Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 9 of 290
Found at i:2986349 original size:27 final size:28
Alignment explanation
Indices: 2986319--2986382 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
2986309 TTTAAAAAAA
* * *
2986319 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
2986346 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
2986373 TATTTAAAAA
1 TATTTAAAAA
2986383 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 20 0.65
27 4 0.13
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:2986390 original size:26 final size:26
Alignment explanation
Indices: 2986319--2986384 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
2986309 TTTAAAAAAA
* *
2986319 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
* *
2986346 TATTAAAAAATTATAATTTTTTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
2986372 GTATTTAAAAATT
1 -TATTTAAAAATT
2986385 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:2986564 original size:16 final size:18
Alignment explanation
Indices: 2986534--2986581 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
2986524 GTCAAAAAAA
*
2986534 TATATT-AAATATATATT
1 TATATTAAAATTTATATT
2986551 T-T-TTAAAATTTATATT
1 TATATTAAAATTTATATT
*
2986567 TATATTTAAATTTAT
1 TATATTAAAATTTAT
2986582 TAATAGTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 12 0.46
17 2 0.08
18 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTAAAATTTATATT
Found at i:2986898 original size:21 final size:20
Alignment explanation
Indices: 2986828--2986904 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 20
2986818 GTTAAAAAAT
2986828 ATTTTTAAAAATAATAATTAC-A
1 ATTTTT-AAAAT-AT-ATTACAA
* *
2986850 ATTTTTAAAAAATATTATAAA
1 ATTTTTAAAATATATTA-CAA
*
2986871 ACATTTTAAATATATATTACAA
1 A-TTTTTAAA-ATATATTACAA
2986893 ATTTTTTAAAAT
1 A-TTTTTAAAAT
2986905 TAATAATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.09
20 2 0.05
21 8 0.18
22 23 0.52
23 7 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTTAAAATATATTACAA
Found at i:2986904 original size:23 final size:22
Alignment explanation
Indices: 2986828--2986918 Score: 64
Period size: 23 Copynumber: 4.1 Consensus size: 22
2986818 GTTAAAAAAT
*
2986828 ATTTTTAAAAATAATAATTAC-A
1 ATTTTTTAAAATAAT-ATTACAA
*
2986850 A-TTTTTAAAA-AATATTATAAA
1 ATTTTTTAAAATAATATTA-CAA
**
2986871 ACATTTT-AAATATATATTACAA
1 ATTTTTTAAAATA-ATATTACAA
* *
2986893 ATTTTTTAAAATTAATAATATAA
1 ATTTTTTAAAA-TAATATTACAA
2986916 ATT
1 ATT
2986919 AAATAAGCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.07
20 3 0.06
21 13 0.24
22 13 0.24
23 19 0.35
24 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTTTTAAAATAATATTACAA
Found at i:2986951 original size:18 final size:18
Alignment explanation
Indices: 2986901--2986952 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2986891 AAATTTTTTA
*
2986901 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
2986919 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
2986937 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
2986953 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:2987021 original size:10 final size:9
Alignment explanation
Indices: 2986996--2987020 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2986986 AAAATATAAG
2986996 AAAAAAAGT
1 AAAAAAAGT
2987005 AAAAAAAGT
1 AAAAAAAGT
2987014 AAAAAAA
1 AAAAAAA
2987021 ATATAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:2987478 original size:91 final size:89
Alignment explanation
Indices: 2987325--2987499 Score: 323
Period size: 91 Copynumber: 1.9 Consensus size: 89
2987315 AAGCCAACAT
*
2987325 TACGAGGAAAAAGAAAAAAAAATGATGGTTCAGGTCAGGGGTCAACTCATTGAGCTATGATGGAT
1 TACGAGGAAAAAGAAAAAAAAATGACGGTTCAGGTCAGGGGTCAACTCATTGAGCTATGATGGAT
2987390 CCGAGTGGAACCAACTTCTAAGAA
66 CCGAGTGGAACCAACTTCTAAGAA
2987414 TACGAGGAAAAAGAAAAAAAAAAATGACGGTTCAGGTCAGGGGTCAACTCATTGAGCTATGATGG
1 TACGAGGAAAAAG--AAAAAAAAATGACGGTTCAGGTCAGGGGTCAACTCATTGAGCTATGATGG
2987479 ATCCGAGTGGAACCAACTTCT
64 ATCCGAGTGGAACCAACTTCT
2987500 TATCCTTCCA
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
89 13 0.16
91 70 0.84
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (89 bp):
TACGAGGAAAAAGAAAAAAAAATGACGGTTCAGGTCAGGGGTCAACTCATTGAGCTATGATGGAT
CCGAGTGGAACCAACTTCTAAGAA
