Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 77 of 163
Found at i:25075578 original size:51 final size:51
Alignment explanation
Indices: 25075369--25075640 Score: 262
Period size: 51 Copynumber: 5.4 Consensus size: 51
25075359 CTAGGGAGAT
* * ** *
25075369 AAGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTACAATGCTAGGGAAAC
1 AAGATTCGCTGCCTTCAGCTTTAATCTATTCCACTGTAATGCCAGGGAAAC
* ** * *
25075420 AAGATTCGCTGCCTTCAGCTTTAATCTACT-CGTTGCAATGCTAGGGAAAC
1 AAGATTCGCTGCCTTCAGCTTTAATCTATTCCACTGTAATGCCAGGGAAAC
* * * * * * *
25075470 AAGATTCGCTACCTTTACCTTTAATC-AGTTCCACTGTAACGCCAAGGAGAT
1 AAGATTCGCTGCCTTCAGCTTTAATCTA-TTCCACTGTAATGCCAGGGAAAC
* **
25075521 AGGATTC-CTTGCCTTCAGCTTTAATCTATTTTACTGTAATGCCAGGGAAAC
1 AAGATTCGC-TGCCTTCAGCTTTAATCTATTCCACTGTAATGCCAGGGAAAC
* * * * * * *
25075572 AAGATTCACTACCTTTAGATGTAATCTGTTCCACTGTAAAGCCAGGGAAAC
1 AAGATTCGCTGCCTTCAGCTTTAATCTATTCCACTGTAATGCCAGGGAAAC
25075623 AAGATTCGCTGCCTTCAG
1 AAGATTCGCTGCCTTCAG
25075641 TCTGCTCCAC
Statistics
Matches: 180, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
49 1 0.01
50 43 0.24
51 134 0.74
52 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (51 bp):
AAGATTCGCTGCCTTCAGCTTTAATCTATTCCACTGTAATGCCAGGGAAAC
Found at i:25075629 original size:102 final size:101
Alignment explanation
Indices: 25075412--25075640 Score: 291
Period size: 102 Copynumber: 2.3 Consensus size: 101
25075402 CTACAATGCT
*
25075412 AGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTACTCGTTGCAATGCTAGGGAAACAAGATTC
1 AGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTACTCGTTGCAATGCCAGGGAAACAAGATTC
* * * *
25075477 GCTACCTTTACCTTTAATCAGTTCCACTGTAACGCC
66 ACTACCTTTACATGTAATCAGTTCCACTGTAAAGCC
* * * * ** *
25075513 AAGGAGATAGGATTC-CTTGCCTTCAGCTTTAATCTA-TTTTACTGTAATGCCAGGGAAACAAGA
1 AGGGAAACAAGATTCGC-TGCCTTCAGCTTTAATCTACTCGT--TGCAATGCCAGGGAAACAAGA
* *
25075576 TTCACTACCTTTAGATGTAATCTGTTCCACTGTAAAGCC
63 TTCACTACCTTTACATGTAATCAGTTCCACTGTAAAGCC
25075615 AGGGAAACAAGATTCGCTGCCTTCAG
1 AGGGAAACAAGATTCGCTGCCTTCAG
25075641 TCTGCTCCAC
Statistics
Matches: 106, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
100 3 0.03
101 30 0.28
102 72 0.68
103 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (101 bp):
AGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTACTCGTTGCAATGCCAGGGAAACAAGATTC
ACTACCTTTACATGTAATCAGTTCCACTGTAAAGCC
Found at i:25076012 original size:24 final size:24
Alignment explanation
Indices: 25075980--25076031 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
25075970 CCCCCTACTA
* *
25075980 TAATCTTCAAGGTTTAATCCACTT
1 TAATCTTCAAGGTTCAATCCACTG
25076004 TAATCTTCAAGGTTCAATCCACTG
1 TAATCTTCAAGGTTCAATCCACTG
25076028 TAAT
1 TAAT
25076032 TTTGGGACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (24 bp):
TAATCTTCAAGGTTCAATCCACTG
Found at i:25090784 original size:14 final size:14
Alignment explanation
Indices: 25090750--25090785 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25090740 TCAATTTATT
*
25090750 AATAAAATATTAAA
1 AATAAATTATTAAA
25090764 AATAAATTATTAAA
1 AATAAATTATTAAA
*
25090778 TATAAATT
1 AATAAATT
25090786 TATATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAATTATTAAA
Found at i:25099779 original size:151 final size:149
Alignment explanation
Indices: 25099460--25099967 Score: 698
Period size: 151 Copynumber: 3.4 Consensus size: 149
25099450 TCAAGAATTA
* * *
25099460 TTTTCAATTTCT-ATTTTTCAAAAATCAACTTATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * * *
25099524 TGCAGGGGAATTTTTAAATTTCTATTTTTTCAAAAGTCAACTCATAATGCGAGAGGTGAGTTGAG
66 TGCCGAGGTATTTTTCAA-TTCTATTTTTTCAAAA-TCAACTCATAATGCGAGAGGTGAGTTGAG
*
25099589 CTTCGGGCACATACCGAGGTAT
129 CCTCGGGCACAT-CCGAGGTAT
*
25099611 TTTTCAATTTATG-TTTTTCAAAAATCAACTCATAATGGGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * *
25099675 TGCCGAGGTATTTTTCAATT-TATGTTTTTCACAAATTAAGTCAGAATGCGAGAGGTGAGTTGAG
66 TGCCGAGGTATTTTTCAATTCTAT-TTTTTCA-AAATCAACTCATAATGCGAGAGGTGAGTTGAG
* *
25099739 CCTCGGGCACATGTCAAGGTAT
129 CCTCGGGCACAT-CCGAGGTAT
* * *
25099761 TTTTCAATTTTTGTTTTTTCAAAAATCAACTCAAAATGCGAGAGGTGAGTTTAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
**
25099826 TGCCGAGGTATTTTTCAAATTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGCAAGTTGAG
66 TGCCGAGGTATTTTTC-AATTCTATTTTTTC-AAAATCAACTCATAATGCGAGAGGTGAGTTGAG
25099891 CCTCGGGTCACACTCCGAGGTAT
129 CCTCGGG-CACA-TCCGAGGTAT
* ** *
25099914 TTTCCAATTTATGTTTTTTTTAAAATCAAATCATAATGCGAGAGGTGAGTTGAG
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
25099968 GTTCAGATCC
Statistics
Matches: 316, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
149 3 0.01
150 65 0.21
151 141 0.45
152 44 0.14
153 62 0.20
154 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (149 bp):
TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
TGCCGAGGTATTTTTCAATTCTATTTTTTCAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC
TCGGGCACATCCGAGGTAT
Found at i:25099994 original size:77 final size:76
Alignment explanation
Indices: 25099460--25099967 Score: 691
Period size: 76 Copynumber: 6.7 Consensus size: 76
25099450 TCAAGAATTA
* * *
25099460 TTTTCAATTTCT-ATTTTTCAAAAATCAACTTATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * *
25099524 TGCAGGGGAAT
66 TGCCGAGGTAT
* * * * *
25099535 TTTTAAATTTCTATTTTTTCAAAAGTCAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25099600 TACCGAGGTAT
66 TGCCGAGGTAT
*
25099611 TTTTCAATTTATG-TTTTTCAAAAATCAACTCATAATGGGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
25099675 TGCCGAGGTAT
66 TGCCGAGGTAT
* * * *
25099686 TTTTCAATTTATG-TTTTTCACAAATTAAGTCAGAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25099750 TGTCAAGGTAT
66 TGCCGAGGTAT
* * *
25099761 TTTTCAATTTTTGTTTTTTCAAAAATCAACTCAAAATGCGAGAGGTGAGTTTAGCCTCGGGCACA
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
25099826 TGCCGAGGTAT
66 TGCCGAGGTAT
* * * **
25099837 TTTTCAAATTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGCAAGTTGAGCCTCGGGTCAC
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CAC
25099902 ACT-CCGAGGTAT
65 A-TGCCGAGGTAT
* ** *
25099914 TTTCCAATTTATGTTTTTTTTAAAATCAAATCATAATGCGAGAGGTGAGTTGAG
1 TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
25099968 GTTCAGATCC
Statistics
Matches: 382, Mismatches: 47, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
75 149 0.39
76 174 0.46
77 58 0.15
78 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (76 bp):
TTTTCAATTTATGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
TGCCGAGGTAT
Found at i:25100205 original size:30 final size:29
Alignment explanation
Indices: 25100157--25100242 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
25100147 TTAATAATAT
* *
25100157 CATTTTGACCCT-AACTTTCCAAAAATTA
1 CATTTTAACCCTAAACTTTCCTAAAATTA
25100185 CATTTTAACCCCTAAACTTTCCTAAAATTA
1 CATTTTAA-CCCTAAACTTTCCTAAAATTA
* * *
25100215 AATTTTAACCCAAAAATTTCCTAAAATT
1 CATTTTAACCCTAAACTTTCCTAAAATT
25100243 TCACTTTGAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
28 7 0.14
29 22 0.43
30 22 0.43
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (29 bp):
CATTTTAACCCTAAACTTTCCTAAAATTA
Found at i:25101197 original size:28 final size:30
Alignment explanation
Indices: 25101159--25101230 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
25101149 TTTTTTTAAA
25101159 AAAATT-CATTTTGACCCC-AA-CTTTCCT
1 AAAATTACATTTTGACCCCTAACCTTTCCT
*
25101186 TAAATTACA-TTTGACCCCTAACCTTTCCT
1 AAAATTACATTTTGACCCCTAACCTTTCCT
25101215 AAAATTACATTTTGAC
1 AAAATTACATTTTGAC
25101231 ATCAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.36
28 4 0.10
29 15 0.38
30 6 0.15
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAACCTTTCCT
Found at i:25102447 original size:76 final size:76
Alignment explanation
Indices: 25102317--25102624 Score: 273
Period size: 76 Copynumber: 4.0 Consensus size: 76
25102307 TTTAAATGGT
* * * *
25102317 AAATCAACTCATAATGCAAGAGGTGAGTTGGGCCTCAGGCACATGCCGAGTTATTTTTCAATTTC
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCACATGCCGAATTATTTTTCAATGTC
*
25102382 TGTTTTTTCAA
66 TATTTTTTCAA
** * * *
25102393 AAATCAACTTTTAATGCGAGAGGTGAGTTTAGCCTGAGGCACTTGCCGAATTATTTTTCAATGTC
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCACATGCCGAATTATTTTTCAATGTC
25102458 TATTTTTTCAA
66 TATTTTTTCAA
* * * ** ** * *
25102469 AAATGAACTCATAATGCGAGAGGTGAGTTAATCCTTGGGTCACACT-CCGAGGTATTTTCCAATT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGG-CACA-TGCCGAATTATTTTTCAATG
* * ***
25102533 TATGTTTTTTTTTT
64 TCT-ATTTTTTCAA
* * * * **
25102547 AAATCAATTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTCATATGCCGAGCTA-TTTTCGAAT-
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGG-CACATGCCGAATTATTTTTC-AATG
25102610 TCTA-TTTTTCAA
64 TCTATTTTTTCAA
25102622 AAA
1 AAA
25102625 AAAAGAATAA
Statistics
Matches: 186, Mismatches: 41, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
75 8 0.04
76 98 0.53
77 26 0.14
78 54 0.29
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (76 bp):
AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCACATGCCGAATTATTTTTCAATGTC
TATTTTTTCAA
Found at i:25102625 original size:154 final size:152
Alignment explanation
Indices: 25102317--25102624 Score: 333
Period size: 154 Copynumber: 2.0 Consensus size: 152
25102307 TTTAAATGGT
** * * *
25102317 AAATCAACTCATAATGCAAGAGGTGAGTTGGGCCTCAGGCACATGCCGAGTTATTTTTCAATTTC
1 AAATCAACTCATAATGCAAGAGGTGAGTTAAGCCTCAGGCACATGCCGAGGTATTTTCCAATTTA
* * *
25102382 TGTTTTTTCAAAAATCAACTTTTAATGCGAGAGGTGAGTTTAGCCTGAGGCACTTGCCGAATTAT
66 TGTTTTTTCAAAAATCAACTTATAATGCGAGAGGTGAGTTGAGCCTGAGGCACTTGCCGAACTAT
25102447 TTTTCAATGTCTATTTTTTCAA
131 TTTTCAATGTCTATTTTTTCAA
* * * **
25102469 AAATGAACTCATAATGCGAGAGGTGAGTTAATCCTTGGGTCACACT-CCGAGGTATTTTCCAATT
1 AAATCAACTCATAATGCAAGAGGTGAGTTAAGCCTCAGG-CACA-TGCCGAGGTATTTTCCAATT
*** *
25102533 TATGTTTTTTTTTTAAATCAA-TTCATAATGCGAGAGGTGAGTTGAGCTTCG-GGTCA-TATGCC
64 TATG-TTTTTTCAAAAATCAACTT-ATAATGCGAGAGGTGAGTTGAGCCT-GAGG-CACT-TGCC
*
25102595 GAGCTA-TTTTCGAAT-TCTA-TTTTTCAA
124 GAACTATTTTTC-AATGTCTATTTTTTCAA
25102622 AAA
1 AAA
25102625 AAAAGAATAA
Statistics
Matches: 130, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
152 32 0.25
153 36 0.28
154 48 0.37
155 14 0.11
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (152 bp):
AAATCAACTCATAATGCAAGAGGTGAGTTAAGCCTCAGGCACATGCCGAGGTATTTTCCAATTTA
TGTTTTTTCAAAAATCAACTTATAATGCGAGAGGTGAGTTGAGCCTGAGGCACTTGCCGAACTAT
TTTTCAATGTCTATTTTTTCAA
Found at i:25102827 original size:30 final size:29
Alignment explanation
Indices: 25102779--25102906 Score: 150
Period size: 30 Copynumber: 4.4 Consensus size: 29
25102769 TTTATAATAT
*
25102779 CATTTTAACCC-CAACTTTCCTAAAATTA
1 CATTTTAACCCTAAACTTTCCTAAAATTA
25102807 CATTTTAACCCTTAAACTTTCCTAAAATTA
1 CATTTTAACCC-TAAACTTTCCTAAAATTA
* * *
25102837 CATTTTGACCCTTAAATTTTCTTAAAATTA
1 CATTTTAACCC-TAAACTTTCCTAAAATTA
* * * *
25102867 CATTTTGACCCTAAAATTTCCCAAAATTT
1 CATTTTAACCCTAAACTTTCCTAAAATTA
*
25102896 TATTTTAACCC
1 CATTTTAACCC
