Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 59 of 182
Found at i:19177668 original size:97 final size:97
Alignment explanation
Indices: 19177565--19177758 Score: 264
Period size: 97 Copynumber: 2.0 Consensus size: 97
19177555 TAAACCTTTA
* * * * *
19177565 AAATCGAGGCAATATTCCTTTATTTC-GAGATTTGAAAATTTGCGTCTTAACTTACTAGGTGTGA
1 AAATCGAGGCAATATTCCTTTATCTCTG-GATTTGAAAATTTACGCCTTAACTTACTAGGCGCGA
*
19177629 TTTTTCTTCAAATCGGAATAATCGAATACCCTT
65 CTTTTCTTCAAATCGGAATAATCGAATACCCTT
* * * * *
19177662 AAATCGAGGTAATGTTTCTTTATCTCTGGTTTTGAAAATTTATGCCTTAACTTACTAGGCGCGAC
1 AAATCGAGGCAATATTCCTTTATCTCTGGATTTGAAAATTTACGCCTTAACTTACTAGGCGCGAC
*
19177727 TTTTCTTCAAATCGGGATAATCGAATACCCTT
66 TTTTCTTCAAATCGGAATAATCGAATACCCTT
19177759 TTCCAAGGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 83 0.99
98 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCTGGATTTGAAAATTTACGCCTTAACTTACTAGGCGCGAC
TTTTCTTCAAATCGGAATAATCGAATACCCTT
Found at i:19186124 original size:29 final size:29
Alignment explanation
Indices: 19186061--19186124 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
19186051 TATATATATG
* *
19186061 TAATATTATATATGAATTATTATTTTGTT
1 TAATTTTATATATGAATTATTATTTTGAT
*
19186090 TAATTTTATATATGAATT-TTTTATTTGAT
1 TAATTTTATATATGAATTATTAT-TTTGAT
*
19186119 TCATTT
1 TAATTT
19186125 ATAAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (29 bp):
TAATTTTATATATGAATTATTATTTTGAT
Found at i:19188589 original size:18 final size:18
Alignment explanation
Indices: 19188566--19188604 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19188556 AAAAATCAAA
*
19188566 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
19188584 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
19188602 TTT
1 TTT
19188605 GTCTCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:19189675 original size:18 final size:17
Alignment explanation
Indices: 19189646--19189696 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
19189636 ATAATATAAA
*
19189646 TAATAAAATATTATTAT
1 TAATTAAATATTATTAT
*
19189663 TTATTATAATATTATTAT
1 TAATTA-AATATTATTAT
19189681 TAATTAATATATTATT
1 TAATTAA-ATATTATT
19189697 TGACAACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTAAATATTATTAT
Found at i:19189680 original size:21 final size:21
Alignment explanation
Indices: 19189654--19189696 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19189644 AATAATAAAA
* *
19189654 TATTATTATTTATTATAATAT
1 TATTATTAATTAATATAATAT
*
19189675 TATTATTAATTAATATATTAT
1 TATTATTAATTAATATAATAT
19189696 T
1 T
19189697 TGACAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTAATTAATATAATAT
Found at i:19198346 original size:32 final size:30
Alignment explanation
Indices: 19198308--19198392 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 30
19198298 ATTATATTAT
* *
19198308 TATTTTGGTGTTTTTTTATTGTTTTGGTTGC
1 TATTTT-GTGTTTTTTTACTGTTTCGGTTGC
*
19198339 TGTTTT-TGTTTTTTTTACTGTTTCGGTTGC
1 TATTTTGTG-TTTTTTTACTGTTTCGGTTGC
19198369 TATTTTCGTGTTGTTTTTACTGTT
1 TATTTT-GTGTT-TTTTTACTGTT
19198393 ATTTTGTTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.04
30 24 0.52
31 7 0.15
32 13 0.28
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.67
Consensus pattern (30 bp):
TATTTTGTGTTTTTTTACTGTTTCGGTTGC
Found at i:19198421 original size:18 final size:20
Alignment explanation
Indices: 19198380--19198421 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
19198370 ATTTTCGTGT
* *
19198380 TGTTTTTACTGTTATTTTGT
1 TGTTTTTAATGTTATTTTGC
19198400 TGTTTTTAAT-TT-TTTTGC
1 TGTTTTTAATGTTATTTTGC
19198418 TGTT
1 TGTT
19198422 ATTTTTGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.10, C:0.05, G:0.14, T:0.71
Consensus pattern (20 bp):
TGTTTTTAATGTTATTTTGC
Found at i:19205426 original size:9 final size:9
Alignment explanation
Indices: 19205407--19205444 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
19205397 TAAATTTTCG
19205407 AATTCGAAT
1 AATTCGAAT
19205416 AACTT-GAAT
1 AA-TTCGAAT
19205425 AATTCGAAT
1 AATTCGAAT
*
19205434 AAATCGAAT
1 AATTCGAAT
19205443 AA
1 AA
19205445 AACTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:19205442 original size:18 final size:18
Alignment explanation
Indices: 19205407--19205444 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19205397 TAAATTTTCG
* *
19205407 AATTCGAATAACTTGAAT
1 AATTCGAATAAATCGAAT
19205425 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
19205443 AA
1 AA
19205445 AACTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:19207264 original size:11 final size:11
Alignment explanation
Indices: 19207250--19207359 Score: 80
Period size: 11 Copynumber: 9.6 Consensus size: 11
19207240 AATGCCTCTC
19207250 AAATAATAATA
1 AAATAATAATA
*
19207261 AAATTAACAATA
1 AAA-TAATAATA
* *
19207273 AAATAAAAATT
1 AAATAATAATA
*
19207284 ATATAAT-ATCCAA
1 AAATAATAAT---A
19207297 ACAATAATAATA
1 A-AATAATAATA
19207309 AAATAATAACT-
1 AAATAATAA-TA
* *
19207320 ATATAATAACA
1 AAATAATAATA
*
19207331 AAATAACAATA
1 AAATAATAATA
*
19207342 AAATAACAATA
1 AAATAATAATA
19207353 AAATAAT
1 AAATAAT
19207360 TAATCCTAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
10 2 0.03
11 55 0.71
12 13 0.17
13 1 0.01
14 5 0.06
15 2 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATAATA
Found at i:19207310 original size:36 final size:33
Alignment explanation
Indices: 19207252--19207347 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 33
19207242 TGCCTCTCAA
* *
19207252 ATAATAATAAAATTAACAATAAAATAAAAATTAT
1 ATAATAACAAAA-TAACAATAAAATAAAAACTAT
* * *
19207286 ATAATATCCAAACAATAATAATAAAATAATAACTAT
1 ATAATA-AC-AA-AATAACAATAAAATAAAAACTAT
19207322 ATAATAACAAAATAACAATAAAATAA
1 ATAATAACAAAATAACAATAAAATAA
19207348 CAATAAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
33 15 0.29
34 8 0.15
35 1 0.02
36 26 0.50
37 2 0.04
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (33 bp):
ATAATAACAAAATAACAATAAAATAAAAACTAT
Found at i:19207327 original size:19 final size:20
Alignment explanation
Indices: 19207296--19207353 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
19207286 ATAATATCCA
19207296 AACAATAATAATAA-AATAAT
1 AACAAT-ATAATAACAATAAT
*
19207316 AACTATATAATAACAA-AAT
1 AACAATATAATAACAATAAT
*
19207335 AACAATAAAATAACAATAA
1 AACAATATAATAACAATAA
19207354 AATAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (20 bp):
AACAATATAATAACAATAAT
Found at i:19209562 original size:33 final size:34
Alignment explanation
Indices: 19209506--19209588 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
19209496 AAAAATAATT
* *
19209506 ATAATA-ATAAATAAGATTTAAATAATTTAATATA
1 ATAATACAT-AATAATATTTAAATAATTAAATATA
*
19209540 ATTATACATAA-AATATTTAAATAATTAAATATA
1 ATAATACATAATAATATTTAAATAATTAAATATA
*
19209573 ATAATATATAATAATA
1 ATAATACATAATAATA
19209589 GTAAAACCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 29 0.69
34 11 0.26
35 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (34 bp):
ATAATACATAATAATATTTAAATAATTAAATATA
Found at i:19213547 original size:25 final size:25
Alignment explanation
Indices: 19213513--19213561 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
19213503 TAATTCAAAC
19213513 AACAAGAATAAAGTGAAAGAATGAG
1 AACAAGAATAAAGTGAAAGAATGAG
* *
19213538 AACAATAATAAATTGAAAGAATGA
1 AACAAGAATAAAGTGAAAGAATGA
19213562 AAAATGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.61, C:0.04, G:0.18, T:0.16
Consensus pattern (25 bp):
AACAAGAATAAAGTGAAAGAATGAG
Found at i:19223911 original size:96 final size:96
Alignment explanation
Indices: 19223802--19223998 Score: 313
Period size: 96 Copynumber: 2.1 Consensus size: 96
19223792 ACACTAGCAG
* * * * *
19223802 CAAATAAAATTATAAACCCAGAAAATAAATGGAATCAAAATCTTTGCTAAAAAAATGCCCAAATT
1 CAAATAAAATTATAAACCCAAAAAAGAAATGAAACCAAAATCTTTGCTAAAAAAATACCCAAATT
*
19223867 TATACAAAGATAATGGAAGAAAACGCTCTTT
66 TATACAAAAATAATGGAAGAAAACGCTCTTT
*
19223898 CAAATAAAATTATAAACCCAAAAAAGAAATGAAACCAAAATCTTTGTTAAAAAAATACCCAAATT
1 CAAATAAAATTATAAACCCAAAAAAGAAATGAAACCAAAATCTTTGCTAAAAAAATACCCAAATT
* *
19223963 TATATAAAAATAATGGAGGAAAACGCTCTTT
66 TATACAAAAATAATGGAAGAAAACGCTCTTT
19223994 CAAAT
1 CAAAT
19223999 TCTTCTTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (96 bp):
CAAATAAAATTATAAACCCAAAAAAGAAATGAAACCAAAATCTTTGCTAAAAAAATACCCAAATT
TATACAAAAATAATGGAAGAAAACGCTCTTT
Found at i:19224047 original size:9 final size:9
Alignment explanation
Indices: 19224019--19224062 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
19224009 GCATCTCCAT
19224019 TTTTTCTCTC
1 TTTTTCT-TC
*
19224029 ATTCTTCTTC
1 -TTTTTCTTC
19224039 TTTTTCTTC
1 TTTTTCTTC
19224048 -TTTTCTTC
1 TTTTTCTTC
19224056 TTTTTCT
1 TTTTTCT
19224063 CTTCTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 8 0.27
9 14 0.47
10 2 0.07
11 6 0.20
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:19224055 original size:17 final size:20
Alignment explanation
Indices: 19224019--19224064 Score: 71
Period size: 17 Copynumber: 2.5 Consensus size: 20
19224009 GCATCTCCAT
19224019 TTTTTCTCTCATTCTTCTTC
1 TTTTTCTCTCATTCTTCTTC
19224039 TTTTTCT-TC-TT-TTCTTC
1 TTTTTCTCTCATTCTTCTTC
19224056 TTTTTCTCT
1 TTTTTCTCT
19224065 TCTTAAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 13 0.52
18 3 0.12
19 2 0.08
20 7 0.28
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTCTCATTCTTCTTC
Found at i:19225129 original size:22 final size:22
Alignment explanation
Indices: 19225104--19225147 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19225094 CTAGTTTCAA
19225104 CTTTAAATTTAT-ACTAATTATT
1 CTTT-AATTTATGACTAATTATT
* *
19225126 CTTTATTTTATGTCTAATTATT
1 CTTTAATTTATGACTAATTATT
19225148 GTGATACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (22 bp):
CTTTAATTTATGACTAATTATT
Found at i:19225521 original size:17 final size:17
Alignment explanation
Indices: 19225478--19225524 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
19225468 AAATTGAATG
19225478 TTTAGTTATTTGT-TTTTA
1 TTTAGTT-TTT-TATTTTA
* *
19225496 ATTAATTTTTTATTTTA
1 TTTAGTTTTTTATTTTA
19225513 TTTAGTTTTTTA
1 TTTAGTTTTTTA
19225525 ATAATGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.04
