Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 22 of 213
Found at i:5708469 original size:10 final size:9
Alignment explanation
Indices: 5708454--5708487 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5708444 TTTTTTTTGT
*
5708454 AATTTTGAC
1 AATTTTTAC
5708463 AATTTTTTAC
1 AA-TTTTTAC
5708473 AATTTTTAC
1 AATTTTTAC
5708482 AATTTT
1 AATTTT
5708488 AAATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (9 bp):
AATTTTTAC
Found at i:5708752 original size:95 final size:95
Alignment explanation
Indices: 5708584--5708768 Score: 221
Period size: 95 Copynumber: 1.9 Consensus size: 95
5708574 TATAAAGAAC
* * ** * * * *
5708584 TTATTTAATATGTTAATTAAAAAGTACTAATTAATCCAAATCTTAATCCCTAACCCGACTCCAAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAACCTTAAACCATAACCCAACTCCAAA
*
5708649 TCCATAACCCCTAACCCCT-AACCCTAAACT
66 CCCATAACCCCTAA-CCCTAAACCCTAAACT
* *
5708679 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCATAACCCAA-TCCCTA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAACCTTAAACCATAACCCAACT-CCAA
* *
5708743 ACCCCTAACCCTTAACCCTAAACCCT
65 ACCCATAACCCCTAACCCTAAACCCT
5708769 TAAATCATAA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
94 5 0.07
95 70 0.93
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.29
Consensus pattern (95 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAACCTTAAACCATAACCCAACTCCAAA
CCCATAACCCCTAACCCTAAACCCTAAACT
Found at i:5708908 original size:7 final size:7
Alignment explanation
Indices: 5708898--5708936 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
5708888 CTCTTAACAT
5708898 CTAACCC
1 CTAACCC
5708905 CTAACCC
1 CTAACCC
5708912 CTAACCC
1 CTAACCC
*
5708919 ATAACCC
1 CTAACCC
* *
5708926 ATAACCA
1 CTAACCC
5708933 CTAA
1 CTAA
5708937 TCTATAAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:5708995 original size:14 final size:15
Alignment explanation
Indices: 5708973--5709006 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5708963 CTTAAACCAG
*
5708973 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
5708987 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
5709002 AATCT
1 AATCT
5709007 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:5709453 original size:114 final size:113
Alignment explanation
Indices: 5709316--5709574 Score: 262
Period size: 114 Copynumber: 2.3 Consensus size: 113
5709306 GCTGAAGTAG
* * *
5709316 TTTTGCGGCGCTTTCCCAAAAACGCCGCTAA-TACTATTC-TTTAGCGGCGTTTCACC-ATAAAC
1 TTTTGCGGCGCTTTACAAAAAACGCCACTAATTA-TATTCTTTTA-CGGCGTTTCACCAAT-AAC
* * *
5709378 GCCAC-AAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTA
63 GCCACTAAA-ACTAATATACCTC-AAACCAAACGCTGCGTTTTCGTTAAGATA
* ****
5709430 TTTTGCGGCGC-TTACAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAATAACGC
1 TTTTGCGGCGCTTTACAAA-AAACGCCACTAATTATATTCTTTTACGGCGTTTCACCAATAACGC
* *
5709494 CACTAAAACTAATCTACCTCAAACCAAACGGTGCGTTTTCGTTAAGATA
65 CACTAAAACTAATATACCTCAAACCAAACGCTGCGTTTTCGTTAAGATA
* **
5709543 -TTTGCGGCGTTTTATC-GTAAACGCCACTAATT
1 TTTTGCGGCGCTTTA-CAAAAAACGCCACTAATT
5709575 CTAATATACC
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
112 23 0.19
113 34 0.28
114 54 0.44
115 11 0.09
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (113 bp):
TTTTGCGGCGCTTTACAAAAAACGCCACTAATTATATTCTTTTACGGCGTTTCACCAATAACGCC
ACTAAAACTAATATACCTCAAACCAAACGCTGCGTTTTCGTTAAGATA
Found at i:5709567 original size:73 final size:75
Alignment explanation
Indices: 5709489--5709626 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
5709479 TTTTTTTAAT
* * *
5709489 AACGCCACTAAAACTAATCTACC-TCAAACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCGGCG
1 AACGCCACTAAAACTAATATACCTTAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGCG
5709552 TTTTATCGTA
66 TTTTATCGTA
** * *
5709562 AACGCCACTAATTCTAATATACCTTAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
1 AACGCCACTAAAACTAATATACCTTAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGCG
5709627 CTAACAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 20 0.36
74 27 0.48
75 9 0.16
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (75 bp):
AACGCCACTAAAACTAATATACCTTAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGCG
TTTTATCGTA
Found at i:5709578 original size:187 final size:187
Alignment explanation
Indices: 5709359--5709700 Score: 567
Period size: 187 Copynumber: 1.8 Consensus size: 187
5709349 CTATTCTTTA
5709359 GCGGCGTTTCACCATAAACGCCACAAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTT
1 GCGGCGTTTCACCATAAACGCCACAAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTT
* * * *
5709424 AAGGTATTTTGCGGCGCTTACAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAAT
66 AAGGTATTTTGCGGCGCTAACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAA
5709489 AACGCCACTAAAACTAATCTACCTCAAACCAAACGGTGCGTTTTCGTTAAGATATTT
131 AACGCCACTAAAACTAATCTACCTCAAACCAAACGGTGCGTTTTCGTTAAGATATTT
* * * * *
5709546 GCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTTAAAACCAAACGCTGCGTTTTGGTT
1 GCGGCGTTTCACCATAAACGCCACAAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTT
5709611 AAGGTATTTTGCGGCGCTAACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAA
66 AAGGTATTTTGCGGCGCTAACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAA
* * * *
5709676 AAGGGCACTAATATTAATCTACCTC
131 AACGCCACTAAAACTAATCTACCTC
5709701 TGGTTAAGAT
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
187 142 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (187 bp):
GCGGCGTTTCACCATAAACGCCACAAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTT
AAGGTATTTTGCGGCGCTAACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAA
AACGCCACTAAAACTAATCTACCTCAAACCAAACGGTGCGTTTTCGTTAAGATATTT
Found at i:5710072 original size:188 final size:188
Alignment explanation
Indices: 5709754--5710133 Score: 575
Period size: 188 Copynumber: 2.0 Consensus size: 188
5709744 CTATTCTTTA
* ** * *
5709754 GCGGCGTTTTATAGAAAACGCCACTAATTCTGATATACAATTGATCCAAACGCTGCGTTTTGGTT
1 GCGGCGTTTTATAGAAAACGCCACTAATTCTAATATACAATAAAACCAAACGCTACGTTTTGGTT
** * * *
5709819 AAGGTATTTTGCGGTGCTTAAGAGTAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAAA
66 AAGGTATTTTGCGACGCTTAAGAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAA
* *
5709884 AACGCCACTAACACTAATCTACCTCAAGACCAAACGGTGTGTTTTCGTTAAGATATTT
131 AACGCCACTAACACTAATCTACCTCAAGACCAAACGCTGCGTTTTCGTTAAGATATTT
* * *
5709942 GCGGCGTTTTATCGTAAACGCCACTAATTCTAATATAC-CTCAAAACCAAACGCTACGTTTTGGT
1 GCGGCGTTTTATAGAAAACGCCACTAATTCTAATATACAAT-AAAACCAAACGCTACGTTTTGGT
5710006 TAAGGTATTTTGCGACGCTTACA-AATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTA
65 TAAGGTATTTTGCGACGCTTA-AGAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTA
* *
5710070 AAAACGCCACTAATACTAATCTACCTCGAGACCAAACGCTGCGTTTTCGTTAAGATATTT
129 AAAACGCCACTAACACTAATCTACCTCAAGACCAAACGCTGCGTTTTCGTTAAGATATTT
5710130 GCGG
1 GCGG
5710134 TGCTTTTTGT
Statistics
Matches: 173, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
187 1 0.01
188 171 0.99
189 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (188 bp):
GCGGCGTTTTATAGAAAACGCCACTAATTCTAATATACAATAAAACCAAACGCTACGTTTTGGTT
AAGGTATTTTGCGACGCTTAAGAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAA
AACGCCACTAACACTAATCTACCTCAAGACCAAACGCTGCGTTTTCGTTAAGATATTT
Found at i:5710072 original size:396 final size:397
Alignment explanation
Indices: 5709337--5710307 Score: 1457
Period size: 396 Copynumber: 2.4 Consensus size: 397
5709327 TTTCCCAAAA
* * * * *
5709337 ACGCCGCTAATACTATTCTTTAGCGGCGTTTCACCA-TAAACGCCACAAATTCTAATATAC-CTC
1 ACGCCGCTAATACTATTCTTTAGCGGCGTTTTA-TAGAAAACGCCACTAATTCTAATATACAAT-
**
5709400 AAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAAACGCCACTAATTAT
64 TGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTA-AAATAAACGCCACTAATTAT
*
5709465 GTTCTTTTACGGCGTTTTTTTAATAACGCCACTAAAACTAATCTACCTCAAACCAAACGGTGCGT
128 GTTCTTTTACGGCGTTTTTTTAAAAACGCCACTAAAACTAATCTACCTCAAACCAAACGGTGCGT
*
5709530 TTTCGTTAAGATATTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTTAAAACCAA
193 TTTCGTTAAGATATTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAA
* *
5709595 ACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTAACAAATAAACGCCACTAATGATGTTCTTTT
258 ACGCTACGTTTTGGTTAAGGTATTTTGCGACGCTAACAAATAAACGCCACTAATGATGTTCTTTT
* * *
5709660 ACGGCGTTTGTTTAAAAAGGGCACTAATATTAATCTACCT-CT-G-GTTAAGATATTTGCGGCGC
323 ACGGCGTTTGTTTAAAAACGCCACTAATACTAATCTACCTACTCGTGTTAAGATATTTGCGGCGC
* *
5709722 TTCTTGTGAT
388 TTCTTGTAAG
*
5709732 ACGCCGCTAATACTATTCTTTAGCGGCGTTTTATAGAAAACGCCACTAATTCTGATATACAATTG
1 ACGCCGCTAATACTATTCTTTAGCGGCGTTTTATAGAAAACGCCACTAATTCTAATATACAATTG
* * *
5709797 ATCCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGTGCTTAAGAGTAAACGCCACTAATTATGT
66 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAA-AATAAACGCCACTAATTATGT
* *
5709862 TCTTTTACGGCGTTTTTTTAAAAACGCCACTAACACTAATCTACCTCAAGACCAAACGGTGTGTT
130 TCTTTTACGGCGTTTTTTTAAAAACGCCACTAAAACTAATCTACCTCAA-ACCAAACGGTGCGTT
5709927 TTCGTTAAGATATTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAA
194 TTCGTTAAGATATTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAA
*
5709992 CGCTACGTTTTGGTTAAGGTATTTTGCGACGCTTACAAATAAACGCCACTAATGATGTTCTTTTA
259 CGCTACGTTTTGGTTAAGGTATTTTGCGACGCTAACAAATAAACGCCACTAATGATGTTCTTTTA
5710057 CGGCGTTTGTTTAAAAACGCCACTAATACTAATCTACCTCGAGACCAAACGCTGCGTTTTCGTTA
324 CGGCGTTTGTTTAAAAACGCCACTAATACTAATCTACCT---------A--CT-CG---T-GTTA
* *
5710122 AGATATTTGCGGTGCTTTTTGTAAG
373 AGATATTTGCGGCGCTTCTTGTAAG
* *
5710147 ACGCCGCTAATACTATTCTTTAGTGGCGTTTTATCGAAAACGCCACTAATTCTAATATACAATTG
1 ACGCCGCTAATACTATTCTTTAGCGGCGTTTTATAGAAAACGCCACTAATTCTAATATACAATTG
*
5710212 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGTTTAAAATAAACGCCACTAATTATGTT
66 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAAAATAAACGCCACTAATTATGTT
*
5710277 CTTTTACGGCGTTTTTTTAGAAACGCCACTA
131 CTTTTACGGCGTTTTTTTAAAAACGCCACTA
5710308 GTTGTTCTGG
Statistics
Matches: 520, Mismatches: 33, Indels: 27
0.90 0.06 0.05
Matches are distributed among these distances:
394 2 0.00
395 160 0.31
396 177 0.34
408 2 0.00
410 1 0.00
414 51 0.10
415 127 0.24
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (397 bp):
ACGCCGCTAATACTATTCTTTAGCGGCGTTTTATAGAAAACGCCACTAATTCTAATATACAATTG
AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAAAATAAACGCCACTAATTATGTT
CTTTTACGGCGTTTTTTTAAAAACGCCACTAAAACTAATCTACCTCAAACCAAACGGTGCGTTTT
CGTTAAGATATTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACG
CTACGTTTTGGTTAAGGTATTTTGCGACGCTAACAAATAAACGCCACTAATGATGTTCTTTTACG
GCGTTTGTTTAAAAACGCCACTAATACTAATCTACCTACTCGTGTTAAGATATTTGCGGCGCTTC
TTGTAAG
Found at i:5710202 original size:113 final size:113
Alignment explanation
Indices: 5709943--5710291 Score: 386
Period size: 113 Copynumber: 3.1 Consensus size: 113
5709933 AAGATATTTG
