Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold401
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: 1910012
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 13
Found at i:398661 original size:22 final size:25
Alignment explanation
Indices: 398609--398663 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
398599 AAAATAAATA
*
398609 TAATTTAATATTCATATTTTTATAT
1 TAATATAATATTCATATTTTTATAT
398634 TAATATAATATT-ATATTTTTAT-T
1 TAATATAATATTCATATTTTTATAT
398657 TATATAT
1 TA-ATAT
398664 TTAATACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 3 0.11
24 14 0.50
25 11 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TAATATAATATTCATATTTTTATAT
Found at i:398692 original size:24 final size:23
Alignment explanation
Indices: 398623--398693 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 23
398613 TTAATATTCA
*
398623 TATTTTTATATTAAT-ATAATAT
1 TATTTTTATATTTATAATAATAT
398645 TATATTTT-TATTTATATATTTAATACT
1 TAT-TTTTATATTTATA-A--TAATA-T
*
398672 TATTTTTAAATTTATAATAATA
1 TATTTTTATATTTATAATAATA
398694 AATTAAAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
22 9 0.22
23 4 0.10
24 6 0.15
26 10 0.25
27 11 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTATATTTATAATAATAT
Found at i:399133 original size:12 final size:12
Alignment explanation
Indices: 399104--399141 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
399094 TTATTTAAAT
399104 TTAATTATAAAAA
1 TTAA-TATAAAAA
399117 -T-ATATAAAAA
1 TTAATATAAAAA
399127 TTAATATAAAAA
1 TTAATATAAAAA
399139 TTA
1 TTA
399142 TATTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAATATAAAAA
Found at i:399876 original size:12 final size:13
Alignment explanation
Indices: 399853--399881 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
399843 TTAAATGTAA
399853 TAATTAATCATTT
1 TAATTAATCATTT
399866 TAATT-ATCATTT
1 TAATTAATCATTT
399878 TAAT
1 TAAT
399882 GTATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTAATCATTT
Found at i:405928 original size:10 final size:10
Alignment explanation
Indices: 405899--405928 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
405889 AGGTCAGTCA
*
405899 TCTCTCTCTC
1 TCTCTCTCTT
405909 TCTCTCTCTT
1 TCTCTCTCTT
405919 TCTCTCTCTT
1 TCTCTCTCTT
405929 CCACAAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (10 bp):
TCTCTCTCTT
Found at i:407680 original size:79 final size:79
Alignment explanation
Indices: 407549--407711 Score: 326
Period size: 79 Copynumber: 2.1 Consensus size: 79
407539 CTGTTGGATT
407549 TTGTGGTCTCTTGTTAATATGTATTAATATGAAATTAGTTGTGGAAGTAAGGTGCACCATTGTTG
1 TTGTGGTCTCTTGTTAATATGTATTAATATGAAATTAGTTGTGGAAGTAAGGTGCACCATTGTTG
407614 CATGGACTCGTGAG
66 CATGGACTCGTGAG
407628 TTGTGGTCTCTTGTTAATATGTATTAATATGAAATTAGTTGTGGAAGTAAGGTGCACCATTGTTG
1 TTGTGGTCTCTTGTTAATATGTATTAATATGAAATTAGTTGTGGAAGTAAGGTGCACCATTGTTG
407693 CATGGACTCGTGAG
66 CATGGACTCGTGAG
407707 TTGTG
1 TTGTG
407712 ATAAGAGTGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 84 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.39
Consensus pattern (79 bp):
TTGTGGTCTCTTGTTAATATGTATTAATATGAAATTAGTTGTGGAAGTAAGGTGCACCATTGTTG
CATGGACTCGTGAG
Found at i:411531 original size:2 final size:2
Alignment explanation
Indices: 411524--411560 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
411514 GGTGGGTCTT
* *
411524 TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
411561 GCATTCGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.43, G:0.03, T:0.54
Consensus pattern (2 bp):
TC
Found at i:412677 original size:22 final size:22
Alignment explanation
Indices: 412652--412770 Score: 68
Period size: 21 Copynumber: 5.3 Consensus size: 22
412642 TGTAATATGA
412652 TTATATAGAATTTT-TTATATAT
1 TTATATA-AATTTTATTATATAT
412674 TTATATAAATTTTA-T-TATAT
1 TTATATAAATTTTATTATATAT
* *
412694 TAATAATAAATTTTA-TATAAAT
1 TTAT-ATAAATTTTATTATATAT
* *
412716 TT-TGATATAATTTAATTTTTATAT
1 TTAT-ATA-AATTTTA-TTATATAT
* * *
412740 TATATTTATATTTTTTATATTATAT
1 T-TATATAAATTTTAT-TA-TATAT
412765 TTATAT
1 TTATAT
412771 CATATTTAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
20 8 0.11
21 22 0.30
22 18 0.24
23 1 0.01
24 15 0.20
25 9 0.12
26 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATAAATTTTATTATATAT
Found at i:412686 original size:20 final size:19
Alignment explanation
Indices: 412664--412712 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
412654 ATATAGAATT
412664 TTTTATATATTTATATAAA
1 TTTTATATATTTATATAAA
*
412683 TTTTATTATATTAATAATAAA
1 TTTTA-TATATTTAT-ATAAA
412704 TTTTATATA
1 TTTTATATA
412713 AATTTTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTATATATTTATATAAA
Found at i:412728 original size:11 final size:11
Alignment explanation
Indices: 412652--412725 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
412642 TGTAATATGA
412652 TTATATAGAATT
1 TTATATA-AATT
* *
412664 TTTTATATA-T
1 TTATATAAATT
412674 TTATATAAATT
1 TTATATAAATT
*
412685 TTAT-TATA-T
1 TTATATAAATT
*
412694 TAATAATAAATT
1 TTAT-ATAAATT
412706 TTATATAAATT
1 TTATATAAATT
412717 TTGATATAA
1 TT-ATATAA
412726 TTTAATTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 4 0.08
10 11 0.22
11 18 0.37
12 16 0.33
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TTATATAAATT
Found at i:412747 original size:11 final size:11
Alignment explanation
Indices: 412733--412778 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
412723 TAATTTAATT
412733 TTTATATTATA
1 TTTATATTATA
412744 TTTATATT-T-
1 TTTATATTATA
412753 TTTATATTATA
1 TTTATATTATA
*
412764 TTTATATCATA
1 TTTATATTATA
412775 TTTA
1 TTTA
412779 AAATTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 8 0.25
10 2 0.06
11 22 0.69
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTATATTATA
Found at i:412756 original size:20 final size:20
Alignment explanation
Indices: 412731--412770 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
412721 TATAATTTAA
412731 TTTTTATATTATATTTATAT
1 TTTTTATATTATATTTATAT
412751 TTTTTATATTATATTTATAT
1 TTTTTATATTATATTTATAT
412771 CATATTTAAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTATATTATATTTATAT
Found at i:413244 original size:2 final size:2
Alignment explanation
Indices: 413237--413280 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
413227 AATGTAATCT
413237 TA TA TA TA 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 TA TA TA TA
413279 TA
1 TA
413281 CACACATACG
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):
TA
Found at i:424277 original size:18 final size:18
Alignment explanation
Indices: 424247--424295 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
424237 TATTTTTTTA
424247 AAAAT-AATGTAAA-TATAT
1 AAAATAAAT-TAAAGTAT-T
424265 AAAATAAATTAAAGTATT
1 AAAATAAATTAAAGTATT
*
424283 AAAAAAAATTAAA
1 AAAATAAATTAAA
424296 AACAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAATAAATTAAAGTATT
Found at i:424304 original size:15 final size:16
Alignment explanation