17 18 0.75
18 5 0.21
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTAGTTTTTTATTTTA
Found at i:19225537 original size:28 final size:27
Alignment explanation
Indices: 19225483--19225537 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
19225473 GAATGTTTAG
* *
19225483 TTATTTGTTTTTAATTAATTTTTTATT
1 TTATTTGTTTTTAATTAATGTTATATT
19225510 TTATTTAGTTTTTTAA-TAATGTTATATT
1 TTATTT-G-TTTTTAATTAATGTTATATT
19225538 GTCCATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 11 0.46
29 7 0.29
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (27 bp):
TTATTTGTTTTTAATTAATGTTATATT
Found at i:19227159 original size:21 final size:18
Alignment explanation
Indices: 19227124--19227185 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
19227114 ATTTTACAAA
19227124 AAAAATAATTTAGTTAAT
1 AAAAATAATTTAGTTAAT
19227142 AAAAATAACTTATAAGTTAAT
1 AAAAATAA-TT-T-AGTTAAT
*
19227163 ATAAAATAAATTT-TTTAAT
1 A-AAAAT-AATTTAGTTAAT
19227182 AAAA
1 AAAA
19227186 TTATTTATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 11 0.29
19 8 0.21
20 1 0.03
21 9 0.24
22 7 0.18
23 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATAATTTAGTTAAT
Found at i:19234479 original size:252 final size:252
Alignment explanation
Indices: 19234057--19235034 Score: 1554
Period size: 252 Copynumber: 3.9 Consensus size: 252
19234047 GCGGAATCAG
* * * * *
19234057 AAGCAGGGGAGGATCTGAAACTAGAA-AAGAGGGAGGAGGCAGAAGAACATGATTCTGTTAGAAC
1 AAGCAAGGGAGGATCTGAAACTAGAAGAGGA-GGAAGATGCAAAAGAACATGATTCTGTTAGAAC
* *
19234121 TTCTACAAATGAAGGAGGTGTTAACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGG
65 TTCTACAAATGAAGGAGATGTTCACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGG
* * *
19234186 TAGCAGAAGACAAAGTTGATAAGCAAGCTCCTTTGCTGACAGTGGACGCTGTTGCTAAAGTTGGA
130 TAGCAGAAGACAAAGTTGACAAGCAAGCTCCTTTGCTGACAATGGACGCTGTTGCCAAAGTTGGA
* *
19234251 TCGAAAGATCAGGAGAGAGGGCAAGAAGATGAATCAAAGGGTGGGGATACAAAACCAA
195 TCAAAAGACCAGGAGAGAGGGCAAGAAGATGAATCAAAGGGTGGGGATACAAAACCAA
19234309 AAGCAAGGGAGGATCTGAAACTAGAAGAGGAGGAAGATGCAAAAGAACATGATTCTGTTAGAACT
1 AAGCAAGGGAGGATCTGAAACTAGAAGAGGAGGAAGATGCAAAAGAACATGATTCTGTTAGAACT
* *
19234374 TTTACAGATGAAGGAGATGTTCACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGGT
66 TCTACAAATGAAGGAGATGTTCACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGGT
* * * *
19234439 AGCAGAAGACAAAGTTGATAAGCAACCTCCTTTACTGACAGTGGACGCTGTTGCCAAAGTTGGAT
131 AGCAGAAGACAAAGTTGACAAGCAAGCTCCTTTGCTGACAATGGACGCTGTTGCCAAAGTTGGAT
* *
19234504 CGAAAGATCAGGAGAGAGGGCAAGAAGATGAATCAAAGGGTGGGGATACAAAACCAA
196 CAAAAGACCAGGAGAGAGGGCAAGAAGATGAATCAAAGGGTGGGGATACAAAACCAA
19234561 AAGCAAGGGAGGATCTGAAACTAGAAGAGGAGGAAGATGCAAAAGAACATGATTCTGTTAGAACT
1 AAGCAAGGGAGGATCTGAAACTAGAAGAGGAGGAAGATGCAAAAGAACATGATTCTGTTAGAACT
* * *
19234626 TTTACAGATGAAGGAGATGTTCACCGTGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGGT
66 TCTACAAATGAAGGAGATGTTCACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGGT
* *
19234691 AGCAGAAGACAAAGTTGACAAGCAAGTTCCTTTGCTGACAATGGATGCTGTTGCCAAAGTTGGAT
131 AGCAGAAGACAAAGTTGACAAGCAAGCTCCTTTGCTGACAATGGACGCTGTTGCCAAAGTTGGAT
* * * * *
19234756 CAAAAGACCAGGAAAAAGGGGAAGAACATGAATCAAAGGGTGGGGATACAGAACCAA
196 CAAAAGACCAGGAGAGAGGGCAAGAAGATGAATCAAAGGGTGGGGATACAAAACCAA
*
19234813 AAGCAAGGGAGGGTCTGAAACTAGAAGAGGA-G--GATGCAAAAGAACATGATTCTGTTAGAACT
1 AAGCAAGGGAGGATCTGAAACTAGAAGAGGAGGAAGATGCAAAAGAACATGATTCTGTTAGAACT
* * * * *
19234875 TCTACAAATGAAGGAGGTGTTCACCATGAAACTTCTAAGCCTTCGGAGAAATGTGAAGATCTGTT
66 TCTACAAATGAAGGAGATGTTCACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGGT
* *
19234940 AGCAGAAGACAAAGTTGACAAGCAAGCTCCTTTGCTGACAATGGATGTTGTTGCCAAAGTTGGAT
131 AGCAGAAGACAAAGTTGACAAGCAAGCTCCTTTGCTGACAATGGACGCTGTTGCCAAAGTTGGAT
19235005 CAAAAGACCAGGA-AGGAGGG-AAGAAGATGA
196 CAAAAGACCAGGAGA-GAGGGCAAGAAGATGA
19235035 GCCTGACTGG
Statistics
Matches: 685, Mismatches: 39, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
248 10 0.01
249 167 0.24
251 1 0.00
252 504 0.74
253 3 0.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (252 bp):
AAGCAAGGGAGGATCTGAAACTAGAAGAGGAGGAAGATGCAAAAGAACATGATTCTGTTAGAACT
TCTACAAATGAAGGAGATGTTCACCATGAAACTTCTAAGCCTTCAGAGAAACGTGAAGACCTGGT
AGCAGAAGACAAAGTTGACAAGCAAGCTCCTTTGCTGACAATGGACGCTGTTGCCAAAGTTGGAT
CAAAAGACCAGGAGAGAGGGCAAGAAGATGAATCAAAGGGTGGGGATACAAAACCAA
Found at i:19240144 original size:252 final size:252
Alignment explanation
Indices: 19239553--19240531 Score: 1554
Period size: 252 Copynumber: 3.9 Consensus size: 252
19239543 CCAGTCAGGC
* * * *
19239553 TCATCTTCTTCCCCTC-CTTCCTGGTCTTTTGATCCAACTTTGGCAACAACATCCATTGTCAGCA
1 TCATCTTCTTCCCCTCTC-TCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCA
* * * * *
19239617 AAGGAGCTTGCTTGTCAACTTTGTCTTCTGCTAACAGATCTTCACATTTCTCCGAAGGCTTAGAA
65 AAGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAA
* *
19239682 GTTTCATGGTGAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTTTGCA---TC
130 GTTTCATGGTGAACACCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTGCATCTTC
* *
19239744 CTCCTCTTCTAGTTTCAGACCCTCCCTTGCTTTTGGTTCTGTATCCCCACCCTTTGAT
195 CTCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTTTGTATCCCCACCCTTTGAT
* * * * *
19239802 TCATGTTCTTCCCCTCTTTCCTGGTCTTTTGATCCAACTTTGGCAACAGCATCCATTGTCAGCAA
1 TCATCTTCTTCCCCTCTCTCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCAA
* *
19239867 AGGAACTTGCTTGTCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
66 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
* * *
19239932 TTTCACGGTGAACATCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTACATCTTCC
131 TTTCATGGTGAACACCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTGCATCTTCC
19239997 TCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTTTGTATCCCCACCCTTTGAT
196 TCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTTTGTATCCCCACCCTTTGAT
* * *
19240054 TCATCTTCTTGCCCTCTCTCCTGATCTTTCGATCCAACTTTGGCAACAGCGTCCACTGTCAGTAA
1 TCATCTTCTTCCCCTCTCTCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCAA
*
19240119 AGGAGGTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
66 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
*
19240184 TTTCATGGTGAACATCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTGCATCTTCC
131 TTTCATGGTGAACACCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTGCATCTTCC
19240249 TCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTTTGTATCCCCACCCTTTGAT
196 TCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTTTGTATCCCCACCCTTTGAT
* * *
19240306 TCATCTTCTTGCCCTCTCTCCTGATCTTTCGATCCAACTTTAGCAACAGCGTCCACTGTCAGCAA
1 TCATCTTCTTCCCCTCTCTCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCAA
19240371 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
66 AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
* * * * * *
19240436 TTTCATGGTTAACACCTCCTTCATTTGTAGAAGTTCTAACAGAATCATGTTCTTCTGCCTCCTCC
131 TTTCATGGTGAACACCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTGCATCTTCC
* *
19240501 -CTCTTTTCTAGTTTCAGATCCTCCCCTGCTT
196 TC-CTCTTCTAGTTTCAGATCCTCCCTTGCTT
19240532 CTGATTCCGC
Statistics
Matches: 685, Mismatches: 40, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
249 175 0.26
251 1 0.00
252 509 0.74
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (252 bp):
TCATCTTCTTCCCCTCTCTCCTGATCTTTCGATCCAACTTTGGCAACAGCATCCACTGTCAGCAA
AGGAGCTTGCTTATCAACTTTGTCTTCTGCTACCAGGTCTTCACGTTTCTCTGAAGGCTTAGAAG
TTTCATGGTGAACACCTCCTTCATCTGTAAAAGTTCTAACAGAATCATGTTCTTTTGCATCTTCC
TCCTCTTCTAGTTTCAGATCCTCCCTTGCTTTTGGTTTTGTATCCCCACCCTTTGAT
Found at i:19250001 original size:19 final size:19
Alignment explanation
Indices: 19249955--19250002 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
19249945 TAATAAAGTT
* * *
19249955 TATATTAAAATTCTTGAAG
1 TATATTGAAATGCTAGAAG
*
19249974 GAT-TTGAAATGCTAGAAG
1 TATATTGAAATGCTAGAAG
19249992 TATATTGAAAT
1 TATATTGAAAT
19250003 TATCAGGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (19 bp):
TATATTGAAATGCTAGAAG
Found at i:19252502 original size:15 final size:15
Alignment explanation
Indices: 19252482--19252511 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19252472 CATATAGTTT
19252482 GAAACTGATTAATAA
1 GAAACTGATTAATAA
19252497 GAAACTGATTAATAA
1 GAAACTGATTAATAA
19252512 TAACACATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
GAAACTGATTAATAA
Found at i:19252578 original size:257 final size:254
Alignment explanation
Indices: 19252242--19252755 Score: 694
Period size: 259 Copynumber: 2.0 Consensus size: 254
19252232 CTTATGGTTT
*
19252242 GAAACTGATTAATAATAACACATAAAATATGTACAATATTAAAATTAAAAAATAGATTAAATTGT
1 GAAACTGATTAATAATAACACATAAAATATGCACAATATTAAAATTAAAAAATAGATTAAATTGT
* *** *
19252307 TTATCATTGTGTTGTCATCAATCATGAGTTGGTGTTTTGTTAACTTGTAACAACAACTCAATCGA
66 TTATCAATGTGTTGTCATCAATCATGAGTTGGTGTCGAGTTAACTTGTAACAACAACTAAATCGA
*
19252372 ATACATTACTAATACTAGAATTTC-T-ATGCGTATGCATGTAAAAACCACAAATTTAGAACACAA
131 ATACA-T--TAATACTAAAATTTCATCATGCGTATGCATGTAAAAACCACAAATTTAGAACACAA
* *
19252435 ATGTGTGTCAAAAAATAA-CAAACTATAAATAGTGACACATATAGTTTGAAACTGATTAATAA
193 ATGTGTGTCAAAAAATAATC-AACTATAAATAGTGAAACATATAGTTTGAAACTAATTAATAA
** *
19252497 GAAACTGATTAATAATAACACATGAAAA-ATGCATGATATTACAATTTAAAAAATTAGATTAAAT
1 GAAACTGATTAATAATAACACAT-AAAATATGCACAATATTA-AAATTAAAAAA-TAGATTAAAT
* *
19252561 TGTTTATCAATGTGTTGTCATCAATCTTGAGTTGGTGTCGAGTTAACTTGTGACAACAACTAAAT
63 TGTTTATCAATGTGTTGTCATCAATCATGAGTTGGTGTCGAGTTAACTTGTAACAACAACTAAAT
* * * *
19252626 CGAATACATTAATACTAAAATTTCTATCACATGTGTATGCGTGTAGAAACCACAAATTTAGAACG
128 CGAATACATTAATACTAAAATTTC-AT--CATGCGTATGCATGTAAAAACCACAAATTTAGAACA
* ** * * *
19252691 TAAATGTGTGTTTAAAACTAATCTACTATAAATAGTGAAACATATGGTTTGAAACTAATTAATAA
190 CAAATGTGTGTCAAAAAATAATCAACTATAAATAGTGAAACATATAGTTTGAAACTAATTAATAA
19252756 AAATACATAA
Statistics
Matches: 226, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
254 14 0.06
255 33 0.15
256 16 0.07
257 76 0.34
259 86 0.38
260 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (254 bp):
GAAACTGATTAATAATAACACATAAAATATGCACAATATTAAAATTAAAAAATAGATTAAATTGT
