Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 115 of 135
Found at i:42202251 original size:438 final size:437
Alignment explanation
Indices: 42201406--42202752 Score: 1849
Period size: 438 Copynumber: 3.1 Consensus size: 437
42201396 ATATATATGA
* * * *
42201406 TTGTACTAGGTGCCGGCCATTGACAGGTCAACACCCAAAAAATTTTTTTTTATTTTTTTCGTATA
1 TTGTACTGGGTGCCGGCCATTGACAGGCCAACACCC-AAAAATTTTTTTTAATTTTTCTCGTATA
* * *
42201471 TTTATATCTGACTCTGACAC-GAAAAAA-AAAATTTTTTTTAAAATTTGTACTGAGTGCCGGCCA
65 TTTATATCTGATTCTGACACAAAAAAAAGAAAATTTTTTTT-AAATTTGTACTGGGTGCCGGCCA
* * * * **
42201534 TTGA-AGGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATATTTATATCTGACCCTGA--CAA
129 TTGACAGGCCAGCACCTAAAATTTTTTTAAATTTTTTCGTATATTTATATCTGATTCTGACCCAA
42201596 AAAAAAAGAAATTTTTTTT-TTAAAAAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACC
194 AAAAAAAGAAATTTTTTTTATT--------TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACC
* * * * * *
42201660 CAAAAATTTTTTTTAAATTTTTTTCGTATATTTATATCTGACTCTGACATGAAAAAAAAAAGTAA
251 CAAAATTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCTGACACG-AAAAAAAAAGTAA
42201725 ATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAACTTTTTTTT
315 ATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAACTTTTTTTT
* * *
42201790 TAATTTTCCTTGTATATTTATATCTGATTCTGACACAAAAAAAAAGGATTTTTTTTATT
379 TTATTTTTCTCGTATATTTATATCTGATTCTGACACAAAAAAAAAGGATTTTTTTTATT
* *
42201849 TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTAAATTTTTCTCGTATAT
1 TTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAATTTTTTTTAATTTTTCTCGTATAT
****
42201914 TTATATCTGATTCTGACACAAAAAAAAGAAAAAAAATTTT-AATTTGTACTGGGTGCCGGCCATT
66 TTATATCTGATTCTGACACAAAAAAAAGAAAATTTTTTTTAAATTTGTACTGGGTGCCGGCCATT
*
42201978 GACAGGCCCGCACCTAAACATTTTTTTAAATTTTTTCGTATATTTATATCTGATTCTGACCCAAA
131 GACAGGCCAGCACCTAAA-ATTTTTTTAAATTTTTTCGTATATTTATATCTGATTCTGACCCAAA
42202043 AAAAAAGAAATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
195 AAAAAAGAAATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
*
42202108 TTTTTTACTTTTTCTCGTATATTTATATATGATTCTGACACGAAAAAAAAAGTAAATTTTTTTTT
260 TTTTTTACTTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGTAAATTTTTTTTT
* *
42202173 TAATTTGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAAAGCTTTTTTTTTTATTTTTCT
325 AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAA-CTTTTTTTTTTATTTTTCT
** *
42202238 CGTATATTTATATCTGATTCTGACA-TTAAAAAAAGAATTTTTTTTATT
389 CGTATATTTATATCTGATTCTGACACAAAAAAAAAGGATTTTTTTTATT
**
42202286 TTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAATTTTTTTTTTAATTTTTCTCGTATAT
1 TTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAATTTTTTTTAATTTTTCTCGTATAT
42202351 TTATATCTGATTCTGACACGAAAAAAAAG-AAATTTTTTTTAAATTTGTAC-GGGTGCCGGCCAT
66 TTATATCTGATTCTGACAC-AAAAAAAAGAAAATTTTTTTTAAATTTGTACTGGGTGCCGGCCAT
* * *
42202414 TGACAGGCCAGCACCTAAAAATTTTTTTTAAATTTTTTTCGTATATTTGTATCTGATTTTGACCG
130 TGACAGGCCAGCACCT-AAAA-TTTTTTTAAA-TTTTTTCGTATATTTATATCTGATTCTGACCC
42202479 AAAAAAAAA-AGAATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
192 AAAAAAAAAGA-AATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
42202543 TTTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCTGACACG--AAAAAAAG--AATTTT
256 -TTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGTAAATTTT
*
42202604 TTTTTAAAAATTTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCC-AAAA---------TT-T
320 TTTTT--AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAACTTTTTTTTTTAT
*
42202658 TTTT-TCGTATATTTATATCTTATTCT-A-ACAAAAAAAAAGGAAATTTTTTTT-TT
383 TTTTCTCGTATATTTATATCTGATTCTGACACAAAAAAAAAGG--ATTTTTTTTATT
* *
42202711 ACTGT--TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATT
1 -TTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAATT
42202753 AATTTTTTTT
Statistics
Matches: 824, Mismatches: 59, Indels: 61
0.87 0.06 0.06
Matches are distributed among these distances:
423 1 0.00
424 43 0.05
425 23 0.03
426 17 0.02
427 2 0.00
436 11 0.01
437 145 0.18
438 179 0.22
439 170 0.21
440 45 0.05
442 69 0.08
443 52 0.06
444 43 0.05
446 22 0.03
447 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (437 bp):
TTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAATTTTTTTTAATTTTTCTCGTATAT
TTATATCTGATTCTGACACAAAAAAAAGAAAATTTTTTTTAAATTTGTACTGGGTGCCGGCCATT
GACAGGCCAGCACCTAAAATTTTTTTAAATTTTTTCGTATATTTATATCTGATTCTGACCCAAAA
AAAAAGAAATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
TTTTTACTTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGTAAATTTTTTTTTA
AATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAACTTTTTTTTTTATTTTTCTCG
TATATTTATATCTGATTCTGACACAAAAAAAAAGGATTTTTTTTATT
Found at i:42202675 original size:100 final size:95
Alignment explanation
Indices: 42202556--42202749 Score: 248
Period size: 95 Copynumber: 2.0 Consensus size: 95
42202546 TTTTTTTTAC
* * *
42202556 TTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAA-G-AATTTTTTTTTAAAAATTTGT
1 TTTTTCTCGTATATTTATATCTGATTCTAACA-AAAAAAAAGGAAATTTTTTTTT---AA-CTGT
42202619 ACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
61 --TAGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * * *
42202656 TTTTTTTCGTATATTTATATCTTATTCTAACAAAAAAAAAGGAAATTTTTTTTTTACTGTTGGGT
1 TTTTTCTCGTATATTTATATCTGATTCTAACAAAAAAAAAGGAAATTTTTTTTTAACTGTTAGGT
42202721 GCCGGCCATTGACAGGCCAGCACCCAAAA
66 GCCGGCCATTGACAGGCCAGCACCCAAAA
42202750 ATTAATTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
95 33 0.39
97 3 0.04
98 1 0.01
99 7 0.08
100 30 0.35
101 11 0.13
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (95 bp):
TTTTTCTCGTATATTTATATCTGATTCTAACAAAAAAAAAGGAAATTTTTTTTTAACTGTTAGGT
GCCGGCCATTGACAGGCCAGCACCCAAAAT
Found at i:42202772 original size:438 final size:433
Alignment explanation
Indices: 42201447--42202752 Score: 1617
Period size: 439 Copynumber: 3.0 Consensus size: 433
42201437 CACCCAAAAA
* * *
42201447 ATTTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACG-AAAAAAA-AAATTTTTTTT
1 ATTTTTTTTAATTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTT
* * *
42201510 AAAATTTGTACTGAGTGCCGGCCATTGA-AGGCCAGCACC--CAAATTTTTTTT-TATTTTTTTC
66 -AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCTAAAAATTTTTTTTAAATTTTTTTC
**
42201571 GTATATTTATATCTGACCCTGA-CAAAAAAAAAGAAATTTTTTTT-TTAAAAAAAATTGTACTGG
130 GTATATTTATATCTGATTCTGACCAAAAAAAAAGAAATTTTTTTTATT--------TTGTACTGG
* * * *
42201634 GTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTAAATTTTTTTCGTATATTTATATCT
187 GTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTTTCTCGTATATTTATATCT
* *
42201699 GACTCTGACATGAAAAAAAAAAGTAAATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACA
252 GATTCTGACACG--AAAAAAAAG-AAATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACA
42201764 GGCCAGCACCCAAAAAACTTTTTTTTTAATTTTCCTTGTATATTTATATCTGATTCTGACACAAA
314 GGCCAGCACCC-AAAAA-----TTTTT--TTTT-C--GTATATTTATATCTGATTCT-A-ACAAA
42201829 AAAAAAGG-ATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTT
366 AAAAAAGGAATTTTTTTTATTTTGTA-TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTT
42201893 TTTT
430 TTTT
****
42201897 A--------AATTTTTCTCGTATATTTATATCTGATTCTGACAC-AAAAAAAAGAAAAAAAATTT
1 ATTTTTTTTAATTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAG-AAATTTTTTT
* *
42201953 T-AATTTGTACTGGGTGCCGGCCATTGACAGGCCCGCACCTAAACA-TTTTTTTAAA-TTTTTTC
65 TAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCTAAAAATTTTTTTTAAATTTTTTTC
42202015 GTATATTTATATCTGATTCTGACCCAAAAAAAAAGAAATTTTTTTTATTTTGTACTGGGTGCCGG
130 GTATATTTATATCTGATTCTGA-CCAAAAAAAAAGAAATTTTTTTTATTTTGTACTGGGTGCCGG
*
42202080 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTTTCTCGTATATTTATATATGATTCTG
194 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCTG
* *
42202145 ACACGAAAAAAAAAGTAAATTTTTTTTTTAATTTGTACTGGGTGCCGACCATTGACAGGCCAGCA
259 ACACG-AAAAAAAAG-AAATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA
* *
42202210 CCCAAAAAGCTTTTTTTTTTATTTTTCTCGTATATTTATATCTGATTCTGACATTAAAAAAA-GA
322 CCCAAAAA---------TTT-TTTTT-TCGTATATTTATATCTGATTCTAACA-AAAAAAAAGGA
*
42202274 ATTTTTTTTATTTTGTACTGGGTGCCGGCCATTGACAGGCCAACACCC--AAA-----TT
375 ATTTTTTTTATTTTGTA-TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
42202327 -TTTTTTTTAATTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTT
1 ATTTTTTTTAATTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTT
42202391 AAATTTGTAC-GGGTGCCGGCCATTGACAGGCCAGCACCTAAAAATTTTTTTTAAATTTTTTTCG
66 AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCTAAAAATTTTTTTTAAATTTTTTTCG
* *
42202455 TATATTTGTATCTGATTTTGACCGAAAAAAAAA-AGAATTTTTTTTATTTTGTACTGGGTGCCGG
131 TATATTTATATCTGATTCTGACC-AAAAAAAAAGA-AATTTTTTTTATTTTGTACTGGGTGCCGG
42202519 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCT
194 CCATTGACAGGCCAGCACCCAAAA-TTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCT
*
42202584 GACACG-AAAAAAAG-AATTTTTTTTTAAAAATTTGTACTAGGTGCCGGCCATTGACAGGCCAGC
258 GACACGAAAAAAAAGAAATTTTTTTTT--AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGC
*
42202647 ACCC-AAAA-TTTTTTTTCGTATATTTATATCTTATTCTAACAAAAAAAAAGGAAATTTTTTTT-
321 ACCCAAAAATTTTTTTTTCGTATATTTATATCTGATTCTAACAAAAAAAAAGG-AATTTTTTTTA
*
42202709 TTACTGT-TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATT
385 TT-TTGTATGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATT
42202753 AATTTTTTTT
Statistics
Matches: 770, Mismatches: 44, Indels: 106
0.84 0.05 0.12
Matches are distributed among these distances:
424 36 0.05
425 27 0.04
426 21 0.03
427 2 0.00
430 2 0.00
435 3 0.00
436 15 0.02
437 137 0.18
438 157 0.20
439 168 0.22
440 49 0.06
441 8 0.01
442 66 0.09
443 10 0.01
444 41 0.05
445 3 0.00
446 22 0.03
447 2 0.00
450 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (433 bp):
ATTTTTTTTAATTTTTCTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTT
AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCTAAAAATTTTTTTTAAATTTTTTTCG
TATATTTATATCTGATTCTGACCAAAAAAAAAGAAATTTTTTTTATTTTGTACTGGGTGCCGGCC
ATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTTTCTCGTATATTTATATCTGATTCTGAC
ACGAAAAAAAAGAAATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
AAAATTTTTTTTTCGTATATTTATATCTGATTCTAACAAAAAAAAAGGAATTTTTTTTATTTTGT
ATGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
Found at i:42204365 original size:3 final size:3
Alignment explanation
Indices: 42204357--42204416 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
42204347 GATTTAGTCC
42204357 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42204405 TAT TAT TAT TAT
1 TAT TAT TAT TAT
42204417 ATATAGGAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42206528 original size:3 final size:3
Alignment explanation
Indices: 42206520--42206589 Score: 106
Period size: 3 Copynumber: 23.3 Consensus size: 3
42206510 TTTAGTAATT
*
42206520 TTA TTA TTA TT- TTCT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
42206565 TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
42206590 ATTTCCATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42211452 original size:9 final size:9
Alignment explanation
Indices: 42211438--42211468 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
42211428 TGAGTCAAAC
42211438 AAAAAATGA
1 AAAAAATGA
42211447 AAAAAATG-
1 AAAAAATGA
42211455 AAAAAATGA
1 AAAAAATGA
42211464 AAAAA
1 AAAAA
42211469 TAAAAATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:42211458 original size:7 final size:8
Alignment explanation
Indices: 42211438--42211474 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
42211428 TGAGTCAAAC
42211438 AAAAAATG
1 AAAAAATG
