGTTTAGGGAACAATTTAGAATAGAGCCATA
*
672966 GTTTGGGGACGTTTAGTGCAATTAACACATTAAATTAACCCA-AAGAAA
64 GTTTGAGGACGTTTAGTGCAATTAACAC-TTAAATTAA-CCATAAGAAA
673014 ATTGAAACTT
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
125 35 0.38
126 9 0.10
127 41 0.44
128 8 0.09
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35
Consensus pattern (125 bp):
GATAGTTTAGGGATGTAATTAGAATGATTTAAAGTTTAGGGAACAATTTAGAATAGAGCCATAGT
TTGAGGACGTTTAGTGCAATTAACACTTAAATTAACCATAAGAAATGAAATAACCTTATT
Found at i:673179 original size:28 final size:27
Alignment explanation
Indices: 673138--673190 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
673128 ATAAACCCTA
* *
673138 AAATTCAATTTAAAAGCCCAAATCCCC
1 AAATTCAATCTAAAAACCCAAATCCCC
*
673165 AAATTCCAATCTAAAAACCCTAATCC
1 AAATT-CAATCTAAAAACCCAAATCC
673191 TCAACCCCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (27 bp):
AAATTCAATCTAAAAACCCAAATCCCC
Found at i:676879 original size:59 final size:59
Alignment explanation
Indices: 676787--676905 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
676777 GAGGCTTAAA
676787 CCGGGAATGACACTCCTAATAGCTATACAACATATACAGTATATAGCTGCATAAAGAAC
1 CCGGGAATGACACTCCTAATAGCTATACAACATATACAGTATATAGCTGCATAAAGAAC
676846 CCGGGAATGACACTCCTAATAGCTATACAACATATACAGTATATAGCTGCATAAAGAAC
1 CCGGGAATGACACTCCTAATAGCTATACAACATATACAGTATATAGCTGCATAAAGAAC
676905 C
1 C
676906 TGTCTTGTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (59 bp):
CCGGGAATGACACTCCTAATAGCTATACAACATATACAGTATATAGCTGCATAAAGAAC
Found at i:679510 original size:20 final size:20
Alignment explanation
Indices: 679485--679524 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
679475 AATATAGTCA
679485 TTTGATGAATAAAGTTAAAC
1 TTTGATGAATAAAGTTAAAC
679505 TTTGATGAATAAAGTTAAAC
1 TTTGATGAATAAAGTTAAAC
679525 ATCTTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (20 bp):
TTTGATGAATAAAGTTAAAC
Found at i:679673 original size:12 final size:13
Alignment explanation
Indices: 679656--679703 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
679646 ATATAATATT
679656 TTTTTAAA-ATAA
1 TTTTTAAATATAA
*
679668 TTTTTAAATATTA
1 TTTTTAAATATAA
*
679681 TTTTTAAGT-T-A
1 TTTTTAAATATAA
679692 -TTTTAAATATAA
1 TTTTTAAATATAA
679704 AATATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 7 0.23
11 2 0.07
12 10 0.33
13 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTTTAAATATAA
Found at i:679693 original size:14 final size:13
Alignment explanation
Indices: 679650--679687 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
679640 ATTTTCATAT
679650 AATATT-TTTTTA
1 AATATTATTTTTA
*
679662 AA-ATAATTTTTA
1 AATATTATTTTTA
679674 AATATTATTTTTA
1 AATATTATTTTTA
679687 A
1 A
679688 GTTATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 10 0.45
13 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATATTATTTTTA
Found at i:679694 original size:24 final size:23
Alignment explanation
Indices: 679650--679701 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
679640 ATTTTCATAT
679650 AATATTTTTTTAAAATAATTTTTA
1 AATATTTTTTTAAAATAA-TTTTA
* *