TTATCAATGTGTTGTCATCAATCATGAGTTGGTGTCGAGTTAACTTGTAACAACAACTAAATCGA
ATACATTAATACTAAAATTTCATCATGCGTATGCATGTAAAAACCACAAATTTAGAACACAAATG
TGTGTCAAAAAATAATCAACTATAAATAGTGAAACATATAGTTTGAAACTAATTAATAA
Found at i:19256751 original size:19 final size:18
Alignment explanation
Indices: 19256712--19256747 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19256702 TTGTGCTCTC
*
19256712 AAAAAACACTTTTTATTT
1 AAAAAACACTTTTAATTT
*
19256730 AAAAAATACTTTTAATTT
1 AAAAAACACTTTTAATTT
19256748 TAAAGTACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAAACACTTTTAATTT
Found at i:19258919 original size:21 final size:22
Alignment explanation
Indices: 19258886--19258928 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
19258876 TAGTCAACAC
* * *
19258886 CGATCAAAGGTTGGTCAGCTAT
1 CGATCAAACGTTGATCAACTAT
19258908 CGATC-AACGTTGATCAACTAT
1 CGATCAAACGTTGATCAACTAT
19258929 TAATCAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (22 bp):
CGATCAAACGTTGATCAACTAT
Found at i:19276877 original size:4 final size:4
Alignment explanation
Indices: 19276870--19276895 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19276860 TGTGTATTTA
19276870 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
19276896 ATTATTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:19277868 original size:9 final size:9
Alignment explanation
Indices: 19277850--19277951 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 9
19277840 TTATAAAAAA
19277850 TTTAAA-TT
1 TTTAAATTT
19277858 TTTAAATTT
1 TTTAAATTT
19277867 TTTATATATTT
1 TTTA-A-ATTT
*
19277878 TTTAGATTTTT
1 TTTA-A-ATTT
19277889 TTTAAATATAAAT
1 TTTAAAT-T---T
19277902 TTTAGAATTT
1 TTTA-AATTT
*
19277912 TTATAAATAT
1 TT-TAAATTT
19277922 TTTAAATTT
1 TTTAAATTT
**
19277931 TAAAAATTAT
1 TTTAAATT-T
*
19277941 TTTCAATTT
1 TTTAAATTT
19277950 TT
1 TT
19277952 GAAAATTATT
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.08
9 22 0.30
10 18 0.24
11 19 0.26
13 6 0.08
14 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTAAATTT
Found at i:19277925 original size:44 final size:45
Alignment explanation
Indices: 19277847--19277931 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 45
19277837 TATTTATAAA
* * * *
19277847 AAATTTAAATTTTTAAATTTTTTATATATTTTTTAGATTTTTTTT
1 AAATATAAATTTTTAAATTTTTTATAAATATTTTAAATTTTTTTT
19277892 AAATATAAA-TTTTAGAA-TTTTTATAAATATTTTAAATTTT
1 AAATATAAATTTTTA-AATTTTTTATAAATATTTTAAATTTT
19277932 AAAAATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 25 0.71
45 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (45 bp):
AAATATAAATTTTTAAATTTTTTATAAATATTTTAAATTTTTTTT
Found at i:19277931 original size:19 final size:20
Alignment explanation
Indices: 19277900--19277963 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
19277890 TTAAATATAA
*
19277900 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AATTTTTAAAAATT
19277920 ATTTTAAA-TTTTAAAAATT
1 ATTTTAAATTTTTAAAAATT
* *
19277939 ATTTTCAATTTTTGAAAATT
1 ATTTTAAATTTTTAAAAATT
19277959 ATTTT
1 ATTTT
19277964 GATTATTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 21 0.54
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTAAATTTTTAAAAATT
Found at i:19277956 original size:20 final size:18
Alignment explanation
Indices: 19277907--19277963 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
19277897 TAAATTTTAG
19277907 AATTTTTATAAA-TATTTT
1 AATTTTTA-AAATTATTTT
*
19277925 AAATTTTAAAAATTATTTT
1 -AATTTTTAAAATTATTTT
19277944 CAATTTTTGAAAATTATTTT
1 -AATTTTT-AAAATTATTTT
19277964 GATTATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.09
19 19 0.58
20 11 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTTTAAAATTATTTT
Found at i:19284234 original size:21 final size:20
Alignment explanation
Indices: 19284186--19284234 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
19284176 TTAAATTATG
19284186 TAATTTGGATTTATAAACTT
1 TAATTTGGATTTATAAACTT
*
19284206 TAAGTTTGGATTTTTAAACTT
1 TAA-TTTGGATTTATAAACTT
19284227 TATATTTG
1 TA-ATTTG
19284235 AATTATACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 22 0.85
22 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (20 bp):
TAATTTGGATTTATAAACTT
Found at i:19292574 original size:14 final size:14
Alignment explanation
Indices: 19292557--19292586 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19292547 TTTAAACTCT
*
19292557 AAAAGATAAATATA
1 AAAAGATAAACATA
19292571 AAAAGATAAACATA
1 AAAAGATAAACATA
19292585 AA
1 AA
19292587 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:19295424 original size:21 final size:21
Alignment explanation
Indices: 19295398--19295439 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19295388 ATAGATGCCT
19295398 CAGTTT-TCTTTTGAAAATCTA
1 CAGTTTGT-TTTTGAAAATCTA
19295419 CAGTTTGTTTTTGAAAATCTA
1 CAGTTTGTTTTTGAAAATCTA
19295440 TAGATTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (21 bp):
CAGTTTGTTTTTGAAAATCTA
Found at i:19303412 original size:18 final size:19
Alignment explanation
Indices: 19303381--19303418 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19303371 CATCGTTTTG
*
19303381 TGGTGATGTCACAA-TCAT
1 TGGTGATGTAACAATTCAT
*
19303399 TGGTGTTGTAACAATTCAT
1 TGGTGATGTAACAATTCAT
19303418 T
1 T
19303419 TTTTAGTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (19 bp):
TGGTGATGTAACAATTCAT
Found at i:19304030 original size:15 final size:15
Alignment explanation
Indices: 19304010--19304040 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19304000 TTTCACTTTT
19304010 CGTTAACTTAAAATC
1 CGTTAACTTAAAATC
19304025 CGTTAACTTAAAATC
1 CGTTAACTTAAAATC
19304040 C
1 C
19304041 CCTTTATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (15 bp):
CGTTAACTTAAAATC
Found at i:19306112 original size:59 final size:59
Alignment explanation
Indices: 19305925--19306146 Score: 202
Period size: 58 Copynumber: 3.8 Consensus size: 59
19305915 TTGGGATTGG
* * * ** * *
19305925 AAATGGAATTTTAGG-CATTCGAGGGTAAAACGGTAATTTTTTCAAAAATCGGGATCAA
1 AAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAATATCGAGATCAA
* * * * *
19305983 AAATAG-ATTTTTTGACATTCGAGGGTAGAATGGTAATTTTTAGAAATATCGAGATCAAA
1 AAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAATATCGAGATC-AA
* * * *
19306042 AAATGAAATTTTTGGACATTCGGGGGTAAAATAGTGATTTTTGGTGAA-ATC-AGAGTCAA
1 AAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGG-AAATATCGAGA-TCAA
* **
19306101 AAATGGAA-TTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAA
1 AAATGGAATTTTTGGACA-TTCGGGGGTAAAATGGTAATTTTTGGAA
19306147 CTTTAGGGGT
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
57 6 0.05
58 49 0.37
59 40 0.30
60 36 0.27
61 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (59 bp):
AAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAATATCGAGATCAA
Found at i:19306131 original size:29 final size:29
Alignment explanation
Indices: 19306099--19306229 Score: 160
Period size: 29 Copynumber: 4.5 Consensus size: 29
19306089 AATCAGAGTC
19306099 AAAAATGGAA-TTTTGGAAAGTTTAGGGGT
1 AAAAATGGAATTTTTGG-AAGTTTAGGGGT
*
19306128 -AAAATGGTAATTTTTGGAACTTTAGGGGT
1 AAAAATGG-AATTTTTGGAAGTTTAGGGGT
* * *
19306157 AAAAATGTAATTTTTGGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGAAGTTT-AGGGGT
19306187 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
1 AAAAATGGAATTTTTGGAAGTTTAG-GGGT
*
19306216 AAAAATGTAATTTT
1 AAAAATGGAATTTT
19306230 AAAGAAGTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
28 7 0.08
29 43 0.49
30 38 0.43
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:19306172 original size:59 final size:59
Alignment explanation
Indices: 19306099--19306229 Score: 171
Period size: 59 Copynumber: 2.2 Consensus size: 59
19306089 AATCAGAGTC
* *
19306099 AAAAATGGAA-TTTTGGAAAGTTT-AGGGGT-AAAATGGTAATTTTTGGAACTTT-AGGGGT
1 AAAAATGTAATTTTTGG-AAGTTTCAAGGGTAAAAATGG-AATTTTTGGAACTTTGA-GGGT
* *
19306157 AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGGAATTTTTGGAACTTTGAGGGT
19306216 AAAAATGTAATTTT
1 AAAAATGTAATTTT
19306230 AAAGAAGTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
58 15 0.23
59 42 0.65
60 8 0.12
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (59 bp):
AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGGAATTTTTGGAACTTTGAGGGT
Found at i:19306251 original size:30 final size:30
Alignment explanation
Indices: 19306203--19306269 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
19306193 GGAATTTTTG
**
19306203 GAAGTTTGAGGGTAAAAATGTAATTTTAAA
1 GAAGTTTGAGGGTAAAAATACAATTTTAAA
** * **
19306233 GAAGTTTTTGGGTCAAAATACAATTTTGGA
1 GAAGTTTGAGGGTAAAAATACAATTTTAAA
19306263 GAAGTTT
1 GAAGTTT
19306270 AAGGACCTCC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
GAAGTTTGAGGGTAAAAATACAATTTTAAA
Found at i:19306258 original size:59 final size:59
Alignment explanation
Indices: 19306136--19306270 Score: 139
Period size: 59 Copynumber: 2.3 Consensus size: 59
19306126 GTAAAATGGT
* ** * **
19306136 AATTTTTGGAACTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGG
1 AATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTAAGAAGTTTCAAGGGTAAAAATAC
** *
19306195 AATTTTTGGAAGTTT-GAGGGTAAAAATGTAATTTTAAAGAAGTTT-TTGGGTCAAAATAC
1 AATTTTTGGAAGTTTAG-GGGTAAAAATGTAATTTT-AAGAAGTTTCAAGGGTAAAAATAC
*
19306254 AATTTTGGAGAAGTTTA
1 AATTTTTG-GAAGTTTA
19306271 AGGACCTCCA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 1 0.02
59 47 0.76
60 14 0.23
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (59 bp):
AATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTAAGAAGTTTCAAGGGTAAAAATAC
Found at i:19308728 original size:201 final size:201
Alignment explanation
Indices: 19308001--19309060 Score: 1253
Period size: 201 Copynumber: 5.2 Consensus size: 201
19307991 CTGGTTTCAT
* * * * **
19308001 TGAGTTGGTATACTTCTCTGTATCTCATTAGGAAGATGATCGCCTCACTTCTTTTGATCCATTTC
1 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTC
* * * * * * * *
19308066 TCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCGGGAAGATAACCACT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
* ** * *
19308131 TTATTGCTTAAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGGTTCAAAGACTTGCTCATAT
131 TTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTCATAT
*
19308196 CGAG-CG
195 CGAGCCC
* * * * * ** *
19308202 TGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATC
1 TGA----G--TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATC
* * * * * *
19308267 CGCTTCTCTGTATCTCAGCAGGAAGACGAATTTGGTCCACTTCTTAGTATGTTATTAAGAAGCTA
60 CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
* * *
19308332 ACCATTTTATTACTTCGGCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGGTTTGAAGACTTGC
125 ACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGC
**
19308397 TCATATCGAGCATAGGTT
189 TCATATCGAGC-----CC
* * * * * * ** *
19308415 TGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATTGCTTGTTTCAATCCGCTTC
1 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTC
* * * * * *
19308480 TCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTTAGTGTCTCATTAGGAAGCTATCCATT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
* * * *
19308545 TTATTACTTCGACCCGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATC
131 TTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATC
19308610 GAGCCC
196 GAGCCC
* *
19308616 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTGATCCACTTC
1 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTC
* * * * * * *
19308681 TCTGTGTTTCATCAGGAAAACAAATTTGGTTCACTTCTCCGTGTCTCATCAGGAAGCTAACCATT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
*
19308746 TTATTACTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTCATATC
131 TTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATC
*
19308811 AAGCCC
196 GAGCCC
* * * *
19308817 TGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTTAATTCGCTTC
1 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTC
*
19308882 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTAACCATT
66 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
* *
19308947 TTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCAT-
131 TTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCT--CATA
*
19309011 TTGAG-CC
194 TCGAGCCC
*
19309018 TCGAGTTGGCATACTTCTCTGTATCTCATCAGGAAGATGACCG
1 T-GAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCG
19309061 TCTCGCTGTT
Statistics
Matches: 735, Mismatches: 109, Indels: 29
0.84 0.12 0.03
Matches are distributed among these distances:
201 351 0.48
202 40 0.05
203 3 0.00
205 1 0.00
206 24 0.03
207 313 0.43
213 3 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (201 bp):
TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATC
GAGCCC
Found at i:19309254 original size:78 final size:78
Alignment explanation
Indices: 19309138--19309281 Score: 191
Period size: 78 Copynumber: 1.8 Consensus size: 78
19309128 ACCAGGTTCG
* ** * *
19309138 GGGTAAAAGATCAAATGGCTGCAATCTACCCCTGGCTCGGGGTAAGAGATTGGTTGACGATGATC
1 GGGTAAAAGATCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGATTGACAATGATC
19309203 TATCCTAGACTTA
66 TATCCTAGACTTA
* * * *
19309216 GGGTAAAAGATCAAATGG-TCACAATTTTCCCCAAGCTCGGGGTAAGAGTTTGATTGATAATGAT
1 GGGTAAAAGATCAAATGGCT-ACAATCTACCCCAAGCTCGGGGTAAGAGATTGATTGACAATGAT
19309280 CT
65 CT
19309282 GCCCCAAGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 1 0.02
78 55 0.98
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (78 bp):
GGGTAAAAGATCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGATTGACAATGATC
TATCCTAGACTTA
Found at i:19309297 original size:78 final size:78
Alignment explanation
Indices: 19309138--19309304 Score: 176
Period size: 78 Copynumber: 2.1 Consensus size: 78
19309128 ACCAGGTTCG
* ** * *
19309138 GGGTAAAAGATCAAATGGCTGCAATCTACCCCTGGCTCGGGGTAAGAGATTGGTTGACGATGATC
1 GGGTAAAAGATCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGATTGACAATGATC
* * *
19309203 TATCCTAGACTTA
66 TACCCAAGACTCA
* * * *
19309216 GGGTAAAAGATCAAATGG-TCACAATTTTCCCCAAGCTCGGGGTAAGAGTTTGATTGATAATGAT
1 GGGTAAAAGATCAAATGGCT-ACAATCTACCCCAAGCTCGGGGTAAGAGATTGATTGACAATGAT
*
19309280 CTGCCCCAAG-CTCA
65 CT-ACCCAAGACTCA
*
19309294 GGGTAATAGAT
1 GGGTAAAAGAT
19309305 TGGTTGATGA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
77 1 0.01
78 68 0.93
79 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (78 bp):
GGGTAAAAGATCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGATTGACAATGATC
TACCCAAGACTCA
Found at i:19309888 original size:150 final size:150
Alignment explanation
Indices: 19309662--19310157 Score: 703
Period size: 150 Copynumber: 3.3 Consensus size: 150
19309652 TTCCCTTCAA
* * * *
19309662 ATCTTCGTGGTACTGGATCCGTCGTTGCGG-CTTAGATCTTTCCCTT-GTGTCTTCATGATACTG
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
* * * *
19309725 GATTCATCGTTGCGACTTAAATCTTTCCTTTCCTGTCTTCTGAGGTACACGGTCTGCCGTAGCGA
66 GATTCATCGTTGCGGCTTAAATCTTTCCTTTCTTGTCTTCTGAGGTACATGGTCCGCCGTAGCGA
* *
19309790 TTTAAACCTTTCCCTTTTGT
131 CTTAGACCTTTCCCTTTTGT
* * *
19309810 ATCTTTGTGGTACTGGTTCCGCCATTACGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
* * * * * *
19309875 GGTTCGTCATTGCGGCTTAAATCTTTCCCTTCTTATCTTCTGAGGTACATGGTCCGCCGTTA-AG
66 GATTCATCGTTGCGGCTTAAATCTTTCCTTTCTTGTCTTCTGAGGTACATGGTCCGCCG-TAGCG
19309939 ACTTAGACCTTTCCCTTTTGT
130 ACTTAGACCTTTCCCTTTTGT
* *
19309960 ATTTTTGTGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
* ** *
19310025 GATTCACCGTTATGGCTTAAATCTTTCCCTTT-TTGTCTTCTGAGGTACATGGTCCGCCGTTGCG
66 GATTCATCGTTGCGGCTTAAATCTTT-CCTTTCTTGTCTTCTGAGGTACATGGTCCGCCGTAGCG
19310089 ACTTAGACCTTTCCCTTTTGT
130 ACTTAGACCTTTCCCTTTTGT
**
19310110 ATCTTTGTGGTACTGGATATGCCGTTGCGGTCTTAGATCTTTCCCTTC
1 ATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTC
19310158 GTGTTTCTGT
Statistics
Matches: 305, Mismatches: 38, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
148 25 0.08
149 17 0.06
150 257 0.84
151 6 0.02
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (150 bp):
ATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
GATTCATCGTTGCGGCTTAAATCTTTCCTTTCTTGTCTTCTGAGGTACATGGTCCGCCGTAGCGA
CTTAGACCTTTCCCTTTTGT
Found at i:19310169 original size:50 final size:51
Alignment explanation
Indices: 19309663--19310174 Score: 337
Period size: 50 Copynumber: 10.3 Consensus size: 51
19309653 TCCCTTCAAA
* *
19309663 TCTTC-GTGGTACTGGATCCGTCGTTGCGG-CTTAGATCTTTCCCTT-GTG
1 TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * * ** * * * *
19309711 TCTTC-ATGATACTGGATTCATCGTTGC-GACTTAAATCTTTCCTTTCCTG
1 TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * * * * * *
19309760 TCTTCTGAGGTACACGG-TCTGCCGTAGCGAT-TTAAACCTTTCCCTT-TTG
1 TCTTCTGTGGTAC-TGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * * *
19309809 TATCTT-TGTGGTACTGGTTCCGCCATTACGGTCTTAGATCTTTCCCTTCATG
1 --TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * * * * * *
19309861 TCTTC-ATGGTACTGGGTTCGTCATTGCGG-CTTAAATCTTTCCCTTCTTA
1 TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* ** * *
19309910 TCTTCTGAGGTACATGG-TCCGCCGTT-AAGACTTAGACCTTTCCCTT-TTG
1 TCTTCTGTGGTAC-TGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * * *
19309959 TATTTTTGTGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCTTCATG
1 T-CTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * * ** * *
19310011 TCTTC-ATGGTACTGGATTCACCGTTATGG-CTTAAATCTTTCCCTTTTTG
1 TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
* * *
19310060 TCTTCTGAGGTACATGG-TCCGCCGTTGC-GACTTAGACCTTTCCCTT-TTG
1 TCTTCTGTGGTAC-TGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
** *
19310109 TATCTT-TGTGGTACTGGATATGCCGTTGCGGTCTTAGATCTTTCCCTTCGTG
1 --TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
*
19310161 T-TTCTGTGGCACTG
1 TCTTCTGTGGTACTG
19310175 AGACCTGTAG
Statistics
Matches: 355, Mismatches: 82, Indels: 52
0.73 0.17 0.11
Matches are distributed among these distances:
47 1 0.00
48 37 0.10
49 71 0.20
50 176 0.50
51 63 0.18
52 7 0.02
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.41
Consensus pattern (51 bp):
TCTTCTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCTTG
Found at i:19311295 original size:6 final size:5
Alignment explanation
Indices: 19311285--19311413 Score: 97
Period size: 5 Copynumber: 25.0 Consensus size: 5
19311275 TCACCTCGAC
* * * *
19311285 CTTTC CTTTT CTTTTT CTTTTT TTTTT CTCTCT CTTTT TTTTT CTTTTT
1 CTTTT CTTTT C-TTTT C-TTTT CTTTT CT-TTT CTTTT CTTTT C-TTTT
*
19311334 CTTCTT CTTCTT -TTTT CTTTT CTCTTT CTTCTT CTTCTT CTTCT -TTTT
1 CTT-TT CTT-TT CTTTT CTTTT CT-TTT CTT-TT CTT-TT CTTTT CTTTT
19311382 CTTTT CTTTT -TTTT C-TTT -TTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
19311414 ATTCATTGAA
Statistics
Matches: 104, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
4 15 0.14
5 46 0.44
6 43 0.41
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:19311331 original size:27 final size:27
Alignment explanation
Indices: 19311291--19311413 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
19311281 CGACCTTTCC
19311291 TTTTCTTTTTCTTTTTTTTTTCTCTCTCT
1 TTTTC-TTTTCTTTTTTTTTTCT-TCTCT
*
19311320 TTTT-TTTTCTTTTTCTTCTTCTTCT-T
1 TTTTCTTTTCTTTTT-TTTTTCTTCTCT
19311346 TTTTCTTTTCTCTTTCTTCTTCTTCTTCTTCT
1 TTTTCTTTTCT-TTT-TT-TT-TTCTTC-TCT
* *
19311378 TTTTCTTTTCTTTTTTTTCTTTTTTTC-
1 TTTTCTTTTCTTTTTTTT-TTCTTCTCT
19311405 TTTTCTTTT
1 TTTTCTTTT
19311414 ATTCATTGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
26 5 0.06
27 28 0.34
28 12 0.15
29 13 0.16
30 8 0.10
31 4 0.05
32 12 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTCTTTTCTTTTTTTTTTCTTCTCT
Found at i:19311334 original size:39 final size:38
Alignment explanation
Indices: 19311286--19311413 Score: 150
Period size: 39 Copynumber: 3.2 Consensus size: 38
19311276 CACCTCGACC
*
19311286 TTTCCTTTTCTTTTTCTTTTTTTTTTCTCTCTCTTTTT-T
1 TTTCTTTTTCTTTTTCTTTTTTTTTT-T-TCTCTTTTTCT
*
19311325 TTTCTTTTTCTTCTTCTTCTTTTTTCTTTTCTCTTTCTTCT
1 TTTCTTTTTCTTTTTCTT-TTTTTT-TTTTCTCTTT-TTCT
* *
19311366 TCTTCTTCTTCTTTTTCTTTTCTTTTTTTTCTTTTTTTCT
1 T-TTCTTTTTCTTTTTCTTTT-TTTTTTTTCTCTTTTTCT
19311406 TTTCTTTT
1 TTTCTTTT
19311414 ATTCATTGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
39 29 0.38
40 14 0.18
41 15 0.19