42211446 AAAAAAATG
1 -AAAAAATG
42211455 AAAAAATG
1 AAAAAATG
42211463 AAAAAAT-
1 AAAAAATG
42211470 AAAAA
1 AAAAA
42211475 TGGAGAGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 5 0.18
8 15 0.54
9 8 0.29
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:42212960 original size:44 final size:43
Alignment explanation
Indices: 42212888--42213477 Score: 224
Period size: 44 Copynumber: 13.5 Consensus size: 43
42212878 AGAATTTCAG
*
42212888 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-A
* * * * * *
42212932 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAACCAAGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-GAAGCTAGA
* * * * * *
42212976 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCA-A
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGA
* * * * * ** * *
42213017 GTCTTATTTCTCTGAGATTACAGTGGAACAAACCGAAGAATTGCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CTAG-A
*
42213062 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-A
* * * * * *
42213107 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAACCAAGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-GAAGCTAGA
* * * * * *
42213151 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGA
* * * *
42213192 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAACTTCAG-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--C-T-AGA
* * * * * *
42213238 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGA
* * * ***
42213279 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAG-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--C-T-AGA
* * * * * *
42213325 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGA
* * * * ** *
42213366 GTCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAG-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG---CT-AGA
* *
42213412 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-A
*
42213456 ATCCTATCTCCCTGAGATTACA
1 ATCTTATCTCCCTGAGATTACA
42213478 NNNNNNNNNN
Statistics
Matches: 399, Mismatches: 115, Indels: 64
0.69 0.20 0.11
Matches are distributed among these distances:
41 109 0.27
42 11 0.03
43 7 0.02
44 137 0.34
45 16 0.04
46 119 0.30
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGA
Found at i:42213084 original size:87 final size:86
Alignment explanation
Indices: 42212839--42213434 Score: 593
Period size: 87 Copynumber: 6.8 Consensus size: 86
42212829 GTTCATTATA
* *
42212839 CAGGTCTTATTTCCCTGAGATTATAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTG-A
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAA-TTCAGATCTTATCTCTCTGAA
** * * *
42212903 GATTACAGCGGAGCAGATTGAAGC
65 G-TTACAGTAGAGTAGATCGCA-C
* * * * * * ** *
42212927 TAGTAATCCTATCTCCCTGA-AGTTACAGTGGAGCGGA-TTAA-AA-CCAAGGATCTTATCTCTC
1 CAG--GTCTTATTTCCCTGAGA-TTACAGTGGAACAGACCGAAGAATTC-A-GATCTTATCTCTC
42212988 TGAAGTTACAGTAGAGTAGATCGCAC
61 TGAAGTTACAGTAGAGTAGATCGCAC
* * * *
42213014 CAAGTCTTATTTCTCTGAGATTACAGTGGAACAAACCGAAGAATTGCAGATCTTATCTCCCTG-A
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATT-CAGATCTTATCTCTCTGAA
** * * *
42213078 GATTACAGCGGAGCAGATTGAAGC
65 G-TTACAGTAGAGTAGATCGCA-C
* * * * * * ** *
42213102 TAGTAATCCTATCTCCCTGA-AGTTACAGTGGAGCGGA-TTAA-AA-CCAAGGATCTTATCTCTC
1 CAG--GTCTTATTTCCCTGAGA-TTACAGTGGAACAGACCGAAGAATTC-A-GATCTTATCTCTC
42213163 TGAAGTTACAGTAGAGTAGATCGCAC
61 TGAAGTTACAGTAGAGTAGATCGCAC
*
42213189 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAACTTCAGATCTTATCTCTCTGAA
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAA-TTCAGATCTTATCTCTCTGAA
42213254 GTTACAGTAGAGTAGATCGCAC
65 GTTACAGTAGAGTAGATCGCAC
*
42213276 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAA
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAA-TTCAGATCTTATCTCTCTGAA
42213341 GTTACAGTAGAGTAGATCGCAC
65 GTTACAGTAGAGTAGATCGCAC
* *
42213363 CAGGTCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTG-A
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAA-TTCAGATCTTATCTCTCTGAA
42213427 GATTACAG
65 G-TTACAG
42213435 CGGAGCAGAT
Statistics
Matches: 417, Mismatches: 66, Indels: 51
0.78 0.12 0.10
Matches are distributed among these distances:
85 48 0.12
86 13 0.03
87 229 0.55
88 68 0.16
89 12 0.03
90 47 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (86 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTCAGATCTTATCTCTCTGAAG
TTACAGTAGAGTAGATCGCAC
Found at i:42213133 original size:175 final size:175
Alignment explanation
Indices: 42212839--42213470 Score: 954
Period size: 175 Copynumber: 3.6 Consensus size: 175
42212829 GTTCATTATA
*
42212839 CAGGTCTTATTTCCCTGAGATTATAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
42212904 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
42212969 ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
131 ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
* * * *
42213014 CAAGTCTTATTTCTCTGAGATTACAGTGGAACAAACCGAAGAATTGCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
42213079 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
42213144 ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
131 ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
* * *
42213189 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAACTTCAGATCTTATCTCTCTGA-
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
** * * * * * * * * * **
42213253 AGTTACAGTAGAGTAGATCGCA-CCAG--GTCTTATTTCCCTG-AGATTACAGTGGAACAGACCA
66 A-TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAG-TTACAGTGGAGCGGA-TT
42213314 AAGAACTTC-A-GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
128 AA-AAC--CAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
*
42213363 CAGGTCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
*
42213428 ATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGA
42213471 GATTACANNN
Statistics
Matches: 407, Mismatches: 39, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
171 2 0.00
172 24 0.06
173 2 0.00
174 121 0.30
175 246 0.60
176 1 0.00
177 11 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (175 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
Found at i:42213213 original size:41 final size:41
Alignment explanation
Indices: 42213168--42213389 Score: 169
Period size: 41 Copynumber: 5.2 Consensus size: 41
42213158 CTCTCTGAAG
42213168 TTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGA
1 TTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGA
* ** * * * * *
42213209 TTACAGTGGAACAGACTGAAGAACTTCAGATCTTATCTCTCTGA-A
1 TTACAGTAGAGTAGA-T--CGCAC--CAGGTCTTATTTCCCTGAGA
42213254 GTTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGA
1 -TTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGA
* ** * * * * *
42213296 TTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGA-A
1 TTACAGTAGAGTAGATC---GCAC--CAGGTCTTATTTCCCTGAGA
*
42213341 GTTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTAAGA
1 -TTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGA
42213383 TTACAGT
1 TTACAGT
42213390 GGAACAGACC
Statistics
Matches: 134, Mismatches: 33, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
41 61 0.46
42 3 0.02
43 6 0.04
44 6 0.04
45 3 0.02
46 55 0.41
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
TTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGA
Found at i:42214159 original size:44 final size:43
Alignment explanation
Indices: 42214111--42214425 Score: 139
Period size: 44 Copynumber: 7.2 Consensus size: 43
42214101 GACAAAAGAT
42214111 CTTGCCTTCCTGTATTGACAGCGAAGTAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGTAGGTCGAAGACACAAAC
* * ** * * *
42214155 CTTGCCTCCCTCGGT-TGTGA-TGGATCT-GGTTGAAGACAACAGAT
1 CTTGCCTTCCT--GTAT-TGACAGGAAGTAGGTCGAAGAC-ACAAAC
* * ** *
42214199 CTTGCCTTCTTGCATTGACAGTGAAACAGGTCGAAAACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGTAGGTCGAAGACACAAAC
* * * * *
42214243 CTTGCCTCTCTCGGT-TGTGA-TGG-AGCT-GGTTGAAGACAAAAGAT
1 CTTGCCT-TC-CTGTAT-TGACAGGAAG-TAGGTCGAAGACACAA-AC
* *
42214287 CTTGCCTTCCTGCATTGACAGCGAAGTAAGTCGAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGTAGGTCGAAGACACAAAC
* * * * *
42214331 CTTGCCACTCTCGGT-TGTGA-TGG-AGCT-GGTCGAAGACAAAAGAT
1 CTTGCC-TTC-CTGTAT-TGACAGGAAG-TAGGTCGAAGACACAA-AC
* * * *
42214375 CTTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACATAAAC
1 CTTGCCTTCCTGTATTGAC-AGGAAGTAGGTCGAAGACACAAAC
42214419 CTTGCCT
1 CTTGCCT
42214426 CTCTCGGTTG
Statistics
Matches: 193, Mismatches: 50, Indels: 56
0.65 0.17 0.19
Matches are distributed among these distances:
42 14 0.07
43 44 0.23
44 75 0.39
45 46 0.24
46 14 0.07
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (43 bp):
CTTGCCTTCCTGTATTGACAGGAAGTAGGTCGAAGACACAAAC
Found at i:42214216 original size:88 final size:88
Alignment explanation
Indices: 42214059--42214439 Score: 627
Period size: 88 Copynumber: 4.3 Consensus size: 88
42214049 NNNNNNNNNN
*
42214059 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGT
1 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGC
*
42214124 ATTGACAGCGAAGTAGGTCGAAG
66 ATTGACAGCGAAGCAGGTCGAAG
* * * *
42214147 ACACAAACCTTGCCTCCCTCGGTTGTGATGGATCTGGTTGAAGACAACAGATCTTGCCTTCTTGC
1 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGC
* * *
42214212 ATTGACAGTGAAACAGGTCGAAA
66 ATTGACAGCGAAGCAGGTCGAAG
42214235 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGC
1 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGC
* *
42214300 ATTGACAGCGAAGTAAGTCGAAG
66 ATTGACAGCGAAGCAGGTCGAAG
* *
42214323 ACACAAACCTTGCCACTCTCGGTTGTGATGGAGCTGGTCGAAGACAAAAGATCTTGCCTTCCTGC
1 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGC
*
42214388 ATTGACAACGAAGCAGGTCGAAG
66 ATTGACAGCGAAGCAGGTCGAAG
*
42214411 ACATAAACCTTGCCTCTCTCGGTTGTGAT
1 ACACAAACCTTGCCTCTCTCGGTTGTGAT
42214440 NNNNNNNNNN
Statistics
Matches: 268, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 268 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGC
ATTGACAGCGAAGCAGGTCGAAG
Found at i:42214713 original size:88 final size:88
Alignment explanation
Indices: 42214542--42214713 Score: 254
Period size: 88 Copynumber: 2.0 Consensus size: 88
42214532 NNNNNNNNNN
* * * * *
42214542 TGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGGTT
1 TGCATTGACAGCGAAACAGGTCAAAAACACAAACCTTACCTCCCTCGGTTGTGATGAAGCTGGTT
*
42214607 GAAGACAACAGATCTTGCCTTCT
66 GAAGACAACAGATATTGCCTTCT
* *
42214630 TGCATTGACAGCGAAACAGGTCAAAAACACAAACCTTACCTCTCTCGGTTGTGGTGAAGCTGGTT
1 TGCATTGACAGCGAAACAGGTCAAAAACACAAACCTTACCTCCCTCGGTTGTGATGAAGCTGGTT
**
42214695 GAAGACAGTAGATATTGCC
66 GAAGACAACAGATATTGCC
42214714 CTCCTGTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (88 bp):
TGCATTGACAGCGAAACAGGTCAAAAACACAAACCTTACCTCCCTCGGTTGTGATGAAGCTGGTT
GAAGACAACAGATATTGCCTTCT
Found at i:42214984 original size:96 final size:96
Alignment explanation
Indices: 42214744--42215025 Score: 476
Period size: 96 Copynumber: 2.9 Consensus size: 96
42214734 CAGATCAAAT
* * *
42214744 ATGGAAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCTTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
*
42214809 GTTGGCAGTGGAATGGATTGAA-AATCGAAG
66 GTTGGCAGTGGAATAGATTGAAGAATCGAAG
42214839 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
* *
42214904 GTTGTCAGCGGAATAGATTGAAGAATCGAAG
66 GTTGGCAGTGGAATAGATTGAAGAATCGAAG
* * *
42214935 ATGGCAGATTTTACCTTCCTGTGACTACAGTAGAGTACATTGAATCCGATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
42215000 GTTGGCAGTGGAATAGATTGAAGAAT
66 GTTGGCAGTGGAATAGATTGAAGAAT
42215026 TTCAGATCTT
Statistics
Matches: 175, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
95 81 0.46
96 94 0.54
