Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 180 of 226
Found at i:57645666 original size:30 final size:30
Alignment explanation
Indices: 57645452--57645668 Score: 150
Period size: 30 Copynumber: 7.2 Consensus size: 30
57645442 ATTCCAACCT
** *
57645452 TTTTCATGGCTCGATAGTCGAAGCTATCCC
1 TTTTCATAACTCGATAGCCGAAGCTATCCC
* ** * *
57645482 TTTTCGTGGCTCGATAGTCGAAGCTATCCA
1 TTTTCATAACTCGATAGCCGAAGCTATCCC
* *
57645512 TTTTCATAGCTCGATAGCTGAAGCTATCCC
1 TTTTCATAACTCGATAGCCGAAGCTATCCC
* ** * *
57645542 TTTTCGTGGCTCGATAGTCGAAGCTATCGC
1 TTTTCATAACTCGATAGCCGAAGCTATCCC
* *
57645572 TTTTCGTAACTCGATA-CCTGAAGCTAGCCC
1 TTTTCATAACTCGATAGCC-GAAGCTATCCC
* * ** * * * *
57645602 TTTTCATTATTTAATGGTCGTCA-CCATCCC
1 TTTTCATAACTCGATAGCCG-AAGCTATCCC
* * *
57645632 TTTTCATAATTTGATAGCCGAAGCTATCCA
1 TTTTCATAACTCGATAGCCGAAGCTATCCC
57645662 TTTTCAT
1 TTTTCAT
57645669 TAGTCAATGA
Statistics
Matches: 149, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
29 2 0.01
30 145 0.97
31 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.36
Consensus pattern (30 bp):
TTTTCATAACTCGATAGCCGAAGCTATCCC
Found at i:57660658 original size:11 final size:11
Alignment explanation
Indices: 57660632--57660666 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
57660622 TTGATGATTT
57660632 TTTATTTTT-A
1 TTTATTTTTCA
*
57660642 TATATTTTTCA
1 TTTATTTTTCA
57660653 TTTATTTTTCA
1 TTTATTTTTCA
57660664 TTT
1 TTT
57660667 TCATTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTTCA
Found at i:57665539 original size:32 final size:32
Alignment explanation
Indices: 57665495--57665582 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
57665485 TACTTCACAC
* *
57665495 GCCCGTGTGGTTTCACATGGCCTAAATATCTT
1 GCCCGTGTGGTTTCACATGGCCTAAATATATG
* * *
57665527 GCTCGTGTGGTTTCACATGTCCTGAATATATG
1 GCCCGTGTGGTTTCACATGGCCTAAATATATG
* * *
57665559 GCCCGTGTTGTTCCACACGGCCTA
1 GCCCGTGTGGTTTCACATGGCCTA
57665583 GCACACGCCC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (32 bp):
GCCCGTGTGGTTTCACATGGCCTAAATATATG
Found at i:57665842 original size:17 final size:17
Alignment explanation
Indices: 57665801--57665842 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
57665791 AGTGAGTTAC
57665801 ACGGCCATGTGGCATCG
1 ACGGCCATGTGGCATCG
* *
57665818 ACGACCATGTGGCGTCG
1 ACGGCCATGTGGCATCG
*
57665835 ATGGCCAT
1 ACGGCCAT
57665843 ATTTTCCGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (17 bp):
ACGGCCATGTGGCATCG
Found at i:57666389 original size:37 final size:36
Alignment explanation
Indices: 57666317--57666390 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 36
57666307 CAAGGTAATC
*
57666317 AAACAAAAAGAAAGAAAAAGAAATGGAAGAAAAGGAA
1 AAACAAAAAGAAAGAAAAAGAAA-GAAAGAAAAGGAA
57666354 AAACAAAAAGAAA-ATAAAATGAAA-AAAGAAGAAGGAA
1 AAACAAAAAGAAAGA-AAAA-GAAAGAAAGAA-AAGGAA
57666391 TGTTAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 6 0.18
37 23 0.70
38 4 0.12
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.04
Consensus pattern (36 bp):
AAACAAAAAGAAAGAAAAAGAAAGAAAGAAAAGGAA
Found at i:57674079 original size:3 final size:3
Alignment explanation
Indices: 57674073--57674103 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
57674063 ATACCTTTTG
57674073 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
57674104 TTATCCACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:57674580 original size:22 final size:22
Alignment explanation
Indices: 57674552--57674611 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
57674542 ATAAAATTAA
*
57674552 TATTTAAAAATATTTATAATT-
1 TATTTAAAAATAATTATAATTC
57674573 TAATTTAAAATTATTAATTATAATTC
1 T-ATTTAAAA--A-TAATTATAATTC
57674599 TATTTAAAAATAA
1 TATTTAAAAATAA
57674612 GTTGTGATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 1 0.03
22 11 0.33
23 1 0.03
24 1 0.03
25 18 0.55
26 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTAAAAATAATTATAATTC
Found at i:57678803 original size:26 final size:27
Alignment explanation
Indices: 57678774--57678877 Score: 119
Period size: 26 Copynumber: 4.0 Consensus size: 27
57678764 CTTGAATAGT
57678774 AGGCCTTGAGCTGA-TGTTTATTTAGC
1 AGGCCTTGAGCTGAGTGTTTATTTAGC
* *
57678800 AGGCCTTGAGTTG-GTGTTTATTTAGA
1 AGGCCTTGAGCTGAGTGTTTATTTAGC
* *
57678826 AGGCCTTGAG-TCAGTGATTATTTAGC
1 AGGCCTTGAGCTGAGTGTTTATTTAGC
* *
57678852 AGGCTTTGATCT-AGTGTTT-TTTAGC
1 AGGCCTTGAGCTGAGTGTTTATTTAGC
57678877 A
1 A
57678878 TGCTTTGATC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
25 8 0.12
26 58 0.87
27 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.40
Consensus pattern (27 bp):
AGGCCTTGAGCTGAGTGTTTATTTAGC
Found at i:57683690 original size:38 final size:38
Alignment explanation
Indices: 57683639--57683713 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
57683629 GTTGAATTTG
57683639 CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATAA
1 CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATAA
57683677 CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATA
1 CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATA
57683714 TCTATATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (38 bp):
CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATAA
Found at i:57686644 original size:26 final size:26
Alignment explanation
Indices: 57686615--57686870 Score: 185
Period size: 26 Copynumber: 9.9 Consensus size: 26
57686605 AATAGCAGGG
*
57686615 CTTGAGTCGGTGTTTATTTAGCAAGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * * *
57686641 CTTG-GAACTGTGTTTCTTTAGTAGGC
1 CTTGAG-CCGGTGTTTATTTAGCAAGC
* * *
57686667 CTTGAGACGGTGTTTATTTAGTAGGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * *
57686693 CTTGGGCTGATGTTTCTTTAGCAAGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* *
57686719 CTTGAGCCGGTGTTTATTTAGTAGGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * * *
57686745 TTTGGGCAGGTGTTTCTTTAGCAAGT
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* ** *
57686771 TTTGAGCCATTGTTTATTTAGCACGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* *
57686797 CTTGAGCCAGTGGTTATTTAGC-AGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * *
57686822 TTTGAGCTGGTGTTTATTTAG-ATGGC
1 CTTGAGCCGGTGTTTATTTAGCA-AGC
* **
57686848 TTTGAGCCGGTGAATATTTAGCA
1 CTTGAGCCGGTGTTTATTTAGCA
57686871 GGTACTATGT
Statistics
Matches: 179, Mismatches: 46, Indels: 9
0.76 0.20 0.04
Matches are distributed among these distances:
25 20 0.11
26 157 0.88
27 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.39
Consensus pattern (26 bp):
CTTGAGCCGGTGTTTATTTAGCAAGC
Found at i:57686757 original size:78 final size:78
Alignment explanation
Indices: 57686625--57686842 Score: 219
Period size: 78 Copynumber: 2.8 Consensus size: 78
57686615 CTTGAGTCGG
* * * *
57686625 TGTTTATTTAGCAAGCCTTG-GAACTGTGTTTCTTTAGTAGGCCTTGAG-ACGGTGTTTATTTAG
1 TGTTTATTTAGCAAGCCTTGAG-CCAGTGTTTATTTAGTAGGCTTTGAGCA-GGTGTTTATTTAG
* * * *
57686688 TAGGCCTTGGGCTGA-
64 CAAGCCTTGAGC-CAT
* * * *
57686703 TGTTTCTTTAGCAAGCCTTGAGCCGGTGTTTATTTAGTAGGCTTTGGGCAGGTGTTTCTTTAGCA
1 TGTTTATTTAGCAAGCCTTGAGCCAGTGTTTATTTAGTAGGCTTTGAGCAGGTGTTTATTTAGCA
**
57686768 AGTTTTGAGCCAT
66 AGCCTTGAGCCAT
* * * *
57686781 TGTTTATTTAGCACGCCTTGAGCCAGTGGTTATTTAGCA-GCTTTGAGCTGGTGTTTATTTAG
1 TGTTTATTTAGCAAGCCTTGAGCCAGTGTTTATTTAGTAGGCTTTGAGCAGGTGTTTATTTAG
57686843 ATGGCTTTGA
Statistics
Matches: 116, Mismatches: 21, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
77 21 0.18
78 93 0.80
79 2 0.02
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.41
Consensus pattern (78 bp):
TGTTTATTTAGCAAGCCTTGAGCCAGTGTTTATTTAGTAGGCTTTGAGCAGGTGTTTATTTAGCA
AGCCTTGAGCCAT
Found at i:57686776 original size:52 final size:52
Alignment explanation
Indices: 57686615--57686842 Score: 219
Period size: 52 Copynumber: 4.4 Consensus size: 52
57686605 AATAGCAGGG
* * * * * * *
57686615 CTTGAGTCGGTGTTTATTTAGCAAGCCTT-GGAACTGTGTTTCTTTAGTAGGC
1 CTTGAGCCGGTGTTTATTTAGTAGGCCTTGGGCA-GGTGTTTCTTTAGCAAGC
* * *
57686667 CTTGAGACGGTGTTTATTTAGTAGGCCTTGGGCTGATGTTTCTTTAGCAAGC
1 CTTGAGCCGGTGTTTATTTAGTAGGCCTTGGGCAGGTGTTTCTTTAGCAAGC
* *
57686719 CTTGAGCCGGTGTTTATTTAGTAGGCTTTGGGCAGGTGTTTCTTTAGCAAGT
1 CTTGAGCCGGTGTTTATTTAGTAGGCCTTGGGCAGGTGTTTCTTTAGCAAGC
* ** * * * * *
57686771 TTTGAGCCATTGTTTATTTAGCACGCCTTGAGCCA-GTGGTTATTTAGC-AGC
1 CTTGAGCCGGTGTTTATTTAGTAGGCCTTG-GGCAGGTGTTTCTTTAGCAAGC
* *
57686822 TTTGAGCTGGTGTTTATTTAG
1 CTTGAGCCGGTGTTTATTTAG
57686843 ATGGCTTTGA
Statistics
Matches: 147, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
51 20 0.14
52 122 0.83
53 5 0.03
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (52 bp):
CTTGAGCCGGTGTTTATTTAGTAGGCCTTGGGCAGGTGTTTCTTTAGCAAGC
Found at i:57693686 original size:18 final size:17
Alignment explanation
Indices: 57693652--57693691 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
57693642 TATGTTGTTT
57693652 TCTCCTTCATTTCTTTC