Indices: 424284--424313 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
424274 TAAAGTATTA
424284 AAAAAAATTA-AAAAC
1 AAAAAAATTACAAAAC
424299 AAAAAAATTACAAAA
1 AAAAAAATTACAAAA
424314 TTTTTGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAATTACAAAAC
Found at i:424374 original size:15 final size:15
Alignment explanation
Indices: 424357--424407 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
424347 AAAAATTTAT
* *
424357 ATTATGTTAATATAT
1 ATTATGTTTATATAA
* *
424372 ATTATTTTTATTTAA
1 ATTATGTTTATATAA
424387 ATTAT-TTTATATAA
1 ATTATGTTTATATAA
424401 ATTATGT
1 ATTATGT
424408 CACTTAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTATGTTTATATAA
Found at i:424396 original size:14 final size:14
Alignment explanation
Indices: 424366--424405 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
424356 TATTATGTTA
*
424366 ATATATATTATTTTT
1 ATATAAATTA-TTTT
*
424381 ATTTAAATTATTTT
1 ATATAAATTATTTT
424395 ATATAAATTAT
1 ATATAAATTAT
424406 GTCACTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATAAATTATTTT
Found at i:424519 original size:18 final size:17
Alignment explanation
Indices: 424498--424531 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
424488 ATTATTATAT
424498 ATAATTTAAAATAAATAA
1 ATAATTTAAAA-AAATAA
*
424516 ATAATTTTAAAAAATA
1 ATAATTTAAAAAAATA
424532 TAATTAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATTTAAAAAAATAA
Found at i:424534 original size:19 final size:19
Alignment explanation
Indices: 424493--424534 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
424483 ATTTAATTAT
*
424493 TATATATAATTTAAAATAA
1 TATAAATAATTTAAAATAA
424512 -ATAAATAATTTTAAAA-AA
1 TATAAATAA-TTTAAAATAA
424530 TATAA
1 TATAA
424535 TTAAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAAATAATTTAAAATAA
Found at i:424868 original size:27 final size:27
Alignment explanation
Indices: 424830--424883 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
424820 CCAATCAAAC
*
424830 TATCGGCTGATAT-TTCTTACTAGCAGT
1 TATCGGCTGATATCTT-TCACTAGCAGT
424857 TATCGGCTGATATCTTTCACTAGCAGT
1 TATCGGCTGATATCTTTCACTAGCAGT
424884 AGCAGTCGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (27 bp):
TATCGGCTGATATCTTTCACTAGCAGT
Found at i:425299 original size:23 final size:23
Alignment explanation
Indices: 425282--425343 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
425272 TAATTTTTTA
*
425282 AAATTATTTAATAAAATTAATTT
1 AAATAATTTAATAAAATTAATTT
** *
425305 AAATAATTTAAT-TTATTAATAAT
1 AAATAATTTAATAAAATTAAT-TT
425328 AAA-AATTTAATAAAAT
1 AAATAATTTAATAAAAT
425344 GTATTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAATTTAATAAAATTAATTT
Found at i:425304 original size:14 final size:14
Alignment explanation
Indices: 425269--425371 Score: 57
Period size: 14 Copynumber: 6.8 Consensus size: 14
425259 AAAAGATACG
**
425269 AATTAATTTTTTAA
1 AATTAATTTAATAA
425283 AATT-ATTTAATAA
1 AATTAATTTAATAA
425296 AATTAATTTAA-ATA
1 AATTAATTTAATA-A
* *
425310 ATTTAATTTATTAA
1 AATTAATTTAATAA
*
425324 TAATAAAAATTTAATAA
1 -AAT--TAATTTAATAA
425341 AATGTATTATTTATATAAA
1 AAT-TA--ATTTA-AT-AA
425360 AATTAATATTAA
1 AATTAAT-TTAA
425372 ATTTAATAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 20
0.70 0.09 0.20
Matches are distributed among these distances:
13 12 0.17
14 21 0.30
15 4 0.06
16 6 0.09
17 17 0.25
18 4 0.06
19 5 0.07
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (14 bp):
AATTAATTTAATAA
Found at i:431253 original size:2 final size:2
Alignment explanation
Indices: 431246--431286 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
431236 AGAGTCTAGG
431246 AT AT AT 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 AT AT AT A
431287 CACACATCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:432742 original size:15 final size:15
Alignment explanation
Indices: 432701--432757 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
432691 ATAGCTCTCA
*
432701 TTTGGCACAAATTATT
1 TTTGGCAC-AAGTATT
* *
432717 TTT-ACAGAAGTATT
1 TTTGGCACAAGTATT
*
432731 TTTGGCACAAGTA-C
1 TTTGGCACAAGTATT
432745 TTTGGCACAAGTA
1 TTTGGCACAAGTA
432758 CCTTAGCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 22 0.65
15 9 0.26
16 3 0.09
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (15 bp):
TTTGGCACAAGTATT
Found at i:432748 original size:14 final size:14
Alignment explanation
Indices: 432731--432758 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
432721 CAGAAGTATT
432731 TTTGGCACAAGTAC
1 TTTGGCACAAGTAC
432745 TTTGGCACAAGTAC
1 TTTGGCACAAGTAC
432759 CTTAGCATAG
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:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
TTTGGCACAAGTAC
Found at i:433471 original size:43 final size:43
Alignment explanation
Indices: 433424--433581 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 43
433414 GGCATTGGTA
* * *
433424 CTTTGGCATAGGTATTTTGGCATAAGTATTCTAGCACAATTAT
1 CTTTGGCATAGGTACTTTGGCATAAGTATTCTAGCACAAGTAC
** * * * *
433467 CTTTGGCATAGGTACTTTGATATAAATACTCTGGCATAAGTAC
1 CTTTGGCATAGGTACTTTGGCATAAGTATTCTAGCACAAGTAC
* * * *
433510 CTTTGGCGTAGGTACTTTGGCATAGGTATTTTTGGCACAAGTA-
1 CTTTGGCATAGGTACTTTGGCATAAGTA-TTCTAGCACAAGTAC
* * *
433553 CTTTCGACATAGATACTTTGACATAAGTA
1 CTTT-GGCATAGGTACTTTGGCATAAGTA
433582 CCTTTGGCAC
Statistics
Matches: 91, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
43 61 0.67
44 30 0.33
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (43 bp):
CTTTGGCATAGGTACTTTGGCATAAGTATTCTAGCACAAGTAC
Found at i:433595 original size:15 final size:14
Alignment explanation
Indices: 433397--433597 Score: 118
Period size: 14 Copynumber: 14.0 Consensus size: 14
433387 CACAAGCATT
* * *
433397 TTTGGCACAAGAAA
1 TTTGGCATAAGTAC
**
433411 TTTGGCATTGGTAC
1 TTTGGCATAAGTAC
* *
433425 TTTGGCATAGGTAT
1 TTTGGCATAAGTAC
433439 TTTGGCATAAGTA-
1 TTTGGCATAAGTAC
* * *
433452 TTCTAGCACAATTATC
1 TT-TGGCATAAGTA-C
*
433468 TTTGGCATAGGTAC
1 TTTGGCATAAGTAC
** *
433482 TTTGATATAAATAC
1 TTTGGCATAAGTAC
*
433496 TCTGGCATAAGTACC
1 TTTGGCATAAGTA-C
* *
433511 TTTGGCGTAGGTAC
1 TTTGGCATAAGTAC
* *
433525 TTTGGCATAGGTATT
1 TTTGGCATAAGTA-C
*
433540 TTTGGCACAAGTAC
1 TTTGGCATAAGTAC
*
433554 TTTCGACAT-AGATAC
1 TTT-GGCATAAG-TAC
*
433569 TTTGACATAAGTACC
1 TTTGGCATAAGTA-C
*
433584 TTTGGCACAAGTAC
1 TTTGGCATAAGTAC
433598 ATTAGCACGT
Statistics
Matches: 143, Mismatches: 35, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
13 2 0.01
14 87 0.61
15 52 0.36
16 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (14 bp):
TTTGGCATAAGTAC
Found at i:435941 original size:34 final size:34
Alignment explanation
Indices: 435902--435968 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
435892 AAAAAGGTTA
435902 AATAATCCACTTCATTTAAGGTTGAGATACAATG
1 AATAATCCACTTCATTTAAGGTTGAGATACAATG
* *
435936 AATAATCTATTTCATTTAAGGTTGAGATACAAT
1 AATAATCCACTTCATTTAAGGTTGAGATACAAT
435969 CTCCCTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (34 bp):
AATAATCCACTTCATTTAAGGTTGAGATACAATG