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (96 bp):
ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
GTTGGCAGTGGAATAGATTGAAGAATCGAAG
Found at i:42215096 original size:44 final size:44
Alignment explanation
Indices: 42215035--42215190 Score: 147
Period size: 44 Copynumber: 3.5 Consensus size: 44
42215025 TTTCAGATCT
42215035 TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
* * * ** ** * *
42215079 TATCTCTCTGA-AGTTACAGTGAAGCGGATT-AAAATAAAG-GATCT
1 TATCTCCCTGAGA-TTACAGCGGAGTAGATTGAAGCT--AGTAATCC
*
42215123 TATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
* * *
42215167 TATCTCTCTGAAATTACAGTGGAG
1 TATCTCCCTGAGATTACAGCGGAG
42215191 CGGATTAAAA
Statistics
Matches: 83, Mismatches: 23, Indels: 12
0.70 0.19 0.10
Matches are distributed among these distances:
43 6 0.07
44 71 0.86
45 6 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
Found at i:42215140 original size:88 final size:88
Alignment explanation
Indices: 42215030--42215239 Score: 350
Period size: 88 Copynumber: 2.4 Consensus size: 88
42215020 AAGAATTTCA
* *
42215030 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAGTTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
42215095 CAGTGAAGCGGATTAAAATAAAG
66 CAGTGAAGCGGATTAAAATAAAG
42215118 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
*
42215183 CAGTGGAGCGGATTAAAATAAAG
66 CAGTGAAGCGGATTAAAATAAAG
* * *
42215206 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGTAGAT
42215240 CACATCAGAT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 2 0.02
88 113 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (88 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
CAGTGAAGCGGATTAAAATAAAG
Found at i:42215215 original size:44 final size:44
Alignment explanation
Indices: 42215079--42215230 Score: 148
Period size: 44 Copynumber: 3.5 Consensus size: 44
42215069 CTAGTAATCC
* *
42215079 TATCTCTCTGAAGTTACAGTGAAGCGGATTAAAATAAAGGATCT
1 TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
* * ** ** ** * *
42215123 TATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCT--AGTAATCC
1 TATCTCTCTGAAATTACAGTGGAGCGGATT-AAAATAAAG-GATCT
42215167 TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
42215211 TATCTCTCT-AAAGTTACAGT
1 TATCTCTCTGAAA-TTACAGT
42215231 AGAGTAGATC
Statistics
Matches: 81, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
43 8 0.10
44 68 0.84
45 5 0.06
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (44 bp):
TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
Found at i:42215357 original size:44 final size:44
Alignment explanation
Indices: 42215245--42215371 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 44
42215235 TAGATCACAT
* * **
42215245 CAGATTGAAGCCAGAGATCTTATCTCCCT-GAGATTACAATGGAG
1 CAGATTAAAGCCACAGATCTTATCTCCCTGGAG-TTACAGCGGAG
* * * *
42215289 TAGATTAAAGCTAGTA-ATCCTATCTCCCTGGAGTTACAGCGGAG
1 CAGATTAAAGCCA-CAGATCTTATCTCCCTGGAGTTACAGCGGAG
* * *
42215333 CAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAG
1 CAGATTAAAGCCACAGATCTTATCTCCCTGGAGTTACAG
42215372 TAGAGTGGAT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 1 0.02
44 61 0.92
45 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
CAGATTAAAGCCACAGATCTTATCTCCCTGGAGTTACAGCGGAG
Found at i:42215389 original size:142 final size:142
Alignment explanation
Indices: 42215118--42215382 Score: 397
Period size: 142 Copynumber: 1.9 Consensus size: 142
42215108 TAAAATAAAG
* * *
42215118 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
1 GATCTTATCTCCCTGAGATTACAACAGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGAAATTA
* * *
42215183 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAG
66 CAGCGGAGCAGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAG
42215248 ATTGAAGCCAGA
131 ATTGAAGCCAGA
** * *
42215260 GATCTTATCTCCCTGAGATTACAATGGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGGAGTTA
1 GATCTTATCTCCCTGAGATTACAACAGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGAAATTA
* * *
42215325 CAGCGGAGCAGATTAAAACCACA-GATCTTATCTCTCTGAAGTTACAGTAGAGTGGATC
66 CAGCGGAGCAGATTAAAA-CAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATC
42215383 GTATCAGGTC
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
142 107 0.98
143 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (142 bp):
GATCTTATCTCCCTGAGATTACAACAGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGAAATTA
CAGCGGAGCAGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAG
ATTGAAGCCAGA
Found at i:42215743 original size:17 final size:16
Alignment explanation
Indices: 42215717--42215749 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
42215707 AACCCAAGAC
42215717 CCAAAACAGACCCAAA
1 CCAAAACAGACCCAAA
42215733 CCAAGAACAGACCCAAA
1 CCAA-AACAGACCCAAA
42215750 AACAAGCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.55, C:0.36, G:0.09, T:0.00
Consensus pattern (16 bp):
CCAAAACAGACCCAAA
Found at i:42216838 original size:110 final size:110
Alignment explanation
Indices: 42216695--42217644 Score: 1830
Period size: 110 Copynumber: 8.6 Consensus size: 110
42216685 CTAATTGGCC
42216695 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42216760 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42216805 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42216870 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42216915 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42216980 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42217025 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42217090 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42217135 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42217200 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42217245 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42217310 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42217355 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42217420 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
42217465 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
*
42217530 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
* * * * * *
42217575 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTGCTCTAAGGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
42217639 CGATTT
66 CGATTT
42217645 CTCGTCTAAC
Statistics
Matches: 833, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
109 26 0.03
110 807 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (110 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGT
CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCAAAAA
Found at i:42219109 original size:10 final size:10
Alignment explanation
Indices: 42219084--42219117 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
42219074 ACTTTGTTTC
42219084 TTCTTTTTCCTT
1 TTCTTTTT--TT
42219096 TTCTTTTTTT
1 TTCTTTTTTT
42219106 TTCTTTTTTT
1 TTCTTTTTTT
42219116 TT
1 TT
42219118 TTGGCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.64
12 8 0.36
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:42219117 original size:15 final size:15
Alignment explanation
Indices: 42219080--42219119 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
42219070 TACTACTTTG
*
42219080 TTTCTTCTTTTTCCT
1 TTTCTTTTTTTTCCT
*
42219095 TTTCTTTTTTTTTCT
1 TTTCTTTTTTTTCCT
42219110 TTT-TTTTTTT
1 TTTCTTTTTTT
42219120 GGCAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTTTTCCT
Found at i:42223138 original size:13 final size:13
Alignment explanation
Indices: 42223120--42223144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42223110 AATCTTCCCC
42223120 ATTTTTTTTTAAA
1 ATTTTTTTTTAAA
42223133 ATTTTTTTTTAA
1 ATTTTTTTTTAA
42223145 GCTTAAGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTTTAAA
Found at i:42225746 original size:27 final size:27
Alignment explanation
Indices: 42225682--42225757 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
42225672 AAAAGATTTT
* *
42225682 CTTTCATATTACACCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
42225709 CTTTCATATTGCGCCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
* *
42225736 CTTTCATATTGTGCCATAAAGG
1 CTTTCATATTGCGCCACAAAGG
42225758 CATTCATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (27 bp):
CTTTCATATTGCGCCACAAAGGTGTTC
Found at i:42228204 original size:13 final size:13
Alignment explanation
Indices: 42228165--42228217 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
42228155 AGTTTAGCAA
42228165 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
42228178 TG-TTATGGAAAAG
1 TGCTT-TTGAAAAG
*
42228191 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
42228204 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42228217 T
1 T
42228218 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 30 0.88
14 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:42230082 original size:19 final size:19
Alignment explanation
Indices: 42230058--42230114 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
42230048 ATTATGTTTT
42230058 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
42230077 TATATTATATTATATTATA
1 TATATTATATTATATTATA
42230096 TATA-TATA-TATA-TATA
1 TATATTATATTATATTATA
42230112 TAT
1 TAT
42230115 CAAAAGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 9 0.24
19 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:42230092 original size:10 final size:10
Alignment explanation
Indices: 42230030--42230114 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 10
42230020 AAAAAAATAT
42230030 TATTATATTA
1 TATTATATTA
*
42230040 TAGTAATGATTA
1 TA-TTAT-ATTA
*
42230052 TGTT-T-TTA
1 TATTATATTA
42230060 TATTATATTA
1 TATTATATTA
42230070 TTATTA-A-TA
1 -TATTATATTA
42230079 TATTATATTA
1 TATTATATTA
42230089 TATTATATATA
1 TATTATAT-TA
42230100 TATATATATATA
1 TAT-TATAT-TA
42230112 TAT
1 TAT
42230115 CAAAAGAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
8 11 0.18
9 4 0.06
10 17 0.27
11 14 0.23
12 16 0.26
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (10 bp):
TATTATATTA
Found at i:42230097 original size:2 final size:2
Alignment explanation
Indices: 42230058--42230114 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
42230048 ATTATGTTTT
42230058 TA TA T- TA TA T- TA T- TA T- TA -A TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42230092 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
42230115 CAAAAGAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
1 8 0.17
2 39 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:42230105 original size:8 final size:8
Alignment explanation
Indices: 42230058--42230114 Score: 58
Period size: 7 Copynumber: 8.1 Consensus size: 8
42230048 ATTATGTTTT
42230058 TATAT-TA
1 TATATATA
42230065 TAT-TAT-
1 TATATATA
42230071 TAT-TA-A
1 TATATATA
42230077 TATAT-TA
1 TATATATA
42230084 TAT-TATA
1 TATATATA
42230091 T-TATATA
1 TATATATA
42230098 TATATATA
1 TATATATA
42230106 TATATATA
1 TATATATA
42230114 T
1 T
42230115 CAAAAGAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
6 11 0.26
7 17 0.40
8 15 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TATATATA
Found at i:42239904 original size:145 final size:145
Alignment explanation
Indices: 42239641--42239931 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 145
42239631 AATCTACAGC
42239641 TAGGAGCTTTGGGCGCTTCCTCTTTGTCTTAGGTCCAAATGCATTCTCGAAAGGCTCTGTGTCCA
1 TAGGAGCTTTGGGCGCTTCCTCTTTGTCTTAGGTCCAAATGCATTCTCGAAAGGCTCTGTGTCCA
42239706 GAAGATGAGCTCTAGCTTGCTTCATATACATACATTTTAATCAACAATACAATAGAATTAGAAGT
66 GAAGATGAGCTCTAGCTTGCTTCATATACATACATTTTAATCAACAATACAATAGAATTAGAAGT