42 19 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (38 bp):
TTTCTTTTTCTTTTTCTTTTTTTTTTTTCTCTTTTTCT
Found at i:19311338 original size:3 final size:3
Alignment explanation
Indices: 19311326--19311411 Score: 69
Period size: 3 Copynumber: 30.7 Consensus size: 3
19311316 CTCTTTTTTT
*
19311326 TTC TTT TTC TTC TTC TTC TT- TT- TTC TT- TTC -TC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
* * * *
19311368 TTC TTC TTC TTT TTC TT- TTC TTT TTT TTC TT- TTT TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19311412 TTATTCATTG
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
2 14 0.20
3 53 0.77
4 2 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (3 bp):
TTC
Found at i:19316953 original size:59 final size:58
Alignment explanation
Indices: 19316845--19316965 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 58
19316835 AAACGACAAT
* *
19316845 TTTTAGAGAAATCGGGATCAAAAATAGAATTTTGGACATTTGAGGGTAAAATGGTAA-
1 TTTTAGAGAAATCGAGATCAAAAATAGAATTTTGGACATTCGAGGGTAAAATGGTAAG
19316902 TTTTAGA-AATATCGAGATCATAAAAT-GAAATTTTTGGACATTCG-GTGGTAAAATGGTAAG
1 TTTTAGAGAA-ATCGAGATCA-AAAATAG-AA-TTTTGGACATTCGAG-GGTAAAATGGTAAG
19316962 TTTT
1 TTTT
19316966 GGAAGTTCCG
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
56 2 0.04
57 17 0.30
58 8 0.14
59 25 0.45
60 4 0.07
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (58 bp):
TTTTAGAGAAATCGAGATCAAAAATAGAATTTTGGACATTCGAGGGTAAAATGGTAAG
Found at i:19316998 original size:30 final size:28
Alignment explanation
Indices: 19316923--19317031 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 28
19316913 TCGAGATCAT
*
19316923 AAAATGAAATTTTTGGACA-TTCGGTGGT-
1 AAAATGGAATTTTTGGA-AGTTCGG-GGTA
*
19316951 AAAATGGTAAGTTTTGGAAGTTCCGGGGTAA
1 AAAATGG-AATTTTTGGAAGTT-CGGGGT-A
**
19316982 AAAATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGTA
* *
19317011 AAAATGTAATTTTTGAAAGTT
1 AAAATGGAATTTTTGGAAGTT
19317032 TTAGAGTCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
28 9 0.13
29 32 0.47
30 18 0.26
31 9 0.13
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:19317052 original size:30 final size:28
Alignment explanation
Indices: 19316981--19317054 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
19316971 TTCCGGGGTA
* *
19316981 AAAAATGGAATTTTTGGAAGTTTAAGGGT
1 AAAAAT-GAATTTTTGAAAGTTTAAGAGT
*
19317010 AAAAATGTAATTTTTGAAAGTTTTAGAGT
1 AAAAATG-AATTTTTGAAAGTTTAAGAGT
19317039 CAAAAATAGAATTTTT
1 -AAAAAT-GAATTTTT
19317055 AGAGGTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 24 0.62
30 13 0.33
31 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (28 bp):
AAAAATGAATTTTTGAAAGTTTAAGAGT
Found at i:19317073 original size:60 final size:60
Alignment explanation
Indices: 19316981--19317127 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
19316971 TTCCGGGGTA
* * *
19316981 AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGA-AAGTTTTAGAGTC
1 AAAAATAGAATTTTTAGAAGTTTAAGGGTAAAAATGTAATTTTGGAGAAGTTTTAGAGTC
* * *
19317040 AAAAATAGAATTTTTAGAGGTTTGAGGGGTAAAAATGTAATTTTGGAGAAGTTTGT-GGGTC
1 AAAAATAGAATTTTTAGAAGTTT-AAGGGTAAAAATGTAATTTTGGAGAAGTTT-TAGAGTC
* *
19317101 -AAAATACAATTTTGGAGAAGTTTAAGG
1 AAAAATAGAATTTT-TAGAAGTTTAAGG
19317128 ACCTCCAGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
59 20 0.27
60 36 0.49
61 17 0.23
62 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (60 bp):
AAAAATAGAATTTTTAGAAGTTTAAGGGTAAAAATGTAATTTTGGAGAAGTTTTAGAGTC
Found at i:19317074 original size:30 final size:29
Alignment explanation
Indices: 19316951--19317083 Score: 94
Period size: 30 Copynumber: 4.4 Consensus size: 29
19316941 ATTCGGTGGT
* **
19316951 AAAATGGTAAGTTTTGGAAGTTCCGGGGTAA
1 AAAAT-GTAA-TTTTTGAAGTTTAGGGGTAA
* *
19316982 AAAATGGAATTTTTGGAAGTTTAAGGGT-A
1 AAAATGTAATTTTT-GAAGTTTAGGGGTAA
* *
19317011 AAAATGTAATTTTTGAAAGTTTTA-GAGTCA
1 AAAATGTAATTTTTG-AAG-TTTAGGGGTAA
*
19317041 AAAATAG-AATTTTTAGAGGTTTGAGGGGT-A
1 AAAAT-GTAATTTTT-GAAGTTT-AGGGGTAA
19317071 AAAATGTAATTTT
1 AAAATGTAATTTT
19317084 GGAGAAGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
28 1 0.01
29 28 0.33
30 45 0.54
31 10 0.12
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAGTTTAGGGGTAA
Found at i:19317105 original size:30 final size:30
Alignment explanation
Indices: 19316976--19317123 Score: 108
Period size: 30 Copynumber: 4.9 Consensus size: 30
19316966 GGAAGTTCCG
* * **
19316976 GGGTAAAAAATGGAATTTTTG-GAAGTTTAA
1 GGGT-AAAAATGTAATTTTGGAGAAGTTTGT
*
19317006 GGGTAAAAATGTAATTTTTGA-AAGTTT-T
1 GGGTAAAAATGTAATTTTGGAGAAGTTTGT
* * * *
19317034 AGAGTCAAAAATAG-AATTTT-TAGAGGTTTGAG
1 -GGGT-AAAAAT-GTAATTTTGGAGAAGTTTG-T
19317066 GGGTAAAAATGTAATTTTGGAGAAGTTTGT
1 GGGTAAAAATGTAATTTTGGAGAAGTTTGT
* **
19317096 GGGTCAAAATACAATTTTGGAGAAGTTT
1 GGGTAAAAATGTAATTTTGGAGAAGTTT
19317124 AAGGACCTCC
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
29 26 0.27
30 58 0.60
31 12 0.12
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTGGAGAAGTTTGT
Found at i:19319547 original size:158 final size:158
Alignment explanation
Indices: 19319249--19319576 Score: 381
Period size: 158 Copynumber: 2.1 Consensus size: 158
19319239 TAACGTCTCC
* * * * * * *
19319249 ATAACATGTAGTGTTCACACGAGCGGTGAAATAGGTTTGCTCACACGAGCTGTGGGTCGAGATGT
1 ATAACCTGTAATGCTCACACGAGCGATGAAATAGGTCTGCTCACACGAGCTATGAGTCGAGATGT
* * * * * * *
19319314 TAGGCTAAACGATGCTGCTGACACAAGCTATGGAGAATCTGTAATAAATGCGGGATCTCATCCAT
66 TAAGCTAAACGATGCTGCTCACACAAGCTATGGAGAATCCGAAAGAAATGCGGAATCTCAGCCAT
* * * *
19319379 CGGTAGGACATCTAGGACCTGCATCCAT
131 CGGTAAGACATCTAAGACCAGCACCCAT
* * * *
19319407 ATAACCTGTAATGCTCACACGAGCTATGAAGTGGGTCTGCTCACACGAGTTATGAGTCGAGATGT
1 ATAACCTGTAATGCTCACACGAGCGATGAAATAGGTCTGCTCACACGAGCTATGAGTCGAGATGT
* * * * *
19319472 TAAGCTACATGATGTTGCTCACACGAGCTGTGGAGAATCCGAAAGAAATGTC-GAATCTCAGCCA
66 TAAGCTAAACGATGCTGCTCACACAAGCTATGGAGAATCCGAAAGAAATG-CGGAATCTCAGCCA
19319536 -CTGGTAAGACATCTAAGACCAGCACCCAT
130 TC-GGTAAGACATCTAAGACCAGCACCCAT
19319565 ATAACCTGTAAT
1 ATAACCTGTAAT
19319577 CCTGAAATCA
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
157 1 0.01
158 139 0.99
159 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (158 bp):
ATAACCTGTAATGCTCACACGAGCGATGAAATAGGTCTGCTCACACGAGCTATGAGTCGAGATGT
TAAGCTAAACGATGCTGCTCACACAAGCTATGGAGAATCCGAAAGAAATGCGGAATCTCAGCCAT
CGGTAAGACATCTAAGACCAGCACCCAT
Found at i:19322012 original size:41 final size:41
Alignment explanation
Indices: 19321963--19322096 Score: 133
Period size: 41 Copynumber: 3.3 Consensus size: 41
19321953 ATTTGAGCTT
* *
19321963 GTGAATTGAATCAGGCCTTGAGCCTAGCAGGATTTGTGTCG
1 GTGAATTGAATCAGGCCTTGAGCCTAGCAGGCTTAGTGTCG
* * * * * * * * *
19322004 GTGGATTGATTCAAGCTTTGTGCCTAACAGGCTTCGAGCCG
1 GTGAATTGAATCAGGCCTTGAGCCTAGCAGGCTTAGTGTCG
* * *
19322045 GTCAATTGAATCAGGTCTTGAGCCTAGCAAGCTTAGTGTCG
1 GTGAATTGAATCAGGCCTTGAGCCTAGCAGGCTTAGTGTCG
*
19322086 ATGAATTGAAT
1 GTGAATTGAAT
19322097 AAGATAAATT
Statistics
Matches: 69, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (41 bp):
GTGAATTGAATCAGGCCTTGAGCCTAGCAGGCTTAGTGTCG
Found at i:19329994 original size:27 final size:27
Alignment explanation
Indices: 19329935--19329996 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
19329925 ATGGGAAAGA
*
19329935 CGGCACCAGTGGTGGCCATGTCATAGG
1 CGGCACCAGTGGTGGCCATCTCATAGG
*
19329962 CAGCACCAGTGGT-GCCAATCTCATAGG
1 CGGCACCAGTGGTGGCC-ATCTCATAGG
*
19329989 TGGCACCA
1 CGGCACCA
19329997 ATAGTGCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.18
Consensus pattern (27 bp):
CGGCACCAGTGGTGGCCATCTCATAGG
Found at i:19337794 original size:20 final size:20
Alignment explanation
Indices: 19337766--19337823 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
19337756 TCACATCAGT
*
19337766 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
19337786 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
*
19337806 AAATTATTATAAAATTAT
1 AAATTATTTTAAAATTAT
19337824 AATCATTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 7 0.22
19 2 0.06
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:19339681 original size:36 final size:36
Alignment explanation
Indices: 19339641--19339709 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
19339631 TGACTTTTGG
* *
19339641 GTCAATAGGGAGTAAAATGAGAATCATGACCTTCGA
1 GTCAACAGGGAGTAAAATGAGAATCAAGACCTTCGA
*
19339677 GTCAACAGGGAGTAAAATGAGCATCAAGACCTT
1 GTCAACAGGGAGTAAAATGAGAATCAAGACCTT
19339710 AGGTTCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (36 bp):
GTCAACAGGGAGTAAAATGAGAATCAAGACCTTCGA
Found at i:19339729 original size:36 final size:36
Alignment explanation
Indices: 19339641--19339729 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
19339631 TGACTTTTGG
* *
19339641 GTCAATAGGGAGTAAAATGAGAATCATGACCTTCGA
1 GTCAATAGGGAGTAAAATGAGAATCAAGACCTTAGA
* *
19339677 GTCAACAGGGAGTAAAATGAGCATCAAGACCTTAG-
1 GTCAATAGGGAGTAAAATGAGAATCAAGACCTTAGA
* *
19339712 GTTCAATAGAGAATAAAA
1 G-TCAATAGGGAGTAAAA
19339730 CAAAAACAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (36 bp):
GTCAATAGGGAGTAAAATGAGAATCAAGACCTTAGA
Found at i:19340328 original size:24 final size:21
Alignment explanation
Indices: 19340301--19340355 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
19340291 AACAATTTAA
19340301 GTATCGGTAGTTCTG-TATACTCAT
1 GTATCGGTAG-T-TGATATACT--T
*
19340325 GTATCGATAGTTGATATACTT
1 GTATCGGTAGTTGATATACTT
19340346 GTATCGGTAG
1 GTATCGGTAG
19340356 AAGTTGCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 10 0.36
22 2 0.07
23 7 0.25
24 9 0.32
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (21 bp):
GTATCGGTAGTTGATATACTT
Found at i:19352746 original size:22 final size:22
Alignment explanation
Indices: 19352721--19352768 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
19352711 TTGAGGAAGG
* *
19352721 GAAAA-GAGAAAAGAAGAAGGAG
1 GAAAAGGAAAAAAGAA-AAGAAG
19352743 GAAAAGGAAAAAAGAAAAGAAG
1 GAAAAGGAAAAAAGAAAAGAAG
19352765 GAAA
1 GAAA
19352769 GACCCGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (22 bp):
GAAAAGGAAAAAAGAAAAGAAG
Found at i:19353816 original size:16 final size:15
Alignment explanation