1 TCTCCTTCATTTCTTTC
57693669 TCTCCTCTCATCTT-TTTC
1 TCTCCT-TCAT-TTCTTTC
57693687 TCTCC
1 TCTCC
57693692 CCTTCCACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (17 bp):
TCTCCTTCATTTCTTTC
Found at i:57698454 original size:20 final size:20
Alignment explanation
Indices: 57698440--57698502 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
57698430 AGCTTGTCTT
57698440 CAATTCTGGTGGCTTGTCCA
1 CAATTCTGGTGGCTTGTCCA
* * *
57698460 CATTTCTGGTGGTTTAT-CA
1 CAATTCTGGTGGCTTGTCCA
57698479 GC-ATTACTGGTGGCTTGTCCA
1 -CAATT-CTGGTGGCTTGTCCA
57698500 CAA
1 CAA
57698503 ACTATTGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
CAATTCTGGTGGCTTGTCCA
Found at i:57708473 original size:15 final size:15
Alignment explanation
Indices: 57708453--57708482 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57708443 ATTTTACTTA
*
57708453 GTAGTTTTATTTAAT
1 GTAGTTTAATTTAAT
57708468 GTAGTTTAATTTAAT
1 GTAGTTTAATTTAAT
57708483 TTTTACAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (15 bp):
GTAGTTTAATTTAAT
Found at i:57709545 original size:49 final size:49
Alignment explanation
Indices: 57709473--57709577 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
57709463 ATGAATGTCC
* *
57709473 ATCCAATCCAGTGTCAATATACTATATGGGGAACTCTAACTAAAACAATA
1 ATCC-ATCCAGTGTCAACATACTATATAGGGAACTCTAACTAAAACAATA
57709523 ATCCATCCAGTGTCAACATACTATATAGGGAACTCTAACTAAAACAATA
1 ATCCATCCAGTGTCAACATACTATATAGGGAACTCTAACTAAAACAATA
57709572 ATCCAT
1 ATCCAT
57709578 ACTGCAATAC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
49 49 0.92
50 4 0.08
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (49 bp):
ATCCATCCAGTGTCAACATACTATATAGGGAACTCTAACTAAAACAATA
Found at i:57719073 original size:8 final size:8
Alignment explanation
Indices: 57719060--57719084 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
57719050 GCGGACACAA
57719060 TCGACTAC
1 TCGACTAC
57719068 TCGACTAC
1 TCGACTAC
57719076 TCGACTAC
1 TCGACTAC
57719084 T
1 T
57719085 TTCGTTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.28
Consensus pattern (8 bp):
TCGACTAC
Found at i:57737544 original size:18 final size:18
Alignment explanation
Indices: 57737521--57737559 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
57737511 CAATAGTTTA
57737521 TTTACCATTTAATATCGT
1 TTTACCATTTAATATCGT
*
57737539 TTTACCATTTAATATTGT
1 TTTACCATTTAATATCGT
57737557 TTT
1 TTT
57737560 CATTTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTACCATTTAATATCGT
Found at i:57738179 original size:40 final size:40
Alignment explanation
Indices: 57738135--57738245 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
57738125 CTTCGGATAA
*
57738135 AAAACGCAGCTAAAAATC-AGGCATTACCGGCGCTTCTAAG
1 AAAACGCCGCTAAAAATCGA-GCATTACCGGCGCTTCTAAG
* * * *
57738175 AAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTTAAG
1 AAAACGCCGCTAAAAATCGAGCATTACCGGCGCTTCTAAG
* *
57738215 AAAACGCCGCTAAAAA-GGAGCATTAGCGGCG
1 AAAACGCCGCTAAAAATCGAGCATTACCGGCG
57738246 TTTTCCAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 13 0.21
40 48 0.77
41 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTACCGGCGCTTCTAAG
Found at i:57738380 original size:41 final size:41
Alignment explanation
Indices: 57738301--57738649 Score: 407
Period size: 41 Copynumber: 8.5 Consensus size: 41
57738291 TTTTGAGTTT
* * *
57738301 TCGGGGCTTTAGCGGTGTTTTT-AAGAAGCGCTGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
** * *
57738341 TCAAGTCTTTAGCGGCATTTTTGAAGAAGTGCCGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
57738382 TCAGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* **
57738423 TCGGGTCTTTAGCGTCGTTTTTGAAGAAGCGTTGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
57738464 TCGGGTCTTTAGCGGTGTTTTTGAAGTAGCGCCG-TGAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCT-AATGC
* * * *
57738505 TCGTGTCTTTAGCAGCGTTTTTGAAGAAGCACTGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
** * * *
57738546 -CTGGGTCTTTAGCGGTATTTTTTAAGAAGCACCGCTAATTC
1 TC-GGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* * * *
57738587 TCGTGTATTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATTC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
*
57738628 TCGGGTCTTTAGCAGCGTTTTT
1 TCGGGTCTTTAGCGGCGTTTTT
57738650 TAAAAAACAC
Statistics
Matches: 263, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
40 19 0.07
41 242 0.92
42 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (41 bp):
TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
Found at i:57741314 original size:20 final size:20
Alignment explanation
Indices: 57741289--57741329 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57741279 AAGAAAGCAG
57741289 TGGAAATCTTAGATGTATAT
1 TGGAAATCTTAGATGTATAT
57741309 TGGAAATCTTAGATGTATAT
1 TGGAAATCTTAGATGTATAT
57741329 T
1 T
57741330 AAAAGAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (20 bp):
TGGAAATCTTAGATGTATAT
Found at i:57743006 original size:43 final size:43
Alignment explanation
Indices: 57742953--57743141 Score: 263
Period size: 43 Copynumber: 4.4 Consensus size: 43
57742943 TTTTTAATAG
* * *
57742953 AAGCGTCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGGGA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* * * * *
57742996 AAGAGCCGCTATAGGTCATGTTCTTTAGCGGCGTTTTTGAGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* *
57743039 AAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTGTGGGAGA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGA-A
*
57743083 AA-CGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
57743125 AAGCGCCGCTAAAGGTC
1 AAGCGCCGCTAAAGGTC
57743142 TTGTTAGCGA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 3 0.02
43 123 0.95
44 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:57745040 original size:40 final size:41
Alignment explanation
Indices: 57744966--57745164 Score: 159
Period size: 41 Copynumber: 4.8 Consensus size: 41
57744956 AGCGTTTACA
* * * * *
57744966 GAAATAAACGCTGCTAAAGGTTATATTCTTTAGCGGCGC-T
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
*
57745006 GAAAAAAACGCCGCTAAAGATCATGTTCTGTAGCGGCGCTT
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * * *
57745047 CAAAAAAAAGTCGCTAAAGGTCATGTTCTTTAGCAGCGCTTT
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TT
* * * ** * *
57745089 TACAAAAAACGCTGCTAAAGAACATGACCTATAGCGGCGCCT
1 GA-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * *
57745131 -ACCAACAAACGCCACTAAAGCTCATGTTCTTTAG
1 GA--AAAAAACGCCGCTAAAGATCATGTTCTTTAG
57745165 TGACGCTTTA
Statistics
Matches: 124, Mismatches: 31, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
40 33 0.27
41 35 0.28
42 28 0.23
43 28 0.23
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:57745125 original size:84 final size:82
Alignment explanation
Indices: 57744978--57745164 Score: 196
Period size: 84 Copynumber: 2.3 Consensus size: 82
57744968 AATAAACGCT
* * * * ** *
57744978 GCTAAAGGTTATATTCTTTAGCGGCGCTGAAAAAAACGCCGCTAAAGATCATGTTCTGTAGCGGC
1 GCTAAAGGTCATGTTCTTTAGCAGCGCTGAAAAAAACGCCGCTAAAGAACATGACCTATAGCGGC
* *
57745043 G-CTTCAAAAAAAAGTC
66 GCCTACAAAAAAAAGCC
* *
57745059 GCTAAAGGTCATGTTCTTTAGCAGCGCTTTTACAAAAAACGCTGCTAAAGAACATGACCTATAGC
1 GCTAAAGGTCATGTTCTTTAGCAGCGC--TGA-AAAAAACGCCGCTAAAGAACATGACCTATAGC
* * *
57745124 GGCGCCTACCAACAAACGCC
63 GGCGCCTACAAAAAAAAGCC
* *
57745144 ACTAAAGCTCATGTTCTTTAG
1 GCTAAAGGTCATGTTCTTTAG
57745165 TGACGCTTTA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 24 0.28
83 2 0.02
84 31 0.36
85 29 0.34
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (82 bp):
GCTAAAGGTCATGTTCTTTAGCAGCGCTGAAAAAAACGCCGCTAAAGAACATGACCTATAGCGGC
GCCTACAAAAAAAAGCC
Found at i:57745233 original size:45 final size:42
Alignment explanation
Indices: 57745135--57745278 Score: 148
Period size: 45 Copynumber: 3.3 Consensus size: 42
57745125 GCGCCTACCA
* * * *
57745135 ACAAACGCCACTAAAGCTCATGTTCTTTAGTGACGCTTTATT-C
1 ACAAACGCCGCTAAAG-TCATGTTCTTTAGCGGCG-TTTTTTCC
* *
57745178 ACAAATGCCGCTCAAAGTAATGTTCTTTAGCGGCGTTTTTTTTCC
1 ACAAACGCCGCT-AAAGTCATGTTCTTTAGCGGCG--TTTTTTCC
* *
57745223 ACAAACGCCGCTAAAGGTCATGCTCTTTAGCGGCG-ATTTTCC
1 ACAAACGCCGCTAAA-GTCATGTTCTTTAGCGGCGTTTTTTCC
57745265 ACAAACGCCGCTAA
1 ACAAACGCCGCTAA
57745279 TTTTGGGATT
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
42 20 0.23
43 25 0.29
44 12 0.14
45 29 0.34
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGTCATGTTCTTTAGCGGCGTTTTTTCC
Found at i:57745276 original size:42 final size:42
Alignment explanation
Indices: 57744971--57745278 Score: 196
Period size: 43 Copynumber: 7.3 Consensus size: 42
57744961 TTACAGAAAT
* * * *** *
57744971 AAACGCTGCTAAAGGTTATATTCTTTAGCGGCGC--TGAAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCAC
* * * *
57745011 AAACGCCGCTAAAGATCATGTTCTGTAGCGGCGC--TTCAAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTC-CAC
* * * * *