42239771 ATCTTTTTTTTTTTT
131 ATCTTTTTTTTTTTT
42239786 TAGGAGCTTTGGGCGCTTCCTCTTTGTCTTAGGTCCAAATGCATTCTCGAAAGGCTCTGTGTCCA
1 TAGGAGCTTTGGGCGCTTCCTCTTTGTCTTAGGTCCAAATGCATTCTCGAAAGGCTCTGTGTCCA
42239851 GAAGATGAGCTCTAGCTTGCTTCATATACATACATTTTAATCAACAATACAATAGAATTAGAAGT
66 GAAGATGAGCTCTAGCTTGCTTCATATACATACATTTTAATCAACAATACAATAGAATTAGAAGT
*
42239916 ATTTTTTTTTTTTTT
131 ATCTTTTTTTTTTTT
42239931 T
1 T
42239932 TTTTTTTAAG
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (145 bp):
TAGGAGCTTTGGGCGCTTCCTCTTTGTCTTAGGTCCAAATGCATTCTCGAAAGGCTCTGTGTCCA
GAAGATGAGCTCTAGCTTGCTTCATATACATACATTTTAATCAACAATACAATAGAATTAGAAGT
ATCTTTTTTTTTTTT
Found at i:42241399 original size:8 final size:8
Alignment explanation
Indices: 42241386--42241416 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
42241376 GCCTTGACTC
42241386 TTAAAATT
1 TTAAAATT
42241394 TTAAAATT
1 TTAAAATT
42241402 TTAAAATT
1 TTAAAATT
42241410 TTAAAAT
1 TTAAAAT
42241417 AATGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTAAAATT
Found at i:42243897 original size:2 final size:2
Alignment explanation
Indices: 42243890--42243945 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
42243880 GTTTATTTGA
42243890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
42243932 AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT
42243946 GTGTGTATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42244142 original size:53 final size:54
Alignment explanation
Indices: 42244080--42244186 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 54
42244070 AGACCATGTC
42244080 TTGGACGTTGGCATCGATTTGATATTTACGTGTAAGACCATGT-TGGGACATTG
1 TTGGACGTTGGCATCGATTTGATATTTACGTGTAAGACCATGTCTGGGACATTG
42244133 TTGGACGTTGGCATCGATTTGATATTTACGTGTAAGACCATGTCTGGGACATTG
1 TTGGACGTTGGCATCGATTTGATATTTACGTGTAAGACCATGTCTGGGACATTG
42244187 GCATCATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 43 0.81
54 10 0.19
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (54 bp):
TTGGACGTTGGCATCGATTTGATATTTACGTGTAAGACCATGTCTGGGACATTG
Found at i:42252202 original size:16 final size:16
Alignment explanation
Indices: 42252168--42252217 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
42252158 AAAACTAAAG
* *
42252168 TTTTTAAAACATTTA-
1 TTTTTAAAATATTCAT
*
42252183 TTTTTATAATATTCAT
1 TTTTTAAAATATTCAT
*
42252199 TTTTTAAAATTTTCAT
1 TTTTTAAAATATTCAT
42252215 TTT
1 TTT
42252218 AAATTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAATATTCAT
Found at i:42254309 original size:42 final size:44
Alignment explanation
Indices: 42254207--42254318 Score: 149
Period size: 42 Copynumber: 2.6 Consensus size: 44
42254197 ATGTGATTTT
* *
42254207 GTGTAAGACCATGTCTTGGACGTTGGCATCGATTTGATATTTAC
1 GTGTAAGACCATGTCTGGGACGTTGGCATCGATATGATATTTAC
*
42254251 GTGTAAGACCATGTCTGGGACATTGGCATC-ATAT-ATGA-TTAC
1 GTGTAAGACCATGTCTGGGACGTTGGCATCGATATGAT-ATTTAC
* *
42254293 GTGTAATACCACGTCTGGGACGTTGG
1 GTGTAAGACCATGTCTGGGACGTTGG
42254319 TATTGTACGA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 29 0.48
43 4 0.07
44 28 0.46
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (44 bp):
GTGTAAGACCATGTCTGGGACGTTGGCATCGATATGATATTTAC
Found at i:42260540 original size:18 final size:21
Alignment explanation
Indices: 42260505--42260548 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
42260495 TGAAAATAAC
*
42260505 TTTTAGAAAATAGATTGAT-T
1 TTTTTGAAAATAGATTGATAT
42260525 TTTTTGAAAA-AG-TTGATAT
1 TTTTTGAAAATAGATTGATAT
42260544 TTTTT
1 TTTTT
42260549 TTATGTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTTTGAAAATAGATTGATAT
Found at i:42265924 original size:11 final size:11
Alignment explanation
Indices: 42265908--42265933 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42265898 TATTTTTTAA
42265908 TTTTAAAATAC
1 TTTTAAAATAC
42265919 TTTTAAAATAC
1 TTTTAAAATAC
42265930 TTTT
1 TTTT
42265934 TTTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:42269190 original size:22 final size:22
Alignment explanation
Indices: 42269155--42269198 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42269145 AGCTAGAATC
42269155 AGAACTGAAGAATTGAA-TTGA
1 AGAACTGAAGAATTGAACTTGA
*
42269176 AGAACTTGGAGAATTGAACTTGA
1 AGAAC-TGAAGAATTGAACTTGA
42269199 GGTTCATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (22 bp):
AGAACTGAAGAATTGAACTTGA
Found at i:42273420 original size:34 final size:35
Alignment explanation
Indices: 42273347--42273421 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
42273337 GCTTTGTTGA
* *
42273347 ATGAGCTCAGGTGAGTTTTAATCTGTCTTGGCATG
1 ATGAACTCAGGTGAGTTCTAATCTGTCTTGGCATG
*
42273382 ATGAACTCAGGTGAGTTCTAATCTG-CTTTGCATG
1 ATGAACTCAGGTGAGTTCTAATCTGTCTTGGCATG
42273416 ATGAAC
1 ATGAAC
42273422 CAAGCTCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 14 0.38
35 23 0.62
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (35 bp):
ATGAACTCAGGTGAGTTCTAATCTGTCTTGGCATG
Found at i:42278011 original size:32 final size:32
Alignment explanation
Indices: 42277975--42278046 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
42277965 GTTGCTATGT
* *
42277975 TTAAAAATTTAACATTTTAGTTGGTATTTTCA
1 TTAAAAATTTAACATTTTAGTCGGCATTTTCA
** *
42278007 TTAAAAGCTTAACGTTTTAGTCGGCATTTTCA
1 TTAAAAATTTAACATTTTAGTCGGCATTTTCA
42278039 TTAAAAAT
1 TTAAAAAT
42278047 GATGGTCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (32 bp):
TTAAAAATTTAACATTTTAGTCGGCATTTTCA
Found at i:42279332 original size:92 final size:93
Alignment explanation
Indices: 42279175--42279359 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 93
42279165 GAGTTTGAGT
42279175 CATATTAATCGTGTTGGTTGTTTGAGTTTTATCCTATTACTGTAATTCATCAAAATAATAATAAT
1 CATATTAATCGTGTTGGTTGTTTGAGTTTTATCCTATTACTGTAATTCATCAAAATAATAATAAT
42279240 ATAATATTTTATCATT-AATAAATATTA
66 ATAATATTTTATCATTAAATAAATATTA
42279267 CATATTAATCGTGTTGGTTGTTTGAGTTTTATCCTATTACTGTAATTCATCAAAATAATAATAAT
1 CATATTAATCGTGTTGGTTGTTTGAGTTTTATCCTATTACTGTAATTCATCAAAATAATAATAAT
42279332 ATAATATTTTATCATTAAATAAATATTA
66 ATAATATTTTATCATTAAATAAATATTA
42279360 ATAATTTTTT
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 81 0.88
93 11 0.12
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (93 bp):
CATATTAATCGTGTTGGTTGTTTGAGTTTTATCCTATTACTGTAATTCATCAAAATAATAATAAT
ATAATATTTTATCATTAAATAAATATTA
Found at i:42281816 original size:6 final size:7
Alignment explanation
Indices: 42281796--42281828 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
42281786 TTTGTAAAAT
42281796 GAAGGGG
1 GAAGGGG
42281803 GAAGGGG
1 GAAGGGG
42281810 GAAGGGG
1 GAAGGGG
42281817 GAA-GGG
1 GAAGGGG
42281823 GAAGGG
1 GAAGGG
42281829 CAAAAGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (7 bp):
GAAGGGG
Found at i:42283574 original size:2 final size:2
Alignment explanation
Indices: 42283569--42283593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42283559 TTTCCTAATT
42283569 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
42283594 TGAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42285787 original size:20 final size:20
Alignment explanation
Indices: 42285764--42285802 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42285754 AAAAGTAATG
42285764 TAGTTTTAG-TTTAATTTTTT
1 TAGTTTT-GTTTTAATTTTTT
42285784 TAGTTTTGTTTTAATTTTT
1 TAGTTTTGTTTTAATTTTT
42285803 GTTAAAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TAGTTTTGTTTTAATTTTTT
Found at i:42286624 original size:2 final size:2
Alignment explanation
Indices: 42286617--42286641 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42286607 TTCTTTTTAA
42286617 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
42286642 ATTACTGACA
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:42288887 original size:21 final size:21
Alignment explanation
Indices: 42288846--42288897 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
42288836 CAACCATAAT
* *
42288846 AATAAACTATACAAAATAAAA
1 AATAAATTATACAAAACAAAA
* *
42288867 TATAAATTATACATAACAAAA
1 AATAAATTATACAAAACAAAA
42288888 AATAATATTA
1 AATAA-ATTA
42288898 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAATTATACAAAACAAAA
Found at i:42289751 original size:40 final size:40
Alignment explanation
Indices: 42289643--42289734 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
42289633 GATAAAGCAG
42289643 GAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
1 GAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
* *
42289683 GAAAATGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACC
1 GAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
42289723 GAAAACGCTTCC
1 GAAAACGCTTCC
42289735 CTGAGGGCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (40 bp):
GAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
Found at i:42289985 original size:99 final size:97
Alignment explanation
Indices: 42289866--42290085 Score: 248
Period size: 99 Copynumber: 2.2 Consensus size: 97
42289856 GATTTTAAGG
* * * *
42289866 TTTTAAGGAAAAAAAT-AAATAAGAGTTTAGAATTTAGGGTTTCTTAATTAAATTAATTATAAA-
1 TTTTAAGG-AAAAAATCAAATAA-A--TTAGAATCTAGAGTTACTTAAGTAAATTAATTATAAAT
** * *
42289929 TTTTAAAAAATTAGATTAGCTTTTAGTGTTTATGGT
62 TTTTAAAAAATTAGATTAGAGTTTAGTATTTAGGGT
** *
42289965 TTTTAAGGAAAAAATCAAATAAATTAGGGTCTAGAGTTACTTGAGTAAATTAATTATAAATTTTT
1 TTTTAAGGAAAAAATCAAATAAATTAGAATCTAGAGTTACTTAAGTAAATTAATTATAAA--TTT
* *
42290030 TTTAAAAATTAGATTGGAGTTTAGTATTTAGGGT
64 TTAAAAAATTAGATTAGAGTTTAGTATTTAGGGT
42290064 TTTTAAGG-AAAAATCAAATAAA
1 TTTTAAGGAAAAAATCAAATAAA
42290086 GCTAGTTACT
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
96 30 0.29
98 22 0.21
99 52 0.50
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (97 bp):
TTTTAAGGAAAAAATCAAATAAATTAGAATCTAGAGTTACTTAAGTAAATTAATTATAAATTTTT
AAAAAATTAGATTAGAGTTTAGTATTTAGGGT
Found at i:42290514 original size:11 final size:11
Alignment explanation
Indices: 42290464--42290489 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42290454 GTTAGACTTA
42290464 ATAAATAATTT
1 ATAAATAATTT
42290475 ATAAATAATTT
1 ATAAATAATTT
42290486 ATAA
1 ATAA
42290490 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:42290718 original size:40 final size:40
Alignment explanation
Indices: 42290645--42290760 Score: 112
Period size: 40 Copynumber: 2.9 Consensus size: 40
42290635 GAAAATGCTT
* *
42290645 CCTCAAGGAAGCG-CTT-TGTCCACGTGGACACAAAGCGCGC
1 CCTCAGGGAAGCGTTTTCTGTCCACGT-GA-ACAAAGCGCGC
**
42290685 CCTCAGGGAAGCGTTTTCTGTCCACGTGAACAAAGCGCTT
1 CCTCAGGGAAGCGTTTTCTGTCCACGTGAACAAAGCGCGC
* * * *
42290725 CCT-TGAGGAAGCGTTTTCAGTCAACGTGGACAAAGC
1 CCTCAG-GGAAGCGTTTTCTGTCCACGTGAACAAAGC
42290761 ACTTCCTTGA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.02
40 51 0.78
41 4 0.06
42 9 0.14
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.21
Consensus pattern (40 bp):
CCTCAGGGAAGCGTTTTCTGTCCACGTGAACAAAGCGCGC
Found at i:42290766 original size:40 final size:40
Alignment explanation
Indices: 42290691--42290782 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
42290681 GCGCCCTCAG
* * *
42290691 GGAAGCGTTTTCTGTCCACGTGAACAAAGCGCTTCCTTGA
1 GGAAGCGTTTTCAGTCAACGTGAACAAAGCACTTCCTTGA
*
42290731 GGAAGCGTTTTCAGTCAACGTGGACAAAGCACTTCCTTGA
1 GGAAGCGTTTTCAGTCAACGTGAACAAAGCACTTCCTTGA
*
42290771 GAAAGCGTTTTC
1 GGAAGCGTTTTC
42290783 CTGCTTTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
GGAAGCGTTTTCAGTCAACGTGAACAAAGCACTTCCTTGA
Found at i:42293199 original size:69 final size:67
Alignment explanation
Indices: 42293081--42293212 Score: 194
Period size: 69 Copynumber: 1.9 Consensus size: 67
42293071 ATAAACAATA
* * *
42293081 TAATGATTTTGTCTTTTAACTTGATGAATAAACATTTATCAAAATGACGTAATTTTACCTTTTAA
1 TAATGATTTTGACTTTTAACTTGATGAATAAACATTTATCAAAACGACGTAATTTTACATTTTAA