* * *
5709943 CGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTACGTTTTGGTTA
1 CGGCGTTTTATCGAAAACGCCACTAATTCTAATATACCTC-GAACCAAACGCTGCGTTTTGGTTA
* *
5710008 AGGTATTTTGCGACGCTTACAAATAAACGCCACTAATGATGTTCTTTTA
65 AGGTATTTTGCGGCGCTTACAAATAAACGCCACTAATGATATTCTTTTA
** * * *
5710057 CGGCGTTTGT-TTAAAAACGCCACTAATACTAATCTACCTCGAGACCAAACGCTGCGTTTTCGTT
1 CGGCGTTT-TATCGAAAACGCCACTAATTCTAATATACCTCGA-ACCAAACGCTGCGTTTTGGTT
* * **** *
5710121 AAGATA-TTTGCGGTGCTT-TTTGTAAGACGCCGCTAAT-ACTATTC-TTTA
64 AAGGTATTTTGCGGCGCTTACAAATAA-ACGCCACTAATGA-TATTCTTTTA
* * *
5710169 GTGGCGTTTTATCGAAAACGCCACTAATTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTT
1 -CGGCGTTTTATCGAAAACGCCACTAATTCTAATATAC-CTCGAACCAAACGCTGCGTTTTGGTT
* * *
5710234 AAGGTATTTTGCGGCGTTTA-AAATAAACGCCACTAATTATGTTCTTTTA
64 AAGGTATTTTGCGGCGCTTACAAATAAACGCCACTAATGATATTCTTTTA
5710283 CGGCGTTTT
1 CGGCGTTTT
5710292 TTTAGAAACG
Statistics
Matches: 190, Mismatches: 34, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
112 9 0.05
113 102 0.54
114 78 0.41
115 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (113 bp):
CGGCGTTTTATCGAAAACGCCACTAATTCTAATATACCTCGAACCAAACGCTGCGTTTTGGTTAA
GGTATTTTGCGGCGCTTACAAATAAACGCCACTAATGATATTCTTTTA
Found at i:5713422 original size:6 final size:6
Alignment explanation
Indices: 5713413--5713486 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
5713403 AAGAAAAAGA
* * * * *
5713413 AAAATC AAAATC AAAGTC AAAATG AAAATG AAAATG AAAAT- GAAA--
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
5713458 AAAATC AAAAATC AAAAATC AAAAT- AAAA
1 AAAATC -AAAATC -AAAATC AAAATC AAAA
5713487 AAACAAAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.05
5 7 0.12
6 37 0.62
7 13 0.22
ACGTcount: A:0.70, C:0.08, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:5713474 original size:14 final size:14
Alignment explanation
Indices: 5713456--5713495 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
5713446 ATGAAAATGA
5713456 AAAAAATCAAAAAT
1 AAAAAATCAAAAAT
*
5713470 CAAAAATC-AAAAT
1 AAAAAATCAAAAAT
*
5713483 AAAAAAACAAAAA
1 AAAAAATCAAAAA
5713496 CAAGAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAATCAAAAAT
Found at i:5713487 original size:20 final size:20
Alignment explanation
Indices: 5713458--5713495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5713448 GAAAATGAAA
* *
5713458 AAAATCAAAAATCAAAAATC
1 AAAATAAAAAAACAAAAATC
5713478 AAAATAAAAAAACAAAAA
1 AAAATAAAAAAACAAAAA
5713496 CAAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAATAAAAAAACAAAAATC
Found at i:5713498 original size:6 final size:7
Alignment explanation
Indices: 5713457--5713495 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5713447 TGAAAATGAA
5713457 AAAAATC
1 AAAAATC
5713464 AAAAATC
1 AAAAATC
5713471 AAAAATC
1 AAAAATC
*
5713478 -AAAATA
1 AAAAATC
*
5713484 AAAAAAC
1 AAAAATC
5713491 AAAAA
1 AAAAA
5713496 CAAGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAATC
Found at i:5714481 original size:7 final size:7
Alignment explanation
Indices: 5714469--5714510 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
5714459 TCTGAGTCAA
5714469 AAAAATG
1 AAAAATG
5714476 AAAAATG
1 AAAAATG
*
5714483 -AGAATG
1 AAAAATG
5714489 AAAAATG
1 AAAAATG
5714496 AAAAA-G
1 AAAAATG
5714502 AAAAATG
1 AAAAATG
5714509 AA
1 AA
5714511 GAGGCTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:5714490 original size:13 final size:13
Alignment explanation
Indices: 5714470--5714510 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
5714460 CTGAGTCAAA
5714470 AAAATGAAAAATG
1 AAAATGAAAAATG
*
5714483 AGAATGAAAAATG
1 AAAATGAAAAATG
*
5714496 AAAAAGAAAAATG
1 AAAATGAAAAATG
5714509 AA
1 AA
5714511 GAGGCTAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:5714508 original size:20 final size:20
Alignment explanation
Indices: 5714469--5714510 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5714459 TCTGAGTCAA
*
5714469 AAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAATG
5714489 AAAAATGAAAAA-GAAAAATG
1 AAAAATGAAAAATG-AAAATG
5714509 AA
1 AA
5714511 GAGGCTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:5715893 original size:85 final size:85
Alignment explanation
Indices: 5715787--5716068 Score: 300
Period size: 87 Copynumber: 3.3 Consensus size: 85
5715777 CTAGTAATCC
*
5715787 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACAGCAG
1 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
*
5715852 AGTTGATCGCATCAGGTATT
66 AGTAGATCGCATCAGGTATT
* * ** ** ** * * *
5715872 ATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCA-GATATTATCTCCCT-AATATTACA
1 ATCTCCCTGAGATTACAGTGGAGCGGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAA-GTTACA
* * * * *
5715935 GCAGAGCAGATTGAAGCTA-GTAACCT
62 GCAGAGTAGATCGCATC-AGGT-A-TT
5715961 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
1 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
*
5716026 AGTAGATCGCATCAGGTCTT
66 AGTAGATCGCATCAGGTATT
*
5716046 ATCTCCCTGAGGTTACAGTGGAG
1 ATCTCCCTGAGATTACAGTGGAG
5716069 TAGATCGAAG
Statistics
Matches: 151, Mismatches: 36, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
85 46 0.30
86 7 0.05
87 66 0.44
88 8 0.05
89 24 0.16
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (85 bp):
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
AGTAGATCGCATCAGGTATT
Found at i:5715920 original size:87 final size:86
Alignment explanation
Indices: 5715721--5716109 Score: 290
Period size: 87 Copynumber: 4.5 Consensus size: 86
5715711 CCCCAGGAAA
* * * * * *
5715721 TAGACCGAAGAATTTTAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGCTA-GTAA
1 TAGA-CGAAGAATTTCAGATCTTATCTCCCTGAAG-TTACAGCAGAGTAGATCGCATC-AGGT-A
* *
5715784 TCCATCTCCCTGAGATTACAGTGGAG
62 T-TATCTCCCTGAGGTTACAGTGGAG
** ** ** ** *
5715810 CGGATTAA-AA-TAAAGGATCTTATCTATCTGAAGTTACAGCAGAGTTGATCGCATCAGGTATTA
1 TAGACGAAGAATTTCA-GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAGGTATTA
*
5715873 TCTCCCTGAGGTTATAGTGGAG
65 TCTCCCTGAGGTTACAGTGGAG
* * * * * *
5715895 TAGACCGAAGAATTTCAGATATTATCTCCCT-AATATTACAGCAGAGCAGATTGAAGCTA-GTAA
1 TAGA-CGAAGAATTTCAGATCTTATCTCCCTGAA-GTTACAGCAGAGTAGATCGCATC-AGGT-A
* *
5715958 CCTATCTCCCTGAGATTACAGTGGAG
62 -TTATCTCCCTGAGGTTACAGTGGAG
** ** ** * *
5715984 CGGATTAA-AA-TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTA
1 TAGACGAAGAATTTCA-GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAGGTATTA
5716047 TCTCCCTGAGGTTACAGTGGAG
65 TCTCCCTGAGGTTACAGTGGAG
*
5716069 TAGATCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAG
1 TAGA-CGAAGAATTTCAGATCTTATCTCCCTGAAGTTACAG
5716110 TGGAGCAGAT
Statistics
Matches: 225, Mismatches: 59, Indels: 34
0.71 0.19 0.11
Matches are distributed among these distances:
85 48 0.21
86 14 0.06
87 123 0.55
88 14 0.06
89 26 0.12
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (86 bp):
TAGACGAAGAATTTCAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAGGTATTAT
CTCCCTGAGGTTACAGTGGAG
Found at i:5716016 original size:174 final size:174
Alignment explanation
Indices: 5715721--5716726 Score: 725
Period size: 174 Copynumber: 5.8 Consensus size: 174
5715711 CCCCAGGAAA
*
5715721 TAGACCGAAGAATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
1 TAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
5715786 CATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACAGCA
66 CATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACAGCA
* *
5715851 GAGTTGATCGCATCAGGTATTATCTCCCTGAGGTTATAGTGGAG
131 GAGTAGATCGCATCAGGTATTATCTCCCTGAGGTTACAGTGGAG
* * * *
5715895 TAGACCGAAGAATTTCAGATATTATCTCCCTAATATTACAGCAGAGCAGATTGAAGCTAGTAA-C
1 TAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
*
5715959 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGC
66 C-ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACAGC
*
5716024 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAG
130 AGAGTAGATCGCATCAGGTATTATCTCCCTGAGGTTACAGTGGAG
* * * *
5716069 TAGATCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG-AGAT
1 TAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA-AT
* * * * * * * ** * ** *
5716133 CTTATCTCCTTGAAATTACAGCGGAGCAGATCT--AAGACACTATCCTATCTCCCT-TAGATTAC
65 C-CATCTCCCTGAGATTACAGTGGAGCGGAT-TAAAATAAAGGATCTTATCTATCTGAAG-TTAC
* ** * * * * * * * *
5716195 AG-TGAAGCGGATTAAAGTAACAGATCTTATCTCTCTGAAGTTACAGTAGAG
127 AGCAG-AGTAGA-T--CGCATCAGGTATTATCTCCCTGAGGTTACAGTGGAG
* * * *
5716246 TAGATC---G--TATCCGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGC-AGATAAT
1 TAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG-TAAT
* * * * * *
5716305 CCTATCTCCTTGAGATTATAGTGGAGTGGGTTAAAGTAACA-GATCTTATCTCTCTGAAGTTACA
65 CC-ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAA-AGGATCTTATCTATCTGAAGTTACA
* * * * * ** *
5716369 GTAGAGTAGATCGTATCCGGTCTTATCTCTCTGAAATTACAGCGGAG
128 GCAGAGTAGATCGCATCAGGTATTATCTCCCTGAGGTTACAGTGGAG
* ** * * * ** **
5716416 CAGATTGAAG--TTGAT-A-ACCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAAG-
1 TAGACCGAAGAATT--TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AGT
* * * * * ** * ** *
5716475 GATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATT-GCAT-CAGG-TCTTATCTCCCTGAGGTT
62 AATC-CATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTT
** * * * *
5716536 ACAGTGGAGTAGAACGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAG
125 ACAGCAGAGTAGATC---GCA--TCAGGTATTATCTCCCTGAGGTTACAGTGGAG
* ** * * * * *
5716591 CAGATTGAAGCCA---GAGATCTTATCTCCCTGAGATTATAACGGAGTAGATTGAAGCTAGTAAT
1 TAGACCGAAG-AATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAAT
* * * * *
5716653 CCTAACTCTCT-AAAGTTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTATCTGAAGTTACA
65 CC-ATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACA
*
5716717 GTAGAGTAGA
128 GCAGAGTAGA
5716727 AGATCTTATC
Statistics
Matches: 664, Mismatches: 122, Indels: 88
0.76 0.14 0.10
Matches are distributed among these distances:
170 63 0.09
171 4 0.01
172 70 0.11
173 87 0.13
174 249 0.38
175 121 0.18
176 6 0.01
177 37 0.06
178 27 0.04
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (174 bp):
TAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
CATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACAGCA
GAGTAGATCGCATCAGGTATTATCTCCCTGAGGTTACAGTGGAG
Found at i:5716061 original size:41 final size:43
Alignment explanation
Indices: 5715825--5716109 Score: 132
Period size: 41 Copynumber: 6.6 Consensus size: 43
5715815 TAAAATAAAG
** * * *
5715825 GATCTTATCTATCTGAAGTTACAGCAGAGTTGATC-GCA-TCA
1 GATCTTATCTCCCTGAGGTTACAGCAGAGTAGATCAGAATTCA
* * * ** *
5715866 GGTATTATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCA
1 GATCTTATCTCCCTGAGGTTACAGCAGAGTAGATC--AGAA-TTCA
* * ** * * *
5715912 GATATTATCTCCCTAATATTACAGCAGAGCAGAT-TGAA-GCTA
1 GATCTTATCTCCCTGAGGTTACAGCAGAGTAGATCAGAATTC-A
* * * ** ** * * **