679674 AATATTATTTTT-AAGTTATTTTA
1 AATATT-TTTTTAAAATAATTTTA
679697 AATAT
1 AATAT
679702 AAAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.40
24 10 0.40
25 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATATTTTTTTAAAATAATTTTA
Found at i:682415 original size:2 final size:2
Alignment explanation
Indices: 682410--682434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
682400 ATGTTACGTC
682410 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 T
682435 ATGTAAATGC
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:685471 original size:16 final size:16
Alignment explanation
Indices: 685437--685500 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
685427 CCTTTAAAAT
* *
685437 TTTAAATTA-TTTCAG
1 TTTAAGTTATTTTGAG
*
685452 TTTAAGTAATTTTGAG
1 TTTAAGTTATTTTGAG
* *
685468 TTTAAATTATTTTAAG
1 TTTAAGTTATTTTGAG
685484 TTTTAAGGTTATTTTGA
1 -TTTAA-GTTATTTTGA
685501 TCAGCTCACT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
15 7 0.18
16 18 0.47
17 5 0.13
18 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (16 bp):
TTTAAGTTATTTTGAG
Found at i:691167 original size:19 final size:20
Alignment explanation
Indices: 691135--691176 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
691125 CTAAACGTAC
691135 AAACCCAAACCTCGAAAACA
1 AAACCCAAACCTCGAAAACA
* *
691155 AAACCCCAA-CTCGAGAACA
1 AAACCCAAACCTCGAAAACA
691174 AAA
1 AAA
691177 TTCTATCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.55, C:0.33, G:0.07, T:0.05
Consensus pattern (20 bp):
AAACCCAAACCTCGAAAACA
Found at i:696351 original size:159 final size:159
Alignment explanation
Indices: 696092--696478 Score: 684
Period size: 159 Copynumber: 2.4 Consensus size: 159
696082 AAAAATCTAG
*
696092 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTTGAT
1 TATCTAGTGAGTTGATGAACACGATTTGATATGTTTATGGATTGCCATTGATGAATTTATTTGAT
*
696157 TCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTAAGAATGTGAAAGCATCTTCGGCT
66 TCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTAAGAATGTGAAAGCATCTTCAGCT
* * *
696222 TGAATGAATGTTTTTGGATACTTTTCTCA
131 CGAATGAAGGTTTTTGGATACTTCTCTCA
*
696251 TATCTAGTGAGTTGATGAACACGATTTGATATGTTTGTGGATTGCCATTGATGAATTTATTTGAT
1 TATCTAGTGAGTTGATGAACACGATTTGATATGTTTATGGATTGCCATTGATGAATTTATTTGAT
696316 TCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTAAGAATGTGAAAGCATCTTCAGCT
66 TCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTAAGAATGTGAAAGCATCTTCAGCT
696381 CGAATGAAGGTTTTTGGATACTTCTCTCA
131 CGAATGAAGGTTTTTGGATACTTCTCTCA
* * *
696410 TATCTAGTGAGTTGATGAACACGATTTGATATGTTTATGAATTGCCATTTGATGAATTGATTTGG
1 TATCTAGTGAGTTGATGAACACGATTTGATATGTTTATGGATTGCCA-TTGATGAATTTATTTGA
696475 TTCT
65 TTCT
696479 GATTGTATTG
Statistics
Matches: 217, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
159 198 0.91
160 19 0.09
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (159 bp):
TATCTAGTGAGTTGATGAACACGATTTGATATGTTTATGGATTGCCATTGATGAATTTATTTGAT
TCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTAAGAATGTGAAAGCATCTTCAGCT
CGAATGAAGGTTTTTGGATACTTCTCTCA