25102907 CAGAAGTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.12
29 23 0.26
30 54 0.61
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (29 bp):
CATTTTAACCCTAAACTTTCCTAAAATTA
Found at i:25103432 original size:15 final size:15
Alignment explanation
Indices: 25103412--25103477 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
25103402 GAAAAAAAAG
25103412 AGAAGAAGGAAAGAA
1 AGAAGAAGGAAAGAA
**
25103427 AGAAGAAAAAAAGAA
1 AGAAGAAGGAAAGAA
*
25103442 GGAAAGAA-GAAAGAA
1 AG-AAGAAGGAAAGAA
*
25103457 A-AA-AAGGAAAACAA
1 AGAAGAAGG-AAAGAA
25103471 AGAAGAA
1 AGAAGAA
25103478 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.05
13 3 0.08
14 6 0.15
15 22 0.55
16 7 0.17
ACGTcount: A:0.73, C:0.02, G:0.26, T:0.00
Consensus pattern (15 bp):
AGAAGAAGGAAAGAA
Found at i:25103441 original size:26 final size:26
Alignment explanation
Indices: 25103401--25103488 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
25103391 TTTGGAGGAG
*
25103401 AGAAAAAAAAGAGAA-GAAGGAAAGAA
1 AGAAAAAAAAGAGAAGGAAAG-AAGAA
25103427 AGAAGAAAAAA-AGAAGGAAAGAAGAA
1 AGAA-AAAAAAGAGAAGGAAAGAAGAA
* **
25103453 AGAAAAAAAGGA-AAACAAAGAAGAA
1 AGAAAAAAAAGAGAAGGAAAGAAGAA
*
25103478 AAAAATAAAAA
1 AGAAA-AAAAA
25103489 ATAAACAGTC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 20 0.38
26 22 0.42
27 10 0.19
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.01
Consensus pattern (26 bp):
AGAAAAAAAAGAGAAGGAAAGAAGAA
Found at i:25103444 original size:23 final size:23
Alignment explanation
Indices: 25103414--25103482 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
25103404 AAAAAAAGAG
25103414 AAGAAGGAAAGAAAGAAGAAAAA
1 AAGAAGGAAAGAAAGAAGAAAAA
25103437 AAGAAGGAAAG-AAGAAAGAAAAA
1 AAGAAGGAAAGAAAG-AAGAAAAA
* *
25103460 AAG--GAAAACAAAGAAGAAAAA
1 AAGAAGGAAAGAAAGAAGAAAAA
25103481 AA
1 AA
25103483 TAAAAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.33
22 6 0.14
23 22 0.52
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.00
Consensus pattern (23 bp):
AAGAAGGAAAGAAAGAAGAAAAA
Found at i:25103448 original size:19 final size:20
Alignment explanation
Indices: 25103424--25103466 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
25103414 AAGAAGGAAA
*
25103424 GAAAGAAGAAA-AAAAGAAG
1 GAAAGAAGAAAGAAAAAAAG
25103443 GAAAGAAGAAAGAAAAAAAG
1 GAAAGAAGAAAGAAAAAAAG
25103463 GAAA
1 GAAA
25103467 ACAAAGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
GAAAGAAGAAAGAAAAAAAG
Found at i:25103480 original size:13 final size:12
Alignment explanation
Indices: 25103404--25103482 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 12
25103394 GGAGGAGAGA
25103404 AAAAAAAGAGAAG
1 AAAAAAA-AGAAG
25103417 AAGGAAAGAAAGAAG
1 AA--AAA-AAAGAAG
25103432 -AAAAAAAGAAG
1 AAAAAAAAGAAG
* *
25103443 -GAAAGAAGAA-
1 AAAAAAAAGAAG
25103453 AGAAAAAAAG--G
1 A-AAAAAAAGAAG
*
25103464 AAAACAAAGAAG
1 AAAAAAAAGAAG
25103476 AAAAAAA
1 AAAAAAA
25103483 TAAAAAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
10 7 0.13
11 16 0.31
12 16 0.31
13 2 0.04
14 1 0.02
15 8 0.15
16 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:25112772 original size:76 final size:76
Alignment explanation
Indices: 25112628--25114747 Score: 2769
Period size: 76 Copynumber: 28.2 Consensus size: 76
25112618 TCAAGAATTA
* * * *
25112628 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCCCGAGCATA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25112693 TGCCGAGGAAG
66 TGCCGAGGTAT
* * *
25112704 TTTTAAATTTCTATCTTTTT-AAAAATCAACTCATAATGCGAGAGGTGAGTTCAGCATCGGGCAC
1 TTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
25112768 ATGCCAAGGTAT
65 ATGCCGAGGTAT
* *
25112780 TTTTCAATTTCTATTTTTT-TAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25112844 TGCCAATGTAT
66 TGCCGAGGTAT
*
25112855 TTTTCAA-TT-TATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCAC
1 TTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
25112918 ATGCCGAGGTAT
65 ATGCCGAGGTAT
* * * * *
25112930 TTTTCGATTTATTTTTTTTTCAAAAATCAACTCA-AATGCGAAAGGTGAGTTAAGCCTCGGGCAC
1 TTTTCAATTT-CTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
25112994 ATGCCGAGGTAT
65 ATGCCGAGGTAT
* * * *
25113006 TTTTCAATTTCTATTTTTTCAAAAAACAACTCATAATGTGAGAGGTGAGTTAAGCCTCGGGCATA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25113071 TGCTGTGGTA-
66 TGCCGAGGTAT
*
25113081 TTTTCAAATTT-T-TGTTTTTCAAAAATCAACTCATAATGCGAGGGGTGAGTTGAGCCTCGGGCA
1 TTTTC-AATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCA
*
25113144 CATGCCGAAGTAT
64 CATGCCGAGGTAT
*
25113157 TTTTCAATTT-T-TGTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
1 TTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
**
25113220 ATGCCGAACTAT
65 ATGCCGAGGTAT
* *
25113232 TTTTCAACTTT-AATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGCAC
1 TTTTCAA-TTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
25113296 ATGCTGAGGTAT
65 ATGCCGAGGTAT
* *
25113308 TTTTCAA----TATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGGCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25113369 TGCTGAGGTAT
66 TGCCGAGGTAT
* * *
25113380 TTTCCAATTTCT-GTTTTTCAAAAATCAACACATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25113444 TGCCGAAGTAT
66 TGCCGAGGTAT
*
25113455 TTTTCAATTT-T-TGTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
1 TTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
**
25113518 ATGCTAAGGTAT
65 ATGCCGAGGTAT
* *
25113530 TTTT-AAATT-T-TTTTTTCAAAAATCAACTCATAATGCGAGAGGTTAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
25113592 TGCCGAGGTA-
66 TGCCGAGGTAT
* *
25113602 TTTTCAATTTCTGTTTTTTCAAAAATCAACTGATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25113667 TGCTGAGGTAT
66 TGCCGAGGTAT
* * * * *
25113678 TTTTCAATTTATTTTTTTTCAAAAATTAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCGC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* *
25113743 ACGCTGAGGTAT
65 ATGCCGAGGTAT
* * *** * *
25113755 TTTTTAATTTCTGTTTTTTTTTTAAATCAACTCATAATGCGAGAGGTGAGTTGATCCTCGAGCAC
1 TTTTCAATTTCT-ATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
25113820 ATGCCGAAGTAT
65 ATGCCGAGGTAT
* * *
25113832 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCTAGAGGTGAG-TGAAGCGTAGGGCAC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTG-AGCCTCGGGCAC
* *
25113896 ATGCTGAGGTGT
65 ATGCCGAGGTAT
** * *
25113908 TTCGCAATTTCTATTTTTTCAAAAATCAAATGATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25113973 TGCCGATGTA-
66 TGCCGAGGTAT
* * * **
25113983 TTTTCAATTGCT-GTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTTGC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* * *
25114047 ACGCTGAGGTAA
65 ATGCCGAGGTAT
* * *
25114059 TTTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGTGAGAGGTGAGTTGAGCCTCAGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
25114124 TGCCGAGGTAT
66 TGCCGAGGTAT
* *
25114135 TTTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGTGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
25114200 TGCCGAGGTAT
66 TGCCGAGGTAT
* * *
25114211 TTTTCAATTTCTATTTTTTCAAAAATCAAATGATAATGCGAGAGGTGAGTTGAGCATCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25114276 TGCCGAGGTAG
66 TGCCGAGGTAT
* *
25114287 TTTTCAATTTCT-GTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25114351 TGTCGAGGTAT
66 TGCCGAGGTAT
* * * ** *
25114362 TTTGCAA-TT-TATGTTTTTCAAAAATAAACTAATAACACGAGAGGTGAGTTGAGCTTCGGGCAC
1 TTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
25114425 ATGCCAAGGTAT
65 ATGCCGAGGTAT
* *
25114437 TTTTCAACTTCTATTTTTTCAAAAATCAACTAATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
25114502 TGCCGAGGTAT
66 TGCCGAGGTAT
* *
25114513 TTTTTAA--T-T-TTTTTT-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAACCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
*
25114573 TGCC-ATGTAT
66 TGCCGAGGTAT
* * *
25114583 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATGATGAGAGAGGAGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * *
25114648 TGCTGAGCTAA
66 TGCCGAGGTAT
* * * * * * **
25114659 TTTACAATTTATGTTTTTTCAAAAACCAACTCATAATTCAAGAGGTGAGTTGAGCCTCGGGTTGC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* * *
25114724 ACGCTGATGTAT
65 ATGCCGAGGTAT
25114736 TTTTCAATTTCT
1 TTTTCAATTTCT
25114748 GTGTAATACC
Statistics
Matches: 1804, Mismatches: 201, Indels: 77
0.87 0.10 0.04
Matches are distributed among these distances:
70 11 0.01
71 47 0.03
72 78 0.04
73 67 0.04
74 69 0.04
75 648 0.36
76 702 0.39
77 138 0.08
78 44 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (76 bp):
TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
TGCCGAGGTAT
Found at i:25113099 original size:151 final size:152
Alignment explanation
Indices: 25112628--25114747 Score: 2769
Period size: 151 Copynumber: 14.1 Consensus size: 152
25112618 TCAAGAATTA
* * * *
25112628 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCCCGAGCATA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * * *
25112693 TGCCGAGGAAGTTTTAAATTTCTATCTTTTT-AAAAATCAACTCATAATGCGAGAGGTGAGTTCA
66 TGCCGAGGTATTTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
* *
25112757 GCATCGGGCACATGCCAAGGTAT
130 GCCTCGGGCACATGCCGAGGTAT
* *
25112780 TTTTCAATTTCTATTTTTT-TAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25112844 TGCCAATGTATTTTTCAA-TT-TATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
66 TGCCGAGGTATTTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
*
25112907 GCCTCAGGCACATGCCGAGGTAT
130 GCCTCGGGCACATGCCGAGGTAT
* * * * *
25112930 TTTTCGATTTATTTTTTTTTCAAAAATCAACTCA-AATGCGAAAGGTGAGTTAAGCCTCGGGCAC
1 TTTTCAATTT-CTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
* * *
25112994 ATGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAAACAACTCATAATGTGAGAGGTGAGTTAA
65 ATGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
* * *
25113059 GCCTCGGGCATATGCTGTGGTA-
130 GCCTCGGGCACATGCCGAGGTAT
*
25113081 TTTTCAAATTT-T-TGTTTTTCAAAAATCAACTCATAATGCGAGGGGTGAGTTGAGCCTCGGGCA
1 TTTTC-AATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCA
* *
25113144 CATGCCGAAGTATTTTTCAATTT-T-TGTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTT
64 CATGCCGAGGTATTTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTT
**
25113207 GAGCCTCGGGCACATGCCGAACTAT
128 GAGCCTCGGGCACATGCCGAGGTAT
* *
25113232 TTTTCAACTTT-AATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGCAC
1 TTTTCAA-TTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCAC
* *
25113296 ATGCTGAGGTATTTTTCAA----TATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAA
65 ATGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
* *
25113357 GGCTCGGGCACATGCTGAGGTAT
130 GCCTCGGGCACATGCCGAGGTAT
* * *
25113380 TTTCCAATTTCT-GTTTTTCAAAAATCAACACATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25113444 TGCCGAAGTATTTTTCAATTT-T-TGTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGA
66 TGCCGAGGTATTTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
**
25113507 GCCTCGGGCACATGCTAAGGTAT
130 GCCTCGGGCACATGCCGAGGTAT
* *