Found at i:3005709 original size:149 final size:149
Alignment explanation
Indices: 3005439--3005738 Score: 447
Period size: 149 Copynumber: 2.0 Consensus size: 149
3005429 CATTTAAATC
3005439 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
1 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
* * * *
3005504 TTTGAAGGGAGTACTCAAAGAACTATACATCTGCAGAAGCCATTTATAGATATCAAATCTTGAAA
66 TCTGAAAGGAGTACTCAAAGAACTATACATCAGCAGAAACCATTTATAGATATCAAATCTTGAAA
*
3005569 TAAATTTCCCTCAAATTAT
131 TAAATTTACCTCAAATTAT
** ** *
3005588 AAAGGGAATTTATGAGTTAGACTTCCAACATGACCATTAATGCACTGCATATAGCAACTAGCAAG
1 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
* * ** *
3005653 TCTGAAAGTAGTGCTCAAAGAACTATGTATCAGCAGAAACCATTTATAGATATCAAATCTTGCAA
66 TCTGAAAGGAGTACTCAAAGAACTATACATCAGCAGAAACCATTTATAGATATCAAATCTTGAAA
* *
3005718 TAAGTTTACCTCAATTTAT
131 TAAATTTACCTCAAATTAT
3005737 AA
1 AA
3005739 CTGTAATCCC
Statistics
Matches: 134, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
149 134 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (149 bp):
AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
TCTGAAAGGAGTACTCAAAGAACTATACATCAGCAGAAACCATTTATAGATATCAAATCTTGAAA
TAAATTTACCTCAAATTAT
Found at i:3006532 original size:53 final size:53
Alignment explanation
Indices: 3006466--3006784 Score: 557
Period size: 53 Copynumber: 6.0 Consensus size: 53
3006456 CAATTAGATA
*
3006466 TGCCATGACCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
3006519 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
3006572 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* *
3006625 TACCATGAGCATTGATAAAAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* *
3006678 GGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATTCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* * * *
3006731 TGTCATGAGCATTGATAACAATACATGGTAACAGTGTGACCATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
3006784 T
1 T
3006785 ATGTAATCAA
Statistics
Matches: 253, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 253 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (53 bp):
TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
Found at i:3008452 original size:25 final size:26
Alignment explanation
Indices: 3008392--3008456 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
3008382 TATATTAAAT
*
3008392 TTAATATAAATTTTAAATATAATTATA
1 TTAATAT-AATTATAAATATAATTATA
* * * *
3008419 TTGAGATAATTAT-AATATAATTTTG
1 TTAATATAATTATAAATATAATTATA
3008444 TTAATATAATTAT
1 TTAATATAATTAT
3008457 TCTAAATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 21 0.68
26 5 0.16
27 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
TTAATATAATTATAAATATAATTATA
Found at i:3014543 original size:106 final size:106
Alignment explanation
Indices: 3014358--3014563 Score: 322
Period size: 106 Copynumber: 1.9 Consensus size: 106
3014348 TTAGTTATAA
* * * *
3014358 TTATTTCGGTAGCCAAAAGCTAATAACGTTAAATATAAAAGGAGTTAACTAATGAGAACTCGTCA
1 TTATTTCGGTAGCCAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAACCAATGAGAACGCGTCA
* *
3014423 CATCATCAATGACATGGCATATTGATCAACAACATAATTTG
66 CATCATCAATGACATAGCATATTGACCAACAACATAATTTG
* *
3014464 TTATTTCGGTAGCTAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAGCCAATGAGAACGCGTCA
1 TTATTTCGGTAGCCAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAACCAATGAGAACGCGTCA
* *
3014529 CGTCATCAATGACATAGCATATTGACCAACGACAT
66 CATCATCAATGACATAGCATATTGACCAACAACAT
3014564 GGTATGTTGA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (106 bp):
TTATTTCGGTAGCCAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAACCAATGAGAACGCGTCA
CATCATCAATGACATAGCATATTGACCAACAACATAATTTG
Found at i:3015635 original size:20 final size:20
Alignment explanation
Indices: 3015612--3015649 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3015602 GTCAATCTAG
*
3015612 CACGTCATTGGTCAACATTT
1 CACGTCATTGGCCAACATTT
3015632 CACGTCATTGGCCAACAT
1 CACGTCATTGGCCAACAT
3015650 GCCTACTCAT
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:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CACGTCATTGGCCAACATTT
Found at i:3016213 original size:59 final size:58
Alignment explanation
Indices: 3016134--3016246 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 58
3016124 AAAATAATTG