57745052 AAAAGTCGCTAAAGGTCATGTTCTTTAGCAGCGCTTTTACAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTT-CCAC
* ** ** * * *
57745095 AAACGCTGCTAAAGAACATGACCTATAGCGGCGC-CTACCAAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCC-AC
* * * * *
57745137 AAACGCCACTAAAGCTCATGTTCTTTAGTGACGCTTTATTCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTT-TCCAC
* * *
57745180 AAATGCCGCTCAAA-GTAATGTTCTTTAGCGGCGTTTTTTTTCCAC
1 AAACGCCGCT-AAAGGTCATGTTCTTTAGCGGCG---CTTTTCCAC
* *
57745225 AAACGCCGCTAAAGGTCATGCTCTTTAGCGGCGATTTTCCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCAC
57745267 AAACGCCGCTAA
1 AAACGCCGCTAA
57745279 TTTTGGGATT
Statistics
Matches: 207, Mismatches: 49, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
40 30 0.14
41 33 0.16
42 47 0.23
43 56 0.27
44 8 0.04
45 30 0.14
46 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCAC
Found at i:57745670 original size:21 final size:21
Alignment explanation
Indices: 57745646--57745696 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
57745636 TTCTTTTGAA
* *
57745646 CCTCTGCTTCTCTTGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
57745667 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
57745688 CCTCTGCTT
1 CCTCTGCTT
57745697 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:57750991 original size:17 final size:16
Alignment explanation
Indices: 57750969--57751003 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
57750959 TAAATATTCA
57750969 AATTTATAAATACTATC
1 AATTT-TAAATACTATC
57750986 AA-TTTAAATACTATC
1 AATTTTAAATACTATC
57751001 AAT
1 AAT
57751004 ATTCAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
15 13 0.76
16 2 0.12
17 2 0.12
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTAAATACTATC
Found at i:57750995 original size:15 final size:15
Alignment explanation
Indices: 57750975--57751003 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57750965 TTCAAATTTA
57750975 TAAATACTATCAATT
1 TAAATACTATCAATT
57750990 TAAATACTATCAAT
1 TAAATACTATCAAT
57751004 ATTCAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATACTATCAATT
Found at i:57751649 original size:20 final size:20
Alignment explanation
Indices: 57751624--57751661 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57751614 AGTAACGCAT
*
57751624 TTTTAAAAAATAATTACACA
1 TTTTAAAAAATAAATACACA
57751644 TTTTAAAAAATAAATACA
1 TTTTAAAAAATAAATACA
57751662 TCAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAATAAATACACA
Found at i:57751886 original size:15 final size:16
Alignment explanation
Indices: 57751862--57751897 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
57751852 TATTTTTTAA
*
57751862 ATATTAATTTATATTT
1 ATATTAATTTACATTT
57751878 ATATT-ATTTACATTT
1 ATATTAATTTACATTT
57751893 ATATT
1 ATATT
57751898 CTAAAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTAATTTACATTT
Found at i:57752065 original size:14 final size:13
Alignment explanation
Indices: 57752033--57752085 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
57752023 CTGTAAATCT
*
57752033 TAAACCCTAAACTA
1 TAAACCCTAAAC-C
57752047 TAAACCCTAAACC
1 TAAACCCTAAACC
* *
57752060 TCAAACCCCAACCC
1 T-AAACCCTAAACC
57752074 GTAAACCCTAAA
1 -TAAACCCTAAA
57752086 TCTTCCAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 1 0.03
14 30 0.94
15 1 0.03
ACGTcount: A:0.45, C:0.38, G:0.02, T:0.15
Consensus pattern (13 bp):
TAAACCCTAAACC
Found at i:57753002 original size:113 final size:112
Alignment explanation
Indices: 57752885--57753207 Score: 390
Period size: 114 Copynumber: 2.8 Consensus size: 112
57752875 TTAGTTAATC
* * * * *
57752885 GCCGCTAATTTCGGTAAATAGCGGCG-TTTTCAACAACCGCTGCT-ATTGGCT-CTATACCTCAA
1 GCCGCTAATTTCGGT-ATTAGCGGCGTTTTTC-ATAAGCGCTACTAATT--CTAATATACCTCAA
* *
57752947 GACCAAACGCTACGTTTTGGTTAAGATATTTTGTGGCGCTTTTTATAATGT
62 GACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGT
57752998 GCCGCTAATTAT-GTGCT-TTAGCGGCGTTTCTTCATAAGCG-TCACTAATTCTAATATACCTCA
1 GCCGCTAATT-TCG-G-TATTAGCGGCGTTT-TTCATAAGCGCT-ACTAATTCTAATATACCTCA
57753060 AGACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGT
61 AGACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGT
* * *
57753112 GCCGCTAA-TTCTGTGATTTAGCGGCGTTTTTTCATAAGCACCACTAATTCTAATATACCTCAAG
1 GCCGCTAATTTCGGT-A-TTAGCGGCG-TTTTTCATAAGCGCTACTAATTCTAATATACCTCAAG
*
57753176 ACCAAATGCTGCGTTTTGGTTAAGATATTTTG
63 ACCAAACGCTGCGTTTTGGTTAAGATATTTTG
57753208 CGACGCTTAC
Statistics
Matches: 185, Mismatches: 11, Indels: 27
0.83 0.05 0.12
Matches are distributed among these distances:
111 1 0.01
112 2 0.01
113 23 0.12
114 149 0.81
115 10 0.05
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (112 bp):
GCCGCTAATTTCGGTATTAGCGGCGTTTTTCATAAGCGCTACTAATTCTAATATACCTCAAGACC
AAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGT
Found at i:57753068 original size:114 final size:114
Alignment explanation
Indices: 57752937--57753207 Score: 470
Period size: 114 Copynumber: 2.4 Consensus size: 114
57752927 CTATTGGCTC
* *
57752937 TATACCTCAAGACCAAACGCTACGTTTTGGTTAAGATATTTTGTGGCGCTTTTTATAATGTGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGTGCCG
* **
57753002 CTAATTATGTGCTTTAGCGGCGTTTCTTCATAAGCGTCACTAATTCTAA
66 CTAATTATGTGATTTAGCGGCGTTTCTTCATAAGCACCACTAATTCTAA
57753051 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGTGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGTGCCG
* *
57753116 CTAATTCTGTGATTTAGCGGCGTTTTTTCATAAGCACCACTAATTCTAA
66 CTAATTATGTGATTTAGCGGCGTTTCTTCATAAGCACCACTAATTCTAA
*
57753165 TATACCTCAAGACCAAATGCTGCGTTTTGGTTAAGATATTTTG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTG
57753208 CGACGCTTAC
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 149 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (114 bp):
TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGGGGCGCTTTTTATAATGTGCCG
CTAATTATGTGATTTAGCGGCGTTTCTTCATAAGCACCACTAATTCTAA
Found at i:57759119 original size:12 final size:11
Alignment explanation
Indices: 57759079--57759121 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
57759069 TTATTAATCC
57759079 TATTATTATTT
1 TATTATTATTT
*
57759090 GTACTATTATTGT
1 -TATTATTATT-T
57759103 TATTATTATTT
1 TATTATTATTT
57759114 TCATTATT
1 T-ATTATT
57759122 TCTTCTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.07
12 24 0.89
13 1 0.04
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTATTATTT
Found at i:57768694 original size:3 final size:3
Alignment explanation
Indices: 57768688--57768721 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
57768678 CTTCAAGAAG
57768688 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
57768722 CCTACAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:57780480 original size:43 final size:42
Alignment explanation
Indices: 57780432--57780556 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
57780422 CGTTTATGTG
*
57780432 GAAAAAAGCCGCTATAGAACATGACCTTTAGCGGTGTTTCTCA
1 GAAAAACGCCGCTATAGAACATGACCTTTAGCGGTGTTT-TCA
* *
57780475 GAAAAACGCCACTATAGAACATGACCTTTAGC-GTGCTTTTCC
1 GAAAAACGCCGCTATAGAACATGACCTTTAGCGGTG-TTTTCA
* ** * * *
57780517 TACGAACGCTGCTAAAGAACATGACCTTTAGCGGCGTTTT
1 GAAAAACGCCGCTATAGAACATGACCTTTAGCGGTGTTTT
57780557 TAGTAAAAGC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 35 0.50
43 35 0.50
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
GAAAAACGCCGCTATAGAACATGACCTTTAGCGGTGTTTTCA
Found at i:57781414 original size:13 final size:14
Alignment explanation
Indices: 57781388--57781416 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
57781378 ACAAATGAAA
57781388 AATTAAACCATTAT
1 AATTAAACCATTAT
57781402 AATTAAA-CATTAT
1 AATTAAACCATTAT
57781415 AA
1 AA
57781417 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:57786482 original size:9 final size:9
Alignment explanation
Indices: 57786464--57786576 Score: 54
Period size: 9 Copynumber: 12.6 Consensus size: 9
57786454 TTTTATGTAA
57786464 GTTATGATAT
1 GTTAT-ATAT
*
57786474 GATATATAT
1 GTTATATAT
*
57786483 -TTATATAA
1 GTTATATAT
* *
57786491 GTTATGTAA
1 GTTATATAT
57786500 GTTATGATAT
1 GTTAT-ATAT
*
57786510 GATATATAT
1 GTTATATAT
* *
57786519 -TTATGTAA
1 GTTATATAT
* *
57786527 GTTATGTAA
1 GTTATATAT
*
57786536 GTTATATAA
1 GTTATATAT
*
57786545 GTTATGTAAT
1 GTTATAT-AT
57786555 -TTATGATAT
1 GTTAT-ATAT
*
57786564 GATATATAT
1 GTTATATAT
57786573 -TTAT
1 GTTAT
57786577 GTATTATGTA
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
8 14 0.17
9 52 0.64
10 15 0.19
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (9 bp):
GTTATATAT
Found at i:57786497 original size:36 final size:36
Alignment explanation
Indices: 57786456--57786540 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
57786446 ATCCAAAGTT
57786456 TTATGTAAGTTATGATATGATATATATTTATATAAG
1 TTATGTAAGTTATGATATGATATATATTTATATAAG
*
57786492 TTATGTAAGTTATGATATGATATATATTTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATATAAG
57786528 TTATGTAAGTTAT
1 TTATGTAAGTTAT
57786541 ATAAGTTATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (36 bp):
TTATGTAAGTTATGATATGATATATATTTATATAAG
Found at i:57786612 original size:54 final size:54
Alignment explanation
Indices: 57786483--57786592 Score: 197
Period size: 54 Copynumber: 2.1 Consensus size: 54
57786473 TGATATATAT
*
57786483 TTATATAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAG
1 TTATATAAGTTATGTAATTTATGATATGATATATATTTATGTAAGTTATGTAAG
57786537 TTATATAAGTTATGTAATTTATGATATGATATATATTTATGT-A-TTATGTAAG
1 TTATATAAGTTATGTAATTTATGATATGATATATATTTATGTAAGTTATGTAAG
57786589 TTAT
1 TTAT
57786593 GATCCAAAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 13 0.24
53 1 0.02
54 41 0.75
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (54 bp):
TTATATAAGTTATGTAATTTATGATATGATATATATTTATGTAAGTTATGTAAG
Found at i:57787451 original size:19 final size:17
Alignment explanation
Indices: 57787423--57787462 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
57787413 TAATTTGTTA
57787423 TTTC-TTTTGTTTACTTAT
1 TTTCATTTTGTTTA-TT-T
57787441 TTTCATTTTGTTTATTT
1 TTTCATTTTGTTTATTT
57787458 TTTCA
1 TTTCA
57787463 ATACTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTCATTTTGTTTATTT
Found at i:57788997 original size:41 final size:41
Alignment explanation
Indices: 57788823--57788967 Score: 245
Period size: 41 Copynumber: 3.5 Consensus size: 41
57788813 TTTAACATAT
*
57788823 TCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
57788864 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
57788905 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
57788946 TCATCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
57788968 ACTTAAAGTC
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:57789009 original size:82 final size:83
Alignment explanation
Indices: 57788821--57788997 Score: 236
Period size: 82 Copynumber: 2.2 Consensus size: 83
57788811 AATTTAACAT
* *
57788821 ATTCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAGGTTCATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
**
57788886 GTTTATAACCTGATTCAG
66 ACTTATAACCTGATTCAG
* * *
57788904 A-TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCAGATCATCGGCACTTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAGGTTCATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
*
57788968 ACTTA-AAGTCTGAATT-A-
66 ACTTATAA-CCTG-ATTCAG
57788985 ATTCACCGGCACT
1 ATTCACCGGCACT
57788998 ACATCTGCTA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
81 3 0.04
82 76 0.92
83 4 0.05
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (83 bp):
ATTCACCGGCACTTAGCCTGCTAGGTTCATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
ACTTATAACCTGATTCAG
Found at i:57790025 original size:14 final size:14
Alignment explanation
Indices: 57790006--57790034 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
57789996 AACATACAAT
57790006 AGATATTCATACAC
1 AGATATTCATACAC
57790020 AGATATTCATACAC
1 AGATATTCATACAC
57790034 A
1 A
57790035 CAAATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (14 bp):
AGATATTCATACAC
Found at i:57791042 original size:13 final size:13
Alignment explanation
Indices: 57791024--57791048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57791014 CAGTCAAATG
57791024 CACACAAAATAAA
1 CACACAAAATAAA
57791037 CACACAAAATAA
1 CACACAAAATAA
57791049 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:57796744 original size:41 final size:41
Alignment explanation
Indices: 57796687--57796836 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
57796677 TTTAACATAT
*
57796687 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * *
57796728 TCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
57796769 TCACCGGCACTTAGCCTGCTAGG-TTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTT-ATAACCTGATTCAGA
*
57796810 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
57796837 AAGTCTAAAT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.02
41 95 0.96
42 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:57796855 original size:82 final size:83
Alignment explanation
Indices: 57796685--57796861 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 83
57796675 AATTTAACAT
*
57796685 ATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACGTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAG
** *
57796750 GTTTATAACCTGATTCAG
66 ACTTATAACCTAATTCAG
* * *
57796768 A-TCACCGGCACTTAGCCTGCTAGG-TTCATAACCTGGTTCAGATCACCGGCACTTAGCCTGCTA
1 ATTCACCGGCACTTAGCCTGCTAGGCTT-ATAACCTGATTCAGATCACCGACACGTAGCCTGCTA
*
57796831 GACTTA-AAGTCTAAATT-A-
65 GACTTATAA-CCT-AATTCAG
57796849 ATTCACCGGCACT
1 ATTCACCGGCACT
57796862 ACATCTGCTA
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
81 5 0.06
82 73 0.89
83 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (83 bp):
ATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAG
ACTTATAACCTAATTCAG
Found at i:57798954 original size:13 final size:13
Alignment explanation
Indices: 57798936--57798960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57798926 CAATCAAATG
57798936 CACACAAAATAAA
1 CACACAAAATAAA
57798949 CACACAAAATAA
1 CACACAAAATAA
57798961 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:57799239 original size:12 final size:12
Alignment explanation
Indices: 57799222--57799247 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57799212 CAATAGCATG
57799222 CTCCATTCTCAA
1 CTCCATTCTCAA
57799234 CTCCATTCTCAA
1 CTCCATTCTCAA
57799246 CT
1 CT
57799248 AAATAGCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCCATTCTCAA
Found at i:57800792 original size:22 final size:22
Alignment explanation
Indices: 57800749--57800792 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
57800739 AACATATAAT
*
57800749 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
57800771 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
57800793 CAGCAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:57801922 original size:21 final size:21
Alignment explanation
Indices: 57801883--57801924 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57801873 TGGGAATTTT
* * *
57801883 GATTTGGGGAATAATTTTAGG
1 GATTTGGGAAAAAAATTTAGG
57801904 GATTTGGGAAAAAAATTTAGG
1 GATTTGGGAAAAAAATTTAGG
57801925 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (21 bp):
GATTTGGGAAAAAAATTTAGG
Found at i:57809227 original size:2 final size:2
Alignment explanation
Indices: 57809169--57809209 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
57809159 TGGAATGAGA
*
57809169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57809210 TTAAAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:57812491 original size:6 final size:6
Alignment explanation
Indices: 57812480--57812508 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
57812470 CCATTTCTCT
57812480 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
57812509 GGAGAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTC
Found at i:57812508 original size:69 final size:71
Alignment explanation
Indices: 57812417--57812553 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 71
57812407 TTTTAGGTCT
* *
57812417 TTTTCATTTTTCATTTTCATTTTGGAGAAAACCATATTCATTTCCAAATGATTCC-ATTTCTCTA
1 TTTTCATTTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCTATTTCTCCA
57812481 TTTTCA
66 TTTTCA
* * *
57812487 TTTTCA-TTTTCATTTTCATTTTGGAGAAAATCATAATCATTTTCAAATGTTTCCTATTTCTCCA
1 TTTTCATTTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCTATTTCTCCA
57812551 TTT
66 TTT
57812554 ATCCATTTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 44 0.72
70 17 0.28
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.51
Consensus pattern (71 bp):
TTTTCATTTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCTATTTCTCCA
TTTTCA
Found at i:57817198 original size:13 final size:13
Alignment explanation
Indices: 57817180--57817205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57817170 TGAGGGGTTT
57817180 TGGACCTCTCTCA
1 TGGACCTCTCTCA
57817193 TGGACCTCTCTCA
1 TGGACCTCTCTCA
57817206 CATCAGATTC
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:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (13 bp):
TGGACCTCTCTCA
Found at i:57819441 original size:70 final size:70
Alignment explanation
Indices: 57819319--57819561 Score: 333
Period size: 70 Copynumber: 3.5 Consensus size: 70
57819309 CGAACATCTA
* * *
57819319 CATGTTGCCATAGTTGAGCTATGGTCTTACACACCATAATTCCCCATCTTTAACATCGTGGTAGA
1 CATGTTGCCATAGTCGAGCTATGGTCTTACACACCATAATTCCCCATGTTTAACATCCTGGTAGA
57819384 CTCTT
66 CTCTT
* * * ** * *
57819389 CATGTTGCCATAGTTGAGCTATGGTCTTACAGACCATAATTCCTCATGTTTAATGTCTTGGCAGA
1 CATGTTGCCATAGTCGAGCTATGGTCTTACACACCATAATTCCCCATGTTTAACATCCTGGTAGA
57819454 CTCTT
66 CTCTT
* * * * *
57819459 CATGTTGCCATAGCCAAGATATTGTCTTACACACCATAATTCCCCATGTTTTAACATCCTGCTAG