42293146 CT
66 CT
*
42293148 TAATGATTTTGACTTTTAACTTTA-GAAAGGTAAACATTTATCAAAACGACGTAATTTTACATTT
1 TAATGATTTTGACTTTTAACTTGATG-AA--TAAACATTTATCAAAACGACGTAATTTTACATTT
42293212 T
63 T
42293213 CTTATTCTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 1 0.02
67 24 0.41
69 33 0.57
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTGATGAATAAACATTTATCAAAACGACGTAATTTTACATTTTAA
CT
Found at i:42295729 original size:3 final size:3
Alignment explanation
Indices: 42295721--42295758 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42295711 TTTTTAAACC
42295721 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42295759 ATTTCTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42306505 original size:94 final size:94
Alignment explanation
Indices: 42306319--42306520 Score: 205
Period size: 94 Copynumber: 2.1 Consensus size: 94
42306309 TCAATGCCTT
* *
42306319 ATAATGAGTAATCTAATGCATCATCAAGATCAACCTTGGAGTTAAGGCAATGACATACGATTGAT
1 ATAATGAGTAATCTAATGCATCATCAAGACCAACCTTAGAGTTAAGGCAATGACATACGATTGAT
* * *
42306384 TCACTATCGAATAAGACGATTAGTATCTT
66 TCACTATCAAATAAGACGATTAATATCTC
* * * * *
42306413 GTAATGAGTAATCTATTGCATTATCATA-ACCAACCTTTAG-GTTAAGG-ATATGACATGCTATT
1 ATAATGAGTAATCTAATGCATCATCA-AGACCAACC-TTAGAGTTAAGGCA-ATGACATACGATT
* * **
42306475 GATTGACTCTCAAATGTGA-GCATTAATATCTC
63 GATTCACTATCAAATAAGACG-ATTAATATCTC
*
42306507 ATAATGAGCAATCT
1 ATAATGAGTAATCT
42306521 TGTAATGAGC
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
93 2 0.02
94 82 0.93
95 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (94 bp):
ATAATGAGTAATCTAATGCATCATCAAGACCAACCTTAGAGTTAAGGCAATGACATACGATTGAT
TCACTATCAAATAAGACGATTAATATCTC
Found at i:42306516 original size:20 final size:20
Alignment explanation
Indices: 42306491--42306546 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
42306481 CTCTCAAATG
42306491 TGAGCATTAATATCTCATAA
1 TGAGCATTAATATCTCATAA
**
42306511 TGAGC----A-ATCTTGTAA
1 TGAGCATTAATATCTCATAA
42306526 TGAGCATTAATATCTCATAA
1 TGAGCATTAATATCTCATAA
42306546 T
1 T
42306547 TTTGTGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
19 1 0.04
20 13 0.48
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAGCATTAATATCTCATAA
Found at i:42309437 original size:19 final size:20
Alignment explanation
Indices: 42309400--42309437 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42309390 ATTATAAAAT
42309400 AATTCAAAATAATTTTTTAA
1 AATTCAAAATAATTTTTTAA
42309420 AATT-AAAA-AATTTATTTA
1 AATTCAAAATAATTT-TTTA
42309438 CCATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTCAAAATAATTTTTTAA
Found at i:42312788 original size:14 final size:14
Alignment explanation
Indices: 42312769--42312816 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
42312759 TCTATTTCTT
42312769 TTATTTTTTTAATA
1 TTATTTTTTTAATA
*
42312783 TTATTTTATTAA-A
1 TTATTTTTTTAATA
*
42312796 TGTAATTTTTTAATA
1 T-TATTTTTTTAATA
42312811 TTATTT
1 TTATTT
42312817 ACAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTTTTTTAATA
Found at i:42313449 original size:14 final size:14
Alignment explanation
Indices: 42313430--42313477 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
42313420 TCTATTTCTT
42313430 TTATTTTTTTAATA
1 TTATTTTTTTAATA
*
42313444 TTATTTTATTAA-A
1 TTATTTTTTTAATA
*
42313457 TGTAATTTTTTAATA
1 T-TATTTTTTTAATA
42313472 TTATTT
1 TTATTT
42313478 ACAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTTTTTTAATA
Found at i:42313891 original size:661 final size:661
Alignment explanation
Indices: 42312631--42313952 Score: 2644
Period size: 661 Copynumber: 2.0 Consensus size: 661
42312621 TCATTATAAT
42312631 CAATTTTTTTTATTTTTTTGTGAATTATATTAAAAAGGTAAAGCTTGAATAATAAATATAATTAA
1 CAATTTTTTTTATTTTTTTGTGAATTATATTAAAAAGGTAAAGCTTGAATAATAAATATAATTAA
42312696 CATGACTCGAACTTAGGTCACAGTTAGCGTAATGAATAATCTTGACCATTAAACTATTAAGATTC
66 CATGACTCGAACTTAGGTCACAGTTAGCGTAATGAATAATCTTGACCATTAAACTATTAAGATTC
42312761 TATTTCTTTTATTTTTTTAATATTATTTTATTAAATGTAATTTTTTAATATTATTTACAAAATTA
131 TATTTCTTTTATTTTTTTAATATTATTTTATTAAATGTAATTTTTTAATATTATTTACAAAATTA
42312826 AATCAAAATTTTAGAAGTAAAATTAAAACAATTGTGTTAAGTGGCGGGTTCAACCTAAACTCGCA
196 AATCAAAATTTTAGAAGTAAAATTAAAACAATTGTGTTAAGTGGCGGGTTCAACCTAAACTCGCA
42312891 ATTGTGTCACAAGAATGCTAAAACCAACACCTAATGTGCTGATTTCACTCTTCTGACATGTCTAC
261 ATTGTGTCACAAGAATGCTAAAACCAACACCTAATGTGCTGATTTCACTCTTCTGACATGTCTAC
42312956 TAACTACTATCATGGCAATTTTCTACCACATCTTGTTTGTAAAAGGCAAGCTGAAATCGCCACCT
326 TAACTACTATCATGGCAATTTTCTACCACATCTTGTTTGTAAAAGGCAAGCTGAAATCGCCACCT
42313021 AATATGGTGATTTCACTCTTTTTTACATGTCTATCGCCATGATAATTTTCTGCCCATGTGTCAGG
391 AATATGGTGATTTCACTCTTTTTTACATGTCTATCGCCATGATAATTTTCTGCCCATGTGTCAGG
42313086 TTGAAGTTGAAACCACCATTTAATGTATTGGTTTCATGTTTACTTTTTGAAAGTTTGATATAATT
456 TTGAAGTTGAAACCACCATTTAATGTATTGGTTTCATGTTTACTTTTTGAAAGTTTGATATAATT
42313151 TTGTAAAAATAATGCGAAACGTAATGTTGAAGTTATTGAGGGAGAGTTTGGATGGGCGGTGCGTT
521 TTGTAAAAATAATGCGAAACGTAATGTTGAAGTTATTGAGGGAGAGTTTGGATGGGCGGTGCGTT
42313216 ATCTGCAGTTAGTGTAAAAACAGCGGTGGCGGTGAGATTAGATACTGTAGCGTGAGACAAAAAGT
586 ATCTGCAGTTAGTGTAAAAACAGCGGTGGCGGTGAGATTAGATACTGTAGCGTGAGACAAAAAGT
42313281 AAGCTAAACGC
651 AAGCTAAACGC
42313292 CAATTTTTTTTATTTTTTTGTGAATTATATTAAAAAGGTAAAGCTTGAATAATAAATATAATTAA
1 CAATTTTTTTTATTTTTTTGTGAATTATATTAAAAAGGTAAAGCTTGAATAATAAATATAATTAA
42313357 CATGACTCGAACTTAGGTCACAGTTAGCGTAATGAATAATCTTGACCATTAAACTATTAAGATTC
66 CATGACTCGAACTTAGGTCACAGTTAGCGTAATGAATAATCTTGACCATTAAACTATTAAGATTC
42313422 TATTTCTTTTATTTTTTTAATATTATTTTATTAAATGTAATTTTTTAATATTATTTACAAAATTA
131 TATTTCTTTTATTTTTTTAATATTATTTTATTAAATGTAATTTTTTAATATTATTTACAAAATTA
42313487 AATCAAAATTTTAGAAGTAAAATTAAAACAATTGTGTTAAGTGGCGGGTTCAACCTAAACTCGCA
196 AATCAAAATTTTAGAAGTAAAATTAAAACAATTGTGTTAAGTGGCGGGTTCAACCTAAACTCGCA
42313552 ATTGTGTCACAAGAATGCTAAAACCAACACCTAATGTGCTGATTTCACTCTTCTGACATGTCTAC
261 ATTGTGTCACAAGAATGCTAAAACCAACACCTAATGTGCTGATTTCACTCTTCTGACATGTCTAC
42313617 TAACTACTATCATGGCAATTTTCTACCACATCTTGTTTGTAAAAGGCAAGCTGAAATCGCCACCT
326 TAACTACTATCATGGCAATTTTCTACCACATCTTGTTTGTAAAAGGCAAGCTGAAATCGCCACCT
42313682 AATATGGTGATTTCACTCTTTTTTACATGTCTATCGCCATGATAATTTTCTGCCCATGTGTCAGG
391 AATATGGTGATTTCACTCTTTTTTACATGTCTATCGCCATGATAATTTTCTGCCCATGTGTCAGG
42313747 TTGAAGTTGAAACCACCATTTAATGTATTGGTTTCATGTTTACTTTTTGAAAGTTTGATATAATT
456 TTGAAGTTGAAACCACCATTTAATGTATTGGTTTCATGTTTACTTTTTGAAAGTTTGATATAATT
42313812 TTGTAAAAATAATGCGAAACGTAATGTTGAAGTTATTGAGGGAGAGTTTGGATGGGCGGTGCGTT
521 TTGTAAAAATAATGCGAAACGTAATGTTGAAGTTATTGAGGGAGAGTTTGGATGGGCGGTGCGTT
42313877 ATCTGCAGTTAGTGTAAAAACAGCGGTGGCGGTGAGATTAGATACTGTAGCGTGAGACAAAAAGT
586 ATCTGCAGTTAGTGTAAAAACAGCGGTGGCGGTGAGATTAGATACTGTAGCGTGAGACAAAAAGT
42313942 AAGCTAAACGC
651 AAGCTAAACGC
42313953 ACCGCACCGC
Statistics
Matches: 661, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
661 661 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (661 bp):
CAATTTTTTTTATTTTTTTGTGAATTATATTAAAAAGGTAAAGCTTGAATAATAAATATAATTAA
CATGACTCGAACTTAGGTCACAGTTAGCGTAATGAATAATCTTGACCATTAAACTATTAAGATTC
TATTTCTTTTATTTTTTTAATATTATTTTATTAAATGTAATTTTTTAATATTATTTACAAAATTA
AATCAAAATTTTAGAAGTAAAATTAAAACAATTGTGTTAAGTGGCGGGTTCAACCTAAACTCGCA
ATTGTGTCACAAGAATGCTAAAACCAACACCTAATGTGCTGATTTCACTCTTCTGACATGTCTAC
TAACTACTATCATGGCAATTTTCTACCACATCTTGTTTGTAAAAGGCAAGCTGAAATCGCCACCT
AATATGGTGATTTCACTCTTTTTTACATGTCTATCGCCATGATAATTTTCTGCCCATGTGTCAGG
TTGAAGTTGAAACCACCATTTAATGTATTGGTTTCATGTTTACTTTTTGAAAGTTTGATATAATT
TTGTAAAAATAATGCGAAACGTAATGTTGAAGTTATTGAGGGAGAGTTTGGATGGGCGGTGCGTT
ATCTGCAGTTAGTGTAAAAACAGCGGTGGCGGTGAGATTAGATACTGTAGCGTGAGACAAAAAGT
AAGCTAAACGC
Found at i:42320068 original size:3 final size:3
Alignment explanation
Indices: 42320060--42320090 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
42320050 CAAGAACCAA
42320060 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42320091 GGTCCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42321868 original size:79 final size:79
Alignment explanation
Indices: 42321777--42321932 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 79
42321767 TTTTAAATTA
* * *
42321777 AAATTAAATTATAATTTTTACGATAATAAAATTGTAATTTTATCGTTTTAATAACCTAAATCTTT
1 AAATTAAATTATAAATTTTACGATAATAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
42321842 ATAATTTTTAAAAG
66 ATAATTTTTAAAAG
* *
42321856 AAATTAAATTATAAATTTTATGATAGTAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
1 AAATTAAATTATAAATTTTACGATAATAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
42321921 ATAATTTTTAAA
66 ATAATTTTTAAA
42321933 GGATTAAATC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (79 bp):
AAATTAAATTATAAATTTTACGATAATAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
ATAATTTTTAAAAG
Found at i:42324315 original size:31 final size:32
Alignment explanation
Indices: 42324264--42324324 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
42324254 TTATAAAATT
* * * *
42324264 AATGATACATTATATTTAAA-TAATTTAATAA
1 AATGATACATAAAATATAAATTAATCTAATAA
42324295 AATGATACATAAAATATAAATTAATCTAAT
1 AATGATACATAAAATATAAATTAATCTAAT
42324325 TTTTTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (32 bp):
AATGATACATAAAATATAAATTAATCTAATAA
Found at i:42331550 original size:17 final size:17
Alignment explanation
Indices: 42331536--42331570 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
42331526 TATTTTTTTA
42331536 TTTTTCTTCTTTTTTCT
1 TTTTTCTTCTTTTTTCT
42331553 TTTTTCTTC-TTTTTCT
1 TTTTTCTTCTTTTTTCT
42331569 TT
1 TT
42331571 CCTTCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTCT
Found at i:42331551 original size:10 final size:10
Alignment explanation
Indices: 42331536--42331590 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
42331526 TATTTTTTTA
42331536 TTTTTCTTCT
1 TTTTTCTTCT
42331546 TTTTTCTT-T
1 TTTTTCTTCT
42331555 TTTCTTCTT-T
1 TTT-TTCTTCT
42331565 TTCTTTCCTTCT
1 TT-TTT-CTTCT
*
42331577 TTCTTCTTCCT
1 TTTTTCTT-CT
42331588 TTT
1 TTT
42331591 CAAACCCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 4 0.11
10 21 0.55
11 10 0.26
12 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:42331576 original size:17 final size:17
Alignment explanation
Indices: 42331529--42331577 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
42331519 GTTTATTTAT
*
42331529 TTTTTTATTT-TTCTTC
1 TTTTTTCTTTCTTCTTC
*
42331545 TTTTTTCTTTTTTCTTC
1 TTTTTTCTTTCTTCTTC
42331562 -TTTTTCTTTCCTTCTT
1 TTTTTTCTTT-CTTCTT
42331578 TCTTCTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTCTTTCTTCTTC
Found at i:42331586 original size:14 final size:14
Alignment explanation
Indices: 42331539--42331588 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
42331529 TTTTTTATTT
*
42331539 TTCTT-CTTTTTTC
1 TTCTTCCTTCTTTC
* *
42331552 TTTTTTCTTCTTT-
1 TTCTTCCTTCTTTC
42331565 TTCTTTCCTTCTTTC
1 TTC-TTCCTTCTTTC
42331580 TTCTTCCTT
1 TTCTTCCTT
42331589 TTCAAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.20
14 21 0.70
15 3 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTCCTTCTTTC
Found at i:42331690 original size:23 final size:23
Alignment explanation
Indices: 42331664--42331712 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
42331654 GCGTCCCCTT
*
42331664 CTTCCCTTC-TCCTTCTTTTCTTC
1 CTTCCCTTCTTCCTT-TTTTCCTC
*
42331687 CTTCTCTTCTTCCTTTTTTCCTC
1 CTTCCCTTCTTCCTTTTTTCCTC
42331710 CTT
1 CTT
42331713 TTTTCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (23 bp):
CTTCCCTTCTTCCTTTTTTCCTC
Found at i:42331730 original size:37 final size:39
Alignment explanation
Indices: 42331676--42331764 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 39
42331666 TCCCTTCTCC
42331676 TTCTTTTCTTCCTTCTCTT-CTTCCTTTTTTCCTCCTTT-T