Found at i:436140 original size:117 final size:117
Alignment explanation
Indices: 435934--436274 Score: 438
Period size: 117 Copynumber: 2.9 Consensus size: 117
435924 TGAGATACAA
** * *
435934 TGAATAATCTATTTCATTTAAGGTTGAGATACAATCTCCCTAATAAAGTGGATAGTTTCC-TTTG
1 TGAATAATCTGCTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATA-ATTCCTTTTG
** * * * *
435998 GTCATAACTATAATCGTTTTTATATTGGCCTAAATTATTTATTC-AAAAAAGAT
65 GTCGCAGCTATAATCATTTATATATTGGCCTAAATCATTTATTCGAAAAAAG-T
*
436051 TGAATAATTTGCTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAATTCCTTTTGG
1 TGAATAATCTGCTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAATTCCTTTTGG
*
436116 TCGCAGCTATAATCATTTATATATTGGCCTAAGTCATTTATTCGAAAAAAGT
66 TCGCAGCTATAATCATTTATATATTGGCCTAAATCATTTATTCGAAAAAAGT
* * *
436168 TGAATAATCTGCTTTATTTAAGGTTAAGATACAATCTCCCTAATGAAGTGGATAGTT-CTCTTTG
1 TGAATAATCTGCTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAATTCCT-TTTG
* * * * *
436232 G-CTGCAGCTATAATCACTCATACATTGGCCTAAGTCACTTATT
65 GTC-GCAGCTATAATCATTTATATATTGGCCTAAATCATTTATT
436275 TAAAAAGAGG
Statistics
Matches: 200, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
116 7 0.04
117 186 0.93
118 7 0.04
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (117 bp):
TGAATAATCTGCTTCATTTAAGGTTGAGATACAATCTCCCTAATGAAGTGGATAATTCCTTTTGG
TCGCAGCTATAATCATTTATATATTGGCCTAAATCATTTATTCGAAAAAAGT
Found at i:436356 original size:120 final size:120
Alignment explanation
Indices: 436074--436474 Score: 479
Period size: 120 Copynumber: 3.4 Consensus size: 120
436064 TCATTTAAGG
* * * * * *
436074 TTGAGATACAATCTCCCTAATGAAGTGGATAATTC-CTTTTGG-TCGCAGCTATAATCATTTATA
1 TTGAGATTCGATCTCCCTAATAAAGTGGATAGTTCTC-TTTGGCT-GCAGCTATAATCACTCATA
* * * ** * * * * * **
436137 TATTGGCCTAAGTCATTTATTCGAAAA-A-A-GTTGAATAATCTGCTTTATTTAAGG
64 CATTAGCCTAAGTCACTTATTTAAAAAGAGAGGTTAAATAATTTACTTTGTTTTATA
* * * *
436191 TTAAGATACAATCTCCCTAATGAAGTGGATAGTTCTCTTTGGCTGCAGCTATAATCACTCATACA
1 TTGAGATTCGATCTCCCTAATAAAGTGGATAGTTCTCTTTGGCTGCAGCTATAATCACTCATACA
* * *
436256 TTGGCCTAAGTCACTTATTTAAAAAGAGGGGTTAAATAGTTTACTTTGTTTTATA
66 TTAGCCTAAGTCACTTATTTAAAAAGAGAGGTTAAATAATTTACTTTGTTTTATA
*
436311 TTGAGATTCGATTTCCCTAATAAAGTGGATAGTTCTCTTTGGCTGCAGCTATAATCACTCATACA
1 TTGAGATTCGATCTCCCTAATAAAGTGGATAGTTCTCTTTGGCTGCAGCTATAATCACTCATACA
*
436376 TTAGCCTAAGTCACTTATTTAAAAAGAGAGGTTAAATAATTTACTTTGTTTTATG
66 TTAGCCTAAGTCACTTATTTAAAAAGAGAGGTTAAATAATTTACTTTGTTTTATA
*
436431 TTGAGATTCGATCTCCCTAATCAATGTGGATAGTTCTCCTTTGG
1 TTGAGATTCGATCTCCCTAAT-AAAGTGGATAGTTCT-CTTTGG
436475 GCACATTCTT
Statistics
Matches: 249, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
117 78 0.31
118 3 0.01
120 148 0.59
121 14 0.06
122 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (120 bp):
TTGAGATTCGATCTCCCTAATAAAGTGGATAGTTCTCTTTGGCTGCAGCTATAATCACTCATACA
TTAGCCTAAGTCACTTATTTAAAAAGAGAGGTTAAATAATTTACTTTGTTTTATA
Found at i:437375 original size:24 final size:24
Alignment explanation
Indices: 437324--437370 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
437314 ATCTAAACTG
*
437324 TGTTCCAAGAGTCATCCCAAAGAA
1 TGTTCCAAGAGTCATCCAAAAGAA
*
437348 TGTTCTAAGAGTCATGCCAAAAG
1 TGTTCCAAGAGTCAT-CCAAAAG
437371 TTGTTTCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGTTCCAAGAGTCATCCAAAAGAA
Found at i:440132 original size:14 final size:14
Alignment explanation
Indices: 440100--440168 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
440090 TTATTGATTC
440100 TTAAAAAAACTA-T
1 TTAAAAAAACTATT
440113 TT--AAAAACTATT
1 TTAAAAAAACTATT
* *
440125 TTAAAAAAAATTGTT
1 TT-AAAAAAACTATT
*
440140 TTAAAAAAAATATT
1 TTAAAAAAACTATT
* *
440154 TAAAAAAAACGATT
1 TTAAAAAAACTATT
440168 T
1 T
440169 GTTAAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 8 0.18
12 3 0.07
13 2 0.04
14 22 0.49
15 10 0.22
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (14 bp):
TTAAAAAAACTATT
Found at i:440162 original size:13 final size:13
Alignment explanation
Indices: 440100--440162 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
440090 TTATTGATTC
*
440100 TTAAAAAAACTAT
1 TTAAAAAAAATAT
**
440113 TTAAAAACTAT-T
1 TTAAAAAAAATAT
*
440125 TTAAAAAAAATTGTT
1 TTAAAAAAAA-T-AT
440140 TTAAAAAAAATAT
1 TTAAAAAAAATAT
440153 TTAAAAAAAA
1 TTAAAAAAAA
440163 CGATTTGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
12 9 0.22
13 20 0.49
14 1 0.02
15 11 0.27
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (13 bp):
TTAAAAAAAATAT
Found at i:440210 original size:13 final size:12
Alignment explanation
Indices: 440187--440220 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
440177 TAAATATATA
*
440187 TTTTATTTTATT
1 TTTTATCTTATT
440199 TTATTATCTTATT
1 TT-TTATCTTATT
440212 TTTTATCTT
1 TTTTATCTT
440221 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATCTTATT
Found at i:440950 original size:3 final size:3
Alignment explanation
Indices: 440914--440982 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
440904 TTTATTTAAT
* * * *
440914 TTA TTA TTTA TCA TAA TTA TTT TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
440960 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
440983 GTAATTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:441019 original size:2 final size:2
Alignment explanation
Indices: 441012--441042 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
441002 ATTCACTCTT
441012 TA TA 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 TA TA T
441043 TACCGTTACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:441315 original size:14 final size:14
Alignment explanation
Indices: 441292--441323 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
441282 TCGACATAAG
441292 TACTCCGGTACAGA
1 TACTCCGGTACAGA
*
441306 TACTCTGGTACAGA
1 TACTCCGGTACAGA
441320 TACT
1 TACT
441324 TTGACACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (14 bp):
TACTCCGGTACAGA
Found at i:441337 original size:14 final size:14
Alignment explanation
Indices: 441320--441383 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
441310 CTGGTACAGA
*
441320 TACTTTGACACAAG
1 TACTTTGGCACAAG
* *
441334 TACTCTGGCACAGG
1 TACTTTGGCACAAG
*
441348 TACTTTTGGCATAAG
1 TAC-TTTGGCACAAG
* * *
441363 TACTTTGCCATAGG
1 TACTTTGGCACAAG
441377 TACTTTG
1 TACTTTG
441384 CTATATATAC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 30 0.73
15 11 0.27
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (14 bp):
TACTTTGGCACAAG
Found at i:441365 original size:15 final size:15
Alignment explanation
Indices: 441347--441418 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 15
441337 TCTGGCACAG
*
441347 GTACTTTTGGCATAA
1 GTACTTTTGCCATAA
*
441362 GTAC-TTTGCCATAG
1 GTACTTTTGCCATAA
*
441376 GTAC-TTTGCTATATA
1 GTACTTTTGCCATA-A
** *
441391 -TACTTTTAACATAG
1 GTACTTTTGCCATAA
*
441405 GTACTTTTGACATA
1 GTACTTTTGCCATA
441419 GATATTTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
14 23 0.51
15 22 0.49