5715954 GTAACCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 G-ATCTTATCTCCCTGAGGTTACAGCAGAGTAGATCAGAATTCA
* * *
5715998 GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC-GCA-TCA
1 -GATCTTATCTCCCTGAGGTTACAGCAGAGTAGATCAGAATTCA
* **
5716040 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTTCA
1 GATCTTATCTCCCTGAGGTTACAGCAGAGTAGATC--AGAA-TTCA
5716086 GATCTTATCTCCCTGAGGTTACAG
1 GATCTTATCTCCCTGAGGTTACAG
5716110 TGGAGCAGAT
Statistics
Matches: 174, Mismatches: 55, Indels: 25
0.69 0.22 0.10
Matches are distributed among these distances:
41 56 0.32
42 3 0.02
43 29 0.17
44 31 0.18
45 1 0.01
46 54 0.31
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGGTTACAGCAGAGTAGATCAGAATTCA
Found at i:5716152 original size:44 final size:44
Alignment explanation
Indices: 5716042--5716645 Score: 221
Period size: 44 Copynumber: 13.9 Consensus size: 44
5716032 TCGCATCAGG
* * * * *
5716042 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG-AATTTCAGA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCA---GAGA
* * *
5716088 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCAGAGA
* * * * **
5716132 TCTTATCTCCTTGAAATTACAGCGGAGCAGATCT-AAGACA-CTA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGAT-TGAAGCCAGAGA
* * ** * ** *
5716175 TCCTATCTCCCTT-AGATTACAGTGAAGCGGATTAAAGTAACAGA
1 TCTTATCT-CCTTGAGATTACAGTGGAGTAGATTGAAGCCAGAGA
* * * *
5716219 TCTTATCT-CTCTGA-AGTTACAGTAGAGTAGATCGTATCC-G-G-
1 TCTTATCTCCT-TGAGA-TTACAGTGGAGTAGATTGAAGCCAGAGA
* * * *
5716260 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CAGATAA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCAGA-GA
* * * * * ** *
5716304 TCCTATCTCCTTGAGATTATAGTGGAGTGGGTTAAAGTAACAGA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCAGAGA
* * * *
5716348 TCTTATCT-CTCTGA-AGTTACAGTAGAGTAGATCGTATCC-G-G-
1 TCTTATCTCCT-TGAGA-TTACAGTGGAGTAGATTGAAGCCAGAGA
* * * ** *
5716389 TCTTATCT-CTCTGAAATTACAGCGGAGCAGATTGAAG-TTGATAA
1 TCTTATCTCCT-TGAGATTACAGTGGAGTAGATTGAAGCCAGA-GA
* * * * *** *
5716433 CCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAAGGA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCAGA-GA
* * * *
5716477 TCTTATCT-CTCTGA-AGTTACAGTAGAGTGGATTGCA-TCAG-G-
1 TCTTATCTCCT-TGAGA-TTACAGTGGAGTAGATTGAAGCCAGAGA
* * ** * *
5716518 TCTTATCTCCCTGAGGTTACAGTGGAGTAGAACGAAG-AATTTCAGA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCA---GAGA
* * *
5716564 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCAGAGA
* * **
5716608 TCTTATCTCCCTGAGATTATAACGGAGTAGATTGAAGC
1 TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGC
5716646 TAGTAATCCT
Statistics
Matches: 412, Mismatches: 110, Indels: 74
0.69 0.18 0.12
Matches are distributed among these distances:
40 1 0.00
41 84 0.20
42 10 0.02
43 36 0.09
44 204 0.50
45 6 0.01
46 69 0.17
47 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
TCTTATCTCCTTGAGATTACAGTGGAGTAGATTGAAGCCAGAGA
Found at i:5716182 original size:87 final size:84
Alignment explanation
Indices: 5716086--5716322 Score: 217
Period size: 87 Copynumber: 2.8 Consensus size: 84
5716076 AAGAATTTCA
* *
5716086 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAAATTA
1 GATCCTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGATCTTATCTCCTTGAAATTA
*
5716151 CAGCGGAGCAGATC-TAAGACAC
65 CAGCAGAGCAGATCGT-A-AC-C
* * * * * * * *
5716173 TATCCTATCTCCCTTAGATTACAGTGAAGCGGATTAAAGTAACAGATCTTATCT-CTCTGAAGTT
1 GATCCTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGATCTTATCTCCT-TGAAATT
* * *
5716237 ACAGTAGAGTAGATCGTATCC
64 ACAGCAGAGCAGATCGTAACC
* * * * * *
5716258 GGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCAGATAATCCTATCTCCTTGAGATTA
1 GATCCTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGA-GATCTTATCTCCTTGAAATTA
5716323 TAGTGGAGTG
Statistics
Matches: 117, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
84 2 0.02
85 46 0.39
86 5 0.04
87 63 0.54
88 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (84 bp):
GATCCTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAGATCTTATCTCCTTGAAATTAC
AGCAGAGCAGATCGTAACC
Found at i:5716538 original size:129 final size:127
Alignment explanation
Indices: 5715740--5716544 Score: 610
Period size: 129 Copynumber: 6.2 Consensus size: 127
5715730 GAATTTTAGA
5715740 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG-TAATCC-ATCTCCCTGAGATTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-TAGAT-ATCCTATCTCCCTGAGATTAC
* * * *
5715803 AGTGGAGCGGATTAAAATAAAGGATCTTATCTATCTGAAGTTACAGCAGAGTTGATCGCATCAGG
64 AGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGG
* * * * * ** * *
5715868 TATTATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCAGATAT--TATCTCCCTAATAT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG----T-AGATATCCTATCTCCCTGAGAT
** * ** * * * * ** **
5715931 TACAGCAGAGCAGATTGAAGCT--AGTAACCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAA
61 TACAGTGGAGCGGATT-AAAATAAAG-ATCTTATCTCTCTGAAG-TTACAGTAGAGTAGA-TCGA
*
5715993 ATAAAGG
122 AT-CAGG
* * * * * * * *
5716000 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG--GTCTTATCTCCCTGAGGTTA
1 -TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGT-AGATATCCTATCTCCCTGAGATTA
** * ** * * * * * *
5716061 CAGTGGAGTAGATCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC
63 CAGTGGAGCGGAT-TAA-AA-TAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAA-T
5716126 CAGAG
124 CAG-G
* * * *
5716131 ATCTTATCTCCTTGAAATTACAGCGGAGCAGATCT-AAG-ACACTATCCTATCTCCCTTAGATTA
1 -TCTTATCTCCCTGAGATTACAGCGGAGCAGAT-TGAAGTAGA-TATCCTATCTCCCTGAGATTA
* * * *
5716194 CAGTGAAGCGGATTAAAGTAACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCCG
63 CAGTGGAGCGGATTAAAATAA-AGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAG
5716259 G
127 G
* * *
5716260 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCAGATAATCCTATCTCCTTGAGATTATA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTAGAT-ATCCTATCTCCCTGAGATTACA
* * * * *
5716325 GTGGAGTGGGTTAAAGTAACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCCGG
65 GTGGAGCGGATTAAAATAA-AGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGG
* * * *
5716389 TCTTATCTCTCTGAAATTACAGCGGAGCAGATTGAAGTTGATAACCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTAGAT-ATCCTATCTCCCTGAGATTACA
* * * *
5716454 GTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCATCAGG
65 GTGGAGCGGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGG
* *
5716518 TCTTATCTCCCTGAGGTTACAGTGGAG
1 TCTTATCTCCCTGAGATTACAGCGGAG
5716545 TAGAACGAAG
Statistics
Matches: 538, Mismatches: 105, Indels: 67
0.76 0.15 0.09
Matches are distributed among these distances:
126 1 0.00
127 1 0.00
128 94 0.17
129 223 0.41
130 32 0.06
131 117 0.22
132 16 0.03
133 54 0.10
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (127 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTAGATATCCTATCTCCCTGAGATTACAG
TGGAGCGGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGG
Found at i:5716715 original size:44 final size:44
Alignment explanation
Indices: 5715960--5716723 Score: 170
Period size: 44 Copynumber: 17.6 Consensus size: 44
5715950 GCTAGTAACC
* *
5715960 TATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATTAAAATAAAAGATCT
* ** * *** * *
5716004 TATCTCTCTGAAGTTACAGCAGAGTAGA-TCGCAT--CAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
* * * ***
5716045 TATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTTCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGAT-TAA-AATAAAAGATCT
* ** * *** *
5716091 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
* * * ** * * ** *
5716135 TATCTCCTTGAAATTACAGCGGAGCAGATCT--AAGACACTATCC
1 TATCTCCCTGAAGTTACAGTGGAGTGGAT-TAAAATAAAAGATCT
* * * * *
5716178 TATCTCCCT-TAGATTACAGTGAAGCGGATTAAAGTAACAGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATTAAAATAAAAGATCT
* * * ** *** *
5716222 TATCTCTCTGAAGTTACAGTAGAGTAGA-T--CGTATCCGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
* ** * ** * *
5716263 TATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGCAGATA-ATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATTAAAATA-AAAGATCT
* * * * *
5716307 TATCTCCTTG-AGATTATAGTGGAGTGGGTTAAAGTAACAGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATTAAAATAAAAGATCT
* * * ** *** *
5716351 TATCTCTCTGAAGTTACAGTAGAGTAGA-T--CGTATCCGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
* * * ** ** * * * *
5716392 TATCTCTCTGAAATTACAGCGGAGCAGATTGAAGTTGATA-ACCC
1 TATCTCCCTGAAGTTACAGTGGAGTGGATT-AAAATAAAAGATCT
*
5716436 TATCTCCCTG-AGATTACAGTGGAGTGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATTAAAATAAAAGATCT
* * ** * *
5716480 TATCTCTCTGAAGTTACAGTAGAGTGGATT-GCAT--CAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
* * ** ***
5716521 TATCTCCCTGAGGTTACAGTGGAGTAGAACGAAGAATTTCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGT-GGATTAA-AATAAAAGATCT
* ** * *** *
5716567 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
* ** * ** ** *
5716611 TATCTCCCTG-AGATTATAACGGAGTAGATTGAAGCTAGTA-ATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTGGATT-AAAATAAAAGATCT
* * *
5716655 TAACTCTCTAAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
** *
5716699 TATCTATCTGAAGTTACAGTAGAGT
1 TATCTCCCTGAAGTTACAGTGGAGT
5716724 AGAAGATCTT
Statistics
Matches: 511, Mismatches: 175, Indels: 68
0.68 0.23 0.09
Matches are distributed among these distances:
40 2 0.00
41 115 0.23
42 6 0.01
43 45 0.09
44 262 0.51
45 17 0.03
46 64 0.13
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCT
Found at i:5716775 original size:40 final size:40
Alignment explanation
Indices: 5716730--5716961 Score: 227
Period size: 40 Copynumber: 5.7 Consensus size: 40
5716720 GAGTAGAAGA
5716730 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAG
* * * *
5716770 TCTTATCTCCCTAAGCAGTAGCGGAGCAGA-CGAAAGAAACATA-
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATC---A-CATCA-AG
* *
5716813 TCTTTTCTCCCTAAGTAGTAGTGGAGTAGATCACATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAG
* * * * **
5716853 TTTTATCTCCCTAAACAGTAGTGGAGCAGA-CGAAAGAAACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATC-ACA-TCA-AG
*
5716895 ATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCACATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAG
* *
5716936 TTTTATCTCCCTAAGCAATAGTGGAG
1 TCTTATCTCCCTAAGCAGTAGTGGAG
5716962 CAGGTCAAAG
Statistics
Matches: 152, Mismatches: 28, Indels: 24
0.75 0.14 0.12
Matches are distributed among these distances:
39 3 0.02
40 81 0.53
41 4 0.03
42 4 0.03
43 57 0.38
44 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAG
Found at i:5717005 original size:44 final size:44
Alignment explanation
Indices: 5716727--5717446 Score: 508
Period size: 44 Copynumber: 16.8 Consensus size: 44
5716717 GTAGAGTAGA
* * **