3016134 AATAGTTGAGTGACCATTTTGCAACT-TTTCATA-TTGGGTGACCAAAAAAGAAAACTACT
1 AATAGTTGAGTGACCATTTTGCAA-TATTTCATAGTTGGGTGA-CAAAAAA-AAAACTACT
* *
3016193 AATAGTTGTA-TGACTATTTTGTAATATTTCATAGTTGGGTGACAAAAAAAAAAC
1 AATAGTTG-AGTGACCATTTTGCAATATTTCATAGTTGGGTGACAAAAAAAAAAC
3016247 CATAGTTGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
58 6 0.12
59 34 0.69
60 9 0.18
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (58 bp):
AATAGTTGAGTGACCATTTTGCAATATTTCATAGTTGGGTGACAAAAAAAAAACTACT
Found at i:3034200 original size:23 final size:23
Alignment explanation
Indices: 3034152--3034200 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3034142 TTGTATCAAA
*
3034152 ATTCATATATAATTTTGATATTT
1 ATTCATATATAATATTGATATTT
*
3034175 ATTCATATATTATATT-ATATTAT
1 ATTCATATATAATATTGATATT-T
3034198 ATT
1 ATT
3034201 ATGGTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTCATATATAATATTGATATTT
Found at i:3034621 original size:14 final size:15
Alignment explanation
Indices: 3034602--3034631 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3034592 ATTACATAAA
3034602 ATACAAAA-AAAGAG
1 ATACAAAATAAAGAG
3034616 ATACAAAATAAAGAG
1 ATACAAAATAAAGAG
3034631 A
1 A
3034632 AATTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (15 bp):
ATACAAAATAAAGAG
Found at i:3042565 original size:14 final size:15
Alignment explanation
Indices: 3042546--3042574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3042536 ATTGATAATT
3042546 AAAAAA-AAAAGGAC
1 AAAAAAGAAAAGGAC
3042560 AAAAAAGAAAAGGAC
1 AAAAAAGAAAAGGAC
3042575 GAGCTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGGAC
Found at i:3044246 original size:39 final size:39
Alignment explanation
Indices: 3044203--3044367 Score: 199
Period size: 39 Copynumber: 4.2 Consensus size: 39
3044193 GGTTGCCATA
*
3044203 CATTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGG
1 CATTTGCTGAGGATACATTGAACCCATCTGGCCAGCTGG
* **
3044242 CATTTGCTGAGGATACATTGAACCCATCTGGGCC-CCCAG
1 CATTTGCTGAGGATACATTGAACCCATCT-GGCCAGCTGG
* * *
3044281 CACTTGCTGAGGATACATTGAACCCATCTGGCCCGTTGG
1 CATTTGCTGAGGATACATTGAACCCATCTGGCCAGCTGG
* * * *
3044320 CATTTGATGAGGATACATGGAACTCATCTGGCCCA-CAGG
1 CATTTGCTGAGGATACATTGAACCCATCTGG-CCAGCTGG
3044359 CATTTGCTG
1 CATTTGCTG
3044368 TGGAAGCATG
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
38 4 0.04
39 96 0.91
40 6 0.06
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (39 bp):
CATTTGCTGAGGATACATTGAACCCATCTGGCCAGCTGG
Found at i:3044293 original size:78 final size:78
Alignment explanation
Indices: 3044206--3044367 Score: 236
Period size: 78 Copynumber: 2.1 Consensus size: 78
3044196 TGCCATACAT
* *
3044206 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATTGAACCCATCT
1 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGATGAGGATACATGGAACCCATCT
*
3044271 GGGCCCCCA-GCAC
66 -GGCCCACAGGCAC
* * * *
3044284 TTGCTGAGGATACATTGAACCCATCTGGCCCGTTGGCATTTGATGAGGATACATGGAACTCATCT
1 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGATGAGGATACATGGAACCCATCT
*
3044349 GGCCCACAGGCAT
66 GGCCCACAGGCAC
3044362 TTGCTG
1 TTGCTG
3044368 TGGAAGCATG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
77 7 0.09
78 68 0.91
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (78 bp):
TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGATGAGGATACATGGAACCCATCT
GGCCCACAGGCAC
Found at i:3046542 original size:110 final size:110
Alignment explanation
Indices: 3046349--3046569 Score: 424
Period size: 110 Copynumber: 2.0 Consensus size: 110
3046339 ATTTTTAACA
3046349 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
1 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
*
3046414 GACACATTCATGAAAACAGATGATAACATCAAGTCTTCAACTTAT
66 GACACATTCATGAAAACAGATGATAACATCAAGTCATCAACTTAT
3046459 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
1 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
*
3046524 GACACATTCATGAAAACAGATGATACCATCAAGTCATCAACTTAT
66 GACACATTCATGAAAACAGATGATAACATCAAGTCATCAACTTAT
3046569 A
1 A
3046570 AAGAGTATGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (110 bp):
AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
GACACATTCATGAAAACAGATGATAACATCAAGTCATCAACTTAT
Found at i:3048780 original size:4 final size:4
Alignment explanation