1 CATGTTGCCATAGTCGAGCTATGGTCTTACACACCATAATTCCCCATG-TTTAACATCCTGGTAG
57819524 ACTCTT
65 ACTCTT
*
57819530 CATGTTGCCATAGTCGAGCTATGTTCTTACAC
1 CATGTTGCCATAGTCGAGCTATGGTCTTACAC
57819562 CTTAAACATC
Statistics
Matches: 148, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
70 104 0.70
71 44 0.30
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (70 bp):
CATGTTGCCATAGTCGAGCTATGGTCTTACACACCATAATTCCCCATGTTTAACATCCTGGTAGA
CTCTT
Found at i:57821217 original size:16 final size:16
Alignment explanation
Indices: 57821196--57821226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57821186 TATACTAATC
*
57821196 AAACACATAATTATTT
1 AAACACATAAATATTT
57821212 AAACACATAAATATT
1 AAACACATAAATATT
57821227 GTATGAACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (16 bp):
AAACACATAAATATTT
Found at i:57828882 original size:2 final size:2
Alignment explanation
Indices: 57828875--57828900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57828865 ATTATAAACC
57828875 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
57828901 CATTACGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57829968 original size:41 final size:43
Alignment explanation
Indices: 57829867--57830011 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 43
57829857 ATATCGAACA
* * * * **
57829867 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
*
57829910 ATGCCACTGTCCCAGACATGGTCTTACACG-AATCAAATAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
* *
57829951 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCACATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCA-A-ATATCG
57829996 ATGCC-ATCGTCCCAGA
1 ATGCCAAT-GTCCCAGA
57830012 AGTCGTCTTA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
41 29 0.33
42 12 0.14
43 27 0.31
44 6 0.07
45 13 0.15
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
Found at i:57833103 original size:6 final size:6
Alignment explanation
Indices: 57833094--57833133 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
57833084 TCAAATTTTT
* *
57833094 TTATAA TTAT-A TTATAA TTATAG TTAAAA TTATAA TTATA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATA
57833134 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
TTATAA
Found at i:57833127 original size:18 final size:18
Alignment explanation
Indices: 57833104--57833138 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57833094 TTATAATTAT
57833104 ATTATAATTATAGTTAAA
1 ATTATAATTATAGTTAAA
*
57833122 ATTATAATTATATTTAA
1 ATTATAATTATAGTTAA
57833139 TTTTTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTATAATTATAGTTAAA
Found at i:57833306 original size:17 final size:17
Alignment explanation
Indices: 57833272--57833306 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
57833262 CAACTTTTAA
57833272 TAAATTATAATTATTTT
1 TAAATTATAATTATTTT
57833289 TAAATGTATAATTATTTT
1 TAAAT-TATAATTATTTT
57833307 GCTTCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TAAATTATAATTATTTT
Found at i:57833645 original size:29 final size:27
Alignment explanation
Indices: 57833606--57833669 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
57833596 TATCTTTTAA
57833606 AAAATATACTTTCAAAAAAAAAACTTTT
1 AAAATATACTTT-AAAAAAAAAACTTTT
* *
57833634 AAAGATATACTTTTAAAAATAAACTTTT
1 AAA-ATATACTTTAAAAAAAAAACTTTT
57833662 AAAATATA
1 AAAATATA
57833670 TAACCAAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 5 0.15
28 19 0.58
29 9 0.27
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAATATACTTTAAAAAAAAAACTTTT
Found at i:57833647 original size:14 final size:13
Alignment explanation
Indices: 57833628--57833669 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
57833618 CAAAAAAAAA
57833628 ACTTTTAAAGATAT
1 ACTTTTAAA-ATAT
*
57833642 ACTTTTAAAAATAA
1 ACTTTT-AAAATAT
57833656 ACTTTTAAAATAT
1 ACTTTTAAAATAT
57833669 A
1 A
57833670 TAACCAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.28
14 15 0.60
15 3 0.12
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (13 bp):
ACTTTTAAAATAT
Found at i:57833670 original size:29 final size:30
Alignment explanation
Indices: 57833599--57833671 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
57833589 ATTATGTTAT
57833599 CTTTTAAAAAATATACTTTCAAAAAAAAAA
1 CTTTTAAAAAATATACTTTCAAAAAAAAAA
* * *
57833629 CTTTT-AAAGATATACTTT-TAAAAATAAA
1 CTTTTAAAAAATATACTTTCAAAAAAAAAA
*
57833657 CTTTTAAAATATATA
1 CTTTTAAAAAATATA
57833672 ACCAAGCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 13 0.34
29 20 0.53
30 5 0.13
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.37
Consensus pattern (30 bp):
CTTTTAAAAAATATACTTTCAAAAAAAAAA
Found at i:57849069 original size:2 final size:2
Alignment explanation
Indices: 57849062--57849091 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57849052 CATCGAATGC
57849062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57849092 TATTCAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57849425 original size:41 final size:41
Alignment explanation
Indices: 57849375--57849551 Score: 282
Period size: 41 Copynumber: 4.3 Consensus size: 41
57849365 TTAAATAGAT
* * * *
57849375 TCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
57849416 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
57849457 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * *
57849498 TCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGTTTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
57849539 TCACCGGCACTTA
1 TCACCGGCACTTA
57849552 TACAGAATAA
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:57850459 original size:2 final size:2
Alignment explanation
Indices: 57850454--57850485 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57850444 TTATATAAGC
57850454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57850486 TCGAACACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57852297 original size:16 final size:17
Alignment explanation
Indices: 57852261--57852297 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
57852251 AATTTTATTT
57852261 TAATAATAAACTTTAAA
1 TAATAATAAACTTTAAA
*
57852278 -AATAAT-AATTTTAAA
1 TAATAATAAACTTTAAA
57852293 TAATA
1 TAATA
57852298 TTACTAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAACTTTAAA
Found at i:57853012 original size:31 final size:31
Alignment explanation
Indices: 57852974--57853050 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 31
57852964 TCTGTCAAAT
57852974 AACAGAAAATATTTTATACAGATTCATCCAA
1 AACAGAAAATATTTTATACAGATTCATCCAA
57853005 AACAGAAAATATTTTATACAGATTCATCCAA
1 AACAGAAAATATTTTATACAGATTCATCCAA
*
57853036 ACACCAAAAAATATT
1 A-A-CAGAAAATATT
57853051 AACTTTTCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 32 0.74
32 1 0.02
33 10 0.23
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (31 bp):
AACAGAAAATATTTTATACAGATTCATCCAA
Found at i:57858191 original size:11 final size:11
Alignment explanation
Indices: 57858146--57858303 Score: 78
Period size: 11 Copynumber: 15.2 Consensus size: 11
57858136 ATTTTTTAAA
57858146 TTTTAAAATATT
1 TTTTAAAAT-TT
*
57858158 TTTTACATATTT
1 TTTTA-AAATTT
*
57858170 TTTT-AATTTT
1 TTTTAAAATTT
57858180 TTTTAAAA---
1 TTTTAAAATTT
*
57858188 TTTTAAAATAT
1 TTTTAAAATTT
57858199 TTTTAAAATAATT
1 TTTTAAAAT--TT
*
57858212 TTTT-TAATTT
1 TTTTAAAATTT
57858222 TTTT--AA---
1 TTTTAAAATTT
*
57858228 TTTTAAAATAT
1 TTTTAAAATTT
57858239 TTTTAAAATAATT
1 TTTTAAAAT--TT
*
57858252 TTTT-TAATTT
1 TTTTAAAATTT
57858262 TTTT--AA---
1 TTTTAAAATTT
*
57858268 TTTTAAAATAT
1 TTTTAAAATTT
57858279 TTTTAAAATATT
1 TTTTAAAAT-TT
57858291 TTTTAAAATTT
1 TTTTAAAATTT
57858302 TT
1 TT
57858304 AAAATAAAAA
Statistics
Matches: 117, Mismatches: 9, Indels: 41
0.70 0.05 0.25
Matches are distributed among these distances:
6 8 0.07
8 12 0.10
9 4 0.03
10 20 0.17
11 33 0.28
12 27 0.23
13 13 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:57858224 original size:8 final size:9
Alignment explanation
Indices: 57858207--57858271 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 9
57858197 ATTTTTAAAA
57858207 TAATTTTTT
1 TAATTTTTT
57858216 TAATTTTTT
1 TAATTTTTT
*
57858225 TAA-TTTTA
1 TAATTTTTT
*
57858233 AAATATTTTT
1 TAAT-TTTTT
57858243 AAAATAATTTTTT
1 ----TAATTTTTT
57858256 TAATTTTTT
1 TAATTTTTT
57858265 TAATTTT
1 TAATTTT
57858272 AAAATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 6 0.13
9 28 0.61
10 4 0.09
13 5 0.11
14 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TAATTTTTT
Found at i:57858234 original size:40 final size:39
Alignment explanation
Indices: 57858136--57858303 Score: 246
Period size: 40 Copynumber: 4.2 Consensus size: 39
57858126 AAATATATTT
* * *
57858136 ATTTTTTAAATTTTAAAATATTTTTTACATATTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
57858175 ATTTTTTTTAAAATTTTAAAATATTTTTAAAATAATTTTTTTA
1 A-TTTTTTT--AATTTTAAAATATTTTTAAAAT-ATTTTTTTA