5716727 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATC--ACAT-CA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* ***
5716768 AG-TCTTATCTCCCTAAGCAGTAGCGGAGCAGA-CGAAAGA-AAC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAGATGGT
* * * * * **
5716810 ATATCTTTTCTCCCTAAGTAGTAGTGGAGTAGATC--ACAT-CA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * ***
5716851 AG-TTTTATCTCCCTAAACAGTAGTGGAGCAGA-CGAAAGA-AAC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAGATGGT
* * * **
5716893 AGATCTTATCTCCCTAAGCAGTAGTAGAGTAGATC--ACAT-CA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * *
5716934 AG-TTTTATCTCCCTAAGCAATAGTGGAGCAGGTCAAAGATGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * * * *
5716977 TGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* ** * * ** *****
5717021 AAATCTTATCTCTTTAAGCAATAGTGAAGCAGATTTAAGCCACC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* *
5717065 AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* ** *
5717108 AGATCCTATCTTTCTAAGCAGTAGTGGAGCAGGTCAAAGATGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* *
5717152 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGGTGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* *
5717196 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG-
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * * * ** *****
5717239 CGAATCTTATCTTCCTAAGCAGTAGTGAAACAGATTTAAGCCACC
1 AG-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * * *
5717284 AGTTC-TATCTCCCTAAGCAGTAATGGAGCAGGTTAAAGATGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * *
5717327 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
* * * * ** *****
5717371 AAATCTTATATTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
*
5717415 AG-TCCTATCTCCCTAAGCAGTAGTGGAGCAGA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
5717447 CAGAATAAAC
Statistics
Matches: 531, Mismatches: 126, Indels: 42
0.76 0.18 0.06
Matches are distributed among these distances:
39 2 0.00
40 80 0.15
41 9 0.02
42 10 0.02
43 142 0.27
44 287 0.54
45 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
Found at i:5717183 original size:219 final size:219
Alignment explanation
Indices: 5716893--5717402 Score: 690
Period size: 219 Copynumber: 2.3 Consensus size: 219
5716883 CGAAAGAAAC
* * * * * * *
5716893 AGATCTTATCTCCCTAAGCAGTAGTAGAGTAGATC--ACAT--CAAGTTTTATCTCCCTAAGCAA
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTCCCTAAGCAG
* *
5716954 TAGTGGAGCAGGTCAAAGATGGTTGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACG
66 TAGTGGAGCAGGTCAAAGATGGTAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACG
* *
5717019 GCAAATCTTATC-TCTTTAAGCAATAGTGAAGCAGATTTAAGCCACCAG-TCTTATCTCCCTAAG
131 GCAAATCTTATCTTC-CTAAGCAATAGTGAAACAGATTTAAGCCACCAGTTC-TATCTCCCTAAG
* *
5717082 CAGTAGTGGAGCAGGTCGAAGATGGT
194 CAGTAATGGAGCAGGTCAAAGATGGT
** * * *
5717108 AGATCCTATCTTTCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAG
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTCCCTAAGCAG
* * *
5717173 TAGTGGAGCAGGTCAAAGGTGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACG
66 TAGTGGAGCAGGTCAAAGATGGTAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACG
* *
5717238 GCGAATCTTATCTTCCTAAGCAGTAGTGAAACAGATTTAAGCCACCAGTTCTATCTCCCTAAGCA
131 GCAAATCTTATCTTCCTAAGCAATAGTGAAACAGATTTAAGCCACCAGTTCTATCTCCCTAAGCA
*
5717303 GTAATGGAGCAGGTTAAAGATGGT
196 GTAATGGAGCAGGTCAAAGATGGT
* * * * *
5717327 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCAAATCTTATATTCCTAAGCAG
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTCCCTAAGCAG
*
5717392 TAGTGAAGCAG
66 TAGTGGAGCAG
5717403 ATTTAAGCCA
Statistics
Matches: 254, Mismatches: 35, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
215 29 0.11
217 3 0.01
219 218 0.86
220 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (219 bp):
AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTCCCTAAGCAG
TAGTGGAGCAGGTCAAAGATGGTAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACG
GCAAATCTTATCTTCCTAAGCAATAGTGAAACAGATTTAAGCCACCAGTTCTATCTCCCTAAGCA
GTAATGGAGCAGGTCAAAGATGGT
Found at i:5717350 original size:131 final size:131
Alignment explanation
Indices: 5717067--5717445 Score: 533
Period size: 131 Copynumber: 2.9 Consensus size: 131
5717057 AAGCCACCAG
* * * * *
5717067 TCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTTTCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCTAAGCAGTAG
* * ** ***** * *
5717132 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGGTGGTA
66 TGAAGCAGATTTAAGCCACCAGTTC-TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
5717197 GA
130 GA
* *
5717199 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCTAAGCAGTAG
* * *
5717264 TGAAACAGATTTAAGCCACCAGTTCTATCTCCCTAAGCAGTAATGGAGCAGGTTAAAGATGGTAG
66 TGAAGCAGATTTAAGCCACCAGTTCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAG
5717329 A
131 A
* *
5717330 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCAAATCTTATATTCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCTAAGCAGTAG
*
5717395 TGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAG
66 TGAAGCAGATTTAAGCCACCAGTTCTATCTCCCTAAGCAGTAGTGGAGCAG
5717446 ACAGAATAAA
Statistics
Matches: 219, Mismatches: 28, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
131 147 0.67
132 72 0.33
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCTAAGCAGTAG
TGAAGCAGATTTAAGCCACCAGTTCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAG
A
Found at i:5722697 original size:20 final size:20
Alignment explanation
Indices: 5722672--5722711 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5722662 AAATATTTTC
*
5722672 AGTAAATCATTTTCTAGAAA
1 AGTAAATCATTTTCCAGAAA
5722692 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
5722712 TCATTTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:5723246 original size:43 final size:43
Alignment explanation
Indices: 5723198--5723283 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
5723188 TGGTGAGATC
* *
5723198 GACAGTGA-GAAGTGAAAGGGAAGGGAGC-AGTGGTGGGGGTTGG
1 GACAGTGATG-AGTGAAAGGGAAGGCAGCGA-CGGTGGGGGTTGG
*
5723241 GACAGTGATGAGTGAGAGGGAAGGCAGCGACGGTGGGGGTTGG
1 GACAGTGATGAGTGAAAGGGAAGGCAGCGACGGTGGGGGTTGG
5723284 ACAAAATAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 36 0.95
44 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.53, T:0.14
Consensus pattern (43 bp):
GACAGTGATGAGTGAAAGGGAAGGCAGCGACGGTGGGGGTTGG
Found at i:5729512 original size:2 final size:2
Alignment explanation
Indices: 5729505--5729539 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5729495 CCTGTCTTAA
5729505 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5729540 TTTATTCGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5730426 original size:13 final size:13
Alignment explanation
Indices: 5730410--5730435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5730400 GCGATATGTT
5730410 ATGTAAATTTTTA
1 ATGTAAATTTTTA
5730423 ATGTAAATTTTTA
1 ATGTAAATTTTTA
5730436 TATCGATGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATGTAAATTTTTA
Found at i:5736989 original size:2 final size:2
Alignment explanation
Indices: 5736982--5737015 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5736972 CTATTTGTAT
5736982 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5737016 ATCTTACATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5754027 original size:3 final size:3
Alignment explanation
Indices: 5754019--5754043 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5754009 ATTATGCCAA
5754019 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5754044 GACTATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5754247 original size:19 final size:19
Alignment explanation
Indices: 5754223--5754276 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
5754213 AATCTTCAAG
5754223 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5754242 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5754261 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
5754277 AAATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5754267 original size:38 final size:40
Alignment explanation
Indices: 5754223--5754299 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
5754213 AATCTTCAAG
5754223 GATATGCAATCTTAG-ATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAGAATATGATTATGTAATCTTAGATAT
*
5754261 GATATGCAATCTTAGAAAATATGATTTTGTAATCTTAGA
1 GATATGCAATCTTAG--AATATGATTATGTAATCTTAGA
5754300 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 15 0.44
41 6 0.18
42 13 0.38
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAGAATATGATTATGTAATCTTAGATAT
Found at i:5754784 original size:17 final size:17
Alignment explanation
Indices: 5754762--5754796 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5754752 TTTATATACA
* *
5754762 TATATATATTTACATTT
1 TATATACATATACATTT
5754779 TATATACATATACATTT
1 TATATACATATACATTT
5754796 T
1 T
5754797 TTATTTCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATACATATACATTT
Found at i:5754992 original size:30 final size:31
Alignment explanation
Indices: 5754958--5755015 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5754948 TATTTGTTTT
*
5754958 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATGTAGATAATCTTTTTTATAATC
*
5754988 TATATATATGTAGATAATTTTTTTTATA
1 TATATATATGTAGATAATCTTTTTTATA
5755016 TATGTACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (31 bp):
TATATATATGTAGATAATCTTTTTTATAATC
Found at i:5756388 original size:7 final size:7
Alignment explanation
Indices: 5756378--5756403 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5756368 ATTTACACCT
5756378 TAAACCC
1 TAAACCC
5756385 TAAACCC
1 TAAACCC
5756392 TAAACCC
1 TAAACCC
5756399 TAAAC
1 TAAAC
5756404 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:5759341 original size:9 final size:9
Alignment explanation
Indices: 5759326--5759365 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
5759316 GAAACCCAGT
5759326 ATTT-TTTA
1 ATTTCTTTA
*
5759334 ATTTTTTTA
1 ATTTCTTTA
5759343 ATTTCTTTA
1 ATTTCTTTA
5759352 ATTTCTTTA
1 ATTTCTTTA
5759361 ATTTC
1 ATTTC
5759366 ATCAAACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 4 0.13
9 26 0.87
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTCTTTA
Found at i:5763883 original size:7 final size:7
Alignment explanation
Indices: 5763873--5763900 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5763863 TTTCAGTGTT
5763873 CATTTCC
1 CATTTCC
5763880 CATTTCC
1 CATTTCC
5763887 CATTTCC
1 CATTTCC
5763894 CATTTCC
1 CATTTCC
5763901 TACCACCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CATTTCC
Found at i:5776794 original size:22 final size:23
Alignment explanation
Indices: 5776748--5776794 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5776738 TCTTCCTTTA
*