1 TTCTTTTC-TCCTTCTCTTCCTTCCTTTTTT-CTCCTTTCT
* *
42331715 TTCTTTTC-CCTTCTCTTCCTTTCTTTTTTCTTCTTTCT
1 TTCTTTTCTCCTTCTCTTCCTTCCTTTTTTCTCCTTTCT
42331753 TCTCTTTTCTCC
1 T-TCTTTTCTCC
42331765 CCTTTTTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
37 15 0.34
38 12 0.27
39 15 0.34
40 2 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (39 bp):
TTCTTTTCTCCTTCTCTTCCTTCCTTTTTTCTCCTTTCT
Found at i:42332588 original size:76 final size:75
Alignment explanation
Indices: 42332400--42334105 Score: 2017
Period size: 78 Copynumber: 22.1 Consensus size: 75
42332390 TTTCTTTCTG
* * * * * * * *
42332400 TTTGAAAAATAGAAATCGAAAATAGCTCAGTGTGCGACCCGAAGCTCAACTCATCTATCGGATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42332465 TGAG-T--TT
66 TGAGTTGATT
* * *
42332472 TTTGAAAATAAACAGAAATTGAAAATACCTCAGCCTGTGACCCGAGGCTCAACTCACCTCTCGGA
1 TTTG--AA-AAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
*
42332537 TTATGATTTGATT
63 TTATGAGTTGATT
* * * *
42332550 TTTGAAAAAACAGAAATTGAAAATACCTCTGCATGTGACCCGAGGCTCAACTCACCTCTCGAATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
42332615 ATGAGTTGATT
65 ATGAGTTGATT
* * * *
42332626 TTTGAAAAAATAGAAATTGAAAGTACCTTAGTGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
42332691 ATGAGTTGATT
65 ATGAGTTGATT
* * *
42332702 TTTGAAAAAATAGAAATTGAAAATACCTCAACGTGCGACCCGAGGATCAACTCACCTCTCGCATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
* *
42332767 TTGAGTTCATTTT
65 ATGAGTTGA--TT
* * * * * *
42332780 TTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCATCTCTCGCATT
1 TTTGAAAAACAGAAATTG-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
42332845 ATGAGTTGATTTTTT
65 ATGAGTTGA----TT
* * *
42332860 TTTAAAAAACA-AAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCATCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42332924 TGAGTTGATT
66 TGAGTTGATT
* * * **
42332934 TTTGAAAAAATAGAAATTGAAAAATACCTCAGCATGTGACCCGAGTTTCAACTCACCTCTCGCAT
1 TTTG-AAAAACAGAAATTG-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAT
42332999 TATGAGTTGATTTTTT
64 TATGAGTTGA----TT
* * *
42333015 TTTGTAAAACAGAAATTAAAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42333080 TGAGTTGATTTTTT
66 TGAGTTGA----TT
* * *
42333094 TTTGTAAAACAGAAATTAAAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42333159 TGAGTTGATT
66 TGAGTTGATT
* * * * * **
42333169 TTTGGAAAAACTGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTTAACTCACCTCTAACAT
1 TTT-GAAAAACAGAAATTG-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAT
*
42333234 TAAGAGTTGATT
64 TATGAGTTGATT
* * *
42333246 TTTGAAAAACAGAAATTGAAAAATACCCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTG-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
42333311 ATGAGTTGATTTTT
65 ATGAGTTGA---TT
* **
42333325 TTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACTAGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
* *
42333390 GGAGTTGTTTTTT
66 TGAGTTG---ATT
*
42333403 TTTGAAAAACAGAAATTGAAAATACCAT-AGCGTGCGACCCGAGACTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTGAAAATACC-TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
42333467 ATGAGTTGATTTTT
65 ATGAGTTGA---TT
* *
42333481 TTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCAACTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42333546 TGAGTTGATTTTT
66 TGAGTTGA---TT
*
42333559 TTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT-
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42333623 TGAGTTGATTTT
66 TGAGTTGA--TT
* * * *
42333635 TTTGAAAAACATAAATTG-AAATACCTCAGCGTGCGGCCCGAGACTCAACCCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
42333699 TGAGTTGATTTT
66 TGAGTTGA--TT
* * * *
42333711 TTTGAAAAACATAAATTTACAATACCTCAGCGTGCGACCAGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
*
42333776 TAAGTTGATT
66 TGAGTTGATT
* * * *
42333786 TTTGAAAAACAGAAATTAAAAAAATACCCCAGCGTGTGACCCGAGACTCAACTCACCTCTCGCAT
1 TTTGAAAAACAGAAATT--GAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAT
42333851 TATGAGTTGATT
64 TATGAGTTGATT
* * * * * *
42333863 TTTGGAAAAAAACAAAAATTAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGT
1 TTT-G--AAAAACAGAAATT-GAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
42333927 ATTATGAGTTGATT
62 ATTATGAGTTGATT
* *
42333941 TTTGAAAAACAAAAATTGAAAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTG-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
42334006 ATGAGTTGATT
65 ATGAGTTGATT
* * * * * * *
42334017 CTTGGAAAAGAACATAAATTAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCAC
1 -TTTG-AAA-AACAGAAATT-GAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
*
42334081 ATTATGAGTTGACT
62 ATTATGAGTTGATT
42334095 TTTGAAAAACA
1 TTTGAAAAACA
42334106 TAAAAAGAAA
Statistics
Matches: 1458, Mismatches: 132, Indels: 85
0.87 0.08 0.05
Matches are distributed among these distances:
72 4 0.00
74 7 0.00
75 156 0.11
76 373 0.26
77 237 0.16
78 443 0.30
79 195 0.13
80 37 0.03
81 6 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (75 bp):
TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
TGAGTTGATT
Found at i:42337812 original size:25 final size:25
Alignment explanation
Indices: 42337759--42337812 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
42337749 TAGAGTCTTG
***
42337759 TGTTTATAAAATCTCTTCAGTGTTG
1 TGTTTATAAAATCTCTTCAGTGAAC
**
42337784 TGTTTATAAAATCTCTTCTTTGAAC
1 TGTTTATAAAATCTCTTCAGTGAAC
42337809 TGTT
1 TGTT
42337813 GCCCCCAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (25 bp):
TGTTTATAAAATCTCTTCAGTGAAC
Found at i:42340227 original size:23 final size:23
Alignment explanation
Indices: 42340183--42340229 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
42340173 ACTTAAATTG
* ** *
42340183 TAATTAATTTTATTTTTTTTAAA
1 TAATCAATTTTATACTTATTAAA
42340206 TAATCAATTTTATACTTATTAAA
1 TAATCAATTTTATACTTATTAAA
42340229 T
1 T
42340230 TAAAATATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATCAATTTTATACTTATTAAA
Found at i:42343146 original size:15 final size:16
Alignment explanation
Indices: 42343128--42343164 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
42343118 TAGGGTCTAG
42343128 AATTTTA-GGATATAA
1 AATTTTAGGGATATAA
*
42343143 AA-TTTAGGGTTATAA
1 AATTTTAGGGATATAA
42343158 AATTTTA
1 AATTTTA
42343165 TAAAAACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 11 0.58
16 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (16 bp):
AATTTTAGGGATATAA
Found at i:42343563 original size:14 final size:14
Alignment explanation
Indices: 42343544--42343583 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42343534 TTGATTGTCA
42343544 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
42343558 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
42343572 GGAAAATGTTTT
1 GTAAAATGTTTT
42343584 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:42348388 original size:20 final size:20
Alignment explanation
Indices: 42348363--42348400 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
42348353 CTTTTCGTTC
42348363 ACAATCACAATACGTAATAG
1 ACAATCACAATACGTAATAG
42348383 ACAATCACAATACGTAAT
1 ACAATCACAATACGTAAT
42348401 TTAGGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (20 bp):
ACAATCACAATACGTAATAG
Found at i:42351954 original size:27 final size:27
Alignment explanation
Indices: 42351915--42352008 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
42351905 AAAGGTTGTT
* * * *
42351915 AAATAATCGTAATGCCCTTGTAGGATA
1 AAATGATCGTAATGCCCCTATAGGGTA
*
42351942 AAATGATCATAATGCCCCTATAGGGTA
1 AAATGATCGTAATGCCCCTATAGGGTA
* *
42351969 AAATGACCGTAATACCCCTATAGGGTA
1 AAATGATCGTAATGCCCCTATAGGGTA
42351996 AAATGATCGTAAT
1 AAATGATCGTAAT
42352009 ATTCTCGAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
AAATGATCGTAATGCCCCTATAGGGTA
Found at i:42352097 original size:24 final size:24
Alignment explanation
Indices: 42352045--42352103 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
42352035 TCTATGGTTA
42352045 AATGACTGATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTTGG
* * *
42352069 TATGACCGATTTGTTTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTGG
42352093 AATGACTGATT
1 AATGACTGATT
42352104 CTAAGCATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTGG
Found at i:42352335 original size:32 final size:32
Alignment explanation
Indices: 42352289--42352491 Score: 230
Period size: 32 Copynumber: 6.4 Consensus size: 32
42352279 GCTGTGATGC
* *
42352289 TACTAATGGCTTTGTGCCGGTCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
42352321 TACTGATGGCTTTGTACTGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
42352353 TACTGATGGCTTTGTGCTGATCATATTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATATTACT-GT
* * **
42352385 TACTGATGGCTTTATGTCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * * *
42352417 TACTGATGGCTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
42352449 TACTGATGGCTTTGTGCCAAACATATTACT-A
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
42352480 TACTTATGGCTT
1 TACTGATGGCTT
42352492 GTAGCCTGTT
Statistics
Matches: 144, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
31 12 0.08
32 132 0.92
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:42352413 original size:96 final size:96
Alignment explanation
Indices: 42352289--42352465 Score: 264
Period size: 96 Copynumber: 1.8 Consensus size: 96
42352279 GCTGTGATGC
* * ** * * * *
42352289 TACTAATGGCTTTGTGCCGGTCATATTACTGTTACTGATGGCTTTGTACTGATCATATTACTGTT
1 TACTAATGGCTTTATGCCGATCATATTACCATTACTGATGGCTGTGTACCGATCATATCACTGCT
42352354 ACTGATGGCTTTGTGCTGATCATATTATCGT
66 ACTGATGGCTTTGTGCTGATCATATTATCGT
* *
42352385 TACTGATGGCTTTATGTCGATCATATTACCATTACTGATGGCTGTGTACCGATCATATCACTGCT
1 TACTAATGGCTTTATGCCGATCATATTACCATTACTGATGGCTGTGTACCGATCATATCACTGCT
42352450 ACTGATGGCTTTGTGC
66 ACTGATGGCTTTGTGC
42352466 CAAACATATT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 71 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (96 bp):
TACTAATGGCTTTATGCCGATCATATTACCATTACTGATGGCTGTGTACCGATCATATCACTGCT
ACTGATGGCTTTGTGCTGATCATATTATCGT
Found at i:42356303 original size:23 final size:25
Alignment explanation
Indices: 42356255--42356310 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
42356245 TATAGTTATG
42356255 AAAAATAATTACATATATAAAATAA
1 AAAAATAATTACATATATAAAATAA
**
42356280 AAAAATAATTACATA-AT-ATTTAA
1 AAAAATAATTACATATATAAAATAA
42356303 AAAAATAA
1 AAAAATAA
42356311 ATATGCGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 12 0.41
24 2 0.07
25 15 0.52
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATAATTACATATATAAAATAA
Found at i:42358088 original size:128 final size:132
Alignment explanation
Indices: 42357804--42358091 Score: 313
Period size: 128 Copynumber: 2.2 Consensus size: 132
42357794 CTTCAATCTA
* * * *
42357804 CTCCTCTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGCTCTCTGCAACTTCAGAGAATAAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCACTGCAACTTCAAAGAATAAG
* * * *
42357869 ATCCAAGATTTGTGGTTCTAATCCGCTCCATTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
66 ATCCAAGA-TTGT-GTTCTAATCCGCTCCACTGCAACTTCAGGAGGATAAGACTTGATCACTTAA
*
42357934 TCTG
129 CCTG
* ** * * *
42357938 CTCCACTACCTCTTCAGAGAGATAAGACTAGATGCGATCTGCTCACTGCAACTTCAAAGAGTTAT
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCACTGCAACTTCAAAGA-ATAA
*
42358003 GATCCAA-A-T-T-TT-TAATCCGCTCCACTGCAACTTCAGG-GAGATAGGA-TT-ATCAGCTTT
65 GATCCAAGATTGTGTTCTAATCCGCTCCACTGCAACTTCAGGAG-GATAAGACTTGATCA-C-TT
42358060 AACCTG
127 AACCTG
*
42358066 CTCCACTGTAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
42358092 GTTTCCAATC