Indices: 19353795--19353824 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19353785 CAGTCAAAAA
19353795 ATATAATAATATGCTT
1 ATATAATAA-ATGCTT
19353811 ATATAATAAATGCT
1 ATATAATAAATGCT
19353825 GTGTTGGTCA
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:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ATATAATAAATGCTT
Found at i:19360487 original size:36 final size:36
Alignment explanation
Indices: 19360428--19360563 Score: 193
Period size: 36 Copynumber: 3.8 Consensus size: 36
19360418 AGTAACAGGA
* * *
19360428 ATGAACTTCGAGTCAACAAGGAGTAAAATAAGCATC
1 ATGACCTTCGGGTCAACAGGGAGTAAAATAAGCATC
* *
19360464 ATGACCTTCGGGTCAATAGGGAGTAAAATGAGCATC
1 ATGACCTTCGGGTCAACAGGGAGTAAAATAAGCATC
19360500 ATGACCTTCGGGTCAACAGGGAGTAAAATAAGCATC
1 ATGACCTTCGGGTCAACAGGGAGTAAAATAAGCATC
* *
19360536 ATGACC-TCAGGGTCAACAAGGAATAAAA
1 ATGACCTTC-GGGTCAACAGGGAGTAAAA
19360564 CGAAAAATGA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 2 0.02
36 88 0.98
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (36 bp):
ATGACCTTCGGGTCAACAGGGAGTAAAATAAGCATC
Found at i:19361272 original size:21 final size:21
Alignment explanation
Indices: 19361247--19361304 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
19361237 TAGATGTATG
*
19361247 ACTTGTTTCGGTAGAACAGTC
1 ACTTGTATCGGTAGAACAGTC
* * *
19361268 TCTTGTATCGGTAAAACTGTC
1 ACTTGTATCGGTAGAACAGTC
*
19361289 ACTTGTATCGATAGAA
1 ACTTGTATCGGTAGAA
19361305 GTCTGCACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:19361817 original size:32 final size:32
Alignment explanation
Indices: 19361776--19361876 Score: 141
Period size: 32 Copynumber: 3.1 Consensus size: 32
19361766 AGTTCTTTGT
* *
19361776 AATGTGTGAGAAGAAGTGGTGATAGATGGAAA
1 AATGGGTGAGAAGAAGTGGTGTTAGATGGAAA
19361808 AATGGGTGAGAAGAAGTGGTGTTAGATGGAAA
1 AATGGGTGAGAAGAAGTGGTGTTAGATGGAAA
*
19361840 AAT-GGTGAGAAGAAAAAGTGGTGTTATATGGAAA
1 AATGGGTGAGAAG---AAGTGGTGTTAGATGGAAA
19361874 AAT
1 AAT
19361877 AGGGAAGAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
31 9 0.14
32 33 0.52
34 21 0.33
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.23
Consensus pattern (32 bp):
AATGGGTGAGAAGAAGTGGTGTTAGATGGAAA
Found at i:19361947 original size:28 final size:28
Alignment explanation
Indices: 19361916--19361971 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
19361906 TTATTTAATA
* * *
19361916 ATTTTAATAATTTTATATTTAACAAAAT
1 ATTTTAAAAAATTTATATTTAAAAAAAT
19361944 ATTTTAAAAAATTTATATTTAAAAAAAT
1 ATTTTAAAAAATTTATATTTAAAAAAAT
19361972 TAATACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTTAAAAAATTTATATTTAAAAAAAT
Found at i:19361963 original size:16 final size:16
Alignment explanation
Indices: 19361941--19361985 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
19361931 TATTTAACAA
19361941 AATATTTTAAAAAATT
1 AATATTTTAAAAAATT
* *
19361957 TATATTTAAAAAAATT
1 AATATTTTAAAAAATT
19361973 AATACTTTTAAAA
1 AATA-TTTTAAAA
19361986 TCATTTGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATTTTAAAAAATT
Found at i:19362885 original size:36 final size:38
Alignment explanation
Indices: 19362829--19362903 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 38
19362819 GGGTTTTAAC
19362829 CTTTAGGGGGAAAATAGGAT-AAGATAAAAAG-TTTGGG
1 CTTTAGGGGGAAAATAGGATAAAG-TAAAAAGATTTGGG
* *
19362866 CTTT-GGGGGAAAATGGGATAAAGTTAAAAGATTTGGG
1 CTTTAGGGGGAAAATAGGATAAAGTAAAAAGATTTGGG
19362903 C
1 C
19362904 CTAGGTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 20 0.59
37 14 0.41
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (38 bp):
CTTTAGGGGGAAAATAGGATAAAGTAAAAAGATTTGGG
Found at i:19363659 original size:26 final size:26
Alignment explanation
Indices: 19363630--19363687 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
19363620 CCACAACTCG
*
19363630 TGTGAGTAAGCCCATTTCATAGCTCA
1 TGTGAGGAAGCCCATTTCATAGCTCA
19363656 TGTGAGGAAGCCCATTTCATAGCTCA
1 TGTGAGGAAGCCCATTTCATAGCTCA
19363682 TGTGAG
1 TGTGAG
19363688 AACTATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (26 bp):
TGTGAGGAAGCCCATTTCATAGCTCA
Found at i:19370336 original size:42 final size:41
Alignment explanation
Indices: 19370207--19370353 Score: 127
Period size: 41 Copynumber: 3.6 Consensus size: 41
19370197 ATGTAAAAAT
* ** * * *
19370207 GGAAGACTCGTGTCTCGGTTTGAGAA-GA-ATTTATATGAAT
1 GGAAGACTCATGTCTCGGAATGAGAATGAGA-ATATATTAAA
* * * * * * *
19370247 GGAAGACTCGTGACTCGAAACGAGCATGAGGATATATTTAA
1 GGAAGACTCATGTCTCGGAATGAGAATGAGAATATATTAAA
* *
19370288 GGAAGACTTATGTCTCGGGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGTCTCGGAATGAGAATGAGAATAT-ATTAAA
19370330 GGAAGACTCATGTCTCGGAATGAG
1 GGAAGACTCATGTCTCGGAATGAG
19370354 CGTGGGATTA
Statistics
Matches: 82, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
40 20 0.24
41 35 0.43
42 27 0.33
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.26
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGGAATGAGAATGAGAATATATTAAA
Found at i:19370371 original size:42 final size:41
Alignment explanation
Indices: 19370247--19370371 Score: 117
Period size: 42 Copynumber: 3.0 Consensus size: 41
19370237 TTATATGAAT
* * * * *
19370247 GGAAGACTCGTGACTCGAAACGAGCATGAGGATATATTT-AA
1 GGAAGACTCATGTCTCGGAATGAGCATG-GGATATGTTTAAA
* * * * *
19370288 GGAAGACTTATGTCTCGGGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGTCTCGGAATGAGCATG-GGATATGTTTAAA
*
19370330 GGAAGACTCATGTCTCGGAATGAGCGTGGGATTATGTTTAAA
1 GGAAGACTCATGTCTCGGAATGAGCATGGGA-TATGTTTAAA
19370372 AAAGAAGATT
Statistics
Matches: 66, Mismatches: 16, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
41 31 0.47
42 35 0.53
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGGAATGAGCATGGGATATGTTTAAA
Found at i:19371750 original size:25 final size:25
Alignment explanation
Indices: 19371722--19371777 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
19371712 TTATTATAAA
*
19371722 TTATTTGTTTTGTTTAAT-TTAATTT
1 TTATTTGGTTTG-TTAATATTAATTT
* *
19371747 TTATTTGGTTTGTTACTATTATTTT
1 TTATTTGGTTTGTTAATATTAATTT
19371772 TTATTT
1 TTATTT
19371778 AGTATAGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (25 bp):
TTATTTGGTTTGTTAATATTAATTT
Found at i:19371834 original size:5 final size:5
Alignment explanation
Indices: 19371823--19371862 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
19371813 GTTTCGTTGT
* *
19371823 TTTTAA TTTAA TTTTA TTTAA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
19371863 GTTAGTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 27 0.90
6 3 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:19371862 original size:10 final size:10
Alignment explanation
Indices: 19371823--19371861 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
19371813 GTTTCGTTGT
19371823 TTTTAATTTAA
1 TTTT-ATTTAA
19371834 TTTTATTTAA
1 TTTTATTTAA
*
19371844 TTTTATTTTA
1 TTTTATTTAA
19371854 TTTTATTT
1 TTTTATTT
19371862 TGTTAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:19371879 original size:21 final size:21
Alignment explanation
Indices: 19371853--19371896 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19371843 ATTTTATTTT
19371853 ATTTTATTTTGTTAGTAAGTA
1 ATTTTATTTTGTTAGTAAGTA
19371874 ATTTTATTTTGTTAGTAAGTA
1 ATTTTATTTTGTTAGTAAGTA
19371895 AT
1 AT
19371897 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTTTATTTTGTTAGTAAGTA
Found at i:19371905 original size:21 final size:21
Alignment explanation
Indices: 19371860--19371906 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
19371850 TTTATTTTAT
* * *
19371860 TTTGTTAGTAAGTAATTTTAT
1 TTTGTTAGTAAGTAATATAAA
19371881 TTTGTTAGTAAGTAATATAAA
1 TTTGTTAGTAAGTAATATAAA
19371902 TTTGT
1 TTTGT
19371907 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (21 bp):
TTTGTTAGTAAGTAATATAAA
Found at i:19377686 original size:24 final size:24
Alignment explanation
Indices: 19377659--19377706 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19377649 AAGAATATTC
* *
19377659 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
*
19377683 AAAGGTCAAAGGAGATGAAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
19377707 GAACATCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.19
Consensus pattern (24 bp):
AAAGGTCAAAGAAGATGAAAGGTT
Found at i:19379437 original size:51 final size:51
Alignment explanation
Indices: 19379318--19379505 Score: 198
Period size: 51 Copynumber: 3.6 Consensus size: 51
19379308 TTTCATTTAA
* * * ** * * *
19379318 TACTCACGATGACA-TATAATCATCGGACCTCTTATTCTGTATAGGAATTCATA
1 TACTCATGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATACATT
* * * * *
19379371 TACTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGATACATT
1 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATACATT
* *
19379422 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATACATT
19379473 TACTCATGATGACACTTAGTCATCGGATCCTTT
1 TACTCATGATGACACTTAGTCATCGGA-CCTTT
19379506 CATTTATAGC
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
51 76 0.66
52 13 0.11
53 25 0.22
54 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATACATT
Found at i:19382267 original size:144 final size:136
Alignment explanation
Indices: 19382060--19382527 Score: 472
Period size: 147 Copynumber: 3.3 Consensus size: 136
19382050 AGGGAAGGTA
* * *
19382060 TTTTTTTGTTGTTTTCAATTTATTTTAAAATTATCTTATTTTTAATTATTATAAAATTTAGTTTA
1 TTTTTTTGTTGTTTTTAATTTATTTTAAAATTA--TT-TTTTAAATTATTATAAAGTTTAGTTTA
** * *
19382125 ATGTTTATGGTTTAATATAATTTTTTTTTGTTTAGTAGAGTAGATTAAAGGGAAAAAA-CTAAAA
63 ATGTTTATGGTTTGTTATAA-TTTTTTTTGTTTAGTAGAGTAAATTAAAGGGAAAAAAGCCAAAA
** *
19382189 GAGGTAATTTTTTGT
127 GA-G--A-GGTAT-T
19382204 TATTGTTGTTGTTGTTTTTAATTTATTTTAAAATTATTTTTTAAATTATTATAAAGTTTAGTTTA
1 T-TT-TT-TTGTTGTTTTTAATTTATTTTAAAATTATTTTTTAAATTATTATAAAGTTTAGTTTA
* * *
19382269 ATGTTTATGATTTGTTATAAATTTTTTTGTTTAATAGAGTAAATTAAAGGGAAAAAAGCCAAAAG
63 ATGTTTATGGTTTGTTATAATTTTTTTTGTTTAGTAGAGTAAATTAAAGGGAAAAAAGCCAAAAG
19382334 AGAGGTATT
128 AGAGGTATT
* *
19382343 TTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTT
1 TTTTTTTGTTGTTTTTAATTTATTTTAAAATTATTTT-TTA--AATTATTAT-AA--A---GTTT
*