57858218 ATTTTTTTAATTTTAAAATATTTTTAAAATAATTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAAT-ATTTTTTTA
*
57858258 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
*
57858297 AATTTTT
1 ATTTTTT
57858304 AAAATAAAAA
Statistics
Matches: 120, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
39 15 0.12
40 68 0.57
42 27 0.22
43 10 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
Found at i:57858307 original size:9 final size:9
Alignment explanation
Indices: 57858179--57858308 Score: 53
Period size: 9 Copynumber: 13.1 Consensus size: 9
57858169 TTTTTAATTT
57858179 TTTTTAAAA
1 TTTTTAAAA
*
57858188 TTTTAAAATA
1 TTTTTAAA-A
57858198 TTTTTAAAATAA
1 TTTTT--AA-AA
**
57858210 TTTTTTTAA
1 TTTTTAAAA
**
57858219 TTTTTTTAA
1 TTTTTAAAA
*
57858228 TTTTAAAATA
1 TTTTTAAA-A
57858238 TTTTTAAAATAA
1 TTTTT--AA-AA
**
57858250 TTTTTTTAA
1 TTTTTAAAA
**
57858259 TTTTTTTAA
1 TTTTTAAAA
*
57858268 TTTTAAAATA
1 TTTTTAAA-A
57858278 TTTTTAAAATA
1 TTTTT-AAA-A
57858289 TTTTTTAAAA
1 -TTTTTAAAA
57858299 TTTTTAAAA
1 TTTTTAAAA
57858308 T
1 T
57858309 AAAAATGGGC
Statistics
Matches: 96, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
9 49 0.51
10 16 0.17
11 8 0.08
12 21 0.22
13 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:57858827 original size:9 final size:9
Alignment explanation
Indices: 57858801--57858846 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
57858791 AAAATTATTT
57858801 TATATTTTA
1 TATATTTTA
57858810 TATTATTTTA
1 TA-TATTTTA
57858820 TATATTTT-
1 TATATTTTA
*
57858828 TAAAATTTTA
1 T-ATATTTTA
57858838 TATATTTTA
1 TATATTTTA
57858847 AAAAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 1 0.03
9 21 0.66
10 10 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATATTTTA
Found at i:57858837 original size:18 final size:18
Alignment explanation
Indices: 57858790--57858849 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
57858780 ATTCTTGATA
*
57858790 TAAAATTATTTTATATTTT
1 TAAAATT-TTATATATTTT
**
57858809 ATATTATTTTATATATTTT
1 -TAAAATTTTATATATTTT
57858828 TAAAATTTTATATA-TTT
1 TAAAATTTTATATATTTT
57858845 TAAAA
1 TAAAA
57858850 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 8 0.23
18 12 0.34
19 10 0.29
20 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAAATTTTATATATTTT
Found at i:57862095 original size:53 final size:55
Alignment explanation
Indices: 57861997--57862101 Score: 178
Period size: 53 Copynumber: 1.9 Consensus size: 55
57861987 AAGAGACAAG
* *
57861997 TTTTTAAGCAAATCAGCTAGTTTTTTTTTTGAATTAAATAAAAGCTAACTTACTA
1 TTTTAAAGCAAATCAACTAGTTTTTTTTTTGAATTAAATAAAAGCTAACTTACTA
57862052 TTTTAAAGCAAATCAACTAG-TTTTTTTTT-AATTAAATAAAAGCTAACTTA
1 TTTTAAAGCAAATCAACTAGTTTTTTTTTTGAATTAAATAAAAGCTAACTTA
57862102 TTGTAACGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 21 0.44
54 9 0.19
55 18 0.38
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (55 bp):
TTTTAAAGCAAATCAACTAGTTTTTTTTTTGAATTAAATAAAAGCTAACTTACTA
Found at i:57871394 original size:17 final size:18
Alignment explanation
Indices: 57871367--57871400 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
57871357 TTGACAAATT
57871367 GAAAGATGAAAAATAGAA
1 GAAAGATGAAAAATAGAA
*
57871385 GAAA-ATGAAAATTAGA
1 GAAAGATGAAAAATAGA
57871401 TATAATCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (18 bp):
GAAAGATGAAAAATAGAA
Found at i:57871428 original size:52 final size:52
Alignment explanation
Indices: 57871344--57871474 Score: 174
Period size: 52 Copynumber: 2.5 Consensus size: 52
57871334 ATCAACCATC
* * *
57871344 TAAGAAATAATCATTGACAAATTGAAAGATGAAAAATAGAAGAAAAT-GAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAG-AAATCAAAAA
* * *
57871396 TTAGATATAATCCTTGATAAATTGAAATATGAAAAATAGAAGAAATCAAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAATCAAAAA
* *
57871448 TAAGATCTAATCCTTGACAAATCGAAA
1 TAAGATATAATCCTTGACAAATTGAAA
57871475 ATAAGATGGA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 4 0.06
52 64 0.94
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.24
Consensus pattern (52 bp):
TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAATCAAAAA
Found at i:57887944 original size:12 final size:11
Alignment explanation
Indices: 57887916--57887945 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
57887906 TTTATTTTTT
57887916 TATTTTTAAAA
1 TATTTTTAAAA
57887927 TATTTTTAAAA
1 TATTTTTAAAA
57887938 TACTTTTT
1 TA-TTTTT
57887946 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:57890414 original size:27 final size:27
Alignment explanation
Indices: 57890384--57890437 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
57890374 TAATATATTA
57890384 TAAAC-TTAAAAATTAATATATTAAATT
1 TAAACTTTAAAAATTAA-ATATTAAATT
**
57890411 TAAACTTTAAATTTTAAATATTAAATT
1 TAAACTTTAAAAATTAAATATTAAATT
57890438 CGAATTCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAACTTTAAAAATTAAATATTAAATT
Found at i:57890420 original size:21 final size:21
Alignment explanation
Indices: 57890370--57890435 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
57890360 ACGATATATC
*
57890370 AATTTAATATATTATAAACTTAA
1 AATTTAATATA-T-TAAATTTAA
*
57890393 AAATTAATATATTAAATTTAA
1 AATTTAATATATTAAATTTAA
* *
57890414 ACTTTAA-ATTTTAAATATTAA
1 AATTTAATATATTAAAT-TTAA
57890435 A
1 A
57890436 TTCGAATTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.22
21 18 0.49
22 1 0.03
23 10 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTAATATATTAAATTTAA
Found at i:57890426 original size:14 final size:14
Alignment explanation
Indices: 57890396--57890437 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
57890386 AACTTAAAAA
57890396 TTAATATATTAAA-T
1 TTAA-ATATTAAATT
57890410 TTAAACT-TTAAATT
1 TTAAA-TATTAAATT
57890424 TTAAATATTAAATT
1 TTAAATATTAAATT
57890438 CGAATTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATATTAAATT
Found at i:57890480 original size:14 final size:14
Alignment explanation
Indices: 57890446--57890483 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
57890436 TTCGAATTCG
57890446 ATTT-ATATTTTAA
1 ATTTAATATTTTAA
*
57890459 A-CTAATATTTTAA
1 ATTTAATATTTTAA
57890472 ATTTAATATTTT
1 ATTTAATATTTT
57890484 TGTACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 1 0.05
13 11 0.52
14 9 0.43
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTAATATTTTAA
Found at i:57896767 original size:23 final size:24
Alignment explanation
Indices: 57896721--57896769 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
57896711 ATATTTATGA
57896721 AAAGTCAAAGATATGAGTATCAAAT
1 AAAGTCAAAGA-ATGAGTATCAAAT
*
57896746 AAAGTCAAAG-ATGTGTATCAAAT
1 AAAGTCAAAGAATGAGTATCAAAT
57896769 A
1 A
57896770 TTGGAAAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (24 bp):
AAAGTCAAAGAATGAGTATCAAAT
Found at i:57896956 original size:2 final size:2
Alignment explanation
Indices: 57896949--57896973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57896939 AAGGCATTGT
57896949 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
57896974 TTGTAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:57901422 original size:25 final size:29
Alignment explanation
Indices: 57901387--57901472 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
57901377 TATATTTATG
57901387 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
57901413 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
57901441 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
57901472 G
1 G
57901473 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:57901449 original size:30 final size:30
Alignment explanation
Indices: 57901385--57901473 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
57901375 TCTATATTTA
57901385 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
57901412 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
57901440 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
57901471 TGG
1 TGG
57901474 CATAAGAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
25 21 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.38
31 8 0.15
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:57902152 original size:17 final size:18
Alignment explanation
Indices: 57902127--57902161 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
57902117 ATAAAAAGAA
57902127 AATTATTTTTT-TCTTTC
1 AATTATTTTTTATCTTTC
*
57902144 AATTTTTTTTTATCTTTC
1 AATTATTTTTTATCTTTC
57902162 TTACCAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTATTTTTTATCTTTC
Found at i:57902509 original size:16 final size:16
Alignment explanation
Indices: 57902479--57902588 Score: 57
Period size: 16 Copynumber: 6.7 Consensus size: 16
57902469 CAAATACCAA
57902479 TATATATTATAATTTTT
1 TATATATT-TAATTTTT
57902496 TATATATTTAATTTATTTCT
1 TATATATTTAA--T-TTT-T
* **
57902516 TATATGTATTAA-AGTT
1 TATATAT-TTAATTTTT
57902532 TATATA--TAATTTTT
1 TATATATTTAATTTTT
* *
57902546 TATAATTTTTAAATTTT
1 TAT-ATATTTAATTTTT
* * *
57902563 TATATCTCTAACTTTT