Statistics
Matches: 129, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
126 2 0.02
127 4 0.03
128 57 0.44
129 2 0.02
131 1 0.01
132 1 0.01
134 53 0.41
135 9 0.07
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCACTGCAACTTCAAAGAATAAG
ATCCAAGATTGTGTTCTAATCCGCTCCACTGCAACTTCAGGAGGATAAGACTTGATCACTTAACC
TG
Found at i:42358165 original size:44 final size:43
Alignment explanation
Indices: 42357893--42358400 Score: 151
Period size: 44 Copynumber: 11.7 Consensus size: 43
42357883 GTTCTAATCC
*
42357893 GCTCCATTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
1 GCTCCACTGCAACTTCAGGAGGATAAGACTTGC-TACTTAGTCT
* ** * * * *
42357937 GCTCCACTACCTCTTCA-GAGAGATAAGACTAGATGC-GA-TCT
1 GCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTACTTAGTCT
* * * **** ** * *
42357978 GCT-CACTGCAACTTCA-AAGAGTTATGATCCAAATTTTTAATCC
1 GCTCCACTGCAACTTCAGGAG-GATAAGA-CTTGCTACTTAGTCT
* * **
42358021 GCTCCACTGCAACTTCAGG-GAGATAGGA-TT-ATCAGCTTTAACCT
1 GCTCCACTGCAACTTCAGGAG-GATAAGACTTGCT-A-C-TTAGTCT
* ** * * *
42358065 GCTCCACTGTAACTTCAGG-GAGATAAGGTTTCCAATCTGCAGTCT
1 GCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTA-CT-TAGTCT
42358110 GC-CTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
1 GCTC-CACTGCAACTTCAGGAGGATAAGACTTGC-TACTTAGTCT
* **
42358154 GCTCCACTGCAACTTCA-GAGAGATAAGACTAG--A-TGGGATCT
1 GCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTACTTAG-TCT
* * * ** * * * *
42358195 GCT-CTCTACAACTTCA-GAGAGATAATATCCAAGGTTC-TAATCC
1 GCTCCACTGCAACTTCAGGAG-GATAAGA--CTTGCTACTTAGTCT
* * **
42358238 GCTCCACTGCAACTTC-GGGGAGATAGGACTATCGGCT--TTAACCT
1 GCTCCACTGCAACTTCAGGAG-GATAAGACT-T--GCTACTTAGTCT
* * ** *
42358282 GCTCTACTGCAACTTCAGGAAGATAAGGTTTGCAATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGAGGATAAGACTTGCTA-CTT-AGTCT
*
42358327 GC-CTCACTGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCT
1 GCTC-CACTGCAACTTCAGGAGGATAAGACTTGC-TACTTAGTCT
*
42358371 GCTCCCCTGCAACTTCAAGGA-GATAAGACT
1 GCTCCACTGCAACTTC-AGGAGGATAAGACT
42358401 AGATGGGATC
Statistics
Matches: 343, Mismatches: 83, Indels: 76
0.68 0.17 0.15
Matches are distributed among these distances:
40 41 0.12
41 21 0.06
42 6 0.02
43 19 0.06
44 177 0.52
45 76 0.22
46 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGAGGATAAGACTTGCTACTTAGTCT
Found at i:42358278 original size:217 final size:217
Alignment explanation
Indices: 42357900--42358482 Score: 891
Period size: 217 Copynumber: 2.7 Consensus size: 217
42357890 TCCGCTCCAT
* **
42357900 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTACCTCTTCAGAGAGATAAGA
1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
* * * * *
42357965 CTAGATGCGATCTGCTCACTGCAACTTCAAAGAG-TTATGATCCAAATTTTTAATCCGCTCCACT
66 CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAGATAAT-ATCCAAAGTTTTAATCCGCTCCACT
* * *
42358029 GCAACTTCAGGGAGATAGGATTATCAGCTTTAACCTGCTCCACTGTAACTTCAGGGAGATAAGGT
130 GCAACTTCAGGGAGATAGGACTATCAGCTTTAACCTGCTCCACTGCAACTTCAGGAAGATAAGGT
42358094 TTCCAATCTGCAGTCTGCCTCAC
195 TTCCAATCTGCAGTCTGCCTCAC
42358117 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
* * *
42358182 CTAGATGGGATCTGCTCTCTACAACTTCAGAGAGATAATATCCAAGGTTCTAATCCGCTCCACTG
66 CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAGATAATATCCAAAGTTTTAATCCGCTCCACTG
* * *
42358247 CAACTTCGGGGAGATAGGACTATCGGCTTTAACCTGCTCTACTGCAACTTCAGGAAGATAAGGTT
131 CAACTTCAGGGAGATAGGACTATCAGCTTTAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTT
* *
42358312 TGCAATCTTCAGTCTGCCTCAC
196 TCCAATCTGCAGTCTGCCTCAC
* *
42358334 TGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCTGCTCCCCTGCAACTTCA-AGGAGATAAG
1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGA-GAGATAAG
* * * *
42358398 ACTAGATGGGATCTACTCTCTGCAACTTCAGAGAGATAAGATCCAATGTTTTAATCCTCTCCACT
65 ACTAGATGGGATCTGCTCTCTGCAACTTCAGAGAGATAATATCCAAAGTTTTAATCCGCTCCACT
* *
42358463 GTAACTTCAGGGAAATAGGA
130 GCAACTTCAGGGAGATAGGA
42358483 TTATTGGCCA
Statistics
Matches: 334, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
216 1 0.00
217 330 0.99
218 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAGATAATATCCAAAGTTTTAATCCGCTCCACTG
CAACTTCAGGGAGATAGGACTATCAGCTTTAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTT
TCCAATCTGCAGTCTGCCTCAC
Found at i:42363007 original size:119 final size:121
Alignment explanation
Indices: 42362795--42363038 Score: 456
Period size: 119 Copynumber: 2.0 Consensus size: 121
42362785 ATATTAAACT
*
42362795 AATTAAATAAAAGAAATAAAATATAGAAAAAAAAGAATAGAAACAGGATAGGCAAATGAAACAGA
1 AATTAAATAAAAGAAATAAAAGATAGAAAAAAAAGAATAGAAACAGGATAGGCAAATGAAACAGA
42362860 GAAGGAAAGAAGGAAAGAAAGAAAAGGGAAAATTTAGGTTTTGAGG-TTCAAGCTC
66 GAAGGAAAGAAGGAAAGAAAGAAAAGGGAAAATTTAGGTTTTGAGGTTTCAAGCTC
*
42362915 AATTAAATAAAAGAAATAAAAGATAG-AAAAAGAGAATAGAAACAGGATAGGCAAATGAAACAGA
1 AATTAAATAAAAGAAATAAAAGATAGAAAAAAAAGAATAGAAACAGGATAGGCAAATGAAACAGA
42362979 GAAGGAAAGAAGGAAAGAAAGAAAAGGGAAAATTTAGGTTTTGAGGTTTCAAGCTC
66 GAAGGAAAGAAGGAAAGAAAGAAAAGGGAAAATTTAGGTTTTGAGGTTTCAAGCTC
42363035 AATT
1 AATT
42363039 GATAAGTCAA
Statistics
Matches: 121, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 83 0.69
120 38 0.31
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.16
Consensus pattern (121 bp):
AATTAAATAAAAGAAATAAAAGATAGAAAAAAAAGAATAGAAACAGGATAGGCAAATGAAACAGA
GAAGGAAAGAAGGAAAGAAAGAAAAGGGAAAATTTAGGTTTTGAGGTTTCAAGCTC
Found at i:42364185 original size:45 final size:45
Alignment explanation
Indices: 42364115--42364215 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
42364105 GCCGACTACT
* * * *
42364115 GTTACTGTTTCCGATTCGGCGCTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTTACC
* * *
42364160 GTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATATTGTTACT
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTTACC
42364205 GTTACTGTTAC
1 GTTACTGTTAC
42364216 TGTTACTACT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTTACC
Found at i:42364209 original size:6 final size:6
Alignment explanation
Indices: 42364198--42364222 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42364188 TGTTGAATAT
42364198 TGTTAC TGTTAC TGTTAC TGTTAC T
1 TGTTAC TGTTAC TGTTAC TGTTAC T
42364223 ACTTCCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTTAC
Found at i:42365352 original size:17 final size:17
Alignment explanation
Indices: 42365311--42365353 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
42365301 ACGTGGCATG
* *
42365311 TACCTAAATAATGTATA
1 TACCTAAGTAATATATA
42365328 TACCTAAGTAATATATA
1 TACCTAAGTAATATATA
42365345 TACCTAAGT
1 TACCTAAGT
42365354 GATGTAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATATATA
Found at i:42367182 original size:27 final size:26
Alignment explanation
Indices: 42367134--42367185 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42367124 ACGCGCCCTT
* * *
42367134 CTTCTTTTCTGTCTTTTTTCTGGCTC
1 CTTCTTTTCTGTCCTCTGTCTGGCTC
42367160 CTTCTTTCTCTGTCCTCTGTCTGGCT
1 CTTCTTT-TCTGTCCTCTGTCTGGCT
42367186 TGTATCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.00, C:0.31, G:0.13, T:0.56
Consensus pattern (26 bp):
CTTCTTTTCTGTCCTCTGTCTGGCTC
Found at i:42380305 original size:9 final size:9
Alignment explanation
Indices: 42380282--42380314 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
42380272 TAAATATATG
42380282 TATATATAAA
1 TATATA-AAA
42380292 T-TATAAAA
1 TATATAAAA
42380300 TATATAAAA
1 TATATAAAA
42380309 TATATA
1 TATATA
42380315 TAAGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 17 0.77
10 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAA
Found at i:42380305 original size:20 final size:19
Alignment explanation
Indices: 42380254--42380305 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
42380244 AAAAATTTAG
* *
42380254 AAAATATGTATATAGATAT
1 AAAATATATATATAAATAT
42380273 AAATATATGTATATATAAATTAT
1 AAA-ATA--TATATATAAA-TAT
42380296 AAAATATATA
1 AAAATATATA
42380306 AAATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
22 11 0.41
23 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (19 bp):
AAAATATATATATAAATAT
Found at i:42380331 original size:51 final size:50
Alignment explanation
Indices: 42380173--42380336 Score: 125
Period size: 51 Copynumber: 3.1 Consensus size: 50
42380163 ATGGATGTAA
** * * *
42380173 ATATGTATATGCAAATTAGAAAGTATAAAAA-ATATATAAGTACGTACATAT
1 ATATGTATATATAAATTATAAAATATAAAAATATATATAAGTATGT--ATAT
* * * * * * *
42380224 AAATATATATATATACTTATAAAAATTTAGAAAATATGTATATAG-ATATAAAT
1 ATATGTATATATA-AATTAT-AAAATATA-AAAATATATATA-AGTATGTATAT
42380277 ATATGTATATATAAATTATAAAATATATAAAATATATATAAGTATGTATGTAT
1 ATATGTATATATAAATTATAAAATATA-AAAATATATATAAGTATGTA--TAT
42380330 ATATGTA
1 ATATGTA
42380337 CCTGTCATAA
Statistics
Matches: 85, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
50 2 0.02
51 31 0.36
52 9 0.11
53 29 0.34
54 4 0.05
55 8 0.09
56 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (50 bp):
ATATGTATATATAAATTATAAAATATAAAAATATATATAAGTATGTATAT
Found at i:42380335 original size:53 final size:52
Alignment explanation
Indices: 42380173--42380336 Score: 138
Period size: 53 Copynumber: 3.1 Consensus size: 52
42380163 ATGGATGTAA
** * * * *
42380173 ATATGTATATGCAAATTAGAAAGTATAAAAA-ATATATAAGTACGTACATAT
1 ATATGTATATATAAATTATAAAATATAAAAATATATATAAGTATGTATATAT
* * * * * *
42380224 AAATATATATATATACTTATAAAAATTTAGAAAATATGTAT-A-TA-GATATAAAT
1 ATATGTATATATA-AATTAT-AAAATATA-AAAATATATATAAGTATG-TATATAT
*
42380277 ATATGTATATATAAATTATAAAATATATAAAATATATATAAGTATGTATGTAT
1 ATATGTATATATAAATTATAAAATATA-AAAATATATATAAGTATGTATATAT
42380330 ATATGTA
1 ATATGTA
42380337 CCTGTCATAA
Statistics
Matches: 86, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
51 26 0.30
52 11 0.13
53 38 0.44
54 6 0.07
55 5 0.06
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (52 bp):
ATATGTATATATAAATTATAAAATATAAAAATATATATAAGTATGTATATAT
Found at i:42380509 original size:3 final size:3
Alignment explanation
Indices: 42380437--42380493 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
42380427 AAATAGAAAT
* * *
42380437 ATA ACA ATA ATA ACA ATA AT- ATA GATA ATA ATA CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
42380482 ATA ATA ATA ATA
1 ATA ATA ATA ATA
42380494 TATTAGTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:42395179 original size:27 final size:27
Alignment explanation
Indices: 42395138--42395205 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
42395128 ATACATGAAT
*
42395138 TCATTTCA-ATATTCATATCCCATTTCA
1 TCATTTCATAT-TTCATATCCCATCTCA
* *
42395165 TCATTTCATATTTCATTTCTCATCTCA
1 TCATTTCATATTTCATATCCCATCTCA
*
42395192 T-A-TTCATTTTTCAT
1 TCATTTCATATTTCAT
42395206 CCTTGTCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.31
26 1 0.03
27 22 0.61
28 2 0.06
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (27 bp):
TCATTTCATATTTCATATCCCATCTCA
Found at i:42395192 original size:19 final size:18
Alignment explanation
Indices: 42395158--42395206 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
42395148 ATTCATATCC
*
42395158 CATTTCATCATTTCATATTT
1 CATTTC-TCATCTCATA-TT
42395178 CATTTCTCATCTCATATT
1 CATTTCTCATCTCATATT
*
42395196 CATTTTTCATC
1 CATTTCTCATC
42395207 CTTGTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 6 0.22
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (18 bp):
CATTTCTCATCTCATATT
Found at i:42400324 original size:27 final size:27
Alignment explanation
Indices: 42400302--42400443 Score: 86
Period size: 27 Copynumber: 5.3 Consensus size: 27
42400292 TGACAAACAT
**
42400302 TACTCTTACATATTTCGCCACAAAGGC
1 TACTCTTACATATTTCGCCACAAAAAC
* *
42400329 TACTATTACATATTTTGCCACAAAAAC