19382408 AGCTTAATGTTTATGTGATTTGTTATAATTTTTTTTGTTTAGTA-AGATAAATTAAAGGGAATAA
57 AGTTTAATGTTTATG-G-TTTGTTATAATTTTTTTTGTTTAGTAGAG-TAAATTAAAGGGAA-AA
* * * **
19382472 AAGGCTAAAACAAAGGTAAA
118 AA-GCCAAAAGAGAGGTATT
* * *
19382492 TTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTT
1 TTTTTTTGTTGTTTTTAATTTATTTTAAAATTATTT
19382528 ATTTTGTTTT
Statistics
Matches: 281, Mismatches: 25, Indels: 31
0.83 0.07 0.09
Matches are distributed among these distances:
136 30 0.11
137 5 0.02
138 2 0.01
139 11 0.04
140 4 0.01
141 1 0.00
142 1 0.00
143 35 0.12
144 50 0.18
145 22 0.08
146 4 0.01
147 65 0.23
148 4 0.01
149 47 0.17
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (136 bp):
TTTTTTTGTTGTTTTTAATTTATTTTAAAATTATTTTTTAAATTATTATAAAGTTTAGTTTAATG
TTTATGGTTTGTTATAATTTTTTTTGTTTAGTAGAGTAAATTAAAGGGAAAAAAGCCAAAAGAGA
GGTATT
Found at i:19382521 original size:149 final size:145
Alignment explanation
Indices: 19382259--19382527 Score: 405
Period size: 149 Copynumber: 1.8 Consensus size: 145
19382249 TTATTATAAA
*
19382259 GTTTAGTTTAATGTTTATGATTTGTTATAAATTTTTTTGTTTAATAGAGTAAATTAAAGGGAAAA
1 GTTTAGCTTAATGTTTATGATTTGTTATAAATTTTTTTGTTTAATAGAGTAAATTAAAGGGAAAA
* * ** *
19382324 AAGCCAAAAGAGAGGTATTTTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAAT
66 AAGCCAAAACAAAGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAAT
19382389 TATTATAAATTATTT
131 TATTATAAATTATTT
* *
19382404 GTTTAGCTTAATGTTTATGTGATTTGTTATAATTTTTTTTGTTTAGTA-AGATAAATTAAAGGGA
1 GTTTAGCTTAATGTTTA--TGATTTGTTATAAATTTTTTTGTTTAATAGAG-TAAATTAAAGGGA
*
19382468 ATAAAAGGCTAAAACAAAGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTT
63 A-AAAA-GCCAAAACAAAGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTT
19382528 ATTTTGTTTT
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
145 16 0.15
146 2 0.02
147 41 0.37
148 4 0.04
149 47 0.43
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (145 bp):
GTTTAGCTTAATGTTTATGATTTGTTATAAATTTTTTTGTTTAATAGAGTAAATTAAAGGGAAAA
AAGCCAAAACAAAGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAAT
TATTATAAATTATTT
Found at i:19382804 original size:21 final size:21
Alignment explanation
Indices: 19382779--19382824 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
19382769 GATTATCCTC
19382779 ACATATCAAACACAGTCAATA
1 ACATATCAAACACAGTCAATA
* *
19382800 ACATATTAAACACGGTCAATA
1 ACATATCAAACACAGTCAATA
19382821 ACAT
1 ACAT
19382825 GGTAATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.07, T:0.22
Consensus pattern (21 bp):
ACATATCAAACACAGTCAATA
Found at i:19390778 original size:147 final size:144
Alignment explanation
Indices: 19390626--19390907 Score: 383
Period size: 146 Copynumber: 1.9 Consensus size: 144
19390616 ATAATTATAA
*
19390626 TATAATTAAAAAC-AAAATAAATAACAAT-AATTAAATTAAAAACAACAA-AACAATTTA-CTTT
1 TATAA-TAAAAACTAAAA-AAATAACAATAAATTAAATTAAAAACAACAACAA-AATTTACCTCT
*
19390687 CCTTTTAGCTTTGTTCGCTTTAATCTACCCTACTAAACAAAAAAAATTATAACAAATCACATAAA
63 -CTTTTAGCTTT-TTCCCTTTAATCTACCCTACTAAACAAAAAAAATTATAACAAAT--CATAAA
19390752 CATTAAACTAAATAAATAATT
124 CATTAAACTAAATAAATAATT
** * **
19390773 TATAATAATTACTAACAAAATAACTTTAAATTAAATTAAAAACAACAACAAAATTTACCTCTCTT
1 TATAATAAAAACTAAAAAAATAACAATAAATTAAATTAAAAACAACAACAAAATTTACCTCTCTT
* * *
19390838 TTAGCTTTTTCCCTTTAATTTACTCTACTAAACAAAAAAATTTATAACAAATCATAAACATTAAA
66 TTAGCTTTTTCCCTTTAATCTACCCTACTAAACAAAAAAAATTATAACAAATCATAAACATTAAA
19390903 CTAAA
131 CTAAA
19390908 CTTTATAATA
Statistics
Matches: 121, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
144 18 0.15
146 53 0.44
147 45 0.37
148 5 0.04
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (144 bp):
TATAATAAAAACTAAAAAAATAACAATAAATTAAATTAAAAACAACAACAAAATTTACCTCTCTT
TTAGCTTTTTCCCTTTAATCTACCCTACTAAACAAAAAAAATTATAACAAATCATAAACATTAAA
CTAAATAAATAATT
Found at i:19393232 original size:43 final size:44
Alignment explanation
Indices: 19393184--19393278 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 44
19393174 TTATTTATTA
* * *
19393184 ACATGTTATC-AAATTATATTACTTGACTCGTGTTAATATGGTT-
1 ACATGTTATCTAAATCATATTACTTGACTCGTATTAATAT-CTTG
*
19393227 ACATGTTA-CTAAATCATATTACTTGACTCTTATTAATATCTTG
1 ACATGTTATCTAAATCATATTACTTGACTCGTATTAATATCTTG
19393270 ACATGTTAT
1 ACATGTTAT
19393279 TAATTGTGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
42 3 0.07
43 42 0.93
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (44 bp):
ACATGTTATCTAAATCATATTACTTGACTCGTATTAATATCTTG
Found at i:19396053 original size:47 final size:47
Alignment explanation
Indices: 19395995--19396087 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
19395985 TAAGTTTTAC
* *
19395995 GATTTTTTACCAATATAATACAAAA-ATAATAATTAAATACCAAAATA
1 GATTATTTACCAAAATAATACAAAATA-AATAATTAAATACCAAAATA
** * *
19396042 GATTATTTACCAAAATGGTACAAAATAAATATTTATATACCAAAAT
1 GATTATTTACCAAAATAATACAAAATAAATAATTAAATACCAAAAT
19396088 GGTATCTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 38 0.97
48 1 0.03
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (47 bp):
GATTATTTACCAAAATAATACAAAATAAATAATTAAATACCAAAATA
Found at i:19396065 original size:27 final size:29
Alignment explanation
Indices: 19396035--19396091 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
19396025 AATTAAATAC
*
19396035 CAAAAT-AGA-TTATTTACCAAAATGGTA
1 CAAAATAAGATTTATATACCAAAATGGTA
*
19396062 CAAAATAAATATTTATATACCAAAATGGTA
1 CAAAAT-AAGATTTATATACCAAAATGGTA
19396092 TCTACACCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
29 2 0.08
30 17 0.68
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (29 bp):
CAAAATAAGATTTATATACCAAAATGGTA
Found at i:19396616 original size:4 final size:4
Alignment explanation
Indices: 19396601--19396652 Score: 90
Period size: 4 Copynumber: 13.5 Consensus size: 4
19396591 CCCTCTCCTT
19396601 TTTC TTTC --TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
19396647 TTTC TT
1 TTTC TT
19396653 CTCTCTCCCG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
4 44 0.96
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:19397108 original size:17 final size:19
Alignment explanation
Indices: 19397073--19397110 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19397063 TAGGATGGAG
19397073 ATATTATTTTGATACATAA
1 ATATTATTTTGATACATAA
*
19397092 ATATT-TTTTTATA-ATAA
1 ATATTATTTTGATACATAA
19397109 AT
1 AT
19397111 TAGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
ATATTATTTTGATACATAA
Found at i:19397864 original size:13 final size:13
Alignment explanation
Indices: 19397846--19397870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19397836 AAAAAGAGGT
19397846 ATTTATTTTATTA
1 ATTTATTTTATTA
19397859 ATTTATTTTATT
1 ATTTATTTTATT
19397871 TTATGTGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTTATTA
Found at i:19398182 original size:86 final size:88
Alignment explanation
Indices: 19398089--19398253 Score: 236
Period size: 89 Copynumber: 1.9 Consensus size: 88
19398079 TAAATTATTT
*
19398089 GTTTTGTT-TTG-TTTT-ATTTTTATGTGATTTG-T-T-ATTA-TTTTTTTATTTAGTAGAGTAC
1 GTTTTGTTGTTGTTTTTAATGTTTATGTGATTTGTTATAATTATTTTTTTTATTTAGTAG-GTAC
19398147 ATTAAAGGAAGAGAAAAAAATGTAA
65 ATTAAAGGAAGA-AAAAAAATGTAA
* *
19398172 GTTTTGTTGTTGTTTTTAATGTTTATGTGATTTGTTATAATTATTTTTTTTGTTTAGTAGGTAGA
1 GTTTTGTTGTTGTTTTTAATGTTTATGTGATTTGTTATAATTATTTTTTTTATTTAGTAGGTACA
19398237 TTAAAGGAAGAAAAAAA
66 TTAAAGGAAGAAAAAAA
19398254 TATAAAAGAA
Statistics
Matches: 72, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
83 8 0.11
84 3 0.04
85 4 0.06
86 15 0.21
87 1 0.01
88 7 0.10
89 19 0.26
90 15 0.21
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (88 bp):
GTTTTGTTGTTGTTTTTAATGTTTATGTGATTTGTTATAATTATTTTTTTTATTTAGTAGGTACA
TTAAAGGAAGAAAAAAAATGTAA
Found at i:19399624 original size:22 final size:24
Alignment explanation
Indices: 19399594--19399640 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
19399584 GGGGATGGGG
* *
19399594 AATTTTATTCCTTGA-CA-TGTTA
1 AATTATATTACTTGACCAGTGTTA
19399616 AATTATATTACTTGACCAGTGTTA
1 AATTATATTACTTGACCAGTGTTA
19399640 A
1 A
19399641 TATCATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 2 0.10
24 6 0.29
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (24 bp):
AATTATATTACTTGACCAGTGTTA
Found at i:19399665 original size:43 final size:43
Alignment explanation
Indices: 19399613--19399702 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
19399603 CCTTGACATG
19399613 TTAAATTATATTACTTGACCAGTGTTAATATCATGACATGTTA
1 TTAAATTATATTACTTGACCAGTGTTAATATCATGACATGTTA
** * *
19399656 TTAAATTATATTACTTGACCCTTGTTAATATCGTGACATTTTA
1 TTAAATTATATTACTTGACCAGTGTTAATATCATGACATGTTA
19399699 TTAA
1 TTAA
19399703 TTGTGCAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (43 bp):
TTAAATTATATTACTTGACCAGTGTTAATATCATGACATGTTA
Found at i:19401726 original size:16 final size:16
Alignment explanation
Indices: 19401705--19401736 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19401695 AACAACAACA
19401705 AAACTTACCTTTCTTT
1 AAACTTACCTTTCTTT
*
19401721 AAACTTATCTTTCTTT
1 AAACTTACCTTTCTTT
19401737 CTCTCCCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (16 bp):
AAACTTACCTTTCTTT
Found at i:19404252 original size:14 final size:15
Alignment explanation
Indices: 19404227--19404256 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19404217 ATTTAAATGT
19404227 TATTTAAATTTTATC
1 TATTTAAATTTTATC
19404242 TATTT-AATTTTATC
1 TATTTAAATTTTATC
19404256 T
1 T
19404257 TAGTTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTAAATTTTATC
Found at i:19409752 original size:71 final size:72
Alignment explanation
Indices: 19409636--19409779 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 72
19409626 TCAGGTAAAC
** *
19409636 TCCACCCAAAAAATACCAAATTCATACTTAAATATCGAATTTCTATCATATCGA-TTTTTTAATT
1 TCCACCCAAAAAATACCAAACCCATACTTAAATATCAAATTTCTATCATATCGATTTTTTTAATT
19409700 AATTTTA
66 AATTTTA
19409707 TCCACCCAAAAAATACCAAACCCATACTTAAATATCAAATTTCTATCATATCGATTTTTTTAATT
1 TCCACCCAAAAAATACCAAACCCATACTTAAATATCAAATTTCTATCATATCGATTTTTTTAATT
19409772 AATTTTA
66 AATTTTA
19409779 T
1 T
19409780 TTTTTTAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 51 0.74
72 18 0.26