1 TATATATTTAATTTTT
57902579 TATA-ATTTAA
1 TATATATTTAA
57902589 GGTATATATA
Statistics
Matches: 71, Mismatches: 13, Indels: 20
0.68 0.12 0.19
Matches are distributed among these distances:
13 3 0.04
14 5 0.07
15 6 0.08
16 23 0.32
17 19 0.27
18 1 0.01
19 3 0.04
20 7 0.10
21 4 0.06
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
TATATATTTAATTTTT
Found at i:57923483 original size:16 final size:16
Alignment explanation
Indices: 57923462--57923493 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
57923452 GTTTTGTTGC
57923462 TAATTTTACTTTTTCA
1 TAATTTTACTTTTTCA
57923478 TAATTTTACTTTTTCA
1 TAATTTTACTTTTTCA
57923494 CTTTCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTTACTTTTTCA
Found at i:57931935 original size:23 final size:23
Alignment explanation
Indices: 57931905--57931958 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
57931895 AGGCATTTAG
*
57931905 AAACTTAAGTAGCTGGTTAGGGA
1 AAACTTAAATAGCTGGTTAGGGA
* *
57931928 AAAGTTAAATGGCTGGTTAGGGA
1 AAACTTAAATAGCTGGTTAGGGA
57931951 AAACTTAA
1 AAACTTAA
57931959 CCGGTTTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (23 bp):
AAACTTAAATAGCTGGTTAGGGA
Found at i:57940893 original size:41 final size:41
Alignment explanation
Indices: 57940832--57941185 Score: 323
Period size: 41 Copynumber: 8.7 Consensus size: 41
57940822 TAATTATTCA
* * **
57940832 CTAAATTGCACATACATGCCCTTGTTTGTACTTCGGCACCC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * *
57940873 CTAAATTGCACATACGTGCCCCTATTTTTACTTTGATACCC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* ** * * *
57940914 CTAAATTACACATAATTGCCCCTATTTGTACTTTGGTACCC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * * * * * ** *
57940955 TTGAATTGTACATACATGCCCCTATTTGCACTTTAATACTC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * * * *
57940996 CTGAATTGCACATATGTGCCCCTGTTTATACTTTGGTACCC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * * *
57941037 CTGAATTGCACATATGTGCCCCTATTTGTACTTCGATACCT
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* *
57941078 TTAAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * * * *
57941119 CAAAATTGTACATATGTGCCCTTGTTTGTACTTCGGTACCC
1 CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * * *
57941160 CTGAATAGCACCTACGT-TCCCTGTTT
1 CTAAATTGCACATACGTGCCCCTGTTT
57941186 ACACTCTGAT
Statistics
Matches: 257, Mismatches: 56, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
40 7 0.03
41 250 0.97
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (41 bp):
CTAAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
Found at i:57941019 original size:21 final size:21
Alignment explanation
Indices: 57940995--57941059 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
57940985 CTTTAATACT
57940995 CCTGAATTGCACATATGTGCC
1 CCTGAATTGCACATATGTGCC
* ** * *
57941016 CCTG-TTTATAC-TTTGGTACC
1 CCTGAATTGCACATAT-GTGCC
57941036 CCTGAATTGCACATATGTGCC
1 CCTGAATTGCACATATGTGCC
57941057 CCT
1 CCT
57941060 ATTTGTACTT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (21 bp):
CCTGAATTGCACATATGTGCC
Found at i:57941057 original size:123 final size:123
Alignment explanation
Indices: 57940833--57941170 Score: 372
Period size: 123 Copynumber: 2.7 Consensus size: 123
57940823 AATTATTCAC
* * * *** * * *
57940833 TAAATTGCACATACATGCCCTTGTTTGTACTTCGGCACCCCTAAATTGCACATACGTGCCCCTAT
1 TAAATTGCACATACATGCCCCTATTTGCACTTCAATACCCCAAAATTGCACATATGTGCCCCTGT
* * * * * *
57940898 TTTTACTTTGATACCCCTAAATTACACATAATTGCCCCTATTTGTACTTTGGTACCCT
66 TTATACTTTGGTACCCCTGAATTGCACATAATTGCCCCTATTTGTACTTCGATACCCT
* * * * **
57940956 TGAATTGTACATACATGCCCCTATTTGCACTTTAATACTCCTGAATTGCACATATGTGCCCCTGT
1 TAAATTGCACATACATGCCCCTATTTGCACTTCAATACCCCAAAATTGCACATATGTGCCCCTGT
*
57941021 TTATACTTTGGTACCCCTGAATTGCACAT-ATGTGCCCCTATTTGTACTTCGATACCTT
66 TTATACTTTGGTACCCCTGAATTGCACATAAT-TGCCCCTATTTGTACTTCGATACCCT
* * * * * * *
57941079 TAAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCCAAAATTGTACATATGTGCCCTTGT
1 TAAATTGCACATACATGCCCCTATTTGCACTTCAATACCCCAAAATTGCACATATGTGCCCCTGT
* * *
57941144 TTGTACTTCGGTACCCCTGAATAGCAC
66 TTATACTTTGGTACCCCTGAATTGCAC
57941171 CTACGTTCCC
Statistics
Matches: 178, Mismatches: 36, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
122 2 0.01
123 176 0.99
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.36
Consensus pattern (123 bp):
TAAATTGCACATACATGCCCCTATTTGCACTTCAATACCCCAAAATTGCACATATGTGCCCCTGT
TTATACTTTGGTACCCCTGAATTGCACATAATTGCCCCTATTTGTACTTCGATACCCT
Found at i:57946292 original size:32 final size:32
Alignment explanation
Indices: 57946251--57946327 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
57946241 ATTTGAGTGA
57946251 TTAAATGGTTAATTGAATAAAGAAAAAGGGAC
1 TTAAATGGTTAATTGAATAAAGAAAAAGGGAC
*
57946283 TTAAATGGTTAATTGAATAAAGGAAAAGGGAC
1 TTAAATGGTTAATTGAATAAAGAAAAAGGGAC
57946315 TTAAATGG-TAATT
1 TTAAATGGTTAATT
57946328 AGACCATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 5 0.11
32 39 0.89
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.29
Consensus pattern (32 bp):
TTAAATGGTTAATTGAATAAAGAAAAAGGGAC
Found at i:57950881 original size:20 final size:20
Alignment explanation
Indices: 57950831--57950881 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
57950821 TGGAGCAGGA
* *
57950831 ATATCGATACCTTAGGAAAT
1 ATATCGATACTTTAAGAAAT
57950851 ATATCGATACTTTAAGAAA-
1 ATATCGATACTTTAAGAAAT
57950870 AGTATCGATACT
1 A-TATCGATACT
57950882 GGATCGATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
ATATCGATACTTTAAGAAAT
Found at i:57955434 original size:18 final size:17
Alignment explanation
Indices: 57955397--57955434 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
57955387 GATAATTTGT
57955397 TTTATTTAATTTATCCA
1 TTTATTTAATTTATCCA
57955414 TTTATTTACTATTTA-CCA
1 TTTATTTA--ATTTATCCA
57955432 TTT
1 TTT
57955435 TAACCTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTTAATTTATCCA
Found at i:57956868 original size:20 final size:20
Alignment explanation
Indices: 57956818--57956868 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
57956808 TGGAGCAGGA
* *
57956818 ATATCGATACCTTAGGAAAT
1 ATATCGATACTTTAAGAAAT
57956838 ATATCGATACTTTAAGAAA-
1 ATATCGATACTTTAAGAAAT
57956857 AGTATCGATACT
1 A-TATCGATACT
57956869 GGATCGATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
ATATCGATACTTTAAGAAAT
Found at i:57959187 original size:25 final size:26
Alignment explanation
Indices: 57959135--57959202 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
57959125 TTACCAATTC
*
57959135 CAGCTCTTATGAGCTTA-CAGATACT
1 CAGCTCGTATGAGCTTACCAGATACT
* *
57959160 CAGCTCGTATGAGCTTACCA-TTATT
1 CAGCTCGTATGAGCTTACCAGATACT
* *
57959185 CAGCTCGGAGGAGCTTAC
1 CAGCTCGTATGAGCTTAC
57959203 TGTTTATCGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (26 bp):
CAGCTCGTATGAGCTTACCAGATACT
Found at i:57960153 original size:43 final size:43
Alignment explanation
Indices: 57960106--57960246 Score: 201
Period size: 43 Copynumber: 3.3 Consensus size: 43
57960096 ACTGCCTAAG
* * * * *
57960106 ACACGGGCGTGTCTCTTAGCCGTGTGACACACACGGCCTAGCC
1 ACACGAGCGTGTCTCTTGGCCATGTGAGACACACGGCCTGGCC
*
57960149 ACACGAGCGTGTCTCTTGGCCTTGTGAGACACACGGCCTGGCC
1 ACACGAGCGTGTCTCTTGGCCATGTGAGACACACGGCCTGGCC
* *
57960192 ACACGAGTGTGTCTCTTGGCCATGTGAGACACACAGCCTGGCC
1 ACACGAGCGTGTCTCTTGGCCATGTGAGACACACGGCCTGGCC
*
57960235 ACACGGGCGTGT
1 ACACGAGCGTGT
57960247 ATCTCCTGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (43 bp):
ACACGAGCGTGTCTCTTGGCCATGTGAGACACACGGCCTGGCC
Found at i:57962681 original size:10 final size:10
Alignment explanation
Indices: 57962668--57962710 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
57962658 ATAAATTAGA
*
57962668 AAAAAATTGT
1 AAAAAATTAT
*
57962678 AAAAATTTAT
1 AAAAAATTAT
*
57962688 -AAAAATCAT
1 AAAAAATTAT
57962697 AAAAAATTAT
1 AAAAAATTAT
57962707 AAAA
1 AAAA
57962711 TGCATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:57962895 original size:10 final size:10
Alignment explanation
Indices: 57962880--57962982 Score: 60
Period size: 9 Copynumber: 10.6 Consensus size: 10
57962870 TTGGTACGAT
57962880 AATTTTTATA
1 AATTTTTATA
*
57962890 AATTTTTTATG
1 AA-TTTTTATA
57962901 AA-TTTTAT-
1 AATTTTTATA
*
57962909 ATTTTTTAT-
1 AATTTTTATA
57962918 AATTTTCT-TA
1 AATTTT-TATA
* *
57962928 CGA-CTTTATA
1 -AATTTTTATA
*
57962938 AAATTTTAT-
1 AATTTTTATA
57962947 AATTTTT-TA
1 AATTTTTATA
57962956 AGATTTTTAT-
1 A-ATTTTTATA
57962966 AATTTTTAATA
1 AATTTTT-ATA
57962977 AATTTT
1 AATTTT
57962983 AAATATTATT
Statistics
Matches: 73, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
8 2 0.03
9 33 0.45
10 21 0.29
11 17 0.23
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (10 bp):
AATTTTTATA
Found at i:57962914 original size:29 final size:29
Alignment explanation
Indices: 57962878--57962982 Score: 99
Period size: 29 Copynumber: 3.7 Consensus size: 29
57962868 TTTTGGTACG
*