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (15 bp):
GTACTTTTGCCATAA
Found at i:441365 original size:29 final size:29
Alignment explanation
Indices: 441306--441382 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
441296 CCGGTACAGA
* *
441306 TACTCTGGTACAGATAC-TTTGACACAAG
1 TACTCTGGCACAGGTACTTTTGACACAAG
* *
441334 TACTCTGGCACAGGTACTTTTGGCATAAG
1 TACTCTGGCACAGGTACTTTTGACACAAG
* * *
441363 TACTTTGCCATAGGTACTTT
1 TACTCTGGCACAGGTACTTT
441383 GCTATATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 15 0.37
29 26 0.63
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (29 bp):
TACTCTGGCACAGGTACTTTTGACACAAG
Found at i:441403 original size:29 final size:29
Alignment explanation
Indices: 441345--441437 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
441335 ACTCTGGCAC
* * **
441345 AGGTACTTTTGGCATA-AGTACTTTGCCAT
1 AGGTACTTTTGACATAGA-TATTTTAACAT
*
441374 AGGTAC-TTTG-CTATATATACTTTTAACAT
1 AGGTACTTTTGAC-ATAGATA-TTTTAACAT
441403 AGGTACTTTTGACATAGATATTTTAACAT
1 AGGTACTTTTGACATAGATATTTTAACAT
*
441432 AAGTAC
1 AGGTAC
441438 CTTAAGCACA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 9 0.17
29 33 0.61
30 10 0.19
31 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (29 bp):
AGGTACTTTTGACATAGATATTTTAACAT
Found at i:441431 original size:14 final size:15
Alignment explanation
Indices: 441390--441432 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
441380 TTTGCTATAT
441390 ATACTTTTAACATAG
1 ATACTTTTAACATAG
* *
441405 GTACTTTTGACATAG
1 ATACTTTTAACATAG
441420 ATA-TTTTAACATA
1 ATACTTTTAACATA
441433 AGTACCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (15 bp):
ATACTTTTAACATAG
Found at i:448685 original size:2 final size:2
Alignment explanation
Indices: 448678--448714 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
448668 TATAGCCTTA
448678 TC TC 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 TC TC T
448715 ATGTCAAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:449953 original size:27 final size:28
Alignment explanation
Indices: 449918--450000 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 28
449908 ATATGATATA
*
449918 ATATAAATATAAATATGTTTTAAAATTT
1 ATATAAATATAAATATATTTTAAAATTT
449946 ATAT-AATATAAATTATTAATATATTAAAATTT
1 ATATAAATATAAA-TA-T-AT-T-TTAAAATTT
449978 ATATAAATATAAA-ATATTTTAAA
1 ATATAAATATAAATATATTTTAAA
450001 CAACATTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
27 13 0.27
28 7 0.15
29 3 0.06
30 2 0.04
31 2 0.04
32 13 0.27
33 8 0.17
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATAAATATAAATATATTTTAAAATTT
Found at i:449955 original size:33 final size:32
Alignment explanation
Indices: 449897--449990 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 32
449887 TGATACAAAA
*
449897 AAATA-ATTAAAATATGATATAATATAAA-TAT
1 AAATATATTAAAAT-TTATATAATATAAATTAT
*
449928 AAATATGTTTTAAAATTTATATAATATAAATTAT
1 AAATA--TATTAAAATTTATATAATATAAATTAT
*
449962 TAATATATTAAAATTTATATAAATATAAA
1 AAATATATTAAAATTTATAT-AATATAAA
449991 ATATTTTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
31 5 0.09
32 14 0.26
33 21 0.39
34 14 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (32 bp):
AAATATATTAAAATTTATATAATATAAATTAT
Found at i:449991 original size:17 final size:17
Alignment explanation
Indices: 449938--449992 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
449928 AAATATGTTT
449938 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
449954 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
449969 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
449987 TAAAAT
1 TAAAAT
449993 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:458552 original size:23 final size:21
Alignment explanation
Indices: 458526--458570 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
458516 ATGATCAAAG
458526 TTTATTTAAATATAAATTAAAAA
1 TTTATTTAAATAT-AA-TAAAAA
458549 TTTATTTAAATATAATAAAAA
1 TTTATTTAAATATAATAAAAA
458570 T
1 T
458571 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
23 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTATTTAAATATAATAAAAA
Found at i:461704 original size:10 final size:10
Alignment explanation
Indices: 461682--461715 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
461672 AATTATTAAA
461682 TTAAATA-TT
1 TTAAATATTT
461691 TTAAATATTT
1 TTAAATATTT
*
461701 TTAAAAATTT
1 TTAAATATTT
461711 TTAAA
1 TTAAA
461716 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTAAATATTT
Found at i:462508 original size:15 final size:17
Alignment explanation
Indices: 462488--462526 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
462478 TATGAAATAA
462488 AAAATTT-ATTT-ATTT
1 AAAATTTGATTTGATTT
462503 AAAATTTGATTTGATTT
1 AAAATTTGATTTGATTT
462520 AATAATT
1 AA-AATT
462527 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 6 0.29
18 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
AAAATTTGATTTGATTT
Found at i:462514 original size:40 final size:42
Alignment explanation
Indices: 462470--462547 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
462460 TATTTGAATA
462470 GATTT-ATTT-ATGAAATAAAAAATT-TATTTATTTAAAATTT
1 GATTTGATTTAAT-AAATAAAAAATTATATTTATTTAAAATTT
* *
462510 GATTTGATTTAATAATTAAAAAATTATTTTTATTTAAA
1 GATTTGATTTAATAAATAAAAAATTATATTTATTTAAA
462548 TATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 5 0.15
41 15 0.45
42 13 0.39
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (42 bp):
GATTTGATTTAATAAATAAAAAATTATATTTATTTAAAATTT
Found at i:462566 original size:16 final size:16
Alignment explanation
Indices: 462530--462563 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
462520 AATAATTAAA
462530 AAAT-TATTTTTATTT
1 AAATATATTTTTATTT
462545 AAATATATTTTTATATT
1 AAATATATTTTTAT-TT
462562 AA
1 AA
462564 TATGTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATATATTTTTATTT
Found at i:463496 original size:15 final size:15
Alignment explanation
Indices: 463469--463502 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
463459 AATTTATATT
*
463469 AATT-ATTTTATTTA
1 AATTAATTTGATTTA
463483 AATTAATTTGATTTA
1 AATTAATTTGATTTA
463498 AATTA
1 AATTA
463503 TTATTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
AATTAATTTGATTTA
Found at i:463578 original size:19 final size:21
Alignment explanation
Indices: 463527--463579 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
463517 ATTTTTTATT
463527 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
463548 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
463568 -ATATTTTAATAT
1 TAAATTTTAATAT
463580 TCTTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:467246 original size:21 final size:20
Alignment explanation
Indices: 467221--467304 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 20
467211 AGGTATAGGG
* *
467221 ATTATTAAAATCATGTTAAA
1 ATTATCAAAATCATATTAAA
467241 TATTATCAAAA-CTATATTAAAA
1 -ATTATCAAAATC-ATATT-AAA
* * *
467263 ATTAACAAAATTATTTTAAA
1 ATTATCAAAATCATATTAAA
* *
467283 ATATATTAAAATTATATTAAA