25113530 TTTT-AAATT-T-TTTTTTCAAAAATCAACTCATAATGCGAGAGGTTAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25113592 TGCCGAGGTA-TTTTCAATTTCTGTTTTTTCAAAAATCAACTGATAATGCGAGAGGTGAGTTGAG
66 TGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
*
25113656 CCTCGGGCACATGCTGAGGTAT
131 CCTCGGGCACATGCCGAGGTAT
* * * * *
25113678 TTTTCAATTTATTTTTTTTCAAAAATTAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCGC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* * * * ***
25113743 ACGCTGAGGTATTTTTTAATTTCTGTTTTTTTTTTAAATCAACTCATAATGCGAGAGGTGAGTTG
65 ATGCCGAGGTATTTTTCAATTTCT-ATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTG
* * *
25113808 ATCCTCGAGCACATGCCGAAGTAT
129 AGCCTCGGGCACATGCCGAGGTAT
* * *
25113832 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCTAGAGGTGAG-TGAAGCGTAGGGCAC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTG-AGCCTCGGGCAC
* * ** * *
25113896 ATGCTGAGGTGTTTCGCAATTTCTATTTTTTCAAAAATCAAATGATAATGCGAGAGGTGAGTTGA
65 ATGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
*
25113961 GCCTCGGGCACATGCCGATGTA-
130 GCCTCGGGCACATGCCGAGGTAT
* * * **
25113983 TTTTCAATTGCT-GTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTTGC
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* * * * *
25114047 ACGCTGAGGTAATTTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGTGAGAGGTGAGTTGA
65 ATGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
*
25114112 GCCTCAGGCACATGCCGAGGTAT
130 GCCTCGGGCACATGCCGAGGTAT
* *
25114135 TTTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGTGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25114200 TGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAAATGATAATGCGAGAGGTGAGTTGAG
66 TGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
* *
25114265 CATCGGGCACATGCCGAGGTAG
131 CCTCGGGCACATGCCGAGGTAT
* *
25114287 TTTTCAATTTCT-GTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * * * **
25114351 TGTCGAGGTATTTTGCAA-TT-TATGTTTTTCAAAAATAAACTAATAACACGAGAGGTGAGTTGA
66 TGCCGAGGTATTTTTCAATTTCTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
* *
25114414 GCTTCGGGCACATGCCAAGGTAT
130 GCCTCGGGCACATGCCGAGGTAT
* *
25114437 TTTTCAACTTCTATTTTTTCAAAAATCAACTAATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* *
25114502 TGCCGAGGTATTTTTTAA--T-T-TTTTTT-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAA
66 TGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
*
25114562 CCTCGGGCACATGCC-ATGTAT
131 CCTCGGGCACATGCCGAGGTAT
* * *
25114583 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATGATGAGAGAGGAGAGTTGAGCCTCGGGCACA
1 TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
* * * * * * * * *
25114648 TGCTGAGCTAATTTACAATTTATGTTTTTTCAAAAACCAACTCATAATTCAAGAGGTGAGTTGAG
66 TGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
** * * *
25114713 CCTCGGGTTGCACGCTGATGTAT
131 CCTCGGG-CACATGCCGAGGTAT
25114736 TTTTCAATTTCT
1 TTTTCAATTTCT
25114748 GTGTAATACC
Statistics
Matches: 1732, Mismatches: 196, Indels: 79
0.86 0.10 0.04
Matches are distributed among these distances:
146 78 0.05
147 121 0.07
148 192 0.11
149 26 0.02
150 316 0.18
151 530 0.31
152 263 0.15
153 100 0.06
154 106 0.06
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (152 bp):
TTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCACA
TGCCGAGGTATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
CCTCGGGCACATGCCGAGGTAT
Found at i:25119803 original size:30 final size:30
Alignment explanation
Indices: 25119762--25119898 Score: 152
Period size: 30 Copynumber: 4.6 Consensus size: 30
25119752 CAACTCTCCT
* *
25119762 AAAATAACATTTTAACCCCTAAAGTTTCCA
1 AAAATTACATTTTAACCCCTAAAATTTCCA
* *
25119792 AAAATTTCATTTTAACCCTTAAAATTTCCA
1 AAAATTACATTTTAACCCCTAAAATTTCCA
* * *
25119822 AACATTA-ATTTTGACCCCTAAAATTTCCT
1 AAAATTACATTTTAACCCCTAAAATTTCCA
* * *
25119851 AAAATTACAATTTAACCCC-AAATTTTTCCT
1 AAAATTACATTTTAACCCCTAAA-ATTTCCA
*
25119881 AAAATTACACTTTAACCC
1 AAAATTACATTTTAACCC
25119899 TAGAAGTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 28 0.31
30 63 0.69
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAAATTTCCA
Found at i:25119879 original size:59 final size:59
Alignment explanation
Indices: 25119758--25119898 Score: 151
Period size: 59 Copynumber: 2.4 Consensus size: 59
25119748 ACCCCAACTC
* * * * *
25119758 TCCTAAAATAACATTTTAACCCCTAAAGTTTCCAAAAATTTCATTTTAACCCTTAAAATT
1 TCCTAAAATTA-ATTTTAACCCCTAAAATTTCCAAAAATTACAATTTAACCCTCAAAATT
* * *
25119818 TCC-AAACATTAATTTTGACCCCTAAAATTTCCTAAAATTACAATTTAACCC-CAAATTTT
1 TCCTAAA-ATTAATTTTAACCCCTAAAATTTCCAAAAATTACAATTTAACCCTCAAA-ATT
*
25119877 TCCTAAAATTACACTTTAACCC
1 TCCTAAAATTA-ATTTTAACCC
25119899 TAGAAGTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
58 3 0.04
59 47 0.70
60 17 0.25
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.35
Consensus pattern (59 bp):
TCCTAAAATTAATTTTAACCCCTAAAATTTCCAAAAATTACAATTTAACCCTCAAAATT
Found at i:25120311 original size:28 final size:27
Alignment explanation
Indices: 25120261--25120314 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
25120251 AAATAAAAAA
25120261 GAAAAAAGAGAAGAGAAGGGGAAAGGAG
1 GAAAAAAGAGAAGAGAA-GGGAAAGGAG
25120289 GAAAAAAGGAAGAAGAGAA-GGAAAGG
1 GAAAAAA-G-AGAAGAGAAGGGAAAGG
25120315 GAACCGTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 14 0.58
29 1 0.04
30 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (27 bp):
GAAAAAAGAGAAGAGAAGGGAAAGGAG
Found at i:25120405 original size:4 final size:4
Alignment explanation
Indices: 25120390--25120462 Score: 75
Period size: 4 Copynumber: 19.5 Consensus size: 4
25120380 TTTGGAGGAG
* * *
25120390 AGAA AAAA AGAA AG-A AGAA GGAA AGAA AG-A AGAA GGAA AGAA AG-A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
25120435 AGAA A-AA AGAA AGAA A-AA AGAA AAAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
25120463 GACAAAAAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
3 15 0.27
4 41 0.73
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:25120414 original size:15 final size:15
Alignment explanation
Indices: 25120396--25120449 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
25120386 GGAGAGAAAA
25120396 AAAGAAAGAAGAAGG
1 AAAGAAAGAAGAAGG
25120411 AAAGAAAGAAGAAGG
1 AAAGAAAGAAGAAGG
*
25120426 AAAGAAAGAAGAA-A
1 AAAGAAAGAAGAAGG
25120440 AAAGAAAGAA
1 AAAGAAAGAA
25120450 AAAAGAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
14 10 0.26
15 28 0.74
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAGG
Found at i:25120415 original size:11 final size:11
Alignment explanation
Indices: 25120397--25120462 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
25120387 GAGAGAAAAA
25120397 AAGAAAG-AAG
1 AAGAAAGAAAG
25120407 AAGGAAAGAAAG
1 AA-GAAAGAAAG
*
25120419 AAGAAGGAAAG
1 AAGAAAGAAAG
*
25120430 AA-AGAAGAAAA
1 AAGA-AAGAAAG
*
25120441 AAGAAAGAAAA
1 AAGAAAGAAAG
*
25120452 AAGAAAAAAAG
1 AAGAAAGAAAG
25120463 GACAAAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
10 3 0.06
11 38 0.81
12 6 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:25120457 original size:7 final size:7
Alignment explanation
Indices: 25120393--25120460 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
25120383 GGAGGAGAGA
25120393 AAAAAAG
1 AAAAAAG
*
25120400 AAAGAAG
1 AAAAAAG
*
25120407 AAGGAAAG
1 AA-AAAAG
*
25120415 AAAGAAG
1 AAAAAAG
*
25120422 AAGGAAAG
1 AA-AAAAG
*
25120430 AAAGAAG
1 AAAAAAG
25120437 AAAAAAG
1 AAAAAAG
25120444 ---AAAG
1 AAAAAAG
25120448 AAAAAAG
1 AAAAAAG
25120455 AAAAAA
1 AAAAAA
25120461 AGGACAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
4 4 0.09
7 32 0.70
8 10 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:25120469 original size:10 final size:9
Alignment explanation
Indices: 25120422--25120479 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 9
25120412 AAGAAAGAAG
*
25120422 AAGGAAAGA
1 AAGGAAAAA
*
25120431 AAGAAGAAAA
1 AAGGA-AAAA
*
25120441 AAGAAAGAAA
1 AAGGAA-AAA
*
25120451 AAAGAAAAA
1 AAGGAAAAA
25120460 AAGGACAAAA
1 AAGGA-AAAA
25120470 AAGGAAAAA
1 AAGGAAAAA
25120479 A
1 A
25120480 TAAAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 17 0.41
10 24 0.59
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGGAAAAA
Found at i:25120487 original size:18 final size:18
Alignment explanation
Indices: 25120436--25120487 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
25120426 AAAGAAAGAA
25120436 GAAAAAAGAAAGAAAAAAG
1 GAAAAAAGAAA-AAAAAAG
* * *
25120455 AAAAAAAGGACAAAAAAG
1 GAAAAAAGAAAAAAAAAG
*
25120473 GAAAAAATAAAAAAA
1 GAAAAAAGAAAAAAA
25120488 TAAAAATATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
GAAAAAAGAAAAAAAAAG
Found at i:25123514 original size:33 final size:33
Alignment explanation
Indices: 25123472--25123537 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
25123462 GCGTAAACTC
*
25123472 CGATCTATTCGTCAAAAATTTTATCTTTTCCTT
1 CGATCTATTCATCAAAAATTTTATCTTTTCCTT
*
25123505 CGATCTATTCATCGAAAATTTTATCTTTTCCTT
1 CGATCTATTCATCAAAAATTTTATCTTTTCCTT
25123538 TCTTTTTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (33 bp):
CGATCTATTCATCAAAAATTTTATCTTTTCCTT
Found at i:25131896 original size:16 final size:16
Alignment explanation
Indices: 25131877--25131911 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
25131867 ATATATATGT
25131877 ATACATGAATTATAAA
1 ATACATGAATTATAAA
25131893 ATACATGAATTATAAA
1 ATACATGAATTATAAA
25131909 ATA
1 ATA
25131912 TATACAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
ATACATGAATTATAAA
Found at i:25133006 original size:3 final size:3
Alignment explanation
Indices: 25132998--25133028 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
25132988 TGTATGCAAA
25132998 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25133029 TAGAAACAGT
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:25157339 original size:50 final size:52
Alignment explanation
Indices: 25157228--25157364 Score: 145
Period size: 56 Copynumber: 2.6 Consensus size: 52
25157218 ATTTGGGTAA
* **
25157228 AGAGATCCCATGTAAGACCATGTC-GGAGACATGGCATTGGTATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGG-GACATGGCATTGG--TCACCGAG--TATG
*
25157284 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG-CACCGAG-ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGTCACCGAGTATG
** *
25157334 AGAGGTCCCCCGTAAGACCATGTTTGGGACA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACA
25157365 NNNNNNNNNN
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
50 31 0.42
53 5 0.07
56 35 0.48
57 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (52 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGTCACCGAGTATG
Found at i:25160332 original size:5 final size:5
Alignment explanation
Indices: 25160318--25160347 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
25160308 ACGTTTAACA
*
25160318 ATTTT GTTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
25160348 TATTAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:25162427 original size:24 final size:24
Alignment explanation