Found at i:698551 original size:31 final size:31
Alignment explanation
Indices: 698506--698637 Score: 99
Period size: 31 Copynumber: 4.4 Consensus size: 31
698496 GTCATATACC
*
698506 ATTTGATACCTGAGTTTAGCTTCAATGTTCA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
* * * *
698537 ATTTGGTACTTGAGTTTGGCTTCCATGTTTA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
* * ** ****
698568 ATTTGGCAGCTGAGTTT-TTTTC--CCCCCA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
* * *
698596 ATTTGGTACCTGAGATTGGCATCAATGTTCA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
698627 ATTTGGTACCT
1 ATTTGGTACCT
698638 AGATCAAACG
Statistics
Matches: 73, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
28 15 0.21
29 2 0.03
30 3 0.04
31 53 0.73
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (31 bp):
ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
Found at i:698868 original size:31 final size:31
Alignment explanation
Indices: 698833--698916 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
698823 CAAATTGAAG
* *
698833 CCAAATTGAACATTAAAGCTAAATTCAGGTA
1 CCAAATTGAACATTAAAGCCAAATTCAGGGA
**
698864 CCAAATTGAACATGGAAGCCAAATTCAGGGA
1 CCAAATTGAACATTAAAGCCAAATTCAGGGA
*
698895 CCAAATTGAACATTGAA-CCAAA
1 CCAAATTGAACATTAAAGCCAAA
698917 CTCAAGTGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 5 0.10
31 43 0.90
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.20
Consensus pattern (31 bp):
CCAAATTGAACATTAAAGCCAAATTCAGGGA
Found at i:712849 original size:166 final size:165
Alignment explanation
Indices: 712548--712978 Score: 585
Period size: 166 Copynumber: 2.6 Consensus size: 165
712538 TCACTGAAAT
* * * * * *
712548 ATATTTCATGATCAACGAGTTATTTTTTTGAAGGTCACCCGCAAGG-ATTTAAGGTTTAGCAATC
1 ATATTTCATGATCAACGAATTACTTCTTTGAA-GACAACC-CACGGAATTTAAGGTTTAGCAATC
* * *
712612 ATGTGATTCCATCATGCATGCATTAAGGAGAGAGAGATAATTACTCACTTCATCCTTCATTTACA
64 ATGTGATTCCATCATGCATGCATTACGTAGAGAGAGATAATTACTCACTTCATCCTTCATTCACA
* * *
712677 TGGTTGAGGGTTAAATTTCCACCTATGAGACTAAAAC
129 TGGTTGAGGGTTAAATCTCCACCTATAAAACTAAAAC
* * * *
712714 ATATTTTATGATTAACGAATTACTTCTTTGAAGACCATCCACGAGAATTTAAGGTTTAGCAATCA
1 ATATTTCATGATCAACGAATTACTTCTTTGAAGACAACCCACG-GAATTTAAGGTTTAGCAATCA
* * *
712779 TGTGATTCCATCATGCATGCATTACGTAGAGAGAGATAATTACTCACTTTATCCTTTATTCACGT
65 TGTGATTCCATCATGCATGCATTACGTAGAGAGAGATAATTACTCACTTCATCCTTCATTCACAT
* *
712844 GGTTGAGGGTTCAATCTCCACCTATAAAACTGAAAC
130 GGTTGAGGGTTAAATCTCCACCTATAAAACTAAAAC
* * * *
712880 ATATTTCATGATCAATGAATTACTTCTTTGAATACAACCCGCGGAAGTTTAAGGTTTAGTAATCA
1 ATATTTCATGATCAACGAATTACTTCTTTGAAGACAACCCACGGAA-TTTAAGGTTTAGCAATCA
*
712945 TGTGATTCCATCATGTATGCATTACGTAGAGAGA
65 TGTGATTCCATCATGCATGCATTACGTAGAGAGA
712979 TGCTGTCATG
Statistics
Matches: 232, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
164 3 0.01
165 7 0.03
166 222 0.96
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (165 bp):
ATATTTCATGATCAACGAATTACTTCTTTGAAGACAACCCACGGAATTTAAGGTTTAGCAATCAT
GTGATTCCATCATGCATGCATTACGTAGAGAGAGATAATTACTCACTTCATCCTTCATTCACATG
GTTGAGGGTTAAATCTCCACCTATAAAACTAAAAC