1 AT-TATCAAAATCATATTAAA
467304 A
1 A
467305 GCAATCAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 6 0.12
21 42 0.82
22 3 0.06
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (20 bp):
ATTATCAAAATCATATTAAA
Found at i:467298 original size:11 final size:11
Alignment explanation
Indices: 467248--467304 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
467238 AAATATTATC
*
467248 AAAACTATATT
1 AAAATTATATT
*
467259 AAAAATTA-A-C
1 -AAAATTATATT
*
467269 AAAATTATTTT
1 AAAATTATATT
467280 AAAA-TATATT
1 AAAATTATATT
467290 AAAATTATATT
1 AAAATTATATT
467301 AAAA
1 AAAA
467305 GCAATCAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 7 0.19
10 9 0.24
11 15 0.41
12 6 0.16
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAATTATATT
Found at i:467314 original size:21 final size:20
Alignment explanation
Indices: 467245--467320 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
467235 GTTAAATATT
*
467245 ATCAAAACTATATTAAAAATTA
1 ATCAAAATTATATT-AAAA-TA
*
467267 A-CAAAATTATTTTAAAATA
1 ATCAAAATTATATTAAAATA
* *
467286 TATTAAAATTATATTAAAAGCA
1 -ATCAAAATTATATTAAAA-TA
467308 ATCAAAATTATAT
1 ATCAAAATTATAT
467321 CATACGCTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 36 0.80
22 2 0.04
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATCAAAATTATATTAAAATA
Found at i:467372 original size:21 final size:20
Alignment explanation
Indices: 467348--467396 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
467338 ATCATGCGGT
*
467348 AAATTATTAAATTCATATCTA
1 AAATTATTAAAATCATAT-TA
*
467369 AAATTACTAAAATCATATTA
1 AAATTATTAAAATCATATTA
467389 AAAGTTAT
1 AAA-TTAT
467397 ATTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATTATTAAAATCATATTA
Found at i:469661 original size:2 final size:2
Alignment explanation
Indices: 469654--469689 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
469644 AACTATTGTC
469654 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
469690 TTGTTTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:475122 original size:30 final size:31
Alignment explanation
Indices: 475061--475137 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
475051 ATTAAAGTTA
**
475061 AAATTTAATAAAATACTTATTATAATAATTT
1 AAATTTAATAAAATAAATATTATAATAATTT
*
475092 -AATTTAATAAAATAAAATATTATGAT-ATTT
1 AAATTTAATAAAAT-AAATATTATAATAATTT
475122 AAATATTTAATAAAAT
1 -AA-ATTTAATAAAAT
475138 TTTTTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
30 17 0.44
31 9 0.23
32 1 0.03
33 12 0.31
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATTTAATAAAATAAATATTATAATAATTT
Found at i:475143 original size:21 final size:21
Alignment explanation
Indices: 475119--475177 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
475109 TATTATGATA
475119 TTTAAATATTTAATAA-AATTT
1 TTTAAATATTTAA-AATAATTT
* *
475140 TTTAATTTTTTAAAATAATTT
1 TTTAAATATTTAAAATAATTT
* *
475161 TGTATTATATTTAAAAT
1 TTTA-AATATTTAAAAT
475178 CAAAAACTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.07
21 19 0.63
22 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAAATATTTAAAATAATTT
Found at i:476185 original size:11 final size:11
Alignment explanation
Indices: 476165--476195 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
476155 TTTATATCAT
476165 ATTATATTTTA
1 ATTATATTTTA
*
476176 ATTATTTTTTA
1 ATTATATTTTA
476187 ATTATATTT
1 ATTATATTT
476196 ATGTTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATATTTTA
Found at i:477859 original size:31 final size:32
Alignment explanation
Indices: 477798--477859 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
477788 TATCTGTAAA
*
477798 GTTTATAAAGATAAATAATTTTTGAAATGAAG
1 GTTTATAAAGATAAATAATTTTTCAAATGAAG
* *
477830 GTTTATCAAGTTAAA-AA-TTTTCAAGATGAA
1 GTTTATAAAGATAAATAATTTTTCAA-ATGAA
477860 AGACGTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 6 0.23
31 7 0.27
32 13 0.50
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (32 bp):
GTTTATAAAGATAAATAATTTTTCAAATGAAG
Found at i:481412 original size:18 final size:18
Alignment explanation
Indices: 481391--481426 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
481381 CTATGGAGTT
481391 TTCTTATACTACTAAAAA
1 TTCTTATACTACTAAAAA
481409 TTCTTATACTACTAAAAA
1 TTCTTATACTACTAAAAA
481427 AATATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
TTCTTATACTACTAAAAA
Found at i:482878 original size:21 final size:21
Alignment explanation
Indices: 482852--482894 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
482842 TTTCAGTGGC
482852 AGTACTTCAATGGCGTTGTTG
1 AGTACTTCAATGGCGTTGTTG
*
482873 AGTACTTCATTGGCGTTGTTG
1 AGTACTTCAATGGCGTTGTTG
482894 A
1 A
482895 AATCTATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.40
Consensus pattern (21 bp):
AGTACTTCAATGGCGTTGTTG
Found at i:483444 original size:11 final size:11
Alignment explanation
Indices: 483428--483481 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
483418 TTATTATTTA
*
483428 ATTTAATTGTT
1 ATTTAATTATT
483439 ATTTAAATTATT
1 ATTT-AATTATT
*
483451 ATTTAAATATT
1 ATTTAATTATT
**
483462 -TTTAATTAAA
1 ATTTAATTATT
483472 ATTTAATTAT
1 ATTTAATTAT
483482 AAATTTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 7 0.20
11 18 0.51
12 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTAATTATT
Found at i:483487 original size:12 final size:13
Alignment explanation
Indices: 483461--483496 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
483451 ATTTAAATAT
483461 TTTTAATTA-AAA
1 TTTTAATTATAAA
483473 -TTTAATTATAAA
1 TTTTAATTATAAA
483485 TTTTAA-TATAAA
1 TTTTAATTATAAA
483497 AATAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.36
12 9 0.41
13 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAATTATAAA
Found at i:484484 original size:21 final size:21
Alignment explanation
Indices: 484459--484500 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
484449 AATCTGAATG
484459 AAAA-TAATTTTAAATATTAAA
1 AAAATTAATTTT-AATATTAAA
*
484480 AAAATTACTTTTAATATTAAA
1 AAAATTAATTTTAATATTAAA
484501 TAAGTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTAATTTTAATATTAAA
Found at i:485987 original size:2 final size:2
Alignment explanation
Indices: 485982--486006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
485972 AAAAAAAAAA
485982 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
486007 CACATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:489502 original size:15 final size:16
Alignment explanation
Indices: 489464--489518 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
489454 ATAAGTAATT
489464 TTATATATTTTTTATA
1 TTATATATTTTTTATA
*
489480 TTTTTATATTTTTT-TA
1 -TTATATATTTTTTATA
489496 TTATATAATTTTTTATA
1 TTATAT-ATTTTTTATA
489513 TTATAT
1 TTATAT
489519 TTTAATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 5 0.15
16 9 0.26
17 20 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATATTTTTTATA
Found at i:489529 original size:23 final size:23
Alignment explanation