Indices: 25162379--25162425 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25162369 ACTGGTCATA
*
25162379 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
25162403 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
25162426 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:25162889 original size:27 final size:27
Alignment explanation
Indices: 25162836--25162985 Score: 214
Period size: 27 Copynumber: 5.6 Consensus size: 27
25162826 TGGGCCATGT
25162836 ATGACCGAAATACCT-CATAGGGTAAA
1 ATGACCGAAATACCTCCATAGGGTAAA
25162862 ATGACCGAAATACCTCCATAGGGTAAA
1 ATGACCGAAATACCTCCATAGGGTAAA
* * * *
25162889 ATGACCGAAATACCCCCATAAGATAGA
1 ATGACCGAAATACCTCCATAGGGTAAA
*
25162916 ATGACCGAAATATCC-ACATAGGGTAAA
1 ATGACCGAAATA-CCTCCATAGGGTAAA
* *
25162943 ATGATCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCTCCATAGGGTAAA
25162970 ATGACCGAAATACCTC
1 ATGACCGAAATACCTC
25162986 TAGGAGATGA
Statistics
Matches: 109, Mismatches: 12, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
26 17 0.16
27 90 0.83
28 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (27 bp):
ATGACCGAAATACCTCCATAGGGTAAA
Found at i:25166375 original size:21 final size:20
Alignment explanation
Indices: 25166336--25166383 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
25166326 AATTATAAAG
25166336 GAAATGAAAGTAAAAGAAATA
1 GAAATGAAAGTAAAAGAAA-A
* * * *
25166357 GAAATGAAGGTTAATGAAAG
1 GAAATGAAAGTAAAAGAAAA
25166377 GAAATGA
1 GAAATGA
25166384 TATATGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (20 bp):
GAAATGAAAGTAAAAGAAAA
Found at i:25167270 original size:10 final size:10
Alignment explanation
Indices: 25167235--25167293 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
25167225 TGGACATGAT
*
25167235 TTAAGAATTA
1 TTAAAAATTA
*
25167245 TTAAGAATTA
1 TTAAAAATTA
*
25167255 TAAAAAAATTA
1 T-TAAAAATTA
* *
25167266 TAAAAAATCA
1 TTAAAAATTA
*
25167276 TTTAAAATTA
1 TTAAAAATTA
25167286 TTAAAAAT
1 TTAAAAAT
25167294 AACATCCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 33 0.80
11 8 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:25168403 original size:20 final size:21
Alignment explanation
Indices: 25168355--25168403 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
25168345 ATAATTCTTG
*
25168355 ATAATTATTAAATAATTTTCT
1 ATAATTATTAAATAAGTTTCT
**
25168376 ATAA-TATTGTATAAGTTT-T
1 ATAATTATTAAATAAGTTTCT
25168395 ATAATTATT
1 ATAATTATT
25168404 TAACAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
ATAATTATTAAATAAGTTTCT
Found at i:25168517 original size:9 final size:9
Alignment explanation
Indices: 25168503--25168562 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
25168493 CCAGACATTG
25168503 TTTTTAATA
1 TTTTTAATA
25168512 TTTTTAATAA
1 TTTTTAAT-A
*
25168522 TTTTTCATA
1 TTTTTAATA
25168531 CTTTTTAATAA
1 -TTTTTAAT-A
* *
25168542 TTATTAAAA
1 TTTTTAATA
*
25168551 GTTTT-ATA
1 TTTTTAATA
25168559 TTTT
1 TTTT
25168563 ATTTTTTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
8 5 0.12
9 13 0.32
10 21 0.52
11 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTAATA
Found at i:25168524 original size:10 final size:10
Alignment explanation
Indices: 25168503--25168548 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
25168493 CCAGACATTG
25168503 TTTTTAAT-A
1 TTTTTAATAA
25168512 TTTTTAATAA
1 TTTTTAATAA
* *
25168522 TTTTTCATAC
1 TTTTTAATAA
25168532 TTTTTAATAA
1 TTTTTAATAA
*
25168542 TTATTAA
1 TTTTTAA
25168549 AAGTTTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:25168535 original size:20 final size:19
Alignment explanation
Indices: 25168503--25168548 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
25168493 CCAGACATTG
25168503 TTTTTAATATTTTTAATAA
1 TTTTTAATATTTTTAATAA
*
25168522 TTTTTCATACTTTTTAATAA
1 TTTTTAATA-TTTTTAATAA
*
25168542 TTATTAA
1 TTTTTAA
25168549 AAGTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAATATTTTTAATAA
Found at i:25168915 original size:16 final size:16
Alignment explanation
Indices: 25168888--25168926 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25168878 GCGAGAACTC
25168888 TAAAATTTAAAGAAATT
1 TAAAA-TTAAAGAAATT
* *
25168905 TAAAATTAAAGTATTT
1 TAAAATTAAAGAAATT
25168921 TAAAAT
1 TAAAAT
25168927 ATTAGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
TAAAATTAAAGAAATT
Found at i:25171837 original size:19 final size:20
Alignment explanation
Indices: 25171813--25171851 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
25171803 TAAATAATCT
*
25171813 TTATTATAAT-TATAATAAA
1 TTATTATAATATACAATAAA
25171832 TTATTATAATATACAATAAA
1 TTATTATAATATACAATAAA
25171852 ACTAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTATAATATACAATAAA
Found at i:25177770 original size:74 final size:74
Alignment explanation
Indices: 25177681--25177831 Score: 284
Period size: 74 Copynumber: 2.0 Consensus size: 74
25177671 TAAAACAGAG
*
25177681 ATATAGAGGAACACACATACAGTAAGCTATTTAAGCTTAGTAAGTCATAAGCAGATATATATATC
1 ATATAGAGGAACACACATACAGTAAGCTATTTAAGCTTAGTAAGTCATAAGCAAATATATATATC
25177746 AACGATTTT
66 AACGATTTT
*
25177755 ATATAGAGGAACACACATACAGTAAGCTGTTTAAGCTTAGTAAGTCATAAGCAAATATATATATC
1 ATATAGAGGAACACACATACAGTAAGCTATTTAAGCTTAGTAAGTCATAAGCAAATATATATATC
25177820 AACGATTTT
66 AACGATTTT
25177829 ATA
1 ATA
25177832 CTAACACTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (74 bp):
ATATAGAGGAACACACATACAGTAAGCTATTTAAGCTTAGTAAGTCATAAGCAAATATATATATC
AACGATTTT
Found at i:25178268 original size:43 final size:43
Alignment explanation
Indices: 25178199--25178327 Score: 147
Period size: 43 Copynumber: 3.0 Consensus size: 43
25178189 AGCTCATAAA
* *
25178199 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACATGTAAACACATATCG
* * *
25178242 ATGTC-ACTGTCCCAGATAG-GGTCTTACACGTAAACACA-ATTCA
1 ATGCCAAC-GTCCCAGA-AGTGGTCTTACATGTAAACACATA-TCG
* *
25178285 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACATGTAAACACATATCG
25178328 GAGATCCTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
42 4 0.06
43 62 0.89
44 4 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGAAGTGGTCTTACATGTAAACACATATCG
Found at i:25179476 original size:11 final size:11
Alignment explanation
Indices: 25179462--25179489 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25179452 ATTAACACAG
25179462 AAAATAATATT
1 AAAATAATATT
25179473 AAAATAATATT
1 AAAATAATATT
25179484 AAAATA
1 AAAATA
25179490 TTTTTCAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATAATATT
Found at i:25185950 original size:43 final size:44
Alignment explanation
Indices: 25185850--25185955 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 44
25185840 AAAGCTTGTA
* *
25185850 CAATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATAT
1 CAATGCCAACGTCCCAGACAGTGGTCTTACACGTAAACACATAT
* *
25185893 CGATGTC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACA-ATT
1 CAATGCCAAC-GTCCCAGACAGTGGTCTTACACGTAAACACATA-T
25185936 CAATGCCAACGTCCCAGACA
1 CAATGCCAACGTCCCAGACA
25185956 TATGTATCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
42 3 0.06
43 47 0.89
44 3 0.06
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (44 bp):
CAATGCCAACGTCCCAGACAGTGGTCTTACACGTAAACACATAT
Found at i:25187973 original size:20 final size:20
Alignment explanation
Indices: 25187945--25187982 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25187935 AATATTTAAA
25187945 TTTTAAAAATTATTTTGATT
1 TTTTAAAAATTATTTTGATT
*
25187965 TTTTGAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
25187983 ATTATTTTTT
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:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGATT
Found at i:25188449 original size:21 final size:21
Alignment explanation
Indices: 25188419--25188461 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
25188409 AATACAACCA
*
25188419 TTTTTTAATA-ATTTTTTTAT
1 TTTTTTAATATATTATTTTAT
25188439 TTTTTTAAATATATTATTTTAT
1 TTTTTT-AATATATTATTTTAT
25188461 T
1 T
25188462 AGTGGTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 4 0.20
22 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTAATATATTATTTTAT
Found at i:25192204 original size:33 final size:32
Alignment explanation
Indices: 25192048--25192212 Score: 152
Period size: 32 Copynumber: 5.1 Consensus size: 32
25192038 ATGAGCTTGA
* * *
25192048 GCCGAGAGAAGTGGAGTGCTGCGATGGATACGG
1 GCCG-GAGAAGTGGAGTACTGCGGTGGATATGG
* * *
25192081 GCCGGAGAAGTGGAGTGCTGCGATGGATACGG
1 GCCGGAGAAGTGGAGTACTGCGGTGGATATGG
* ** *
25192113 ACCGGAGAAGTAAAGTACTGCAGTGGATATGG
1 GCCGGAGAAGTGGAGTACTGCGGTGGATATGG
* * **
25192145 GCCGGAAAGAGTAGAGTACTAAGGTGGATATGG
1 GCCGGAGA-AGTGGAGTACTGCGGTGGATATGG
*
25192178 GCCGGGAGAAGTGGAGTATTGCGGTGG-TAGTGG
1 GCC-GGAGAAGTGGAGTACTGCGGTGGATA-TGG
25192211 GC
1 GC
25192213 TGAAGATATT
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
32 61 0.55
33 46 0.41
34 4 0.04
ACGTcount: A:0.26, C:0.13, G:0.44, T:0.18
Consensus pattern (32 bp):
GCCGGAGAAGTGGAGTACTGCGGTGGATATGG
Found at i:25193732 original size:9 final size:9
Alignment explanation
Indices: 25193716--25193752 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25193706 GAGTTAAACG
25193716 AATCGAGTT
1 AATCGAGTT
*
25193725 ATTCGAGTT
1 AATCGAGTT
25193734 AATCGAGTT
1 AATCGAGTT
25193743 AATCGAGTT
1 AATCGAGTT
25193752 A
1 A
25193753 TTTGAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (9 bp):
AATCGAGTT
Found at i:25193828 original size:9 final size:9
Alignment explanation
Indices: 25193811--25193847 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25193801 TGAGTTTTCA
25193811 AATTCGAAT
1 AATTCGAAT
*
25193820 AACTCGAAT
1 AATTCGAAT
25193829 AATTCGAAT
1 AATTCGAAT
25193838 AATTCGAAT
1 AATTCGAAT
25193847 A
1 A
25193848 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:25194088 original size:30 final size:31
Alignment explanation
Indices: 25194054--25194113 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
25194044 AAACCTTTTA
*
25194054 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
25194084 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
25194114 TCTNNNNNNN
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:25195190 original size:18 final size:17
Alignment explanation
Indices: 25195168--25195210 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
25195158 AATAAATAAA
25195168 AATAAAACAATATTACATT
1 AATAAAA-AAT-TTACATT
*
25195187 -ATAAAAAGTTTACATT
1 AATAAAAAATTTACATT
25195203 AATAAAAA
1 AATAAAAA
25195211 TTCACAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAAAAAATTTACATT
Found at i:25200036 original size:14 final size:14
Alignment explanation
Indices: 25200017--25200055 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
25200007 TTGTTTCGCT
*
25200017 GAAAATGGCTTCTG
1 GAAAATGACTTCTG
*
25200031 GAAAATGATTTCTG
1 GAAAATGACTTCTG
25200045 GAAAATGACTT
1 GAAAATGACTT
25200056 ACTTTTCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (14 bp):
GAAAATGACTTCTG
Found at i:25202479 original size:18 final size:18
Alignment explanation
Indices: 25202453--25202491 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25202443 CGCTGGAAAC