Found at i:715467 original size:22 final size:22
Alignment explanation
Indices: 715439--715521 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 22
715429 CATAAACAAT
715439 GATATAATATAACTATATGATA
1 GATATAATATAACTATATGATA
* *
715461 GATATAATATATGATTGA-ACTTGCCATT
1 GATATAATATA--ACT-ATA--TG--ATA
*
715489 CATATAATATAACTATATGATA
1 GATATAATATAACTATATGATA
715511 GATATAATATA
1 GATATAATATA
715522 TGATTGAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
22 23 0.49
24 5 0.11
25 2 0.04
26 5 0.11
28 12 0.26
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (22 bp):
GATATAATATAACTATATGATA
Found at i:715515 original size:50 final size:50
Alignment explanation
Indices: 715440--715541 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
715430 ATAAACAATG
715440 ATATAATATAACTATATGATAGATATAATATATGATTGAACTTGCCATTC
1 ATATAATATAACTATATGATAGATATAATATATGATTGAACTTGCCATTC
715490 ATATAATATAACTATATGATAGATATAATATATGATTGAACTTGCCATTC
1 ATATAATATAACTATATGATAGATATAATATATGATTGAACTTGCCATTC
715540 AT
1 AT
715542 TGGCCTGCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (50 bp):
ATATAATATAACTATATGATAGATATAATATATGATTGAACTTGCCATTC
Found at i:718355 original size:24 final size:23
Alignment explanation
Indices: 718318--718385 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
718308 TGACGAATCT
718318 AACATAAAAAAAAATTGATGAAAA
1 AACA-AAAAAAAAATTGATGAAAA
* * *
718342 AACAATAAATAAAACTAATGAAAA
1 AACAA-AAAAAAAATTGATGAAAA
718366 AACAAAAAAAAAATTTGATG
1 AACAAAAAAAAAA-TTGATG
718386 GGACAGCACA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 8 0.22
24 28 0.78
ACGTcount: A:0.69, C:0.06, G:0.07, T:0.18
Consensus pattern (23 bp):
AACAAAAAAAAAATTGATGAAAA
Found at i:721174 original size:51 final size:52
Alignment explanation
Indices: 721115--721217 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 52
721105 CATTTACCAC
* *
721115 GTGCAATATCACGCCTTTGTCTCGATGCATGAAAAAGACATTA-ACCTTATA
1 GTGCAATATCACGCCTTTGTCTCGATGCATAAAAAAGACATAATACCTTATA
* * * *
721166 GTGCAATATCATGCCTTTGTTTCGATGTATAAAAAAGATATAATACCTTATA
1 GTGCAATATCACGCCTTTGTCTCGATGCATAAAAAAGACATAATACCTTATA
721218 TGATGATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
51 37 0.82
52 8 0.18
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (52 bp):
GTGCAATATCACGCCTTTGTCTCGATGCATAAAAAAGACATAATACCTTATA
Found at i:721300 original size:153 final size:151
Alignment explanation
Indices: 721019--721317 Score: 431
Period size: 153 Copynumber: 2.0 Consensus size: 151
721009 AGCATGCAAA
* * *
721019 AATATCATGCTTTTGTTTCAATGTATGAAAAAGACATAAACCTTGTATGATGATTTCAGTGCTAA
1 AATATCATGCCTTTGTTTCAATGTATAAAAAAGACATAAACCTTATATGATGATTTCAGTGCTAA
*
721084 TGCATTTGCTTTGATTAAGTTCATTTACCACGTGCAATATCACGCCTTTGTCTCGATGCATGAAA
66 TGCATTTGCTTTGATTAAGTTCATTTACCACGTGCAATATCACACCTTTGTCTCGATGCATGAAA
*
721149 AAGACATTAACCTTATAGTGC
131 AAGACATAAACCTTATAGTGC
* *
721170 AATATCATGCCTTTGTTTCGATGTATAAAAAAGATATAATACCTTATATGATGATTTCAGTGCTA
1 AATATCATGCCTTTGTTTCAATGTATAAAAAAGACATAA-ACCTTATATGATGATTTCAGTGCTA
* * * * *