Indices: 3048771--3048798 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3048761 ACCTTCAGTC
3048771 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
3048799 TTTTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:3050272 original size:20 final size:20
Alignment explanation
Indices: 3050247--3050286 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3050237 CGTAAAATAA
*
3050247 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3050267 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3050287 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3050276 original size:34 final size:34
Alignment explanation
Indices: 3050233--3050298 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
3050223 AGTAAAATAT
*
3050233 TTTTCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATAATTTACTGGAAAATATTTTAC
*
3050266 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATAATTTACTGGAAAATATTTT
3050299 CTGGTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 11 0.38
35 13 0.45
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:3053011 original size:19 final size:19
Alignment explanation
Indices: 3052983--3053044 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
3052973 AATCTTTAAG
*
3052983 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3053002 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3053021 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3053042 GAT
1 GAT
3053045 CTTGTAATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 31 0.77
21 9 0.22
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3058223 original size:11 final size:11
Alignment explanation
Indices: 3058207--3058249 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
3058197 ACTTCTATTT
3058207 AAAAAAAAAGA
1 AAAAAAAAAGA
3058218 AAAAAAAAAGA
1 AAAAAAAAAGA
*
3058229 GAAAAAAAAGA
1 AAAAAAAAAGA
3058240 AAAAAGAAAA
1 AAAAA-AAAA
3058250 AATAGAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:3058236 original size:16 final size:16
Alignment explanation
Indices: 3058207--3058251 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
3058197 ACTTCTATTT
3058207 AAAAAA-AAAGAAAAA-
1 AAAAAAGAAA-AAAAAG
3058222 AAAAAGAGAAAAAAAAG
1 AAAAA-AGAAAAAAAAG
3058239 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
3058252 TAGAGAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 14 0.52
17 8 0.30
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:3058242 original size:27 final size:26
Alignment explanation
Indices: 3058207--3058257 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3058197 ACTTCTATTT
*
3058207 AAAAAAAAAGAA-AAAAAAAAGAGAA
1 AAAAAAAAAAAAGAAAAAAAAGAGAA
*
3058232 AAAAAAGAAAAAAGAAAAAATAGAGA
1 AAAAAA-AAAAAAGAAAAAAAAGAGA
3058258 GGCCGAGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 11 0.50
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (26 bp):
AAAAAAAAAAAAGAAAAAAAAGAGAA
Found at i:3058573 original size:78 final size:79
Alignment explanation
Indices: 3058443--3058596 Score: 301
Period size: 78 Copynumber: 2.0 Consensus size: 79
3058433 CATATGTTGA
3058443 ACTCAAAAAAAAAAGTCTTCATGGAGCTGGTGTATAGACGCTCAAGCGGCGATATCTAGGGCATC
1 ACTCAAAAAAAAAAGTCTTCATGGAGCTGGTGTATAGACGCTCAAGCGGCGATATCTAGGGCATC
3058508 TAACTTTTATCAAG
66 TAACTTTTATCAAG
3058522 ACTC-AAAAAAAAAGTCTTCATGGAGCTGGTGTATAGACGCTCAAGCGGCGATATCTAGGGCATC
1 ACTCAAAAAAAAAAGTCTTCATGGAGCTGGTGTATAGACGCTCAAGCGGCGATATCTAGGGCATC
3058586 TAACTTTTATC
66 TAACTTTTATC
3058597 CTGCTTGGTA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 71 0.95
79 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (79 bp):
ACTCAAAAAAAAAAGTCTTCATGGAGCTGGTGTATAGACGCTCAAGCGGCGATATCTAGGGCATC
TAACTTTTATCAAG
Found at i:3059541 original size:132 final size:132
Alignment explanation
Indices: 3059315--3059636 Score: 434
Period size: 132 Copynumber: 2.4 Consensus size: 132
3059305 TATTGTTAAG
* * * * * *
3059315 GAGCAGATCGAAGATACCAGATTTGACGTCTCTG-TATTGGCAGGGAGTAGATCGAAGACATAGC
1 GAGCAGATCAAAGATAACAGATTTGGCATCTCTGATATTGGCAGAGAGCAGATCGAAGACATAGC
* * * *
3059379 TGATTTGGCTTTCACGTGTTTACATTGAAGCAAATCTAAGATGATTTAGCGTCTCTATATTGGCA
66 TGATTTGGCTTTCACGTGTTTACATTGAAGCAAATCAAAGATGAATTAGCATCTCTATATTGACA
3059444 GA
131 GA
* * *
3059446 GAGTAGATCAAAGATGACTGATTTGGCATCTCTG-TATTCGGC-GAAGAGCAGATCGAAGACATA