*
25202453 TTTATATCCTTC-AGGGAT
1 TTTAAATCCTTCTA-GGAT
25202471 TTTAAATCCTTCTAGGAT
1 TTTAAATCCTTCTAGGAT
25202489 TTT
1 TTT
25202492 CATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAAATCCTTCTAGGAT
Found at i:25206095 original size:12 final size:13
Alignment explanation
Indices: 25206055--25206094 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
25206045 ACATGAAGAA
25206055 TATTATTTAAAATTAT
1 TATT-TTTAAAA--AT
25206071 TATTTTTAAAAAT
1 TATTTTTAAAAAT
25206084 TATTTTTAAAA
1 TATTTTTAAAA
25206095 TAAAATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.54
15 7 0.29
16 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTTAAAAAT
Found at i:25206151 original size:16 final size:15
Alignment explanation
Indices: 25206111--25206156 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
25206101 TGAAATATCA
25206111 AATAATTTATTA-A-
1 AATAATTTATTATAT
**
25206124 AATAATAAATTATATT
1 AATAATTTATTATA-T
25206140 AATAATTTATTATAT
1 AATAATTTATTATAT
25206155 AA
1 AA
25206157 CTAAATACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
15 3 0.12
16 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAATTTATTATAT
Found at i:25213725 original size:44 final size:45
Alignment explanation
Indices: 25213463--25213732 Score: 199
Period size: 44 Copynumber: 6.1 Consensus size: 45
25213453 GCATATCAGT
* * * * * *
25213463 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
* * * ** * * *
25213508 GAAG-ATGCATATCTTGTTTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
* * *
25213552 GAAGAAAGTAGATCTTGTCTTCATGTATTGG-CATGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
* * * * * * *
25213596 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATT
1 GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
* * ** * * *
25213640 GAAG-ATGCAGATTTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
* * *
25213684 AAAGAAAGCAAATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
25213728 GAAGA
1 GAAGA
25213733 TAGTAGATAT
Statistics
Matches: 170, Mismatches: 51, Indels: 9
0.74 0.22 0.04
Matches are distributed among these distances:
43 21 0.12
44 108 0.64
45 41 0.24
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (45 bp):
GAAGAAAGCAGATCTTGTCTTCATATATTGGTCGTGAAGTAGATC
Found at i:25213751 original size:132 final size:133
Alignment explanation
Indices: 25213463--25213740 Score: 459
Period size: 132 Copynumber: 2.1 Consensus size: 133
25213453 GCATATCAGT
* *
25213463 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCATATCTTGTTTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
* * *
25213528 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCATGAAGTAG
66 CCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTATTGGCATGAAGTAG
25213593 ATC
131 ATC
* * *
25213596 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATTGAAGATGCAGATTTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
*
25213660 CCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAG
66 CCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTATTGGCATGAAGTAG
25213725 ATC
131 ATC
*
25213728 GAAGATAGTAGAT
1 GAAGATAGCAGAT
25213741 ATTGCCTTCC
Statistics
Matches: 134, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
132 101 0.75
133 33 0.25
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (133 bp):
GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTATTGGCATGAAGTAG
ATC
Found at i:25213944 original size:45 final size:45
Alignment explanation
Indices: 25213801--25213944 Score: 107
Period size: 44 Copynumber: 3.2 Consensus size: 45
25213791 TCCCTGGTTG
* *
25213801 CAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGA
1 CAGCGAAGCAGGCTAAAAATAGCAAATCTTGCCTTCCTGCACCGA
* * * ** * * * ****
25213846 TAACGAAGCA-GAT-CGAAGA-CACCATCCTTGCCTCCCTGGGTTG-
1 CAGCGAAGCAGGCTAAAAATAGCA-AAT-CTTGCCTTCCTGCACCGA
*
25213889 CAGCGGAGCAGGCTAAAAATAGCAAATCTTGCCTTCCTGCACCGA
1 CAGCGAAGCAGGCTAAAAATAGCAAATCTTGCCTTCCTGCACCGA
25213934 CAGCGAAGCAG
1 CAGCGAAGCAG
25213945 ATCGAAGGCA
Statistics
Matches: 66, Mismatches: 27, Indels: 12
0.63 0.26 0.11
Matches are distributed among these distances:
42 2 0.03
43 12 0.18
44 28 0.42
45 22 0.33
46 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (45 bp):
CAGCGAAGCAGGCTAAAAATAGCAAATCTTGCCTTCCTGCACCGA
Found at i:25214060 original size:88 final size:88
Alignment explanation
Indices: 25213732--25214035 Score: 475
Period size: 88 Copynumber: 3.5 Consensus size: 88
25213722 TAGATCGAAG
* * *
25213732 ATAGTAGATATTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
25213796 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* * *
25213819 ATAGCAGATCTTGCCTTCCTGCACCGATAACGAAGCAGATCGAAGACACCATCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
25213884 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* * *
25213907 ATAGCAAATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGGCACTAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
25213972 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* * * *
25213995 ATAGCAGATCTTGTCTTCCTGCACTGACAGTGAAGTAGATC
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
25214036 AATAACCCCA
Statistics
Matches: 198, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
87 58 0.29
88 140 0.71
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.21
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGCTAAAA
Found at i:25214098 original size:44 final size:43
Alignment explanation
Indices: 25214048--25214257 Score: 217
Period size: 44 Copynumber: 4.8 Consensus size: 43
25214038 TAACCCCAGC
*
25214048 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTATGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTA-GAAT
*
25214092 CCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT-AGAAT
* * * * *
25214136 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGACTGTAG-GT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGA-T-TAGAAT
* * * *
25214180 CGTATCTCCCTGGTCAACAGTGGAATTGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT-AGAAT
* * * *
25214224 CATATCTCCCTAAG-CAGCAGTGGAGTAAGTTGAA
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAA
25214258 AATAGCAGAT
Statistics
Matches: 139, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 130 0.94
45 5 0.04
46 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTAGAAT
Found at i:25215078 original size:21 final size:19
Alignment explanation
Indices: 25215053--25215100 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
25215043 CTTAGATATG
*
25215053 ATCTTAGATATTATATATGCA
1 ATCTTAGATA-T-GATATGCA
25215074 ATCTTAGATATGATATGCA
1 ATCTTAGATATGATATGCA
25215093 ATCTTAGA
1 ATCTTAGA
25215101 AGATATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.58
20 1 0.04
21 10 0.38
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (19 bp):
ATCTTAGATATGATATGCA
Found at i:25215126 original size:22 final size:22
Alignment explanation
Indices: 25215067--25215123 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
25215057 TAGATATTAT
25215067 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
25215086 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
25215108 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
25215124 GATTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
22 8 0.25
23 12 0.38
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:25215304 original size:22 final size:20
Alignment explanation
Indices: 25215279--25215323 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
25215269 TTCACTCAAA
*
25215279 TTTCTCTCTCTTGCGTTCTTAT
1 TTTCTCTCGCTT--GTTCTTAT
*
25215301 TTTCTCTGGCTTGTTCTTAT
1 TTTCTCTCGCTTGTTCTTAT
25215321 TTT
1 TTT
25215324 GTTGATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.04, C:0.22, G:0.11, T:0.62
Consensus pattern (20 bp):
TTTCTCTCGCTTGTTCTTAT
Found at i:25215722 original size:37 final size:37
Alignment explanation
Indices: 25215646--25215722 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
25215636 CATACATACG
*
25215646 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
25215684 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
25215721 TT
1 TT
25215723 CTATGTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:25217133 original size:16 final size:15
Alignment explanation
Indices: 25217107--25217136 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25217097 GAAATTTTTT
25217107 AAATAATATTATTTC
1 AAATAATATTATTTC
25217122 AAATATATATTATTT
1 AAATA-ATATTATTT
25217137 ATAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATAATATTATTTC
Found at i:25218473 original size:16 final size:14
Alignment explanation
Indices: 25218443--25218478 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
25218433 GCATAAAATT
25218443 TTAAAAATATTAAC
1 TTAAAAATATTAAC
25218457 TTAACAAATAGTTAAC
1 TTAA-AAATA-TTAAC
25218473 TTAAAA
1 TTAAAA
25218479 GGATGTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 9 0.45
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (14 bp):
TTAAAAATATTAAC
Found at i:25220619 original size:23 final size:24
Alignment explanation
Indices: 25220592--25220638 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
25220582 GATAATTTTT
*
25220592 ATTTTTTT-ATTTAATTA-TATAA
1 ATTTTTTTAAATTAATTATTATAA
25220614 ATTTTTTTAAATTAATTATTATAA
1 ATTTTTTTAAATTAATTATTATAA
25220638 A
1 A
25220639 ACGTTTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTTTTAAATTAATTATTATAA
Found at i:25224417 original size:9 final size:9
Alignment explanation
Indices: 25224403--25224444 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
25224393 TTGGAGGCAA
25224403 AAAAAAAAC
1 AAAAAAAAC
25224412 AAAAAAAAC
1 AAAAAAAAC
25224421 AAAAAAAA-
1 AAAAAAAAC
*
25224429 AACAAAGAAC
1 AA-AAAAAAC
25224439 AAAAAA
1 AAAAAA
25224445 TAGAAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 2 0.07
9 25 0.86
10 2 0.07
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:25224424 original size:15 final size:15
Alignment explanation
Indices: 25224401--25224458 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
25224391 CATTGGAGGC
25224401 AAAAA-AAAAACAAA
1 AAAAACAAAAACAAA
25224415 AAAAAC---AA-AAA
1 AAAAACAAAAACAAA
25224426 AAAAACAAAGAACAAA
1 AAAAACAAA-AACAAA
* *
25224442 AAATAGAAAAACAAA
1 AAAAACAAAAACAAA
25224457 AA
1 AA
25224459 CCTCTACCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
11 9 0.25
12 2 0.06
14 5 0.14
15 10 0.28
16 10 0.28
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (15 bp):
AAAAACAAAAACAAA
Found at i:25224441 original size:27 final size:27
Alignment explanation
Indices: 25224400--25224459 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
25224390 ACATTGGAGG
25224400 CAAAAA-AAAAACAAAAAAAACAAAAA
1 CAAAAACAAAAACAAAAAAAACAAAAA
* *
25224426 -AAAAACAAAGAACAAAAAATAGAAAAA
1 CAAAAACAAA-AACAAAAAAAACAAAAA
25224453 CAAAAAC
1 CAAAAAC
25224460 CTCTACCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 3 0.10
27 15 0.52
28 6 0.21