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (72 bp):
TCCACCCAAAAAATACCAAACCCATACTTAAATATCAAATTTCTATCATATCGATTTTTTTAATT
AATTTTA
Found at i:19412566 original size:58 final size:58
Alignment explanation
Indices: 19412481--19412598 Score: 177
Period size: 58 Copynumber: 2.0 Consensus size: 58
19412471 AAGAAGTTGA
* *
19412481 TTATGAGTGTTATTTAAGAATAAAATTATATTTTGG-TTTAAAAATATTTGGGTTTAGT
1 TTATAAGTGTTATTTAAAAATAAAATTATA-TTTGGATTTAAAAATATTTGGGTTTAGT
*
19412539 TTATAAGTGTT-TTTGAAAAATGAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
1 TTATAAGTGTTATTT-AAAAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
19412597 TT
1 TT
19412599 GTTGATAGGT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
57 8 0.15
58 47 0.85
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (58 bp):
TTATAAGTGTTATTTAAAAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
Found at i:19420210 original size:8 final size:8
Alignment explanation
Indices: 19420194--19420224 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19420184 ATTGTAAAAG
19420194 TATACAAT
1 TATACAAT
*
19420202 TATAGAAT
1 TATACAAT
19420210 TATACAAT
1 TATACAAT
19420218 TATACAA
1 TATACAA
19420225 ACAAGTTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (8 bp):
TATACAAT
Found at i:19420411 original size:17 final size:17
Alignment explanation
Indices: 19420391--19420427 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19420381 GAAGAAAAAG
*
19420391 AAATTGAAATGAAATGA
1 AAATTCAAATGAAATGA
*
19420408 AAATTCAAATTAAATGA
1 AAATTCAAATGAAATGA
19420425 AAA
1 AAA
19420428 AATAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (17 bp):
AAATTCAAATGAAATGA
Found at i:19420501 original size:32 final size:31
Alignment explanation
Indices: 19420448--19420511 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
19420438 TGAAGATAAT
19420448 TAAATTAAATTATTAATATAAAAAATGAAAA
1 TAAATTAAATTATTAATATAAAAAATGAAAA
**
19420479 TAAAGTTAAATCTATTAA-ATAAAAGTTGAAAA
1 TAAA-TTAAAT-TATTAATATAAAAAATGAAAA
19420511 T
1 T
19420512 TAAGAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 4 0.14
32 19 0.66
33 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (31 bp):
TAAATTAAATTATTAATATAAAAAATGAAAA
Found at i:19420645 original size:17 final size:17
Alignment explanation
Indices: 19420623--19420667 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
19420613 AGTTCCAGCC
*
19420623 ATTAAATTTAAAATGAA
1 ATTAAATTTAAAATCAA
* *
19420640 ATTAAAATGAAAATCAA
1 ATTAAATTTAAAATCAA
*
19420657 ATGAAATTTAA
1 ATTAAATTTAA
19420668 CTAAATTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (17 bp):
ATTAAATTTAAAATCAA
Found at i:19420646 original size:11 final size:11
Alignment explanation
Indices: 19420630--19420664 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19420620 GCCATTAAAT
19420630 TTAAAATGAAA
1 TTAAAATGAAA
19420641 TTAAAATGAAA
1 TTAAAATGAAA
* *
19420652 ATCAAATGAAA
1 TTAAAATGAAA
19420663 TT
1 TT
19420665 TAACTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (11 bp):
TTAAAATGAAA
Found at i:19420749 original size:24 final size:24
Alignment explanation
Indices: 19420687--19420749 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
19420677 AAATTTAATG
*
19420687 GGTGGCAGGCCTAAACCCGCATCA
1 GGTGGCAGGCCTAAGCCCGCATCA
** * *
19420711 GGTGATAGGCGTAAGCCCGCGTCA
1 GGTGGCAGGCCTAAGCCCGCATCA
19420735 GGTGGCAGGCCTAAG
1 GGTGGCAGGCCTAAG
19420750 TCCAATGAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.27, G:0.37, T:0.14
Consensus pattern (24 bp):
GGTGGCAGGCCTAAGCCCGCATCA
Found at i:19427662 original size:2 final size:2
Alignment explanation
Indices: 19427615--19427644 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19427605 CTACAAATTG
19427615 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19427645 CCATTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19427735 original size:19 final size:19
Alignment explanation
Indices: 19427692--19427735 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
19427682 TTATATAATT
*
19427692 TTTATACATCAATTTTTTA
1 TTTATACATCAATTTTATA
*
19427711 TATATACA-CTAATTTTATA
1 TTTATACATC-AATTTTATA
19427730 TTTATA
1 TTTATA
19427736 TATACATGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATACATCAATTTTATA
Found at i:19437839 original size:11 final size:11
Alignment explanation
Indices: 19437823--19437848 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19437813 ACGGGTTGTA
19437823 AAATAAGTGTT
1 AAATAAGTGTT
19437834 AAATAAGTGTT
1 AAATAAGTGTT
19437845 AAAT
1 AAAT
19437849 GATTACCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (11 bp):
AAATAAGTGTT
Found at i:19439024 original size:24 final size:24
Alignment explanation
Indices: 19438992--19439049 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
19438982 CACCTAACGT
19438992 GCCTACCACCTGACGCGGGCTTAA
1 GCCTACCACCTGACGCGGGCTTAA
* * *
19439016 GCCTGCCACCTGACGCGGGTTTAG
1 GCCTACCACCTGACGCGGGCTTAA
*
19439040 GCCTAGCACC
1 GCCTACCACC
19439050 CATTAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.17
Consensus pattern (24 bp):
GCCTACCACCTGACGCGGGCTTAA
Found at i:19439313 original size:22 final size:22
Alignment explanation
Indices: 19439296--19439338 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19439286 AAAATTATTT
19439296 TTTCATTT-AATTTGAATTTTCA
1 TTTCATTTCAATTT-AATTTTCA
19439318 TTTCATTTCAATTTAATTTTC
1 TTTCATTTCAATTTAATTTTC
19439339 TTCCTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTCATTTCAATTTAATTTTCA
Found at i:19439317 original size:17 final size:17
Alignment explanation
Indices: 19439295--19439331 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19439285 AAAAATTATT
*
19439295 TTTTCATTTAATTTGAA
1 TTTTCATTTAATTTCAA
*
19439312 TTTTCATTTCATTTCAA
1 TTTTCATTTAATTTCAA
19439329 TTT
1 TTT
19439332 AATTTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTCATTTAATTTCAA
Found at i:19439510 original size:8 final size:8
Alignment explanation
Indices: 19439497--19439527 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19439487 GGCAACTTAT
19439497 TTGTATAA
1 TTGTATAA
19439505 TTGTATAA
1 TTGTATAA
*
19439513 TTCTATAA
1 TTGTATAA
19439521 TTGTATA
1 TTGTATA
19439528 CTTTTACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (8 bp):
TTGTATAA
Found at i:19443771 original size:21 final size:22
Alignment explanation
Indices: 19443731--19443772 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19443721 TAAACAAACC
*
19443731 TTTTTTTTTCTCTGTTTGGGGG
1 TTTTTTTTTCTCTGTGTGGGGG
*
19443753 TTTTTTTTTC-GTGTGTGGGG
1 TTTTTTTTTCTCTGTGTGGGG
19443773 TTTGATCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.00, C:0.07, G:0.31, T:0.62
Consensus pattern (22 bp):
TTTTTTTTTCTCTGTGTGGGGG
Found at i:19447332 original size:34 final size:34
Alignment explanation
Indices: 19447294--19447370 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
19447284 CGAGGTTATT
19447294 CTTTGCTCTCTTTTTTTTTAACTTCTTTATTTTC
1 CTTTGCTCTCTTTTTTTTTAACTTCTTTATTTTC
19447328 CTTTGCTCTCTTTTTTTTTAACTTCTTTATTTTC
1 CTTTGCTCTCTTTTTTTTTAACTTCTTTATTTTC
19447362 CTTTGCTCT
1 CTTTGCTCT
19447371 TGTTATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.08, C:0.22, G:0.04, T:0.66
Consensus pattern (34 bp):
CTTTGCTCTCTTTTTTTTTAACTTCTTTATTTTC
Found at i:19447339 original size:19 final size:19
Alignment explanation
Indices: 19447317--19447370 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 19
19447307 TTTTTTAACT
19447317 TCTTTATTTTCCTTTGCTC
1 TCTTTATTTTCCTTTGCTC
**
19447336 TCTTT-TTTT--TTAACT-
1 TCTTTATTTTCCTTTGCTC
19447351 TCTTTATTTTCCTTTGCTC
1 TCTTTATTTTCCTTTGCTC
19447370 T
1 T
19447371 TGTTATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
18 8 0.30
19 6 0.22
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (19 bp):
TCTTTATTTTCCTTTGCTC
Found at i:19456601 original size:58 final size:58
Alignment explanation
Indices: 19456515--19456634 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
19456505 AAAAGAAGTT
* *
19456515 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTAGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTAGGTTTAAAAATATTTGGGTTTA
* * *
19456573 GTTTATGAGTATT-TTTGAAGAATGAAATTATATTTGGGTTTAATAATATTTGGGTTTA
1 GTTTATGAGTATTATTT-AAGAATAAAATTATATTTAGGTTTAAAAATATTTGGGTTTA
19456631 GTTT
1 GTTT
19456635 GTTGACGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTATTATTTAAGAATAAAATTATATTTAGGTTTAAAAATATTTGGGTTTA
Found at i:19456900 original size:23 final size:23
Alignment explanation
Indices: 19456856--19456901 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19456846 AAAAAAAATT
**
19456856 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
19456879 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
19456902 ATTCAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:19457562 original size:88 final size:88
Alignment explanation
Indices: 19457413--19457584 Score: 274
Period size: 88 Copynumber: 2.0 Consensus size: 88
19457403 GTACAAAGGA
* * *
19457413 ACCTTGAGCACATGAAAACCCAACTTCAAATTAGCATTCTCAGGAGCCAGAAGGGAAATTGGGGT
1 ACCTTAAGCACATGAAAACCCAACTTCAAATCAGCATTCTCAGGAGCCAAAAGGGAAATTGGGGT
19457478 TTATCTAGGGTTTTTAAAAATCC
66 TTATCTAGGGTTTTTAAAAATCC
* * *
19457501 ACCTTAAGCACATGAAAACCCAACTTCAAGTCCA-CATTCTTAGGAGGCAAAAGGGAAATTGGGG
1 ACCTTAAGCACATGAAAACCCAACTTCAAAT-CAGCATTCTCAGGAGCCAAAAGGGAAATTGGGG
19457565 TTTATCTAGGGTTTTTAAAA
65 TTTATCTAGGGTTTTTAAAA
19457585 TCCTGAACAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 76 0.99
89 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (88 bp):
ACCTTAAGCACATGAAAACCCAACTTCAAATCAGCATTCTCAGGAGCCAAAAGGGAAATTGGGGT
TTATCTAGGGTTTTTAAAAATCC
Found at i:19459375 original size:23 final size:22
Alignment explanation
Indices: 19459332--19459381 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
19459322 ATAGAATATA
* **
19459332 ATTTAAAATTTAATTGGATAAT
1 ATTTAAAATTAAATTAAATAAT
19459354 ATTTAAAATTAAAATTAAATAAT
1 ATTTAAAATT-AAATTAAATAAT
*
19459377 TTTTA
1 ATTTA
19459382 TAAGTTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTTAAAATTAAATTAAATAAT
Done.