1 TACTCTTACATATTTCGCCACAAAAAC
* * ** ** ***
42400356 AACTCTTTCATATTTTACGGCAACGGC
1 TACTCTTACATATTTCGCCACAAAAAC
* * *
42400383 TATTCTTCCATATTTCACCACAAAAAC
1 TACTCTTACATATTTCGCCACAAAAAC
* * ** *
42400410 TAATCTTTCATATTTTTCCACAAATAC
1 TACTCTTACATATTTCGCCACAAAAAC
*
42400437 TAGTCTT
1 TACTCTT
42400444 TCCTGACATG
Statistics
Matches: 87, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (27 bp):
TACTCTTACATATTTCGCCACAAAAAC
Found at i:42401405 original size:2 final size:2
Alignment explanation
Indices: 42401393--42401428 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42401383 TGAAAATCCA
*
42401393 AT AT TT 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
42401429 CTAGTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:42403237 original size:11 final size:11
Alignment explanation
Indices: 42403221--42403251 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42403211 GAGGGAGTAG
42403221 TTTATTTTTGA
1 TTTATTTTTGA
*
42403232 TTTATTTTAGA
1 TTTATTTTTGA
42403243 TTTATTTTT
1 TTTATTTTT
42403252 TTAAGTGTTT
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:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTATTTTTGA
Found at i:42407548 original size:20 final size:20
Alignment explanation
Indices: 42407507--42407551 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42407497 GTTACACGGT
*
42407507 CGTGTGCCTTTCCACACGGG
1 CGTGTGCCTTTCCACACAGG
*
42407527 CGTGTGTCTCTTCCA-ACAGG
1 CGTGTGCCT-TTCCACACAGG
42407547 CGTGT
1 CGTGT
42407552 TGACCCCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.11, C:0.31, G:0.29, T:0.29
Consensus pattern (20 bp):
CGTGTGCCTTTCCACACAGG
Found at i:42410246 original size:22 final size:22
Alignment explanation
Indices: 42410221--42410263 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42410211 CGATTTGAGT
*
42410221 GCATGAATGATTAAAGCAAATA
1 GCATGAATGATTAAAACAAATA
42410243 GCATGAATGATTAAAACAAAT
1 GCATGAATGATTAAAACAAAT
42410264 TTGATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (22 bp):
GCATGAATGATTAAAACAAATA
Found at i:42413584 original size:26 final size:27
Alignment explanation
Indices: 42413547--42413600 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
42413537 AACAATCATT
42413547 GCATAGTCATGAAATAAGCAAAGAAAA
1 GCATAGTCATGAAATAAGCAAAGAAAA
* *
42413574 GCAT-GTCATGAACTAAGCAAATAAAA
1 GCATAGTCATGAAATAAGCAAAGAAAA
42413600 G
1 G
42413601 AAAATTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.17
Consensus pattern (27 bp):
GCATAGTCATGAAATAAGCAAAGAAAA
Found at i:42417178 original size:18 final size:19
Alignment explanation
Indices: 42417140--42417179 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
42417130 ATCGAGTTTC
*
42417140 ATTCATTTTATCAAGACTT
1 ATTCATTTTATCAAGAATT
*
42417159 ATTCA-TTTATCAGGAATT
1 ATTCATTTTATCAAGAATT
42417177 ATT
1 ATT
42417180 GAATATGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTCATTTTATCAAGAATT
Found at i:42423174 original size:25 final size:25
Alignment explanation
Indices: 42423143--42423192 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
42423133 TTGTGTTTAA
42423143 AAATTTAACATTTTAGTCAATATTT
1 AAATTTAACATTTTAGTCAATATTT
*
42423168 AAATTTAACATTTTAGTTAATATTT
1 AAATTTAACATTTTAGTCAATATTT
42423193 TTATTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (25 bp):
AAATTTAACATTTTAGTCAATATTT
Found at i:42431890 original size:73 final size:74
Alignment explanation
Indices: 42431745--42431901 Score: 176
Period size: 73 Copynumber: 2.1 Consensus size: 74
42431735 CGCAGCTATT
* * * * * **
42431745 ATGAACGTCCCGTTAAATGGCTCTTCGTGAGCTTCCTAATTATTGGCTCTCCGGAGCTTCCCGAT
1 ATGAACTTCCCGATAAATGGATATTCGTGAGCTTCCTAATTAATGGCTCTCCAAAGCTTCCCGAT
42431810 ATGGCTCGC
66 ATGGCTCGC
* * *
42431819 TTGAACTTCCCGATAAATGGATATTCG-GAGCTTCCT-ATTAATGGCTCTTCAAAG-TTACCCGT
1 ATGAACTTCCCGATAAATGGATATTCGTGAGCTTCCTAATTAATGGCTCTCCAAAGCTT-CCCGA
42431881 TATTGGCTCGC
65 TA-TGGCTCGC
*
42431892 ATGAGCTTCC
1 ATGAACTTCC
42431902 TGATTATGGC
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
71 2 0.03
72 20 0.29
73 25 0.36
74 22 0.32
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (74 bp):
ATGAACTTCCCGATAAATGGATATTCGTGAGCTTCCTAATTAATGGCTCTCCAAAGCTTCCCGAT
ATGGCTCGC
Found at i:42431911 original size:24 final size:23
Alignment explanation
Indices: 42431879--42431931 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
42431869 AAAGTTACCC
42431879 GTTATTGGCTCGCATGAGCTTCCT
1 GTTA-TGGCTCGCATGAGCTTCCT
**
42431903 GATTATGGCTCTTATGAGCTTCCT
1 G-TTATGGCTCGCATGAGCTTCCT
42431927 GTTAT
1 GTTAT
42431932 ACAGCCCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 19 0.73
25 3 0.12
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (23 bp):
GTTATGGCTCGCATGAGCTTCCT
Found at i:42431969 original size:25 final size:25
Alignment explanation
Indices: 42431941--42431988 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42431931 TACAGCCCGA
**
42431941 ATAAGCTTTTCATTACATGGCTCAC
1 ATAAGCTTCCCATTACATGGCTCAC
*
42431966 ATAAGCTTCCCATTATATGGCTC
1 ATAAGCTTCCCATTACATGGCTC
42431989 GAGAGAGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (25 bp):
ATAAGCTTCCCATTACATGGCTCAC
Found at i:42432702 original size:24 final size:23
Alignment explanation
Indices: 42432670--42432722 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
42432660 AAAGTTACCC
42432670 GTTATTGGCTCGCATGAGCTTCCT
1 GTTA-TGGCTCGCATGAGCTTCCT
**
42432694 GATTATGGCTCTTATGAGCTTCCT
1 G-TTATGGCTCGCATGAGCTTCCT
42432718 GTTAT
1 GTTAT
42432723 ACAGCCCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 19 0.73
25 3 0.12
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (23 bp):
GTTATGGCTCGCATGAGCTTCCT
Found at i:42432760 original size:25 final size:25
Alignment explanation
Indices: 42432732--42432779 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42432722 TACAGCCCGA
**
42432732 ATAAGCTTTTCATTACATGGCTCAC
1 ATAAGCTTCCCATTACATGGCTCAC
*
42432757 ATAAGCTTCCCATTATATGGCTC
1 ATAAGCTTCCCATTACATGGCTC
42432780 GAGAGAGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (25 bp):
ATAAGCTTCCCATTACATGGCTCAC
Found at i:42433678 original size:25 final size:24
Alignment explanation
Indices: 42433612--42433751 Score: 101
Period size: 26 Copynumber: 5.7 Consensus size: 24
42433602 GTCCTGTTAT
*
42433612 ATGGCTCTTCGTGAGCTTTCCAATTA
1 ATGGCTCTTCG-GAGC-TTCCGATTA
* *
42433638 AAGGCTCTTTGTGAGCTTCCTGATTA
1 ATGGCTCTTCG-GAGCTTCC-GATTA
42433664 ATGGCTCTTCGGAGCTTCCCGA-T-
1 ATGGCTCTTCGGAGCTT-CCGATTA
*
42433687 ATGGCTCGCTT--GAACTTCCCGA-TA
1 ATGGCT--CTTCGGAGCTT-CCGATTA
* * *
42433711 TATGGCTATCCGGAGCTTCCCATTA
1 -ATGGCTCTTCGGAGCTTCCGATTA
42433736 ATGGCTCTTCGGAGCT
1 ATGGCTCTTCGGAGCT
42433752 ACCCGTTATT
Statistics
Matches: 93, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
23 18 0.19
24 18 0.19
25 28 0.30
26 29 0.31
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (24 bp):
ATGGCTCTTCGGAGCTTCCGATTA
Found at i:42433825 original size:25 final size:25
Alignment explanation
Indices: 42433797--42433866 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
42433787 GCTCTTATGG
* *
42433797 GCTTCCCGTTATATAGCTCGGATAA
1 GCTTCCTGTTATATAGCTCGCATAA
* * * *
42433822 GCTTCCTGTTACATTGCTCACATGA
1 GCTTCCTGTTATATAGCTCGCATAA
*
42433847 GCTTCCTGTTATATGGCTCG
1 GCTTCCTGTTATATAGCTCG
42433867 AGAGAGGGTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (25 bp):
GCTTCCTGTTATATAGCTCGCATAA
Found at i:42437381 original size:13 final size:13
Alignment explanation
Indices: 42437363--42437387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42437353 TAAAAAGCAT
42437363 AAAAGTTATAAAC
1 AAAAGTTATAAAC
42437376 AAAAGTTATAAA
1 AAAAGTTATAAA
42437388 AATTTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAGTTATAAAC
Found at i:42442627 original size:14 final size:14
Alignment explanation
Indices: 42442608--42442648 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
42442598 TCTGTGATTA
42442608 AATTTTAAAGGTAT
1 AATTTTAAAGGTAT
42442622 AATTTTAAA---AT
1 AATTTTAAAGGTAT
42442633 AATTTTAAAGGTAT
1 AATTTTAAAGGTAT
42442647 AA
1 AA
42442649 CGACTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.46
14 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (14 bp):
AATTTTAAAGGTAT
Found at i:42443092 original size:28 final size:29
Alignment explanation
Indices: 42443053--42443121 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 29
42443043 ATAAAAATTA
42443053 ACCAAAATATTATAAC-TTTTTT-TTATTT
1 ACCAAAATA-TATAACTTTTTTTATTATTT
42443081 ACCAAAATAT-T-ACTTTTTTTATTATTT
1 ACCAAAATATATAACTTTTTTTATTATTT
*
42443108 ACGAAAATATATAA
1 ACCAAAATATATAA
42443122 AAAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 2 0.06
26 7 0.19
27 16 0.44
28 10 0.28
29 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (29 bp):
ACCAAAATATATAACTTTTTTTATTATTT
Found at i:42443223 original size:27 final size:27
Alignment explanation
Indices: 42443185--42443263 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
42443175 GGCTAATTAC
42443185 ATTGGCGGCACCAAAT-GTGCCAAAGAG
1 ATTGGCGGCACC-AATGGTGCCAAAGAG
* *
42443212 ATTGGTGGCACCAATGGTGCCAAAGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
42443239 ACTGCCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
42443264 GACTAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 3 0.07
27 43 0.93
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:42443364 original size:19 final size:19
Alignment explanation
Indices: 42443337--42443406 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
42443327 TCAACTCATT
*
42443337 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
**
42443356 TTTTAATTTAATAA-AATA
1 TTTTAATTTAATAACTCTA
* *
42443374 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
42443393 TTTTAATTTAATAA
1 TTTTAATTTAATAA
42443407 ACTATTAAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:42443385 original size:37 final size:37
Alignment explanation
Indices: 42443342--42443412 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
42443332 TCATTTTTTT
42443342 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
*
42443379 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
42443413 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:42443727 original size:20 final size:19
Alignment explanation
Indices: 42443676--42443736 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
42443666 CTATTCTCAT
42443676 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
42443695 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
42443713 TATAAAATTAAAATAGAGTTA
1 T-T-AAATTAAAATAGAGTTA
42443734 TTA
1 TTA
42443737 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 4 0.12
19 14 0.42
20 11 0.33
21 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:42443958 original size:20 final size:19
Alignment explanation
Indices: 42443919--42443959 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42443909 TTAATAAACT
* *
42443919 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
42443938 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
42443958 TT
1 TT
42443960 GAAGGGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:42444094 original size:27 final size:27
Alignment explanation
Indices: 42444026--42444096 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
42444016 ATTTTAGTCA
* **
42444026 TTTGGCACCATTGGAGCCGGCAATCAC
1 TTTGGCACCATTGGTGCCACCAATCAC
*
42444053 TTTGGCACCATTGGTGCCACCAATCTC
1 TTTGGCACCATTGGTGCCACCAATCAC
*
42444080 TTTGGCACCTTTGGTGC
1 TTTGGCACCATTGGTGC
42444097 AGCCAATGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.30
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCACCAATCAC
Done.