5776748 TTTTTTTCAACAATTTCATTTAT
1 TTTTTTTCAACAATTTCATTAAT
5776771 TTTTCTTTCAAC-ATTT-ATTAAT
1 TTTT-TTTCAACAATTTCATTAAT
5776793 TT
1 TT
5776795 ATTGGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 7 0.32
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTTTCAACAATTTCATTAAT
Found at i:5782042 original size:22 final size:21
Alignment explanation
Indices: 5782003--5782043 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5781993 GAGTGGACAA
*
5782003 TTTAAAAAAAAGCGAAAACCC
1 TTTAAAAAAAAGCAAAAACCC
*
5782024 TTTAAAAATAAAGTAAAAAC
1 TTTAAAAA-AAAGCAAAAAC
5782044 ACAGAGGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.20
Consensus pattern (21 bp):
TTTAAAAAAAAGCAAAAACCC
Found at i:5784213 original size:34 final size:34
Alignment explanation
Indices: 5784170--5784246 Score: 145
Period size: 34 Copynumber: 2.3 Consensus size: 34
5784160 AAAACAGTGA
5784170 AAAAAAAAATAGCAACAAAATAATTAAAAAAAAC
1 AAAAAAAAATAGCAACAAAATAATTAAAAAAAAC
5784204 AAAAAAAAATAGCAACAAAATAATTAAAAAAAAC
1 AAAAAAAAATAGCAACAAAATAATTAAAAAAAAC
*
5784238 AACAAAAAA
1 AAAAAAAAA
5784247 GCAAGAAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.78, C:0.09, G:0.03, T:0.10
Consensus pattern (34 bp):
AAAAAAAAATAGCAACAAAATAATTAAAAAAAAC
Found at i:5788338 original size:19 final size:20
Alignment explanation
Indices: 5788306--5788369 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 20
5788296 ATCTTTGAAT
**
5788306 TCATTTCAAAATTT-ACATC
1 TCATTTCATCATTTCACATC
* *
5788325 TCATTTCATCATTTCATATT
1 TCATTTCATCATTTCACATC
*
5788345 TCATTTC-TCATTTCATAT-
1 TCATTTCATCATTTCACATC
5788363 TCATTTC
1 TCATTTC
5788370 TCAACTTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 7 0.17
19 23 0.57
20 10 0.25
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.52
Consensus pattern (20 bp):
TCATTTCATCATTTCACATC
Found at i:5790616 original size:13 final size:13
Alignment explanation
Indices: 5790598--5790624 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5790588 CTATCATTTT
5790598 AAATTGTATGATA
1 AAATTGTATGATA
5790611 AAATTGTATGATA
1 AAATTGTATGATA
5790624 A
1 A
5790625 TAATACTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (13 bp):
AAATTGTATGATA
Found at i:5791770 original size:20 final size:20
Alignment explanation
Indices: 5791745--5791787 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5791735 ATTTTAAGAG
*
5791745 ATTCTCGTACAAGACTTTTT
1 ATTCTCATACAAGACTTTTT
* *
5791765 ATTCTCATACGAGATTTTTT
1 ATTCTCATACAAGACTTTTT
5791785 ATT
1 ATT
5791788 GGGTCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (20 bp):
ATTCTCATACAAGACTTTTT
Found at i:5794929 original size:72 final size:73
Alignment explanation
Indices: 5794809--5794959 Score: 268
Period size: 72 Copynumber: 2.1 Consensus size: 73
5794799 CGACAAAGGC
*
5794809 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAGAACCATTAAAACTTCTTTT-A
1 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
* *
5794873 TTGGCTCT
66 CTAGCTCT
5794881 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
1 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
5794946 CTAGCTCT
66 CTAGCTCT
5794954 ATTGGC
1 ATTGGC
5794960 TTATCCATGT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 62 0.83
73 13 0.17
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (73 bp):
ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
CTAGCTCT
Found at i:5796827 original size:24 final size:25
Alignment explanation
Indices: 5796800--5796856 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
5796790 GAAGGATGAT
*
5796800 AAGGCTGAGACAAA-A-AAGGAAGTG
1 AAGGCTGAGA-AAAGAGAAGGAAGCG
5796824 AAGGCTGA-AAAAGAGAAGGAAGCG
1 AAGGCTGAGAAAAGAGAAGGAAGCG
5796848 AAGGCTGAG
1 AAGGCTGAG
5796857 TGAAAATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 24 0.83
ACGTcount: A:0.47, C:0.09, G:0.37, T:0.07
Consensus pattern (25 bp):
AAGGCTGAGAAAAGAGAAGGAAGCG
Found at i:5800356 original size:20 final size:20
Alignment explanation
Indices: 5800328--5800376 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
5800318 ATAAATCTGG
5800328 ATAAAAATTGATG-TAATGGA
1 ATAAAAATT-ATGATAATGGA
* *
5800348 ATAACAATTATGATAATGTA
1 ATAAAAATTATGATAATGGA
5800368 AGTAAAAAT
1 A-TAAAAAT
5800377 AATATGGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (20 bp):
ATAAAAATTATGATAATGGA
Found at i:5800674 original size:11 final size:12
Alignment explanation
Indices: 5800652--5800706 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
5800642 TAATGTATAT
*
5800652 ATATATTTAAAA
1 ATATATATAAAA
5800664 ATATAT-TAAAA
1 ATATATATAAAA
*
5800675 ATATATGTATAAA
1 ATATATATA-AAA
*
5800688 GTATATATAAAA
1 ATATATATAAAA
*
5800700 AAATATA
1 ATATATA
5800707 AGTACATACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 11 0.30
12 16 0.43
13 10 0.27
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (12 bp):
ATATATATAAAA
Found at i:5800687 original size:25 final size:27
Alignment explanation
Indices: 5800650--5800706 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
5800640 GGTAATGTAT
* *
5800650 ATATATATTTAAA-AATATAT-TAAAA
1 ATATATATATAAAGAATATATAAAAAA
* *
5800675 ATATATGTATAAAGTATATATAAAAAA
1 ATATATATATAAAGAATATATAAAAAA
5800702 ATATA
1 ATATA
5800707 AGTACATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 11 0.42
26 6 0.23
27 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATAAAGAATATATAAAAAA
Found at i:5800793 original size:3 final size:3
Alignment explanation
Indices: 5800785--5800813 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5800775 TAAATGGGTA
5800785 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5800814 AACTAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5804456 original size:48 final size:48
Alignment explanation
Indices: 5804394--5804489 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
5804384 AATTTAAAGA
5804394 ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
1 ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
* *
5804442 ATATCTGTAGTTTCAATTACAACAATCACAAGATATTATTCACTAAAT
1 ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
5804490 CCTTAGTCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (48 bp):
ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
Found at i:5805414 original size:5 final size:5
Alignment explanation
Indices: 5805400--5805450 Score: 77
Period size: 5 Copynumber: 10.2 Consensus size: 5
5805390 TTTATTTATT
*
5805400 TAAT- TAATA TAATA TAATA TAATA TAATA TAATA TAATA CTAAAA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA -TAATA TAATA
5805450 T
1 T
5805451 TATTTATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
4 4 0.09
5 35 0.81
6 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:5809158 original size:20 final size:20
Alignment explanation
Indices: 5809133--5809172 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5809123 AGTCTTTCTG
5809133 CGATTTCCCCTCATCCTTTC
1 CGATTTCCCCTCATCCTTTC
5809153 CGATTTCCCCTCATCCTTTC
1 CGATTTCCCCTCATCCTTTC
5809173 TTCATCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.45, G:0.05, T:0.40
Consensus pattern (20 bp):
CGATTTCCCCTCATCCTTTC
Found at i:5810848 original size:17 final size:17
Alignment explanation
Indices: 5810826--5810858 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5810816 TTATTTTCTA
5810826 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
*
5810843 TATAAGTTTTGTAAAT
1 TATAAGTTTTCTAAAT
5810859 AATTATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:5810904 original size:15 final size:16
Alignment explanation
Indices: 5810867--5810905 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5810857 ATAATTATTC
*
5810867 TAAATTTATTAGTATA
1 TAAATTTAGTAGTATA
*
5810883 AAAATTTAGTAGTAT-
1 TAAATTTAGTAGTATA
5810898 TAAATTTA
1 TAAATTTA
5810906 TAAGTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
TAAATTTAGTAGTATA
Found at i:5810905 original size:61 final size:61
Alignment explanation
Indices: 5810837--5810986 Score: 178
Period size: 61 Copynumber: 2.5 Consensus size: 61
5810827 ATAAGTTTTC
5810837 TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGT-ATAAAAATTTAGT-AGTAT
1 TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGTAAT-AAAATTTA-TAAGTAT
* * * * * *
5810898 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAGATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * * *
5810959 CAATTTTACACGTTTTGTAAATAATTAT
1 TAAATTTATAAGTTTTGTAAATAATTAT
5810987 ATATTTTTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
60 1 0.01
61 70 0.96
62 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (61 bp):
TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:5811218 original size:8 final size:7
Alignment explanation
Indices: 5811205--5811250 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
5811195 TAACGTATAT
5811205 ATAATAAC
1 ATAAT-AC
5811213 ATAATA-
1 ATAATAC
*
5811219 A-ATTAC
1 ATAATAC
5811225 ATAATAC
1 ATAATAC
5811232 ATAATAAC
1 ATAAT-AC
5811240 ATAATAC
1 ATAATAC
5811247 ATAA
1 ATAA
5811251 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:5811243 original size:15 final size:15
Alignment explanation
Indices: 5811205--5811250 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
5811195 TAACGTATAT
5811205 ATAATAACATAAT--
1 ATAATAACATAATAC
*
5811218 A-AATTACATAATAC
1 ATAATAACATAATAC
5811232 ATAATAACATAATAC
1 ATAATAACATAATAC
5811247 ATAA
1 ATAA
5811251 CTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:5811272 original size:21 final size:20
Alignment explanation
Indices: 5811246--5811303 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
5811236 TAACATAATA
5811246 CATAACTTATATATAAGCTTGT
1 CATAACTTATATATAA-CTT-T
*
5811268 -ATAACTTACATAATAACTTT
1 CATAACTTATAT-ATAACTTT
5811288 CATAACTTATATATAA
1 CATAACTTATATATAA
5811304 TCTGATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 23 0.72
22 4 0.12
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (20 bp):
CATAACTTATATATAACTTT
Found at i:5811299 original size:95 final size:94
Alignment explanation
Indices: 5811130--5811392 Score: 363
Period size: 95 Copynumber: 2.8 Consensus size: 94
5811120 AATCATTTGC
* * * *
5811130 TTACTTAATACATAATAACACAATGCATAA-TTGGTATATAAGC---ATAACTTACATAATAACT
1 TTACATAATACATAATAACATAATACATAACTT-ATATATAAGCTTGATAACTTACATAATAACT
*
5811191 TCCATAACGTATATATAATAACATAATAAA
65 TCCATAACTTATATATAATAACATAATAAA
5811221 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGTATAACTTACATAATAACT
1 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTG-ATAACTTACATAATAACT
* *** *
5811286 TTCATAACTTATATATAATCTGATAATACA
65 TCCATAACTTATATATAATAACATAATAAA
*
5811316 TTACATAATACATAATAACATAATACATAACTTATATTATAATCTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACATAATACATAACTTATA-TATAAGCTTG-ATAACTTACATAATAAC
5811381 TTCCATAACTTA
64 TTCCATAACTTA
5811393 ATACACCACT
Statistics