Indices: 489467--489538 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
489457 AGTAATTTTA
489467 TATATTTT--TTATATTTTTATAT
1 TATATTTTAATTAT-TTTTTATAT
* * *
489489 TTTTTTATTATATAATTTTTTATAT
1 TATATT-TTA-ATTATTTTTTATAT
489514 TATATTTTAATTATTTTTTATAT
1 TATATTTTAATTATTTTTTATAT
489537 TA
1 TA
489539 GATAATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
22 4 0.10
23 17 0.43
24 3 0.08
25 13 0.32
26 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TATATTTTAATTATTTTTTATAT
Found at i:489544 original size:20 final size:19
Alignment explanation
Indices: 489469--489560 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 19
489459 TAATTTTATA
* *
489469 TATTTTTTATATT-TTTA-
1 TATTTTTTATATTAATAAT
489486 TATTTTTT-TATTATATAAT
1 TATTTTTTATATTA-ATAAT
* *
489505 TTTTTATATTATATT-TTAAT
1 TATTT-T-TTATATTAATAAT
489525 TATTTTTTATATTAGATAAT
1 TATTTTTTATATTA-ATAAT
* *
489545 TATATTATA-ATTAATA
1 TATTTTTTATATTAATA
489561 TAAGTTGATA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.07
17 8 0.14
18 12 0.20
19 9 0.15
20 20 0.34
21 2 0.03
22 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (19 bp):
TATTTTTTATATTAATAAT
Found at i:489551 original size:25 final size:24
Alignment explanation
Indices: 489494--489552 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
489484 TATATTTTTT
* *
489494 TATTATATAATTTTTTATATTATA
1 TATTATATTATTTTTTATATTAGA
*
489518 TTTTA-ATTATTTTTTATATTAGA
1 TATTATATTATTTTTTATATTAGA
489541 TAATTATATTAT
1 T-ATTATATTAT
489553 AATTAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 17 0.59
24 7 0.24
25 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTATATTATTTTTTATATTAGA
Found at i:489605 original size:7 final size:7
Alignment explanation
Indices: 489593--489627 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
489583 TAAATTTAAT
489593 TATTTTA
1 TATTTTA
489600 TATTTTA
1 TATTTTA
489607 TATTTTTA
1 TA-TTTTA
489615 TATTTT-
1 TATTTTA
489621 TATTTTA
1 TATTTTA
489628 ATTAATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:489613 original size:8 final size:8
Alignment explanation
Indices: 489595--489623 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
489585 AATTTAATTA
489595 TTTTATA-
1 TTTTATAT
489602 TTTTATAT
1 TTTTATAT
489610 TTTTATAT
1 TTTTATAT
489618 TTTTAT
1 TTTTAT
489624 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATAT
Found at i:489613 original size:15 final size:14
Alignment explanation
Indices: 489595--489626 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
489585 AATTTAATTA
489595 TTTTATATTTTATAT
1 TTTTATATTTT-TAT
489610 TTTTATATTTTTAT
1 TTTTATATTTTTAT
489624 TTT
1 TTT
489627 AATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATATTTTTAT
Found at i:489806 original size:22 final size:22
Alignment explanation
Indices: 489778--489820 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
489768 GATTGATTTG
489778 TTTTTTTTA-TTATATTTTTTA
1 TTTTTTTTATTTATATTTTTTA
*
489799 TTTTTTTTATTTTTATTTTTTA
1 TTTTTTTTATTTATATTTTTTA
489821 AAAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTTATTTATATTTTTTA
Found at i:500102 original size:22 final size:21
Alignment explanation
Indices: 500061--500102 Score: 50
Period size: 22 Copynumber: 1.9 Consensus size: 21
500051 TCAAACATCC
500061 ATAATAATTTAAAACTTTAATA
1 ATAATAATTTAAAAC-TTAATA
500083 ATAATAAATTTTAAAA-TTAA
1 ATAAT-AA-TTTAAAACTTAA
500103 AAAAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
22 9 0.50
23 2 0.11
24 7 0.39
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAATTTAAAACTTAATA
Found at i:506491 original size:6 final size:6
Alignment explanation
Indices: 506479--506514 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
506469 ACTTGGACTT
*
506479 GGGTGA GGATGA -GGTGA GGGTGA GGGTGA GGGTGA G
1 GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA G
506515 AGCGACCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.19, C:0.00, G:0.64, T:0.17
Consensus pattern (6 bp):
GGGTGA
Found at i:506494 original size:11 final size:11
Alignment explanation
Indices: 506480--506514 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
506470 CTTGGACTTG
*
506480 GGTGAGGATGA
1 GGTGAGGGTGA
506491 GGTGAGGGTGA
1 GGTGAGGGTGA
506502 GGGTGAGGGTGA
1 -GGTGAGGGTGA
506514 G
1 G
506515 AGCGACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.20, C:0.00, G:0.63, T:0.17
Consensus pattern (11 bp):
GGTGAGGGTGA
Found at i:506501 original size:17 final size:18
Alignment explanation
Indices: 506479--506514 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
506469 ACTTGGACTT
506479 GGGTGAGGATGA-GGTGA
1 GGGTGAGGATGAGGGTGA
*
506496 GGGTGAGGGTGAGGGTGA
1 GGGTGAGGATGAGGGTGA
506514 G
1 G
506515 AGCGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.64, T:0.17
Consensus pattern (18 bp):
GGGTGAGGATGAGGGTGA
Found at i:508091 original size:43 final size:43
Alignment explanation
Indices: 508027--508111 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
508017 ATGAACGACT
*
508027 ATGCAGGATGCGAAATTCCTATGGTTTGCTAGAATCTACTATC
1 ATGCAGGATGCGAAATCCCTATGGTTTGCTAGAATCTACTATC
*
508070 ATGCAGGATGCGTAATCCCTATGGTTTGCTAGAATCTACTAT
1 ATGCAGGATGCGAAATCCCTATGGTTTGCTAGAATCTACTAT
508112 GTGCTGGGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (43 bp):
ATGCAGGATGCGAAATCCCTATGGTTTGCTAGAATCTACTATC
Found at i:512535 original size:24 final size:23
Alignment explanation
Indices: 512489--512535 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
512479 ATTTTTTATT
*
512489 TATTTATAAAATATAAAAATTTA
1 TATTTATAAAAAATAAAAATTTA
* *
512512 TATTTATGAAAAAATTAAACTTTA
1 TATTTAT-AAAAAATAAAAATTTA
512536 CTTTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TATTTATAAAAAATAAAAATTTA
Found at i:513036 original size:28 final size:27
Alignment explanation
Indices: 512983--513047 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
512973 TGAATAACAA
512983 TTAAAAA-T-TATTTAATTATTATTTT
1 TTAAAAATTATATTTAATTATTATTTT
513008 TTAAAAAATTATATTTAATATATTA-TTT
1 TT-AAAAATTATATTTAAT-TATTATTTT
*
513036 TTAATAATTATA
1 TTAAAAATTATA
513048 ATTTTTATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 2 0.06
26 5 0.14
27 10 0.29
28 13 0.37
29 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAAAAATTATATTTAATTATTATTTT
Found at i:513040 original size:14 final size:14
Alignment explanation
Indices: 512993--513046 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
512983 TTAAAAATTA
512993 TTTAAT-TATTATTT
1 TTTAATATATTA-TT
* * *
513007 TTTAAAAAATTATA
1 TTTAATATATTATT
513021 TTTAATATATTATT
1 TTTAATATATTATT
513035 TTTAATA-ATTAT
1 TTTAATATATTAT
513047 AATTTTTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 5 0.15
14 24 0.73
15 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATATATTATT
Found at i:514801 original size:2 final size:2
Alignment explanation
Indices: 514796--514822 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
514786 TTATCAAGGT
514796 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