1 GAGCAGATCAAAGATAACAGATTTGGCATCTCTGATATT-GGCAG-AGAGCAGATCGAAGACATA
* * * *
3059509 GCTGATTTGGCTTTCATGTGTTTACGTTGAAGCAAATCAAAGATGAATTGGCATCTCTGTATTGA
64 GCTGATTTGGCTTTCACGTGTTTACATTGAAGCAAATCAAAGATGAATTAGCATCTCTATATTGA
3059574 CAGA
129 CAGA
* *
3059578 GAGCAGATCGAAGATAACAGATTTGGCATCTCTGATATTGGCAGAGAGCAGATCAAAGA
1 GAGCAGATCAAAGATAACAGATTTGGCATCTCTGATATTGGCAGAGAGCAGATCGAAGA
3059637 TGACAGATTT
Statistics
Matches: 165, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
131 32 0.19
132 128 0.78
133 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (132 bp):
GAGCAGATCAAAGATAACAGATTTGGCATCTCTGATATTGGCAGAGAGCAGATCGAAGACATAGC
TGATTTGGCTTTCACGTGTTTACATTGAAGCAAATCAAAGATGAATTAGCATCTCTATATTGACA
GA
Found at i:3060058 original size:350 final size:352
Alignment explanation
Indices: 3059421--3060206 Score: 1249
Period size: 350 Copynumber: 2.2 Consensus size: 352
3059411 AATCTAAGAT
* * * * *
3059421 GATTTAGCGTCTCTATATTGGCAGAGAGTAGATCAAAGATGACTGATTTGGCATCTCTGTATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
*
3059486 GC-GAAGAGCAGATCGAAGACATAGCTGATTTGGCTTTCATGTGTTTACGTTGAAGCAAATCAAA
66 GCAG-AGAGCAGATCGAAGACA-AGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCAAA
3059550 GATGAATTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGATA
129 GATGAATTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGATA
*
3059615 TTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTGACGGAGAGCAGATCGAA
194 TTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCGACGGAGAGCAGATCGAA
*
3059680 GACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATCTTTG
259 GACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATCTCTG
*
3059745 TATTGGCAGAGAGCAGATCGAAGATAATA
324 TATTGGCAGAGAGCAGATCGAAGATAACA
*
3059774 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTATATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
* *
3059839 GCAGAGAGCAGATCGAAGAC-AGCTGATTTGGC-TTCTACGTGTTTACGTTGAAGCAAGTCTAAG
66 GCAGAGAGCAGATCGAAGACAAGCTGATTTGGCTTTC-ACGTGTTTACGTTGAAGCAAATCAAAG
* ** **
3059902 ATGATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATGGCAGATTTGGCATCTCTG-TAT
130 ATGAATTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGATAT
* * * *
3059966 TGGCAGAGAGGAGATCAAAGATGACAGATTTGGCATCTCTGTATTCGGCGGATAGCATATCGAAG
195 TGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCGACGGAGAGCAGATCGAAG
*
3060031 ACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGT
260 ACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATCTCTGT
*
3060096 ATTGGTAGAGAGCAGATCGAAGATAACA
325 ATTGGCAGAGAGCAGATCGAAGATAACA
* ** * * *
3060124 GATTTGACATCTCTGTATTGGCAGAGAGCAGATTGAAGATAATAGATTTGGCGTCTCTGTATT-G
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
3060188 GCAGAGAGCAGATCGAAGA
66 GCAGAGAGCAGATCGAAGA
3060207 TAGAAGATTT
Statistics
Matches: 401, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
349 20 0.05
350 211 0.53
351 92 0.23
353 77 0.19
354 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (352 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
GCAGAGAGCAGATCGAAGACAAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCAAAGA
TGAATTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGATATT
GGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCGACGGAGAGCAGATCGAAGA
CATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATCTCTGTA
TTGGCAGAGAGCAGATCGAAGATAACA
Found at i:3060117 original size:176 final size:176
Alignment explanation
Indices: 3059421--3060206 Score: 1236
Period size: 176 Copynumber: 4.5 Consensus size: 176
3059411 AATCTAAGAT
* * * * *
3059421 GATTTAGCGTCTCTATATTGGCAGAGAGTAGATCAAAGATGACTGATTTGGCATCTCTGTATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
* * * * *
3059486 GCGAAGAGCAGATCGAAGACATAGCTGATTTGGCTTTCATGTGTTTACGTTGAAGCAAATCAAAG
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
* *
3059551 ATGAATTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATAACA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
3059597 GATTTGGCATCTCTGATATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTT
1 GATTTGGCATCTCTG-TATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTC
*
3059662 GACGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAA
65 GGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAA
* * *