Matches: 153, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
91 36 0.24
92 2 0.01
95 78 0.51
96 37 0.24
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (94 bp):
TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGATAACTTACATAATAACTT
CCATAACTTATATATAATAACATAATAAA
Found at i:5811325 original size:12 final size:14
Alignment explanation
Indices: 5811308--5811344 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
5811298 ATATAATCTG
5811308 ATAATACAT-T-AC
1 ATAATACATATAAC
5811320 ATAATACATAATAAC
1 ATAATACAT-ATAAC
5811335 ATAATACATA
1 ATAATACATA
5811345 ACTTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATACATATAAC
Found at i:5811338 original size:8 final size:7
Alignment explanation
Indices: 5811308--5811345 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
5811298 ATATAATCTG
5811308 ATAATAC
1 ATAATAC
5811315 AT--TAC
1 ATAATAC
5811320 ATAATAC
1 ATAATAC
5811327 ATAATAAC
1 ATAAT-AC
5811335 ATAATAC
1 ATAATAC
5811342 ATAA
1 ATAA
5811346 CTTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAC
Found at i:5811357 original size:27 final size:27
Alignment explanation
Indices: 5811288--5811358 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 27
5811278 TAATAACTTT
***
5811288 CATAACTTATA-TATAATCTGATAATA
1 CATAACTTATATTATAATAACATAATA
* * *
5811314 CATTACATA-ATACATAATAACATAATA
1 CATAACTTATAT-TATAATAACATAATA
5811341 CATAACTTATATTATAAT
1 CATAACTTATATTATAAT
5811359 CTTGCATAAC
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 23 0.70
28 2 0.06
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (27 bp):
CATAACTTATATTATAATAACATAATA
Found at i:5811366 original size:22 final size:21
Alignment explanation
Indices: 5811341--5811392 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
5811331 TAACATAATA
* * *
5811341 CATAACTTATATTATAATCTTG
1 CATAACTTACATAATAA-CTTC
5811363 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
5811384 CATAACTTA
1 CATAACTTA
5811393 ATACACCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:5811491 original size:9 final size:9
Alignment explanation
Indices: 5811463--5811652 Score: 100
Period size: 9 Copynumber: 22.2 Consensus size: 9
5811453 CATATATAGA
*
5811463 AACTGACAT
1 AACTTACAT
* *
5811472 AAATTAAAT
1 AACTTACAT
5811481 AACTTACAT
1 AACTTACAT
5811490 AACTTACAT
1 AACTTACAT
* *
5811499 AAATTAAAT
1 AACTTACAT
*
5811508 TACTTACAT
1 AACTTACAT
5811517 AACTTACAT
1 AACTTACAT
*
5811526 TA--TACAT
1 AACTTACAT
*
5811533 AACCTT-CTT
1 AA-CTTACAT
5811542 AACTTACAT
1 AACTTACAT
* *
5811551 TA--TACAC
1 AACTTACAT
* *
5811558 GACTCACAT
1 AACTTACAT
5811567 AA-TTA-AT
1 AACTTACAT
* *
5811574 -ATTATACAC
1 AACT-TACAT
5811583 AACTTACAT
1 AACTTACAT
*
5811592 AA-TAAC-T
1 AACTTACAT
**
5811599 TTCTTACAT
1 AACTTACAT
5811608 AACTTACAT
1 AACTTACAT
*
5811617 TACTTACAGT
1 AACTTACA-T
5811627 -ACTTACAT
1 AACTTACAT
5811635 AA--TACAT
1 AACTTACAT
5811642 AACTTACAT
1 AACTTACAT
5811651 AA
1 AA
5811653 TACATAAAAA
Statistics
Matches: 133, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
6 1 0.01
7 22 0.17
8 14 0.11
9 92 0.69
10 4 0.03
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:5811646 original size:16 final size:16
Alignment explanation
Indices: 5811603--5811659 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
5811593 ATAACTTTCT
*
5811603 TACATAACTTACATTACT
1 TACATAACTTACA-TA-A
5811621 TACAGT-ACTTACATAA
1 TACA-TAACTTACATAA
5811637 TACATAACTTACATAA
1 TACATAACTTACATAA
5811653 TACATAA
1 TACATAA
5811660 AAATATATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.03
16 21 0.58
17 2 0.06
18 11 0.31
19 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:5819130 original size:24 final size:24
Alignment explanation
Indices: 5819095--5819140 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5819085 TCATTTAACT
*
5819095 TAATTGAATATGTTCATGAACATA
1 TAATTGAATATGTTCACGAACATA
5819119 TAATT-AATTATGTTCACGAACA
1 TAATTGAA-TATGTTCACGAACA
5819141 ATGTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (24 bp):
TAATTGAATATGTTCACGAACATA
Found at i:5840188 original size:9 final size:8
Alignment explanation
Indices: 5840172--5840214 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
5840162 AAAAATTTCT
5840172 AAAATATA
1 AAAATATA
5840180 AAAATTATA
1 AAAA-TATA
5840189 AAAACTA-A
1 AAAA-TATA
*
5840197 AAAATAAA
1 AAAATATA
5840205 AAAATATA
1 AAAATATA
5840213 AA
1 AA
5840215 TATGTTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 2 0.06
8 19 0.61
9 10 0.32
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAATATA
Found at i:5840192 original size:17 final size:17
Alignment explanation
Indices: 5840154--5840214 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
5840144 CATCATTCGA
*
5840154 AAAAATAAAAAAATT-T
1 AAAAATATAAAAATTAT
*
5840170 CTAAAATATAAAAATTAT
1 -AAAAATATAAAAATTAT
*
5840188 AAAAACTA-AAAAA-TAA
1 AAAAA-TATAAAAATTAT
5840204 AAAAATATAAA
1 AAAAATATAAA
5840215 TATGTTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.05
16 10 0.27
17 22 0.59
18 3 0.08
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATATAAAAATTAT
Found at i:5844235 original size:29 final size:29
Alignment explanation
Indices: 5844193--5844250 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
5844183 TTGAGCGTTG
5844193 GATGAATTAATTTTTTGAACCAAATTATA
1 GATGAATTAATTTTTTGAACCAAATTATA
* *
5844222 GATGAATTAATTTTTTGGACTAAATTATA
1 GATGAATTAATTTTTTGAACCAAATTATA
5844251 AGGTACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (29 bp):
GATGAATTAATTTTTTGAACCAAATTATA
Found at i:5844437 original size:29 final size:29
Alignment explanation
Indices: 5844405--5844463 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5844395 AAATGGTTTT
*
5844405 TTTATAAAAATAACCCAAATTTTTTATTA
1 TTTACAAAAATAACCCAAATTTTTTATTA
* * **
5844434 TTTACAAAAATGACTCACTTTTTTTATTA
1 TTTACAAAAATAACCCAAATTTTTTATTA
5844463 T
1 T
5844464 GTAAATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTACAAAAATAACCCAAATTTTTTATTA
Found at i:5845465 original size:195 final size:192
Alignment explanation
Indices: 5845128--5845537 Score: 511
Period size: 195 Copynumber: 2.1 Consensus size: 192
5845118 GCAACTGGGC
* * * * *
5845128 ATCGAATTATGTCAAAAAATTAAAGTATAGAGATTAAATTTTAAAATTGTGCATATTATTGGGAG
1 ATCGAATTATGTC-AAAAATTAAAGTATAAAGATTAAATTTTAAAATTGAGCATAATATAGGAAG
* * * * **
5845193 CAAAAATTTGACTATTGTTATATAATCTCAAAAAAGAAGTAAAAGGTCGTGTATTTGGACATGTG
65 CAAAAATTTGACCATTATTATATAATCTCAAAAAAGAAGTAAAAGATCGTGCATCGGGACATGTG
* * * **
5845258 TACGTCAACATTTTAATCAGAATGAAGTGTTTAGACTAACCATGACATTATAAAAATCGAGGT
130 TACGTCAACATTTTAATCAGAATGAAGTATTTAGACTAACAATGAAATTATAAAAATCGAAAT
* *
5845321 ATCGAATTATGTCAAAAATTAAAGTATAAAGATTAAA-TTTAAATTTGAGCATAATATAGGAATC
1 ATCGAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTTAAAATTGAGCATAATATAGGAAGC
* * *
5845385 AAAGTTAAAATTTGACCATTATTATATAATCT-AAAAAATAAGTAAAAGATTGTGCATCGGGATA
66 --A---AAAATTTGACCATTATTATATAATCTCAAAAAAGAAGTAAAAGATCGTGCATCGGGACA
* * *
5845449 TGTGTAGGTCAACATTTTAATCAGAATGAAGTATTTAGACTTACAATGAAATTATAAAAGTCGAA
126 TGTGTACGTCAACATTTTAATCAGAATGAAGTATTTAGACTAACAATGAAATTATAAAAATCGAA
5845514 AT
191 AT
* *
5845516 ACCAAATTATGTC-AAAATTAAA
1 ATCGAATTATGTCAAAAATTAAA
5845538 TTCAAAACTT
Statistics
Matches: 186, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
191 21 0.11
192 23 0.12
193 14 0.08
194 9 0.05
195 95 0.51
196 24 0.13
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (192 bp):
ATCGAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTTAAAATTGAGCATAATATAGGAAGC
AAAAATTTGACCATTATTATATAATCTCAAAAAAGAAGTAAAAGATCGTGCATCGGGACATGTGT
ACGTCAACATTTTAATCAGAATGAAGTATTTAGACTAACAATGAAATTATAAAAATCGAAAT
Found at i:5855036 original size:16 final size:16
Alignment explanation
Indices: 5855015--5855054 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
5855005 AGTAAAAATG
5855015 TGGGTAAATATTTGTT
1 TGGGTAAATATTTGTT
5855031 TGGGTAAATATTTGTT
1 TGGGTAAATATTTGTT
5855047 TGGGTAAA
1 TGGGTAAA
5855055 AATGACAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (16 bp):
TGGGTAAATATTTGTT
Found at i:5855748 original size:92 final size:89
Alignment explanation
Indices: 5855594--5855762 Score: 250
Period size: 92 Copynumber: 1.9 Consensus size: 89
5855584 TAAAAACATA
* **
5855594 ATTTTTTTTATTTTTTATGTTTTTCAATTTTTAATTTCAAATTTTTATTGAATTTTTAAATATTA
1 ATTTCTTTTATTTTTTATGTTTTTCAATTTTT-ATTGAAAATTTTTATTGAATTTTTAAATATTA
5855659 AAAATTTCAAAAGTATAAATAATTT
65 AAAATTTCAAAAGTATAAATAATTT
*
5855684 ATTTCTTTTATTTTTCTATGTTTTTCAATTTTT-TTGAAAATTTTTTATTTTGAATTTTTTAATA
1 ATTTCTTTTATTTTT-TATGTTTTTCAATTTTTATTGAAAA-TTTTTA--TTGAATTTTTAAATA
5855748 TTAAAAATTTCAAAA
62 TTAAAAATTTCAAAA
5855763 AAATATAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
89 5 0.07
90 20 0.28
91 17 0.24
92 29 0.41
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (89 bp):
ATTTCTTTTATTTTTTATGTTTTTCAATTTTTATTGAAAATTTTTATTGAATTTTTAAATATTAA
AAATTTCAAAAGTATAAATAATTT
Found at i:5863149 original size:40 final size:40
Alignment explanation
Indices: 5863100--5863222 Score: 174
Period size: 40 Copynumber: 3.0 Consensus size: 40
5863090 ATAAAACAGG
*
5863100 AAAACGCTTCCTTAAGGAAGCACTTTGTCCACGTGGACAA
1 AAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGACAA
* * *
5863140 AAAACGCTTCCTCAAGGAAGTGCTTTGTCCACGTGGACAG
1 AAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGACAA
* *
5863180 AAAACGCTTCCTTGAGGGAGCGCTTTGTGTCCACGTGGACAA
1 AAAACGCTTCCTTAAGGAAGCGC-TT-TGTCCACGTGGACAA
5863222 A
1 A
5863223 GTGCTTCCTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 55 0.76
41 2 0.03
42 15 0.21
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (40 bp):
AAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGACAA
Found at i:5864147 original size:92 final size:92
Alignment explanation
Indices: 5864016--5864267 Score: 371
Period size: 92 Copynumber: 2.7 Consensus size: 92
5864006 ACCCTAAATA
* *
5864016 CTAAACCCCAATCTAA-CTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTA
1 CTAAACCCTAATCTAATTTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTA
5864080 ATTTATTTAATTTTTCCCTTAAAAACC
66 ATTTATTTAATTTTTCCCTTAAAAACC
*
5864107 CTAAACCCTAATCTAATTTTTTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTA
1 CTAAACCCTAATCTAATTTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTA
*
5864172 ATTTATTTAATTTTTTCCTTAAAAACC
66 ATTTATTTAATTTTTCCCTTAAAAACC
* * * * * * *
5864199 ATAAACACTAAACCCTAATCTATTTTTTAAAATTTATAATTAATTTAATTAAGAAACCCTAAACC
1 CTAAACCCT-AA-TCTAAT-TTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACC
5864264 CTAA
63 CTAA
5864268 ACCCTTATTT
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
91 15 0.10
92 79 0.54
93 2 0.01
94 5 0.03
95 44 0.30
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.40
Consensus pattern (92 bp):
CTAAACCCTAATCTAATTTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTA
ATTTATTTAATTTTTCCCTTAAAAACC
Found at i:5875455 original size:23 final size:24
Alignment explanation
Indices: 5875429--5875484 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
5875419 TGTATATATA
*
5875429 AATTTTTTT-ATAATGTTAGAAAT
1 AATTTTTTTAAGAATGTTAGAAAT
5875452 AATTTTTTTTAAAGAATGTTAGAAAT
1 AA-TTTTTTT-AAGAATGTTAGAAAT
*
5875478 AGTTTTT
1 AATTTTT
5875485 GAATGTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 5 0.18
26 14 0.50
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (24 bp):
AATTTTTTTAAGAATGTTAGAAAT
Found at i:5876733 original size:17 final size:17
Alignment explanation
Indices: 5876711--5876744 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5876701 TTTTATAATA
5876711 TATAAA-TTATTTTTTAT
1 TATAAACTT-TTTTTTAT
5876728 TATAAACTTTTTTTTAT
1 TATAAACTTTTTTTTAT
5876745 AATTTTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TATAAACTTTTTTTTAT
Found at i:5880820 original size:226 final size:225
Alignment explanation
Indices: 5880426--5880879 Score: 746
Period size: 226 Copynumber: 2.0 Consensus size: 225
5880416 AACTATCCAT
* *
5880426 TCAAGAAGGCTCAATATACTGCCAATCAATGAGAAAATATTATATTGGGGTACTCGGGGAACTCG
1 TCAAGAAGGCTCAATATACCGCCAATCAATGAGAAAATATTATATTAGGGTACTCGGGGAACTCG
* * * **
5880491 AACGCATGCGACGCATCAGGATTTATGCTCGACATGTGCGCTTCAGGGTCATTGTGTATGACAAT
66 AACACATGCGACACATCAAGATTTACACTCGACATGTGCGCTTCAGGGTCATTGTGTATGACAAT
** * *
5880556 GCCATGACTCGGGTTCTTGATCAAAGGGGCGTAAACATTTTCATCATCATCCACACCTTCGTCAT
131 GCCACAACCCGGGTTCTTGATCAAAGGGGCGTAAACATTTTCATCATAATCCACACCTTCGTCAT
5880621 CGATATCATCTGGGACCTAAAATCTTCACCC
196 CGATATCA-CTGGGACCTAAAATCTTCACCC
* * * *
5880652 TCAAGAAGGCTCGATATGCCGCCAATCAATGAGCAAATATTATATTAGGGTACTTGGGGAACTCG
1 TCAAGAAGGCTCAATATACCGCCAATCAATGAGAAAATATTATATTAGGGTACTCGGGGAACTCG
5880717 AACACATGCGACACATCAAGATTTACACTCGACATGTGCGCTTCAGGGTCATTGTGTATGACAAT
66 AACACATGCGACACATCAAGATTTACACTCGACATGTGCGCTTCAGGGTCATTGTGTATGACAAT
*
5880782 GCCACAACCCGGGTTCTTGATCAAAGGGGCGTAAACATTTTCATCATAATCCACACCTTCGTCGT
131 GCCACAACCCGGGTTCTTGATCAAAGGGGCGTAAACATTTTCATCATAATCCACACCTTCGTCAT
*
5880847 TGATATCACTGGGACCTAAAATCTTCACCC
196 CGATATCACTGGGACCTAAAATCTTCACCC
5880877 TCA
1 TCA
5880880 TTATCAAAAT
Statistics
Matches: 211, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
225 25 0.12
226 186 0.88
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (225 bp):
TCAAGAAGGCTCAATATACCGCCAATCAATGAGAAAATATTATATTAGGGTACTCGGGGAACTCG
AACACATGCGACACATCAAGATTTACACTCGACATGTGCGCTTCAGGGTCATTGTGTATGACAAT
GCCACAACCCGGGTTCTTGATCAAAGGGGCGTAAACATTTTCATCATAATCCACACCTTCGTCAT
CGATATCACTGGGACCTAAAATCTTCACCC
Found at i:5882045 original size:50 final size:54
Alignment explanation
Indices: 5881915--5882063 Score: 207
Period size: 50 Copynumber: 2.8 Consensus size: 54
5881905 ATTTGGGTAA
* *
5881915 AGAGATCCCATGTAAGACCATGTCTGGGACATTGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGATCA-G
* *
5881971 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAGA-C-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCAG
*
5882021 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5882064 GTTATGATCA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
50 41 0.48
52 1 0.01
53 4 0.05
55 2 0.02
56 38 0.44
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (54 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCAG
Found at i:5884487 original size:5 final size:5
Alignment explanation
Indices: 5884479--5884554 Score: 93
Period size: 5 Copynumber: 15.0 Consensus size: 5
5884469 ATATATATTA
* *
5884479 TATAT TATAT TAT-T TA-AT TAATAAGT AATAT TATAT TGTAT TATAT
1 TATAT TATAT TATAT TATAT T-AT-A-T TATAT TATAT TATAT TATAT
5884525 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
5884555 AAAACAAATG
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
4 5 0.08
5 52 0.84
6 1 0.02
7 3 0.05
8 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:5885642 original size:25 final size:25
Alignment explanation
Indices: 5885613--5885717 Score: 99
Period size: 25 Copynumber: 4.3 Consensus size: 25
5885603 ACTTTAGCGC
5885613 GCTCTCTGATTTTTAGCACGTTAGT
1 GCTCTCTGATTTTTAGCACGTTAGT
* * * *
5885638 GCTCTCTGACTATTAGAACGTTGGT
1 GCTCTCTGATTTTTAGCACGTTAGT
* * * *
5885663 GCTCTTTGATATTTAGCATGTCAGT
1 GCTCTCTGATTTTTAGCACGTTAGT
* *
5885688 GCTCTCTG---TATAGCACTTTAGT
1 GCTCTCTGATTTTTAGCACGTTAGT
5885710 GCTCTCTG
1 GCTCTCTG
5885718 TTCATTAGTG
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
22 18 0.29
25 45 0.71
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTTTTAGCACGTTAGT
Found at i:5891490 original size:12 final size:12
Alignment explanation
Indices: 5891473--5891497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5891463 ATATTCTTTT
5891473 ATAAAATAAAAA
1 ATAAAATAAAAA
5891485 ATAAAATAAAAA
1 ATAAAATAAAAA
5891497 A
1 A
5891498 GGACCCGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:5896911 original size:23 final size:23
Alignment explanation
Indices: 5896879--5896924 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5896869 TTCTTACATT
*
5896879 GTAAATCGTTAAAAATATTGGTA
1 GTAAACCGTTAAAAATATTGGTA
*
5896902 GTAAACCGTTAGAAATATTGGTA
1 GTAAACCGTTAAAAATATTGGTA
5896925 AATCGTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (23 bp):
GTAAACCGTTAAAAATATTGGTA
Found at i:5896931 original size:20 final size:20
Alignment explanation
Indices: 5896879--5896946 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
5896869 TTCTTACATT
*
5896879 GTAAATCGTTAAAAATATTGG
1 GTAAATCGTTAGAAATATT-G
*
5896900 TAGTAAACCGTTAGAAATATTG
1 --GTAAATCGTTAGAAATATTG
* *
5896922 GTAAATCGTTAGATATTTTG
1 GTAAATCGTTAGAAATATTG
5896942 GTAAA
1 GTAAA
5896947 AGCTTTTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
20 22 0.55
22 1 0.03
23 17 0.43
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (20 bp):
GTAAATCGTTAGAAATATTG
Found at i:5901257 original size:2 final size:2
Alignment explanation
Indices: 5901250--5901282 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5901240 TTTTTCTTTT
*
5901250 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5901283 TATTTTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:5901827 original size:19 final size:19
Alignment explanation
Indices: 5901803--5901841 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5901793 TATGTATATA
*
5901803 ATCGAAACTAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
*
5901822 ATCGAACCCAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
5901841 A
1 A
5901842 ATTTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (19 bp):
ATCGAAACCAAATTAAAAT
Found at i:5909875 original size:21 final size:20
Alignment explanation
Indices: 5909849--5909905 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
5909839 ATTTGGTAGA
5909849 AAAACATATATGAACATATTT
1 AAAACA-ATATGAACATATTT
5909870 AAAACAAGATAT-AACATATTT
1 AAAAC-A-ATATGAACATATTT
*
5909891 AAAACACTATGAACA
1 AAAACAATATGAACA
5909906 CATACAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 19 0.59
22 5 0.16
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAACAATATGAACATATTT
Found at i:5909881 original size:22 final size:21
Alignment explanation
Indices: 5909856--5909896 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
5909846 AGAAAAACAT
5909856 ATATGAACATATTTAAAACAAG
1 ATAT-AACATATTTAAAACAAG
5909878 ATATAACATATTTAAAACA
1 ATATAACATATTTAAAACA
5909897 CTATGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (21 bp):
ATATAACATATTTAAAACAAG
Found at i:5910101 original size:4 final size:4
Alignment explanation
Indices: 5910092--5910119 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5910082 CAACTTTGCT
5910092 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
5910120 TACTCTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:5914550 original size:13 final size:13
Alignment explanation
Indices: 5914532--5914590 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
5914522 TTTAATATCG
5914532 ATAATTTTAAAAT
1 ATAATTTTAAAAT
*
5914545 ATAATTTAAATAAT
1 ATAATTTTAA-AAT
*
5914559 TTAAATTTTAAAA-
1 AT-AATTTTAAAAT
5914572 ACTAA-TTTAAAAT
1 A-TAATTTTAAAAT
5914585 AATAAT
1 -ATAAT
5914591 CATAATTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
12 7 0.19
13 14 0.39
14 8 0.22
15 7 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATTTTAAAAT
Found at i:5919820 original size:5 final size:5
Alignment explanation
Indices: 5919812--5919844 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5919802 TGAGCTGGGC
*
5919812 TGGTA TGGTA TGGTA TGGTA TGGTA TGGAA TGG
1 TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGG
5919845 CTAATTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.36
Consensus pattern (5 bp):
TGGTA
Found at i:5921803 original size:50 final size:50
Alignment explanation
Indices: 5921645--5921796 Score: 191
Period size: 50 Copynumber: 3.1 Consensus size: 50
5921635 TACTAAATAG
* *
5921645 GCTTCCATCAAATCA--TAAAGAGACTTGTTTTATCATTTCAGTTATCAG
1 GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
* * * * *
5921693 GCTTCCATCAACTCATGCAAACAGACTTGTTTTATCATTTCAGTCGTTAA
1 GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
* * * *
5921743 ACTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATCTCGGCCATCAA
1 GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
5921793 GCTT
1 GCTT
5921797 TTATCAACTC
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
48 14 0.16
50 71 0.84
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (50 bp):
GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
Found at i:5925958 original size:23 final size:22
Alignment explanation
Indices: 5925915--5925958 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
5925905 TTCTAAGTCG
5925915 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
5925938 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
5925959 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:5926067 original size:45 final size:45
Alignment explanation
Indices: 5926003--5926096 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
5925993 AACAGATACT
* *
5926003 CGGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
5926048 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
5926093 CGGT
1 CGGT
5926097 TCACATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:5927720 original size:23 final size:23
Alignment explanation
Indices: 5927687--5927738 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
5927677 ATAAGTGCCA
* *
5927687 CACTGATATGTAGTCAAAGCTAC
1 CACTGAAATGTAGCCAAAGCTAC
*
5927710 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCAAAGCTAC
5927733 CACTGA
1 CACTGA
5927739 TCAATAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCAAAGCTAC
Found at i:5927991 original size:18 final size:17
Alignment explanation