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (27 bp):
CAAAAACAAAAACAAAAAAAACAAAAA
Found at i:25225920 original size:45 final size:44
Alignment explanation
Indices: 25225808--25225933 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 44
25225798 TATGACGGAT
* * *
25225808 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAACCAAC
* * *
25225852 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGACAACGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CAACCAAC
* * * *
25225897 CTTATTTCCCT-AGCGTTGCAGTGGAACAGATTAAAGC
1 CTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAGC
25225934 TACAAATTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.52
45 33 0.48
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAACCAAC
Found at i:25226226 original size:143 final size:142
Alignment explanation
Indices: 25225796--25226450 Score: 895
Period size: 143 Copynumber: 4.6 Consensus size: 142
25225786 GATTGAAGTC
* *
25225796 ATTATGACGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT-C
* * * *
25225861 CTGAAGTTGTAGTGGAGCAGATTGAAGACAACGAATCTTATTTCCCTAGCGTTGCAGTGGAACAG
65 CTGAAGTTGCAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTGGCATTGCAGTGGAACAG
25225926 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* *
25225939 ATTATGGCAGATCTTATCTTCCAGAAGTTGCAGTGGAGCAGATTGATGCCACCAGCCTTATCTCT
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC-
* * * *
25226004 CTG-A-TTGCAGCGGAGCAGATTAAAGATAGCGAATCTTATTTCCTTGGCATTGCAGTGGAACAG
65 CTGAAGTTGCAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTGGCATTGCAGTGGAACAG
25226067 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* * * *
25226080 ATTATGACAGATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAGGCCACCGGCCTTATCTAC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT-C
** *
25226145 CTGAAGTTGCAGCAAAGCAGATTGAAGACAGA-GAATCTTATTTCCCTGGCGTTGCAGTGGAACA
65 CTGAAGTTGCAGCGGAGCAGATTGAAGACA-ACGAATCTTATTTCCCTGGCATTGCAGTGGAACA
*
25226209 GCTTAAAGCTACAA
129 GATTAAAGCTACAA
**
25226223 ATTATGGTGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
25226288 TTAAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTCCCCTGGCATTGTAGTGGAACAG
66 -TGAAGTTGCAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTGGCATTGCAGTGGAACAG
25226353 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* * * * * *
25226366 ATTATGGC-GAATCTTATCTTCCTGAAGTTGCAGCGGAACAGACTGAAGACACAATCCTTATCTC
1 ATTATGGCAG-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
* * *
25226430 GCTTAAGTTGTAGTGGAGCAG
65 -CTGAAGTTGCAGCGGAGCAG
25226451 GATAAAAATA
Statistics
Matches: 453, Mismatches: 50, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
141 125 0.28
142 8 0.02
143 319 0.70
144 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (142 bp):
ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
TGAAGTTGCAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTGGCATTGCAGTGGAACAGA
TTAAAGCTACAA
Found at i:25226721 original size:179 final size:179
Alignment explanation
Indices: 25226415--25226758 Score: 528
Period size: 179 Copynumber: 1.9 Consensus size: 179
25226405 AGACTGAAGA
* * * * * *
25226415 CACAATCCTTATCTCGCTTAAGTTGTAGTGGAGCAGGATAAAAATATACAAACCTTATCTCCCTG
1 CACAATCCTTATCTCCCTAAAGTTGCACTGGAACAGGATAAAAATATACAAACCTTATCTCCCTA
** * * * *
25226480 AAGTTGTAGTGGAGCAGGTTGAAGTTACCGATTCTTATCTCCTTGAAGTTGCAGCGGAGTAGATC
66 AAGTTACAGTGGAGCAGATTGAAATTACCAATTCTTATCTCCTTAAAGTTGCAGCGGAGTAGATC
*
25226545 GAAGCTACAAATCTCTTCTCTCTGAAATTATATTGAAGTAGATCGTAGC
131 GAAGCTACAAATCTCTTCTCCCTGAAATTATATTGAAGTAGATCGTAGC
* *
25226594 CACAATCCTTATCTCCCTAAAGTTGCACTGGAACGGGATAAAAATATACAAACCTTATCTCCTTA
1 CACAATCCTTATCTCCCTAAAGTTGCACTGGAACAGGATAAAAATATACAAACCTTATCTCCCTA
25226659 AAGTTACAGTGGAGCAGATTGAAATTACCAATTCTTATCTCCTTAAAGTTGCAG-GAGAGTAGAT
66 AAGTTACAGTGGAGCAGATTGAAATTACCAATTCTTATCTCCTTAAAGTTGCAGCG-GAGTAGAT
*
25226723 CGAAGCTACAAGTCTCTTCTCCCTGAAATTATATTG
130 CGAAGCTACAAATCTCTTCTCCCTGAAATTATATTG
25226759 GAGCGGATCG
Statistics
Matches: 148, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
178 1 0.01
179 147 0.99
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (179 bp):
CACAATCCTTATCTCCCTAAAGTTGCACTGGAACAGGATAAAAATATACAAACCTTATCTCCCTA
AAGTTACAGTGGAGCAGATTGAAATTACCAATTCTTATCTCCTTAAAGTTGCAGCGGAGTAGATC
GAAGCTACAAATCTCTTCTCCCTGAAATTATATTGAAGTAGATCGTAGC
Found at i:25227965 original size:4 final size:4
Alignment explanation
Indices: 25227956--25227987 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
25227946 TCCTCGACTG
*
25227956 TTTA TTTA TTTA TTTA TTTA TTCA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
25227988 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:25233789 original size:143 final size:143
Alignment explanation
Indices: 25233529--25233987 Score: 675
Period size: 143 Copynumber: 3.2 Consensus size: 143
25233519 GATTGAAGTC
* * * *
25233529 ATTATGGCGGATCTTATCTTTCTAAAGTTGCAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
25233594 TTGAAGTTGTAGCGGAGCAGACTGAAAACAGTGAATCTTATTTCCCTCGCGTTGTAGTGGAATAG
66 TTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
25233659 ATTAAAGCTACAA
131 ATTAAAGCTACAA
*
25233672 ATTATGACGGATCTTATCTTCCTAAAGTTGTAGTGGAGCAGATTGAGGCCACCAGCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
25233737 CTAAAGTTGCAGCGGACCAGATTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 TTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
25233802 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * *
25233815 ATTATGATGGATCTTATCTTCCTGAAGTTGTTGTGGAGTAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
25233880 TTAAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTCCCCTGGCATTGTAGTGGAACAG
66 TTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
25233945 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * *
25233958 ATTATGGCGAATCTTATCTTTCTGAAGTTG
1 ATTATGACGGATCTTATCTTCCTAAAGTTG
25233988 CGGCGAAACA
Statistics
Matches: 284, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
143 284 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (143 bp):
ATTATGACGGATCTTATCTTCCTAAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
TTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
ATTAAAGCTACAA
Found at i:25234005 original size:143 final size:143
Alignment explanation
Indices: 25233529--25234042 Score: 668
Period size: 143 Copynumber: 3.6 Consensus size: 143
25233519 GATTGAAGTC
* * *
25233529 ATTATGGCGGATCTTATCTTTCTAAAGTTGCAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * *
25233594 TTGAAGTTGTAGCGGAGCAGACTGAAAACAGTGAATCTTATTTCCCTCGCGTTGTAGTGGAATAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
25233659 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* *
25233672 ATTATGACGGATCTTATCTTCCTAAAGTTGTAGTGGAGCAGATTGAGGCCACCAGCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * *
25233737 CTAAAGTTGCAGCGGACCAGATTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
25233802 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * ** *
25233815 ATTATGATGGATCTTATCTTCCTGAAGTTGTTGTGGAGTAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
25233880 TTAAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTCCCCTGGCATTGTAGTGGAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
25233945 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * * * * * * * * *
25233958 ATTATGGCGAATCTTATCTTTCTGAAGTTGCGGCGAAACAGACTGAAGACACAATCCTTATCTCC
1 ATTATGACGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * *
25234023 CTGAAGTTGAAGTGGAGCAG
66 CTAAAGTTGCAGCGGAGCAG
25234043 GAGTAAAATA
Statistics
Matches: 325, Mismatches: 46, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
143 325 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (143 bp):
ATTATGACGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
ATTAAAGCTACAA
Found at i:25234206 original size:44 final size:44
Alignment explanation
Indices: 25234008--25234541 Score: 310
Period size: 44 Copynumber: 11.9 Consensus size: 44
25233998 GACTGAAGAC
* ** **
25234008 ACAATCCTTATCTCCCTGAAGTTGAAGTGGAGCAGGAGTAAAATAT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCA-GA-TCGAAGCT
* * * * * *
25234054 ACAAAT-CGTATCTCCCTGAAGTTGTAATGGAGCAGGTTGAAGTT
1 AC-AATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
* * * * *
25234098 ACCAATTCTTATCTCCTTGAAGTAGCAGCGGAGTAGATCGAAGCT
1 A-CAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
* * * * *
25234143 ACAAAT-CTCT-TCTCACTGAAATTACATTGGAGCAGATCGAAGCC
1 AC-AATCCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
* ** **
25234187 ACAATCCTTATCCCCCTGAAGTTGCAGTGGAGCAGGATAAAATTAT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATCGAA-GCT
* * ** * * **
25234233 ACAAACCTTATCTCCCTGAAGTTGTAGTGGAATAGGTTGAAATT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
* * * *
25234277 ACCAATTCTTATCTCCTTGAAGTTGCAGAGGAGTAGATCGAAGCT
1 A-CAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
* * * *
25234322 ACAAGT-CTCT-TCTCCCTGAAATTACATTGGAGCAGATCGAAGCC
1 ACAA-TCCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
** **
25234366 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATAT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCA-GAT-CGAAGCT
* * * **
25234412 ACAAACCTTATCTCCCTGAAGTTGTAGTGGAGC-GAGTTGAAATT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCGAAGCT
* * ** * *
25234456 ACCAATTCTTATCTCCTTGAAGTTGCAGCAGAGTAGATTGAAGCT
1 A-CAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
* * * *
25234501 ACAAGT-CTCT-TCTCCCTGAAATTACATTGGAGCGGATCGAA
1 ACAA-TCCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAA
25234542 ACACCATTTC
Statistics
Matches: 371, Mismatches: 96, Indels: 44
0.73 0.19 0.09
Matches are distributed among these distances:
43 6 0.02
44 153 0.41
45 118 0.32
46 91 0.25
47 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCT
Found at i:25234312 original size:179 final size:178
Alignment explanation
Indices: 25234002--25234541 Score: 877
Period size: 179 Copynumber: 3.0 Consensus size: 178
25233992 GAAACAGACT
* * * *
25234002 GAAGACACAATCCTTATCTCCCTGAAGTTGAAGTGGAGCAGGAGTAAAATATACAAATCGTATCT
1 GAAGCCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGA-TAAAATATACAAACCTTATCT
* * * * *
25234067 CCCTGAAGTTGTAATGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTAGCAGCGGAGT
65 CCCTGAAGTTGTAGTGGAACAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTTGCAGAGGAGT
* *
25234132 AGATCGAAGCTACAAATCTCTTCTCACTGAAATTACATTGGAGCAGATC
130 AGATCGAAGCTACAAGTCTCTTCTCCCTGAAATTACATTGGAGCAGATC
*
25234181 GAAGCCACAATCCTTATCCCCCTGAAGTTGCAGTGGAGCAGGATAAAATTATACAAACCTTATCT
1 GAAGCCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAA-TATACAAACCTTATCT
*
25234246 CCCTGAAGTTGTAGTGGAATAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTTGCAGAGGAGT
65 CCCTGAAGTTGTAGTGGAACAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTTGCAGAGGAGT
25234311 AGATCGAAGCTACAAGTCTCTTCTCCCTGAAATTACATTGGAGCAGATC
130 AGATCGAAGCTACAAGTCTCTTCTCCCTGAAATTACATTGGAGCAGATC