57962878 ATAA-TTTTTATAAATTTTTTATGAATTTT
1 ATAATTTTTTAT-AATTTTTTAAGAATTTT
* *
57962907 AT-ATTTTTTATAATTTTCTTACG-ACTTT
1 ATAATTTTTTATAATTTT-TTAAGAATTTT
** *
57962935 ATAAAATTTTATAATTTTTTAAGATTTTT
1 ATAATTTTTTATAATTTTTTAAGAATTTT
* *
57962964 ATAATTTTTAATAAATTTT
1 ATAATTTTTTATAATTTTT
57962983 AAATATTATT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 17 0.28
29 44 0.72
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (29 bp):
ATAATTTTTTATAATTTTTTAAGAATTTT
Found at i:57962982 original size:19 final size:17
Alignment explanation
Indices: 57962883--57962983 Score: 60
Period size: 19 Copynumber: 5.3 Consensus size: 17
57962873 GTACGATAAT
57962883 TTTTATAAATTTTTTATGAA
1 TTTTAT-AATTTTTTA--AA
57962903 TTTTAT-ATTTTTTATAA
1 TTTTATAATTTTTTA-AA
* * *
57962920 TTTTCTTACGACTTTATAAAA
1 TTTT-ATA--A-TTTTTTAAA
57962941 TTTTATAATTTTTTAAGA
1 TTTTATAATTTTTTAA-A
57962959 TTTTTATAATTTTTAATAAA
1 -TTTTATAATTTTT--TAAA
57962979 TTTTA
1 TTTTA
57962984 AATATTATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
17 12 0.18
18 11 0.17
19 18 0.28
20 9 0.14
21 10 0.15
22 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTATAATTTTTTAAA
Found at i:57970997 original size:30 final size:30
Alignment explanation
Indices: 57970961--57971022 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
57970951 TGGCCATTTG
57970961 TATAATTTACCCTAAAATATAATATGTGAT
1 TATAATTTACCCTAAAATATAATATGTGAT
57970991 TATAATTTACCCTAAAATATAATATGTGAT
1 TATAATTTACCCTAAAATATAATATGTGAT
57971021 TA
1 TA
57971023 GAAAACATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (30 bp):
TATAATTTACCCTAAAATATAATATGTGAT
Found at i:57971343 original size:12 final size:12
Alignment explanation
Indices: 57971324--57971359 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
57971314 GGTCCGGCCG
57971324 TATTATTTTTTA
1 TATTATTTTTTA
*
57971336 TTTTATTTTTTA
1 TATTATTTTTTA
*
57971348 TATAATTTTTTA
1 TATTATTTTTTA
57971360 AAAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:57971378 original size:16 final size:18
Alignment explanation
Indices: 57971359--57971395 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
57971349 ATAATTTTTT
*
57971359 AAAAATA-TAATACA-TA
1 AAAAATACTAAAACATTA
57971375 AAAAATACTAAAACATTA
1 AAAAATACTAAAACATTA
57971393 AAA
1 AAA
57971396 CAAATGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAATACTAAAACATTA
Found at i:57971560 original size:11 final size:11
Alignment explanation
Indices: 57971541--57971586 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
57971531 AATAGTGAAA
57971541 AAAACAACAAG
1 AAAACAACAAG
* *
57971552 AAAATAACAAT
1 AAAACAACAAG
*
57971563 AAAACAATAA-
1 AAAACAACAAG
57971573 AAAACAACAAG
1 AAAACAACAAG
57971584 AAA
1 AAA
57971587 GCAGTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.76, C:0.13, G:0.04, T:0.07
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:57971581 original size:21 final size:21
Alignment explanation
Indices: 57971541--57971597 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
57971531 AATAGTGAAA
* * *
57971541 AAAACAACAAGAAAATAACAAT
1 AAAACAATAA-AAAACAACAAG
57971563 AAAACAATAAAAAACAACAAG
1 AAAACAATAAAAAACAACAAG
* *
57971584 AAAGCAGTAAAAAA
1 AAAACAATAAAAAA
57971598 AATTTCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.74, C:0.12, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAACAATAAAAAACAACAAG
Found at i:57975178 original size:27 final size:27
Alignment explanation
Indices: 57975143--57975220 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
57975133 CAACATTTGG
57975143 AGTCCGTCGAGACATTAAACATGGGGT
1 AGTCCGTCGAGACATTAAACATGGGGT
* *
57975170 AGTCCGTCGGGA-ATATAAAAATGGGGT
1 AGTCCGTCGAGACAT-TAAACATGGGGT
* *
57975197 AGTCCGT-TAGGACGTTAAACATGG
1 AGTCCGTCGA-GACATTAAACATGG
57975221 TATTGTGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 39 0.93
28 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (27 bp):
AGTCCGTCGAGACATTAAACATGGGGT
Found at i:57978335 original size:41 final size:41
Alignment explanation
Indices: 57978298--57978467 Score: 295
Period size: 41 Copynumber: 4.1 Consensus size: 41
57978288 GACTATATGT
57978298 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
57978339 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
57978380 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* * * * *
57978421 CTAGCAGGCTAAGTGCCAGTGAACTGAATTAGACTTTAAAC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
57978462 CTAGCA
1 CTAGCA
57978468 CATGAAGTGC
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:57978412 original size:82 final size:82
Alignment explanation
Indices: 57978270--57978467 Score: 297
Period size: 82 Copynumber: 2.4 Consensus size: 82
57978260 TCGGATTTAT
* * * ***
57978270 TGCCAGTGAAATTATTCAGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTAT
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTAT
57978335 AAGCCTAGCAGGCTAAG
66 AAGCCTAGCAGGCTAAG
* * *
57978352 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTAT
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTAT
57978417 AAGCCTAGCAGGCTAAG
66 AAGCCTAGCAGGCTAAG
* *
57978434 TGCCAGTGAACTGAATTAGACTTTAAACCTAGCA
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCA
57978468 CATGAAGTGC
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 104 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (82 bp):
TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTAT
AAGCCTAGCAGGCTAAG
Found at i:57986436 original size:45 final size:45
Alignment explanation
Indices: 57986367--57986538 Score: 181
Period size: 44 Copynumber: 3.8 Consensus size: 45
57986357 ATTAACTTGA
* *
57986367 GAAAAGAGAAAGACCATGGTTGAAAGATA-TCATGGCACTATAACC
1 GAAATGAGAAAGACCATAGTTGAAAGATACT-ATGGCACTATAACC
* *
57986412 GAAATGAGAAAGACCATAGTTGAAAGATACTATGGAAATA-AACC
1 GAAATGAGAAAGACCATAGTTGAAAGATACTATGGCACTATAACC
** * * * *
57986456 GAAGCGAGTAAGACCCTAGTTGAAAGATACTATGACACTAT-ATC
1 GAAATGAGAAAGACCATAGTTGAAAGATACTATGGCACTATAACC
*
57986500 GAAAAATGA-ACAAGACCATAGTTGAAACATACTATGGCA
1 G--AAATGAGA-AAGACCATAGTTGAAAGATACTATGGCA
57986539 TTAAATGTGA
Statistics
Matches: 104, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
44 40 0.38
45 34 0.33
46 30 0.29
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.19
Consensus pattern (45 bp):
GAAATGAGAAAGACCATAGTTGAAAGATACTATGGCACTATAACC
Found at i:57987798 original size:10 final size:10
Alignment explanation
Indices: 57987783--57987845 Score: 56
Period size: 10 Copynumber: 5.9 Consensus size: 10
57987773 CAAATAAATA
57987783 AAAGAAAAAG
1 AAAGAAAAAG
57987793 AAAGAAAAAGG
1 AAAGAAAAA-G
*
57987804 AATACAAAACCA-
1 AA-AGAAAA--AG
*
57987816 AAACGAAACAG
1 AAA-GAAAAAG
57987827 AAAGAAAAAG
1 AAAGAAAAAG
57987837 AAAGAAAAA
1 AAAGAAAAA
57987846 AAGAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 25 0.58
11 7 0.16
12 10 0.23
14 1 0.02
ACGTcount: A:0.75, C:0.08, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:57989153 original size:55 final size:56
Alignment explanation
Indices: 57989089--57989208 Score: 140
Period size: 55 Copynumber: 2.2 Consensus size: 56
57989079 ATGCGACCTC
* * *
57989089 ATTTGGAATACTCACAC-AGTCGGAG-ACACGGCTTGCA-ACATGATCGTGTGACCC-T
1 ATTTTGAATACTCACACAAG-CGG-GCACACGGCTTG-AGACACGACCGTGTGACCCAT
* *
57989144 ATTTTGAATACTCACACAAGCGGGCACATGGGTTGAGACACGACCGTGTGACCCAT
1 ATTTTGAATACTCACACAAGCGGGCACACGGCTTGAGACACGACCGTGTGACCCAT
57989200 ATTTTGAAT
1 ATTTTGAAT
57989209 TATACACGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
54 2 0.04
55 42 0.75
56 12 0.21
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (56 bp):
ATTTTGAATACTCACACAAGCGGGCACACGGCTTGAGACACGACCGTGTGACCCAT
Found at i:57990528 original size:9 final size:10
Alignment explanation
Indices: 57990509--57990537 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
57990499 CACTTCTCTT
57990509 TTTCTATTCA
1 TTTCTATTCA
57990519 TTTC-ATTCA
1 TTTCTATTCA
57990528 TTTCTATTCA
1 TTTCTATTCA
57990538 AACACGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:58006386 original size:26 final size:25
Alignment explanation
Indices: 58006356--58006413 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
58006346 AAGCTCTGGT
58006356 GAGCCATTAATCAGGAAACTTACAAA
1 GAGCCATTAATCAGGAAAC-TACAAA
* * * *
58006382 GAGCCTTTAATCGGGAAGCTCCAAA
1 GAGCCATTAATCAGGAAACTACAAA
58006407 GAGCCAT
1 GAGCCAT
58006414 ATATCGGGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATCAGGAAACTACAAA
Found at i:58006419 original size:25 final size:25
Alignment explanation
Indices: 58006378--58006427 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
58006368 AGGAAACTTA
*
58006378 CAAAGAGCCTTTAATCGGGAAGCTC
1 CAAAGAGCCTATAATCGGGAAGCTC
*
58006403 CAAAGAGCC-ATATATCGGGATGCTC
1 CAAAGAGCCTATA-ATCGGGAAGCTC
58006428 ATGAGAGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (25 bp):
CAAAGAGCCTATAATCGGGAAGCTC
Done.