514823 GGGGGAAGGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:515068 original size:10 final size:11
Alignment explanation
Indices: 515053--515080 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
515043 TTTTTTTCCC
515053 CTTTTTTCTTT
1 CTTTTTTCTTT
515064 CTTTTTTCTTT
1 CTTTTTTCTTT
515075 CTTTTT
1 CTTTTT
515081 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:515798 original size:25 final size:26
Alignment explanation
Indices: 515752--515800 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
515742 TAATATTTAA
*
515752 AAAATAAAATTATTTAAATTTTATAT
1 AAAATAAAATTATTAAAATTTTATAT
*
515778 AAAATAATATT-TTAAAATTTTAT
1 AAAATAAAATTATTAAAATTTTAT
515801 TTTATAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATAAAATTATTAAAATTTTATAT
Found at i:517691 original size:23 final size:23
Alignment explanation
Indices: 517648--517693 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
517638 AAAAGTTGAT
**
517648 AAATAATTTTAATTATTTTTAAA
1 AAATAATTTTAATTAAATTTAAA
517671 AAATAATATTTAA-TAAATTTAAA
1 AAATAAT-TTTAATTAAATTTAAA
517694 TTTTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATAATTTTAATTAAATTTAAA
Found at i:520381 original size:22 final size:22
Alignment explanation
Indices: 520343--520386 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
520333 ATGACACATG
* *
520343 AAATATAATTATCAAATGAAAT
1 AAATATAATCATCAAATAAAAT
520365 AAATATAAATCAT-AAATAAAAT
1 AAATAT-AATCATCAAATAAAAT
520387 TATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATATAATCATCAAATAAAAT
Found at i:521043 original size:14 final size:14
Alignment explanation
Indices: 521024--521079 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
521014 TAATAAAAAT
521024 TATTTTTATATTAA
1 TATTTTTATATTAA
521038 TATTTTTATATCTAA
1 TATTTTTATAT-TAA
** **
521053 -ATTTAAATAAAAA
1 TATTTTTATATTAA
521066 TATTTTT-TATTAA
1 TATTTTTATATTAA
521079 T
1 T
521080 TAATAATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
13 7 0.22
14 22 0.69
15 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTTTTATATTAA
Found at i:522066 original size:2 final size:2
Alignment explanation
Indices: 522054--522097 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
522044 AATAAATTAA
*
522054 AT AT TT 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
522096 AT
1 AT
522098 GTATGTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:523622 original size:2 final size:2
Alignment explanation
Indices: 523615--523660 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
523605 GACACTTTAA
523615 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
523657 CT CT
1 CT CT
523661 GTGTCTGGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:527527 original size:3 final size:3
Alignment explanation
Indices: 527519--527552 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
527509 CCTGATTAGC
527519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
527553 AAATAAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:530212 original size:7 final size:7
Alignment explanation
Indices: 530200--530225 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
530190 ACAAAAGCTG
530200 GAAAGGT
1 GAAAGGT
530207 GAAAGGT
1 GAAAGGT
530214 GAAAGGT
1 GAAAGGT
530221 GAAAG
1 GAAAG
530226 CAACGGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (7 bp):
GAAAGGT
Found at i:533075 original size:2 final size:2
Alignment explanation
Indices: 533068--533096 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
533058 AAGCAAGGCA
533068 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
533097 AAAGATTGAA
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:534899 original size:23 final size:25
Alignment explanation
Indices: 534854--534905 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
534844 TATTTGATTA
*
534854 AAATTATAAATATATGATCATTTTT
1 AAATTATAAATATATGATAATTTTT
*
534879 AAATTA-AAATATAT-TTAATTTTT
1 AAATTATAAATATATGATAATTTTT
534902 AAAT
1 AAAT
534906 AATATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 8 0.32
25 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AAATTATAAATATATGATAATTTTT
Found at i:535275 original size:16 final size:16
Alignment explanation
Indices: 535254--535284 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
535244 TATAATTTAA
*
535254 ATAAATTTATTTAAAT
1 ATAAATTTAATTAAAT
535270 ATAAATTTAATTAAA
1 ATAAATTTAATTAAA
535285 ATTTTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATTTAATTAAAT
Found at i:535295 original size:26 final size:26
Alignment explanation
Indices: 535247--535297 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
535237 TTTAATTTAT
*
535247 AATTTAAATAAATTTATTTAAATATA
1 AATTTAAATAAATTTATTAAAATATA
*
535273 AATTTAATTAAAATTT-TTAAAATAT
1 AATTTAAAT-AAATTTATTAAAATAT
535298 TTTAAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTTAAATAAATTTATTAAAATATA
Found at i:536576 original size:12 final size:13
Alignment explanation
Indices: 536549--536578 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
536539 TAATTATAAA
536549 AATATAAAATATT
1 AATATAAAATATT
536562 AATATAAAA-ATT
1 AATATAAAATATT
536574 AATAT
1 AATAT
536579 TTTAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAAAATATT
Found at i:536583 original size:20 final size:21
Alignment explanation
Indices: 536543--536585 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
536533 TAAATGTAAT
536543 TATAAAAATATAAAATATTAA
1 TATAAAAATATAAAATATTAA
* *
536564 TATAAAAAT-TAATATTTTAA
1 TATAAAAATATAAAATATTAA
536584 TA
1 TA
536586 ATTTTAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAAATATAAAATATTAA
Found at i:537248 original size:22 final size:20
Alignment explanation
Indices: 537205--537249 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
537195 TTTTGATTAG
* *
537205 TTTTTAAAAAATTAGTATTT
1 TTTTTAAAAAAATAGTAATT
537225 TTTTTCAAAAAAATAGATAATT
1 TTTTT-AAAAAAATAG-TAATT
537247 TTT
1 TTT
537250 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAAAATAGTAATT
Found at i:538381 original size:15 final size:15
Alignment explanation
Indices: 538357--538431 Score: 100
Period size: 16 Copynumber: 4.9 Consensus size: 15
538347 AAGGTTTTAA
538357 AAAAATATAAAATTTT
1 AAAAA-ATAAAATTTT
538373 AAAAAAT-AAATTTT
1 AAAAAATAAAATTTT
538387 AAAAATATAAAATTTT
1 AAAAA-ATAAAATTTT
*
538403 AAAAAAT-AAATTTG
1 AAAAAATAAAATTTT
538417 AAAGAAATAAAATTT
1 AAA-AAATAAAATTT
538432 ATTTAAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
14 21 0.39
15 10 0.19
16 23 0.43
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAAAATAAAATTTT
Found at i:538393 original size:30 final size:30
Alignment explanation
Indices: 538357--538431 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
538347 AAGGTTTTAA
*
538357 AAAAATATAAAATTTTAAAAAATAAATTTT
1 AAAAATATAAAATTTTAAAAAATAAATTTG
538387 AAAAATATAAAATTTTAAAAAATAAATTTG
1 AAAAATATAAAATTTTAAAAAATAAATTTG
538417 AAAGAA-ATAAAATTT
1 AAA-AATATAAAATTT