25234360 GAAGCCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATATACAAACCTTATCT
1 GAAGCCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGAT-AAAATATACAAACCTTATCT
*
25234425 CCCTGAAGTTGTAGTGGAGC-GAGTTGAAATTACCAATTCTTATCTCCTTGAAGTTGCAGCA-GA
65 CCCTGAAGTTGTAGTGGAACAG-GTTGAAATTACCAATTCTTATCTCCTTGAAGTTGCAG-AGGA
* *
25234488 GTAGATTGAAGCTACAAGTCTCTTCTCCCTGAAATTACATTGGAGCGGATC
128 GTAGATCGAAGCTACAAGTCTCTTCTCCCTGAAATTACATTGGAGCAGATC
25234539 GAA
1 GAA
25234542 ACACCATTTC
Statistics
Matches: 339, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
178 6 0.02
179 328 0.97
180 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (178 bp):
GAAGCCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAATATACAAACCTTATCTC
CCTGAAGTTGTAGTGGAACAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTTGCAGAGGAGTA
GATCGAAGCTACAAGTCTCTTCTCCCTGAAATTACATTGGAGCAGATC
Found at i:25234859 original size:23 final size:24
Alignment explanation
Indices: 25234815--25234861 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25234805 AAATACAAGC
25234815 CCCAAAAACTAAAAACTCTAACAG
1 CCCAAAAACTAAAAACTCTAACAG
* *
25234839 CCCAAAACCTAAACACT-TAACAG
1 CCCAAAAACTAAAAACTCTAACAG
25234862 AAACCCTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.51, C:0.32, G:0.04, T:0.13
Consensus pattern (24 bp):
CCCAAAAACTAAAAACTCTAACAG
Found at i:25235771 original size:4 final size:4
Alignment explanation
Indices: 25235748--25235790 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
25235738 TTTTACTTAA
* *
25235748 TATT CTATT TAAT AATT TATT TATT TATT TATT TATT TGATT T
1 TATT -TATT TATT TATT TATT TATT TATT TATT TATT T-ATT T
25235791 CTCTTTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 25 0.76
5 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:25237125 original size:36 final size:37
Alignment explanation
Indices: 25237077--25237149 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
25237067 TTTTAAATTA
25237077 AAAATATTAAAATATCTTTGAATAAAATAATTTATTT
1 AAAATATTAAAATATCTTTGAATAAAATAATTTATTT
* * *
25237114 AAAA-ATTAAAATATTTTTGAATAATATATTTTATTT
1 AAAATATTAAAATATCTTTGAATAAAATAATTTATTT
25237150 TAATTACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
AAAATATTAAAATATCTTTGAATAAAATAATTTATTT
Found at i:25237259 original size:25 final size:27
Alignment explanation
Indices: 25237222--25237274 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
25237212 TAGTATGAAT
*
25237222 TTTTAAGCAAGTATATAATAA-AAAATA
1 TTTTAAGCAAGTACA-AATAATAAAATA
25237249 TTTTAA-C-AGTACAAATAATAAAATA
1 TTTTAAGCAAGTACAAATAATAAAATA
25237274 T
1 T
25237275 GATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 12 0.50
26 1 0.04
27 6 0.25
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (27 bp):
TTTTAAGCAAGTACAAATAATAAAATA
Found at i:25240207 original size:48 final size:48
Alignment explanation
Indices: 25240151--25240253 Score: 188
Period size: 48 Copynumber: 2.1 Consensus size: 48
25240141 GCCAATAGCT
* *
25240151 AAATCCTCAGATAAAGGATGTGTCTATGGGGTGGTTTGGATTTGGACC
1 AAATCCTCAAATAAAGGATGTGTCTATAGGGTGGTTTGGATTTGGACC
25240199 AAATCCTCAAATAAAGGATGTGTCTATAGGGTGGTTTGGATTTGGACC
1 AAATCCTCAAATAAAGGATGTGTCTATAGGGTGGTTTGGATTTGGACC
25240247 AAATCCT
1 AAATCCT
25240254 AAAAGGTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (48 bp):
AAATCCTCAAATAAAGGATGTGTCTATAGGGTGGTTTGGATTTGGACC
Found at i:25245871 original size:19 final size:19
Alignment explanation
Indices: 25245849--25245886 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25245839 ACACTGTCAC
*
25245849 CCACTGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
*
25245868 CCACCGTAATCAAGTTTGT
1 CCACCGTAATCAAATTTGT
25245887 TATTAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:25246689 original size:22 final size:20
Alignment explanation
Indices: 25246652--25246694 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
25246642 GGGAAAGTGA
* *
25246652 GAAAGAGTAAAAGTTTTAGG
1 GAAAAAGTAAAAGTTTGAGG
25246672 GAAAAAGTAAAAAGGTTTGAGG
1 GAAAAAGT-AAAA-GTTTGAGG
25246694 G
1 G
25246695 TTTGGGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.21
Consensus pattern (20 bp):
GAAAAAGTAAAAGTTTGAGG
Found at i:25249629 original size:15 final size:15
Alignment explanation
Indices: 25249605--25249636 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25249595 TATGCATGCA
*
25249605 AAATATAAAAGACAT
1 AAATACAAAAGACAT
25249620 AAATACAAAAGACAT
1 AAATACAAAAGACAT
25249635 AA
1 AA
25249637 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:25251333 original size:88 final size:88
Alignment explanation
Indices: 25251184--25251367 Score: 323
Period size: 88 Copynumber: 2.1 Consensus size: 88
25251174 TCACATGCCT
*
25251184 GTGTGTCAGACCATGTGCTAGGCCGTGTAACTGCCTGACTTGCAATCATCAGAAAGCTACAAGGG
1 GTGTGTCAGACCATGTGCTAGGCCGTGTAACTGCCTGACTTGCAACCATCAGAAAGCTACAAGGG
* *
25251249 ACACATGGTTGTGTTGCCTAGCC
66 ACACATGGCTGTGTCGCCTAGCC
* *
25251272 GTGTGTCAGACCGTGTGCTAGGCCGTGTAACTGCCTGGCTTGCAACCATCAGAAAGCTACAAGGG
1 GTGTGTCAGACCATGTGCTAGGCCGTGTAACTGCCTGACTTGCAACCATCAGAAAGCTACAAGGG
25251337 ACACATGGCTGTGTCGCCTAGCC
66 ACACATGGCTGTGTCGCCTAGCC
25251360 GTGTGTCA
1 GTGTGTCA
25251368 TACACGGCTG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (88 bp):
GTGTGTCAGACCATGTGCTAGGCCGTGTAACTGCCTGACTTGCAACCATCAGAAAGCTACAAGGG
ACACATGGCTGTGTCGCCTAGCC
Found at i:25252266 original size:15 final size:16
Alignment explanation
Indices: 25252237--25252266 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25252227 CAAACATGCT
25252237 TTAACACATTATCAAA
1 TTAACACATTATCAAA
25252253 TTAACACA-TATCAA
1 TTAACACATTATCAA
25252267 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:25252743 original size:20 final size:19
Alignment explanation
Indices: 25252716--25252757 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
25252706 CTTTTCAAAT
25252716 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCATTT-CA
25252735 TTTCATTACTTTCCATTTCA
1 TTTC-TTACTTTCCATTTCA
25252755 TTT
1 TTT
25252758 ACTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTCTTACTTTCCATTTCA
Found at i:25252753 original size:15 final size:16
Alignment explanation
Indices: 25252733--25252762 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25252723 CTTTCATTTG
25252733 CATTTCA-TTACTTTC
1 CATTTCATTTACTTTC
25252748 CATTTCATTTACTTT
1 CATTTCATTTACTTT
25252763 TTTTAGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
CATTTCATTTACTTTC
Found at i:25253437 original size:25 final size:25
Alignment explanation
Indices: 25253403--25253470 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
25253393 CTGTACCTGT
*
25253403 ATGCTCACACGAGTTGTGAATTAGA
1 ATGCTCACACGAGTTGTGAATAAGA
*
25253428 ATGCTCACACGAGCTGTGAATAAGA
1 ATGCTCACACGAGTTGTGAATAAGA
*
25253453 ATGCTCACACAAGTTGTG
1 ATGCTCACACGAGTTGTG
25253471 GGTCGGAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (25 bp):
ATGCTCACACGAGTTGTGAATAAGA
Found at i:25256158 original size:3 final size:3
Alignment explanation
Indices: 25256139--25256177 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
25256129 TGTTCAATAG
*
25256139 TAT T-T TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
25256178 CTCTAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:25261631 original size:16 final size:17
Alignment explanation
Indices: 25261612--25261644 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
25261602 TTTAGTGCAT
25261612 TATATTTTTAAA-AAAA
1 TATATTTTTAAAGAAAA
25261628 TATATTTTTAAAGAAAA
1 TATATTTTTAAAGAAAA
25261645 ATTAATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TATATTTTTAAAGAAAA
Found at i:25262192 original size:2 final size:2
Alignment explanation
Indices: 25262185--25262219 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25262175 GGTTTTACCT
25262185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25262220 GCAGGCATCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25264402 original size:16 final size:17
Alignment explanation
Indices: 25264383--25264415 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
25264373 TTTAGTGCAT
25264383 TATATTTTTAAA-AAAA
1 TATATTTTTAAAGAAAA
25264399 TATATTTTTAAAGAAAA
1 TATATTTTTAAAGAAAA
25264416 ATTAATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TATATTTTTAAAGAAAA
Found at i:25274910 original size:53 final size:53
Alignment explanation
Indices: 25274853--25274954 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
25274843 TCATCTCCTA
25274853 GGGGTATAAAAGTCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCTTAT
1 GGGGTATAAAAGTCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCTTAT
**** * *
25274906 GGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
1 GGGGTATAAAAGTCATTTTACCCTATAGAGGTATTTCGGTCATTTTACC
25274955 CTATAAGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.41
Consensus pattern (53 bp):
GGGGTATAAAAGTCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCTTAT
Found at i:25275035 original size:27 final size:27
Alignment explanation
Indices: 25274864--25275022 Score: 205
Period size: 27 Copynumber: 5.9 Consensus size: 27
25274854 GGGTATAAAA
*
25274864 GTCATTTTACCCTATAGAGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
25274891 GTCATTTTACCTTAT-GGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
25274917 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
25274944 GTCATTTTACCCTATAAGGGTATTTCC
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
25274971 GTTATTTTACCTTAT-GAGGGTATTTCG
1 GTCATTTTACCCTATAG-GGGTATTTCG
* *
25274998 ATTATTTTACCCTATAGGGGTATTT
1 GTCATTTTACCCTATAGGGGTATTT
25275023 ATATCATTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
26 23 0.20
27 91 0.79
28 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:25278769 original size:15 final size:16
Alignment explanation
Indices: 25278742--25278771 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25278732 GATAACGATT
25278742 AATATATATTATATAA
1 AATATATATTATATAA
25278758 AATATA-ATTATATA
1 AATATATATTATATA
25278772 TTAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:25278976 original size:139 final size:140
Alignment explanation
Indices: 25278812--25279091 Score: 553
Period size: 139 Copynumber: 2.0 Consensus size: 140
25278802 TAAATTTAAA
25278812 ACTTTTATTTTAGCTGCTTTTAAAGATATTTACAAAAAGAGACAGCTAATTTCAATCTTTACAAA
1 ACTTTTATTTTAGCTGCTTTTAAAGATATTTACAAAAAGAGACAGCTAATTTCAATCTTTACAAA
25278877 ATGAACAACCAAATTTTGCAAATAATTAAATTAAGTACCTAAACTTAAAGAAAATTTGAAAATTG
66 ATGAACAACCAAATTTTGCAAATAATTAAATTAAGTACCTAAACTTAAAGAAAATTTGAAAATTG
25278942 -GCTGCAATT
131 AGCTGCAATT
25278951 ACTTTTATTTTAGCTGCTTTTAAAGATATTTACAAAAAGAGACAGCTAATTTCAATCTTTACAAA
1 ACTTTTATTTTAGCTGCTTTTAAAGATATTTACAAAAAGAGACAGCTAATTTCAATCTTTACAAA
25279016 ATGAACAACCAAATTTTGCAAATAATTAAATTAAGTACCTAAACTTAAAGAAAATTTGAAAATTG
66 ATGAACAACCAAATTTTGCAAATAATTAAATTAAGTACCTAAACTTAAAGAAAATTTGAAAATTG
25279081 AGCTGCAATT
131 AGCTGCAATT
25279091 A
1 A
25279092 AAACTTGGAT
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 130 0.93