721235 ATGCA-TTGGTTGTGATTTAAGTTCATTTAGCTCGTGCGATATCACACCTTTGT-TCCGATGTAT
65 ATGCATTTGCTT-TGA-TTAAGTTCATTTACCACGTGCAATATCACACCTTTGTCT-CGATGCAT
*
721298 GAAATAGACATAAACCTTAT
127 GAAAAAGACATAAACCTTAT
721318 TTGATGATTT
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
151 40 0.31
152 33 0.25
153 58 0.44
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (151 bp):
AATATCATGCCTTTGTTTCAATGTATAAAAAAGACATAAACCTTATATGATGATTTCAGTGCTAA
TGCATTTGCTTTGATTAAGTTCATTTACCACGTGCAATATCACACCTTTGTCTCGATGCATGAAA
AAGACATAAACCTTATAGTGC
Found at i:721352 original size:101 final size:103
Alignment explanation
Indices: 721179--721364 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 103
721169 CAATATCATG
* * *
721179 CCTTTGTTTCGATGTATAAAAAAGATATAATACCTTATATGATGATTTCAGTGCTAATGCATTGG
1 CCTTTGTTCCGATGTATAAAAAAGACATAATACCTTATATGATGATTTCAATGCTAATGCATTGG
721244 TTGTGATTT-AAGTTCATTTAGCTCGTGCGATATCACA
66 TTGTGATTTAAAGTTCATTTAGCTCGTGCGATATCACA
* * * *
721281 CCTTTGTTCCGATGTATGAAATAGACATAA-ACCTTATTTGATGATTTCAATGCTAATGCATTTG
1 CCTTTGTTCCGATGTATAAAAAAGACATAATACCTTATATGATGATTTCAATGCTAATGCATTGG
*
721345 TTTTGATTTAAAGTTCATTT
66 TTGTGATTTAAAGTTCATTT
721365 TGTTGACATA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
101 39 0.52
102 36 0.48
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (103 bp):
CCTTTGTTCCGATGTATAAAAAAGACATAATACCTTATATGATGATTTCAATGCTAATGCATTGG
TTGTGATTTAAAGTTCATTTAGCTCGTGCGATATCACA
Found at i:724260 original size:30 final size:28
Alignment explanation
Indices: 724207--724275 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
724197 TGATAAACTG
* *
724207 AAAAATTAAATGTTGACATATTAAATGCT
1 AAAATTTAAATATTGACATATTAAATG-T
724236 AAAATTTTAAATATTGAACA-ATTAAATGT
1 AAAA-TTTAAATATTG-ACATATTAAATGT
*
724265 TAAATTTAAAT
1 AAAATTTAAAT
724276 TATAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.20
29 8 0.23
30 17 0.49
31 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
AAAATTTAAATATTGACATATTAAATGT
Found at i:724653 original size:16 final size:17
Alignment explanation
Indices: 724628--724661 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
724618 GTTGAAGCTC
724628 TTAAAAAATAAT-TAAT
1 TTAAAAAATAATATAAT
*
724644 TTAAATAATAATATAAT
1 TTAAAAAATAATATAAT
724661 T
1 T
724662 GTTTTGCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAAATAATATAAT
Found at i:729973 original size:18 final size:17
Alignment explanation
Indices: 729950--729988 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
729940 TAATTTTTGA
*
729950 AATTTTGTTTATGGTTTT
1 AATTTTGTTTA-AGTTTT
*
729968 AATTTTTTTTAAGTTTT
1 AATTTTGTTTAAGTTTT
729985 AATT
1 AATT
729989 AAATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (17 bp):
AATTTTGTTTAAGTTTT
Found at i:735200 original size:20 final size:19
Alignment explanation
Indices: 735153--735189 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
735143 ATTTTAAAAA
*
735153 ATAAAT-TTTAGAGTTTTT
1 ATAAATATTTAGAATTTTT
735171 ATAAATATTTAGAATTTTT
1 ATAAATATTTAGAATTTTT
735190 GAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
ATAAATATTTAGAATTTTT
Done.