538432 ATTTAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 41 0.95
31 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAATATAAAATTTTAAAAAATAAATTTG
Found at i:541053 original size:21 final size:21
Alignment explanation
Indices: 541035--541074 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
541025 ATATTATATT
*
541035 TATATTAATTTTAAATATAAA
1 TATAATAATTTTAAATATAAA
*
541056 TATAATAATATTAAATATA
1 TATAATAATTTTAAATATA
541075 CGGTGTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATAATTTTAAATATAAA
Found at i:542882 original size:21 final size:20
Alignment explanation
Indices: 542856--542895 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
542846 TTAAATTAAA
542856 TAATATCATTTGATTAAAAAG
1 TAATATCATTT-ATTAAAAAG
* *
542877 TAATATTATTTTTTAAAAA
1 TAATATCATTTATTAAAAA
542896 TATATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TAATATCATTTATTAAAAAG
Found at i:543359 original size:18 final size:17
Alignment explanation
Indices: 543338--543390 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
543328 CAATTCAATA
543338 TTAATCTAAAAAATAAAT
1 TTAAT-TAAAAAATAAAT
* *
543356 TTAAATAAAAAATAAAA
1 TTAATTAAAAAATAAAT
*
543373 TCAATTAAAAAAATAAAT
1 TTAATT-AAAAAATAAAT
543391 CTAACCTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAATTAAAAAATAAAT
Found at i:543390 original size:22 final size:22
Alignment explanation
Indices: 543347--543390 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
543337 ATTAATCTAA
*
543347 AAAATAAATTTAAATAAAAAAT
1 AAAATAAATTTAAAAAAAAAAT
*
543369 AAAATCAA-TTAAAAAAATAAAT
1 AAAATAAATTTAAAAAAA-AAAT
543391 CTAACCTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATAAATTTAAAAAAAAAAT
Found at i:543715 original size:2 final size:2
Alignment explanation
Indices: 543708--543741 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
543698 ACATACATAC
543708 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
543742 CATTATCTGC
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):
AT
Found at i:544072 original size:4 final size:4
Alignment explanation
Indices: 544063--544098 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
544053 TACCAATGCG
*
544063 AGAA AGAA AGAA ACAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
544099 TGTATCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:545418 original size:15 final size:17
Alignment explanation
Indices: 545389--545423 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
545379 AATAATATTA
545389 ATTTATTTAATAAAAAT
1 ATTTATTTAATAAAAAT
545406 ATTT-TTTAA-AAAAAT
1 ATTTATTTAATAAAAAT
545421 ATT
1 ATT
545424 AACAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTATTTAATAAAAAT
Found at i:548495 original size:20 final size:19
Alignment explanation
Indices: 548443--548496 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
548433 ATTATTTATT
548443 ATATTT-AATTT-TTTTTA
1 ATATTTAAATTTCTTTTTA
* **
548460 ATATTAAAATCACTTTTTAA
1 ATATTTAAATTTCTTTTT-A
548480 ATATTTAAATTTCTTTT
1 ATATTTAAATTTCTTTT
548497 ATATAAATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 5 0.18
18 3 0.11
19 5 0.18
20 15 0.54
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTAAATTTCTTTTTA
Found at i:558513 original size:27 final size:27
Alignment explanation
Indices: 558482--558537 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
558472 ATCTTGCCAT
*
558482 TTCTAAAATGAATCATATAATTTTTAG
1 TTCTAAAATGAATCATATAATTTCTAG
*
558509 TTCTAAGATGAATCATATAATTTCTAG
1 TTCTAAAATGAATCATATAATTTCTAG
558536 TT
1 TT
558538 GATTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (27 bp):
TTCTAAAATGAATCATATAATTTCTAG
Found at i:558648 original size:30 final size:31
Alignment explanation
Indices: 558614--558674 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
558604 TTGCTAATTT
*
558614 TAAAATGAATCACA-TAATTTTTAGTTCTAA
1 TAAAATGAATCACATTAATATTTAGTTCTAA
* *
558644 TAAAATGAATTATATTAATATTTAGTTCTAA
1 TAAAATGAATCACATTAATATTTAGTTCTAA
558675 GATAAATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
TAAAATGAATCACATTAATATTTAGTTCTAA
Found at i:561268 original size:17 final size:18
Alignment explanation
Indices: 561246--561285 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
561236 ATTTTGACCA
561246 TTTAATTTTAA-AAAATT
1 TTTAATTTTAATAAAATT
561263 TTTAA-TTTAATAAAATT
1 TTTAATTTTAATAAAATT
*
561280 ATTAAT
1 TTTAAT
561286 ATTTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATTTTAATAAAATT
Found at i:562100 original size:20 final size:18
Alignment explanation
Indices: 562077--562115 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
562067 TATTATATTT
562077 AATATTAAAATATTTTTTAA
1 AATATT-AAAT-TTTTTTAA
*
562097 AATATTTAATTTTTTTAA
1 AATATTAAATTTTTTTAA
562115 A
1 A
562116 TAAATGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTAAATTTTTTTAA
Found at i:571639 original size:3 final size:3
Alignment explanation
Indices: 571631--571664 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
571621 AGTAGGTGGT
571631 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
571665 TGGAGGAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:574070 original size:18 final size:19
Alignment explanation
Indices: 574039--574074 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
574029 TGAAATATTA
*
574039 AAAAATTATTTTAAAAAAT
1 AAAAATTATATTAAAAAAT
574058 AAAAA-TATATTAAAAAA
1 AAAAATTATATTAAAAAA
574075 ATAATTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTATATTAAAAAAT
Found at i:574845 original size:28 final size:27
Alignment explanation
Indices: 574814--574894 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
574804 CTTTTATTTG
574814 AAATGACAATTTATTTAAATACAT-ATAA
1 AAATGACAATTTATTTAAA-A-ATAATAA
* *
574842 AAATAATAATTTATTTAAAAATAATAA
1 AAATGACAATTTATTTAAAAATAATAA
*
574869 AAATGTAACAATTTATATAAAAATAA
1 AAATG--ACAATTTATTTAAAAATAA
574895 AATAATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.04
27 9 0.20
28 17 0.38
29 17 0.38
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
AAATGACAATTTATTTAAAAATAATAA
Found at i:574889 original size:29 final size:27
Alignment explanation
Indices: 574814--574894 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 27
574804 CTTTTATTTG
*
574814 AAATGACAATTTATTTAAATACAT-ATAA
1 AAATAACAATTTATTTAAA-A-ATAATAA
*
574842 AAATAATAATTTATTTAAAAATAATAA
1 AAATAACAATTTATTTAAAAATAATAA
*
574869 AAATGTAACAATTTATATAAAAATAA
1 AAA--TAACAATTTATTTAAAAATAA
574895 AATAATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.04
27 8 0.17
28 17 0.37
29 19 0.41
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
AAATAACAATTTATTTAAAAATAATAA
Found at i:577773 original size:20 final size:19
Alignment explanation
Indices: 577748--577786 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
577738 AATTACATCG
*
577748 TAAAATATGATAAAAATATT
1 TAAAATATAAT-AAAATATT
577768 TAAAATATAATAAAATATT
1 TAAAATATAATAAAATATT
577787 ATAGAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TAAAATATAATAAAATATT
Done.