3059727 AATGATTTGGCATCTTTGTATTGGCAGAGAGCAGATCGAAGATAATA
130 GATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
3059774 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTATATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
* *
3059839 GCAGAGAGCAGATCGAAGAC--AGCTGATTTGGCTTCTACGTGTTTACGTTGAAGCAAGTCTAAG
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
* **
3059902 ATGATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATGGCA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
3059948 GATTTGGCATCTCTGTATTGGCAGAGAGGAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
* *
3060013 GCGGATAGCATATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
*
3060078 ATGATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAACA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* ** * * *
3060124 GATTTGACATCTCTGTATTGGCAGAGAGCAGATTGAAGATAATAGATTTGGCGTCTCTGTATT-G
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
*
3060188 GCAGAGAGCAGATCGAAGA
66 GCGGAGAGCAGATCGAAGA
3060207 TAGAAGATTT
Statistics
Matches: 561, Mismatches: 46, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
174 162 0.29
175 17 0.03
176 220 0.39
177 162 0.29
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (176 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
Found at i:3060247 original size:44 final size:44
Alignment explanation
Indices: 3059421--3060250 Score: 535
Period size: 44 Copynumber: 18.9 Consensus size: 44
3059411 AATCTAAGAT
* * * * * *
3059421 GATTTAGCGTCTCTATATTGGCAGAGAGTAGATCAAAGAT-GACT
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
**
3059465 GATTTGGCATCTCTGTATTCGGC-GAAGAGCAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTATT-GGCAG-AGAGCAGATCGAAG--ATAGAA
* * ** * * *
3059512 GATTTGGC-TTTCATGTGTTTAC-GTTGAAGCAAATCAAAGAT-G-A
1 GATTTGGCATCTC-TGTATTGGCAG-AG-AGCAGATCGAAGATAGAA
*
3059555 -A-TTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATA-ACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
*
3059597 GATTTGGCATCTCTGATATTGGCAGAGAGCAGATCAAAGAT-GACA
1 GATTTGGCATCTCTG-TATTGGCAGAGAGCAGATCGAAGATAGA-A
* * **
3059642 GATTTGGCATCTCTGTATTTGACGGAGAGCAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTA-TTGGCAGAGAGCAGATCGAAG--ATAGAA
* * * ** * *
3059689 GATTTGGCTTCCACGTGT-TTACGTTGA-AGCA-AGTC-TA-A-A-AT
1 GATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATAGAA
*
3059730 GATTTGGCATCTTTGTATTGGCAGAGAGCAGATCGAAGATA-ATA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
*
3059774 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGAT-GACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
* * **
3059818 GATTTGGCATCTCTATATTCGGCAGAGAGCAGATCGAAGACAGCT
1 GATTTGGCATCTCTGTATT-GGCAGAGAGCAGATCGAAGATAGAA
* * ** *
3059863 GATTTGGCTTCTACGTGT-TTACGTTGA-AGCA-AGTCTAAGAT----
1 GATTTGGCATCT-C-TGTATT-GGCAGAGAGCAGA-TCGAAGATAGAA
* * *
3059904 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATGGCA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGAA
* *
3059948 GATTTGGCATCTCTGTATTGGCAGAGAGGAGATCAAAGAT-GACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
* * * **
3059992 GATTTGGCATCTCTGTATTCGGCGGATAGCATATCGAAGACATAGCT
1 GATTTGGCATCTCTGTATT-GGCAGAGAGCAGATCGAAG--ATAGAA
* * * ** *
3060039 GATTTGGCTTCCACGTGT-TTACGTTGA-AGCA-AGTCTAAGAT----
1 GATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATAGAA
*
3060080 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATA-ACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
* *
3060124 GATTTGACATCTCTGTATTGGCAGAGAGCAGATTGAAGATA-ATA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
*
3060168 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGAA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGAA
* * *
3060212 GATTTGGCATCTCTGTATTGTCAGAGAGTATATCGAAGA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGA
3060251 GAAGAACAAC
Statistics
Matches: 628, Mismatches: 98, Indels: 120
0.74 0.12 0.14
Matches are distributed among these distances:
39 20 0.03
40 50 0.08
41 47 0.07
42 8 0.01
43 5 0.01
44 262 0.42
45 133 0.21
46 16 0.03
47 67 0.11
48 14 0.02
49 6 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGAA
Found at i:3060445 original size:44 final size:44
Alignment explanation
Indices: 3060303--3060581 Score: 199
Period size: 44 Copynumber: 6.2 Consensus size: 44