Indices: 5927965--5928003 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5927955 ATTTTCCTTC
5927965 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
5927982 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
5928000 CACA
1 CACA
5928004 ATTTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:5930598 original size:30 final size:30
Alignment explanation
Indices: 5930562--5930638 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
5930552 GTTTAATTAG
5930562 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTATCATACTTTTTATCAAAAAAA
5930592 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTATCATACTTTTTATCAAAAAAA
*
5930622 AAACTTTTACCATACTT
1 AAACTTTTATCATACTT
5930639 ATAAAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (30 bp):
AAACTTTTATCATACTTTTTATCAAAAAAA
Found at i:5930654 original size:30 final size:30
Alignment explanation
Indices: 5930562--5930656 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
5930552 GTTTAATTAG
* * *
5930562 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTACCATACTTTATATAAAAAAAA
* * *
5930592 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTACCATACTTTATATAAAAAAAA
* *
5930622 AAACTTTTACCATACTTATAAAATAAATAAAA
1 AAACTTTTACCATACTT-T-ATATAAAAAAAA
5930654 AAA
1 AAA
5930657 TTATCATGGC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 46 0.79
31 1 0.02
32 11 0.19
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.36
Consensus pattern (30 bp):
AAACTTTTACCATACTTTATATAAAAAAAA
Found at i:5931253 original size:19 final size:19
Alignment explanation
Indices: 5931207--5931243 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5931197 AAAATCAAAA
5931207 AAATATTATAAAAATGTTT
1 AAATATTATAAAAATGTTT
*
5931226 AAATATTATAAAAGTGTT
1 AAATATTATAAAAATGTT
5931244 ATATATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATATTATAAAAATGTTT
Found at i:5968669 original size:37 final size:37
Alignment explanation
Indices: 5968608--5968754 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
5968598 TACGTATGAT
* *
5968608 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5968643 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5968680 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
5968717 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5968754 C
1 C
5968755 GAAGCTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:5968770 original size:46 final size:46
Alignment explanation
Indices: 5968717--5968937 Score: 264
Period size: 46 Copynumber: 4.6 Consensus size: 46
5968707 TAAGTGTAGC
*
5968717 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
5968763 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
5968815 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * * ** *
5968861 TACTTATCACTTT-CCACTTGTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCA-----CTTGATCAGATAAGTATAGCCGAAGCTAT
5968911 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
5968938 AGTACTCAAA
Statistics
Matches: 152, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
45 2 0.01
46 66 0.43
49 2 0.01
50 37 0.24
51 2 0.01
52 43 0.28
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:5968796 original size:52 final size:52
Alignment explanation
Indices: 5968717--5968931 Score: 275
Period size: 52 Copynumber: 4.2 Consensus size: 52
5968707 TAAGTGTAGC
* *
5968717 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
5968770 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
5968822 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * ** *
5968868 CACTTTCCACTTGT--CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
5968918 CACTTTGTCACTTG
1 CACTTT-TCACTTG
5968932 ATCAGAAGTA
Statistics
Matches: 143, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
46 43 0.30
49 1 0.01
50 37 0.26
51 6 0.04
52 47 0.33
53 9 0.06
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:5968848 original size:98 final size:96
Alignment explanation
Indices: 5968716--5968937 Score: 372
Period size: 98 Copynumber: 2.3 Consensus size: 96
5968706 ATAAGTGTAG
* *
5968716 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
*
5968781 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
66 TGT--CTTGATCAGATAAGTGTAGCCAAAGCTA
* *
5968814 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
*
5968879 TGTCTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCTTGATCAGATAAGTGTAGCCAAAGCTA
5968910 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
5968938 AGTACTCAAA
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
96 53 0.45
98 64 0.55
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (96 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
TGTCTTGATCAGATAAGTGTAGCCAAAGCTA
Found at i:5984725 original size:16 final size:16
Alignment explanation
Indices: 5984704--5984735 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5984694 TAAAATATAG
5984704 AAATTAGTAGATGAAA
1 AAATTAGTAGATGAAA
*
5984720 AAATTAGTAGTTGAAA
1 AAATTAGTAGATGAAA
5984736 CTGATTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
AAATTAGTAGATGAAA
Found at i:5986368 original size:3 final size:3
Alignment explanation
Indices: 5986360--5986384 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5986350 TTATATTAGT
5986360 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5986385 AAGGGCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5993121 original size:20 final size:20
Alignment explanation
Indices: 5993098--5993162 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
5993088 ATTTAATTAG
*
5993098 AATATATAAATTATATTTTA
1 AATATTTAAATTATATTTTA
5993118 AATATTTAAA-TATAATTATTA
1 AATATTTAAATTAT-ATT-TTA
*
5993139 AATATTTGTAATTAGTATTTTA
1 AATATTT-AAATTA-TATTTTA
5993161 AA
1 AA
5993163 AATTATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 10 0.26
22 7 0.18
23 5 0.13
24 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AATATTTAAATTATATTTTA
Found at i:5993141 original size:21 final size:21
Alignment explanation
Indices: 5993093--5993162 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
5993083 ATAAAATTTA
*
5993093 ATTAGAATATATAAATTATATT
1 ATTA-AATATTTAAATTATATT
5993115 -TTAAATATTTAAA-TATAATT
1 ATTAAATATTTAAATTAT-ATT
*
5993135 ATTAAATATTTGTAATTAGTATT
1 ATTAAATATTT-AAATTA-TATT
5993158 -TTAAA
1 ATTAAA
5993163 AATTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 13 0.32
22 7 0.17
23 5 0.12
24 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTAAATATTTAAATTATATT
Found at i:5993141 original size:33 final size:31
Alignment explanation
Indices: 5993065--5993145 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 31
5993055 ATTTTTAAGT
*
5993065 AATA-AATATT-AATTATTTATAAA-ATTTA
1 AATATAATATTAAATTATTTTTAAATATTTA
* *
5993093 ATTAGAATATATAAATTATATTTTAAATATTTA
1 AATATAATAT-TAAATTAT-TTTTAAATATTTA
5993126 AATATAATTATTAAA-TATTT
1 AATATAA-TATTAAATTATTT
5993146 GTAATTAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 1 0.02
31 8 0.19
32 9 0.21
33 14 0.33
34 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
AATATAATATTAAATTATTTTTAAATATTTA
Found at i:5996868 original size:38 final size:38
Alignment explanation
Indices: 5996817--5996890 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
5996807 TCATAAGTTT
* * *
5996817 AGTAATTCGTTTGTTGTGTATTTCCCGGTTGGTGTCAA
1 AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTCAA
5996855 AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTC
1 AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTC
5996891 TGTCTCTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.45
Consensus pattern (38 bp):
AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTCAA
Found at i:5997916 original size:22 final size:22
Alignment explanation
Indices: 5997891--5997933 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5997881 TATTTAAAAA
5997891 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
*
5997913 ATAATAACAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
5997934 AACAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:5997943 original size:22 final size:22
Alignment explanation
Indices: 5997896--5997943 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5997886 AAAAAATAAC
* * *
5997896 AACAAAATAGTAGCAATATAAT
1 AACAAAATAGTAGCAAAACAAA
5997918 AACAAAAT-GATAGCAAAACAAA
1 AACAAAATAG-TAGCAAAACAAA
5997940 AACA
1 AACA
5997944 TAACAGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (22 bp):
AACAAAATAGTAGCAAAACAAA
Found at i:6005484 original size:3 final size:3
Alignment explanation
Indices: 6005476--6005505 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6005466 TAGTCCCTAA
6005476 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6005506 TTTGCTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6016775 original size:5 final size:5
Alignment explanation
Indices: 6016765--6016789 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6016755 TCACGTTCAC
6016765 TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA
6016790 ACTCATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:6017194 original size:126 final size:128
Alignment explanation
Indices: 6017037--6017294 Score: 375
Period size: 126 Copynumber: 2.0 Consensus size: 128
6017027 ATTCATATTT
6017037 ACAAAAAATATATATATTACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGACAA
1 ACAAAAAATATATATATTACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGACAA
* * *
6017102 CTCGAAC-AGTTACATGATT-TC-A-A-TTATCTATGCAACTAAAATGAAAAACAT-TTCGGAA
66 ATCGAACAAGTTAAATGATTCTCAACAGTTATCTATGCAACT-AAATGAAAAACATGTTCGCAA
*
6017160 ACAAAAAGTATATATATACTTACATTCTCAATGTCATGCTCATACTATCTATTATACAATTCCGA
1 ACAAAAA--ATATATATA-TTACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGA
* *
6017225 CAAATCGGACAAGTTAAATGTTTCTCAACCAGTTATCTATGCAACTAAATGAAAAACATGTTCGC
63 CAAATCGAACAAGTTAAATGATTCTCAA-CAGTTATCTATGCAACTAAATGAAAAACATGTTCGC
6017290 AA
127 AA
6017292 ACA
1 ACA
6017295 GGGAAAACCC
Statistics
Matches: 119, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
123 7 0.06
125 9 0.08
126 53 0.45
127 10 0.08
128 2 0.02
129 1 0.01
131 14 0.12
132 23 0.19
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (128 bp):
ACAAAAAATATATATATTACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGACAA
ATCGAACAAGTTAAATGATTCTCAACAGTTATCTATGCAACTAAATGAAAAACATGTTCGCAA
Found at i:6021459 original size:24 final size:24
Alignment explanation
Indices: 6021403--6021467 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
6021393 CCGGCCTATT
6021403 TTTAATAAACAAAAATTATTCTAAAA
1 TTTAA-AAA-AAAAATTATTCTAAAA
**
6021429 TAAAAAAAAAAAATTATT-TAAATA
1 TTTAAAAAAAAAATTATTCTAAA-A
6021453 TTTAAAATAAAAAAT
1 TTTAAAA-AAAAAAT
6021468 AAAAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 4 0.12
24 16 0.48
25 10 0.30
26 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (24 bp):
TTTAAAAAAAAAATTATTCTAAAA
Done.