140 10 0.07
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (140 bp):
ACTTTTATTTTAGCTGCTTTTAAAGATATTTACAAAAAGAGACAGCTAATTTCAATCTTTACAAA
ATGAACAACCAAATTTTGCAAATAATTAAATTAAGTACCTAAACTTAAAGAAAATTTGAAAATTG
AGCTGCAATT
Found at i:25288866 original size:18 final size:18
Alignment explanation
Indices: 25288843--25288881 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25288833 TGGGAAAATA
*
25288843 AGAAAGGGAATGGAAGAG
1 AGAAAGGGAATGAAAGAG
* *
25288861 AGAAAGTGATTGAAAGAG
1 AGAAAGGGAATGAAAGAG
25288879 AGA
1 AGA
25288882 GAGAGATGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.38, T:0.10
Consensus pattern (18 bp):
AGAAAGGGAATGAAAGAG
Found at i:25300156 original size:25 final size:23
Alignment explanation
Indices: 25300127--25300178 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
25300117 AAGAAGGAGA
25300127 AAAATGAGAGAAAAAGATAAGAGGG
1 AAAATGAGAGAAAAAGA-AAG-GGG
* *
25300152 AAAATGAGAGGAAAATAAAGGGG
1 AAAATGAGAGAAAAAGAAAGGGG
25300175 AAAA
1 AAAA
25300179 GGGAAAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 15 0.60
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (23 bp):
AAAATGAGAGAAAAAGAAAGGGG
Found at i:25301326 original size:19 final size:20
Alignment explanation
Indices: 25301284--25301326 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
25301274 TTTATATTTA
* *
25301284 AAAAAAATATTAATTATTAT
1 AAAAAAATATTAAGTATGAT
25301304 -AAAAAATATT-AGTATGAT
1 AAAAAAATATTAAGTATGAT
25301322 AAAAA
1 AAAAA
25301327 TAATTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAAAATATTAAGTATGAT
Found at i:25301328 original size:17 final size:19
Alignment explanation
Indices: 25301285--25301326 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
25301275 TTATATTTAA
* *
25301285 AAAAAATATTAATTATTAT
1 AAAAAATATTAAGTATGAT
25301304 AAAAAATATT-AGTATGAT
1 AAAAAATATTAAGTATGAT
25301322 AAAAA
1 AAAAA
25301327 TAATTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAAAATATTAAGTATGAT
Found at i:25306944 original size:22 final size:21
Alignment explanation
Indices: 25306898--25306944 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
25306888 GACAATACGT
**
25306898 CTCTTCTCGTCGGGACGACGC
1 CTCTTCTCGTCGGGACGACAA
*
25306919 CTCTTCCTCGTCGGGACGTCAA
1 CTCTT-CTCGTCGGGACGACAA
25306941 CTCT
1 CTCT
25306945 GTTTCTGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.11, C:0.38, G:0.23, T:0.28
Consensus pattern (21 bp):
CTCTTCTCGTCGGGACGACAA
Found at i:25309322 original size:22 final size:23
Alignment explanation
Indices: 25309286--25309334 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
25309276 TCGGTATGCC
*
25309286 AAAT-GTTTTTCTT-AATTATAT
1 AAATAGTTTTTATTAAATTATAT
*
25309307 TAATAGTTTTTATTAAATTATAT
1 AAATAGTTTTTATTAAATTATAT
25309330 AAATA
1 AAATA
25309335 CTAAATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 8 0.35
23 12 0.52
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AAATAGTTTTTATTAAATTATAT
Found at i:25311286 original size:23 final size:23
Alignment explanation
Indices: 25311260--25311422 Score: 175
Period size: 23 Copynumber: 7.1 Consensus size: 23
25311250 TATTGATCAA
* *
25311260 TGGTAGCTTCGGCTAAATTTCAA
1 TGGTAGCTTCGGCTACATTTCAG
* * *
25311283 TGGTAGCTACAGCTACATATCAG
1 TGGTAGCTTCGGCTACATTTCAG
* *
25311306 TGGTAGCTTTGGCTACATTTTAG
1 TGGTAGCTTCGGCTACATTTCAG
* *
25311329 TGGTAGCTACGGCTACATATCAG
1 TGGTAGCTTCGGCTACATTTCAG
*
25311352 TGGTAGCTTCAGCTACATTTCAG
1 TGGTAGCTTCGGCTACATTTCAG
* * *
25311375 TGGTAGCTACAGCTACGTATT-AG
1 TGGTAGCTTCGGCTACAT-TTCAG
* *
25311398 TGGTAACTTCGGCTACATATCAG
1 TGGTAGCTTCGGCTACATTTCAG
25311421 TG
1 TG
25311423 TGGCACTTAT
Statistics
Matches: 114, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
22 1 0.01
23 111 0.97
24 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGTAGCTTCGGCTACATTTCAG
Found at i:25311312 original size:46 final size:46
Alignment explanation
Indices: 25311255--25311422 Score: 237
Period size: 46 Copynumber: 3.7 Consensus size: 46
25311245 AGTGTTATTG
* * *
25311255 ATCAATGGTAGCTTCGGCTAAATTTCAATGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
* * *
25311301 ATCAGTGGTAGCTTTGGCTACATTTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
* *
25311347 ATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACAGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
* * *
25311393 ATTAGTGGTAACTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
25311423 TGGCACTTAT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 107 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
Found at i:25311375 original size:69 final size:69
Alignment explanation
Indices: 25311260--25311422 Score: 218
Period size: 69 Copynumber: 2.4 Consensus size: 69
25311250 TATTGATCAA
* * * *** *
25311260 TGGTAGCTTCGGCTAAATTTCAATGGTAGCTACAGCTACATATCAGTGGTAGCTTTGGCTACATT
1 TGGTAGCTTCGGCTACATATCAGTGGTAGCTACAGCTACATATCAGTGGTAGCTACAGCTACATA
25311325 TTAG
66 TTAG
* * * *
25311329 TGGTAGCTACGGCTACATATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACAGCTACGTA
1 TGGTAGCTTCGGCTACATATCAGTGGTAGCTACAGCTACATATCAGTGGTAGCTACAGCTACATA
25311394 TTAG
66 TTAG
*
25311398 TGGTAACTTCGGCTACATATCAGTG
1 TGGTAGCTTCGGCTACATATCAGTG
25311423 TGGCACTTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (69 bp):
TGGTAGCTTCGGCTACATATCAGTGGTAGCTACAGCTACATATCAGTGGTAGCTACAGCTACATA
TTAG
Found at i:25313700 original size:6 final size:6
Alignment explanation
Indices: 25313689--25313714 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25313679 AGTATAGACA
25313689 TTATAT TTATAT TTATAT TTATAT TT
1 TTATAT TTATAT TTATAT TTATAT TT
25313715 GAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:25314097 original size:16 final size:16
Alignment explanation
Indices: 25314076--25314114 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
25314066 CTTATTCGTT
25314076 CCACTTCACTAGCTCG
1 CCACTTCACTAGCTCG
25314092 CCACTTCACTAGCTCG
1 CCACTTCACTAGCTCG
*
25314108 CCCCTTC
1 CCACTTC
25314115 GCCAGCTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.49, G:0.10, T:0.26
Consensus pattern (16 bp):
CCACTTCACTAGCTCG
Found at i:25314121 original size:16 final size:16
Alignment explanation
Indices: 25314076--25314121 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
25314066 CTTATTCGTT
*
25314076 CCACTTCACTAGCTCG
1 CCACTTCACCAGCTCG
*
25314092 CCACTTCACTAGCTCG
1 CCACTTCACCAGCTCG
* *
25314108 CCCCTTCGCCAGCT
1 CCACTTCACCAGCT
25314122 TGTCACTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.15, C:0.48, G:0.13, T:0.24
Consensus pattern (16 bp):
CCACTTCACCAGCTCG
Found at i:25323198 original size:5 final size:5
Alignment explanation
Indices: 25323188--25323214 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
25323178 TCTCTGCCAG
25323188 CTTTT CTTTT CTTTT CTTTT CTTTT CT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CT
25323215 CCATCTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:25326035 original size:27 final size:27
Alignment explanation
Indices: 25326005--25326057 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
25325995 AAATAATTAA
*
25326005 AATTCAA-TATGTTAATAATTTAAGTGC
1 AATTCAATTAT-TTAATAATTAAAGTGC
* *
25326032 AATTTAATTATTTTATAATTAAAGTG
1 AATTCAATTATTTAATAATTAAAGTG
25326058 TGAATGTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (27 bp):
AATTCAATTATTTAATAATTAAAGTGC
Found at i:25328513 original size:26 final size:26
Alignment explanation
Indices: 25328484--25328533 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
25328474 TTTTACATCG
* *
25328484 TTGCTCACATGAGCTATGAAATGGAT
1 TTGCTCACACGAGCTACGAAATGGAT
25328510 TTGCTCACACGAGCTACGAAATGG
1 TTGCTCACACGAGCTACGAAATGG
25328534 GCTCCTCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (26 bp):
TTGCTCACACGAGCTACGAAATGGAT
Found at i:25332782 original size:29 final size:29
Alignment explanation
Indices: 25332728--25332783 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
25332718 GCTTTTAAAG
* *
25332728 ATATTTACAAAAAGAGACAGCTAATTTCA
1 ATATTTACAAAAAGAGACACCAAATTTCA
25332757 ATATTTACAAAAAGA-ACAACCAAATTT
1 ATATTTACAAAAAGAGAC-ACCAAATTT
25332784 TGCAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (29 bp):
ATATTTACAAAAAGAGACACCAAATTTCA
Found at i:25340266 original size:30 final size:30
Alignment explanation
Indices: 25340232--25340320 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
25340222 TGTTGCCACA
* *
25340232 GGCGTGTGTCTTAGTCATGTGTGAAACATG
1 GGCGTGTGTCTCAGTCATGTGTGAAACACG
*
25340262 GGCGTGTGTCTCAGCCATGTGTGAAACACG
1 GGCGTGTGTCTCAGTCATGTGTGAAACACG
* * *
25340292 GGCGTGTGCCTCAGTCATGAGTGACACAC
1 GGCGTGTGTCTCAGTCATGTGTGAAACAC
25340321 AGCCATGCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.26
Consensus pattern (30 bp):
GGCGTGTGTCTCAGTCATGTGTGAAACACG
Found at i:25345810 original size:27 final size:27
Alignment explanation
Indices: 25345774--25346039 Score: 173
Period size: 27 Copynumber: 10.2 Consensus size: 27
25345764 AAAGGTCAAT
* *
25345774 AAATGATCGAATTACCCCCACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
25345801 AAATGATCGAATTACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
25345828 GAATGA-CTAAAATACCCCCATAGGATA
1 AAATGATC-GAAATACCCCCATAGGGTA
* * *
25345855 GAATGACCGAAATACCCCCATAGGATA
1 AAATGATCGAAATACCCCCATAGGGTA
*
25345882 AAATG-TCTGAAATACCCCCATAAGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
* * * *** *
25345909 GAATTACCGAAATA-CCCCATAAAATG
1 AAATGATCGAAATACCCCCATAGGGTA
* *
25345935 GAATGATCGAAATACCCCCACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
25345962 AAATGA-CCAAA-ACACCCC-TA-GG--
1 AAATGATCGAAATAC-CCCCATAGGGTA
* *
25345984 --A-GAT-GAAATACCCTCATAGGTTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
25346007 AAATGA-CTGAAATACCCTCATAGGTTA
1 AAATGATC-GAAATACCCCCATAGGGTA
25346034 AAATGA
1 AAATGA
25346040 CTGTTATACC
Statistics
Matches: 191, Mismatches: 31, Indels: 34
0.75 0.12 0.13
Matches are distributed among these distances:
19 8 0.04
20 5 0.03
21 1 0.01
24 2 0.01
25 4 0.02
26 33 0.17
27 136 0.71
28 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:25345910 original size:81 final size:80
Alignment explanation
Indices: 25345771--25345967 Score: 245
Period size: 81 Copynumber: 2.5 Consensus size: 80
25345761 TCGAAAGGTC
* * * *
25345771 AATA-AATGATCGAATTACCCCCACAGGGTAAAATGATCGAATTACCCTCATAGGGTAGAATGAC
1 AATAGAATGATCGAAATACCCCCACAGGGTAAAATGATCGAAATACCCCCATAAGGTAGAATGAC
* *
25345835 TAAAATACCCCCATAG
66 CAAAATA-CCCCATAA
* * * * *
25345851 GATAGAATGACCGAAATACCCCCATAGGATAAAATG-TCTGAAATACCCCCATAAGGTAGAATTA
1 AATAGAATGATCGAAATACCCCCACAGGGTAAAATGATC-GAAATACCCCCATAAGGTAGAATGA
*
25345915 CCGAAATACCCCATAA
65 CCAAAATACCCCATAA
*
25345931 AATGGAATGATCGAAATACCCCCACAGGGTAAAATGA
1 AATAGAATGATCGAAATACCCCCACAGGGTAAAATGA
25345968 CCAAAACACC
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
80 43 0.44
81 54 0.56
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (80 bp):
AATAGAATGATCGAAATACCCCCACAGGGTAAAATGATCGAAATACCCCCATAAGGTAGAATGAC
CAAAATACCCCATAA
Done.