3060293 GATCCAAGAT
* *
3060303 GATTTGGCATTCCTGTGTTTACAGGGAACAGATCGAAGACATAGCA
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGATTGAAG--ATAGCA
* * * * * ** ***
3060349 GATCTGACATTCCTGTGCTTACAGCGAAGCAGATCAAAGATTTTA
1 GATTTGGCATCCCTGTGTTTACAGGGAA-CAGATTGAAGATAGCA
** **
3060394 -ACATGGCATCCCTGTGTTTATTGGGAACA-AGTTGAAGATAGCA
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCA
* *
3060437 GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAAACATAGCA
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGATTG--AAGATAGCA
* * * * * **
3060483 GATTTGACATTCCTGTGCTTACAGCGAAGCAGATTAAAGATTTCA
1 GATTTGGCATCCCTGTGTTTACAGGGAA-CAGATTGAAGATAGCA
* *
3060528 GCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGTA
1 G-ATTTGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCA
3060571 GATTTGGCATC
1 GATTTGGCATC
3060582 TTCATATTCG
Statistics
Matches: 177, Mismatches: 45, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
42 3 0.02
43 20 0.11
44 72 0.41
45 11 0.06
46 57 0.32
47 14 0.08
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCCCTGTGTTTACAGGGAACAGATTGAAGATAGCA
Found at i:3060453 original size:134 final size:134
Alignment explanation
Indices: 3060303--3060581 Score: 486
Period size: 134 Copynumber: 2.1 Consensus size: 134
3060293 GATCCAAGAT
* *
3060303 GATTTGGCATTCCTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCT
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAAACATAGCAGATCTGACATTCCTGTGCT
* *
3060368 TACAGCGAAGCAGATCAAAGATTTTAACATGGCATCCCTGTGTTTATTGGGAACAAGTTGAAGAT
66 TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
3060433 AGCA
131 AGCA
*
3060437 GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAAACATAGCAGATTTGACATTCCTGTGCT
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAAACATAGCAGATCTGACATTCCTGTGCT
* *
3060502 TACAGCGAAGCAGATTAAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
66 TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
*
3060567 AGTA
131 AGCA
3060571 GATTTGGCATC
1 GATTTGGCATC
3060582 TTCATATTCG
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 137 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (134 bp):
GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAAACATAGCAGATCTGACATTCCTGTGCT
TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
AGCA
Found at i:3060769 original size:44 final size:45
Alignment explanation
Indices: 3060645--3060793 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 45
3060635 TTTACATCGA
* * * * *
3060645 AGCAGATCCAAGATGATAGATTTGGCATCTTTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAAATTTGGCATCTCTGTATTAGACGGGG
* * * *
3060690 AACAAATCGGAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAAATTTGGCATCTCTGTATTAGACGGGG
* *
3060735 AGCAGATTGAAGA-AGCAAATTTGG-AGTCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAAATTTGGCA-TCTCTGTATTAGACGGGG
*
3060779 AGCAGATCAAAGATA
1 AGCAGATCGAAGATA
3060794 GCAGATATCG
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.01
44 38 0.44
45 48 0.55
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (45 bp):
AGCAGATCGAAGATAACAAATTTGGCATCTCTGTATTAGACGGGG
Found at i:3061176 original size:19 final size:19
Alignment explanation
Indices: 3061152--3061230 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
3061142 AATCTTTAAG
3061152 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3061171 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3061190 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3061207 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3061228 GAT
1 GAT
3061231 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3061182 original size:36 final size:36
Alignment explanation
Indices: 3061142--3061229 Score: 119
Period size: 36 Copynumber: 2.4 Consensus size: 36
3061132 ATGGAAATAT
3061142 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGACAATCTTAGATATGATATGC
3061178 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG--ACAATCTTAGATATGATATGC
*
3061214 AATCTTGAAGATATGA
1 AATCTTTAAGATATGA
3061230 TCTTGTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 2 0.04
36 29 0.63
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (36 bp):
AATCTTTAAGATATGACAATCTTAGATATGATATGC
Found at i:3070768 original size:18 final size:19
Alignment explanation
Indices: 3070747--3070786 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3070737 TACCTAAATT
* *
3070747 TATTTTTTAAA-TTTAATA
1 TATTTTTAAAACTTTAAAA
3070765 TATTTTTAAAACTTTAAAA
1 TATTTTTAAAACTTTAAAA
3070784 TAT
1 TAT
3070787 CATATCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTAAAACTTTAAAA
Found at i:3082059 original size:29 final size:29
Alignment explanation
Indices: 3082017--3082075 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3082007 TATGCTCATG
3082017 TAAGTTTTTTTTAATAAAAAGAAAAACAC
1 TAAGTTTTTTTTAATAAAAAGAAAAACAC
*
3082046 TAAGTTTTTTTTAATAAAAAGACAAACAC
1 TAAGTTTTTTTTAATAAAAAGAAAAACAC
3082075 T
1 T
3082076 TTCAAGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAGTTTTTTTTAATAAAAAGAAAAACAC
Found at i:3083016 original size:17 final size:17
Alignment explanation
Indices: 3082994--3083037 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3082984 TATACTTTCA
*
3082994 TAATTAAATTAAATTTT
1 TAATTAAATTAAAGTTT
* *
3083011 TAATTAAAATAAGGTTT
1 TAATTAAATTAAAGTTT
*
3083028 TAATCAAATT
1 TAATTAAATT
3083038 TCAATGTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (17 bp):
TAATTAAATTAAAGTTT
Found at i:3083929 original size:24 final size:23
Alignment explanation
Indices: 3083902--3083946 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3083892 TTAACACCTT
3083902 AATTGAATGTGATTTTCAATTAAA
1 AATTGAAT-TGATTTTCAATTAAA
* * *
3083926 AATTTAATTTATTTTTAATTA
1 AATTGAATTGATTTTCAATTA
3083947 TTTTAGGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (23 bp):
AATTGAATTGATTTTCAATTAAA
Found at i:3089430 original size:253 final size:253
Alignment explanation
Indices: 3089049--3089557 Score: 964
Period size: 253 Copynumber: 2.0 Consensus size: 253
3089039 CATCAAGCAA
3089049 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTGATGGGAAATAAACAAAAGCAGAGGTT
1 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTGATGGGAAATAAACAAAAGCAGAGGTT
*
3089114 AACATACAAGCACACAGAAAAGCGAAATAATATAACGGTATTGGGGAGCAGTGGAACCTTACATA
66 AACATACAAGCACACAGAAAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
*
3089179 TTACAATTTTCAATAGCAGCACCATTCCCAGCATTATCAGCCAAGTTCTCCAAGGTTGCTGATGA
131 TTACAATTTTCAATAGCAGCACCATTCCCAGCATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
*
3089244 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGATAATTATGCAT
196 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
3089302 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTGATGGGAAATAAACAAAAGCAGAGGTT
1 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTGATGGGAAATAAACAAAAGCAGAGGTT
*
3089367 AACATACAAGCACACAGAGAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
66 AACATACAAGCACACAGAAAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
**
3089432 TTGTAATTTTCAATAGCAGCACCATTCCCAGCATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
131 TTACAATTTTCAATAGCAGCACCATTCCCAGCATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
3089497 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
196 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
3089555 GCA
1 GCA
3089558 TTTCCCGAAA
Statistics
Matches: 250, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
253 250 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (253 bp):
GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTGATGGGAAATAAACAAAAGCAGAGGTT
AACATACAAGCACACAGAAAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
TTACAATTTTCAATAGCAGCACCATTCCCAGCATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
Found at i:3093978 original size:34 final size:34
Alignment explanation
Indices: 3093939--3094006 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3093929 AAGAAAAAGA
3093939 ACTCTTTAAATTCGTAAGATATAAGAAGAAACCC
1 ACTCTTTAAATTCGTAAGATATAAGAAGAAACCC
3093973 ACTCTTTAAATTCGTAAGATATAAGAAGAAACCC
1 ACTCTTTAAATTCGTAAGATATAAGAAGAAACCC
3094007 TAAAAAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (34 bp):
ACTCTTTAAATTCGTAAGATATAAGAAGAAACCC
Found at i:3095071 original size:26 final size:26
Alignment explanation
Indices: 3094995--3095071 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 26
3094985 CATTAAAGCT
*
3094995 AAACTTAGATACCAAATTGAAACAAAAA
1 AAAC-TAGATACTAAATT-AAACAAAAA
* *
3095023 AAATCAAG-TACTAAAGTAGAACAAAAA
1 AAA-CTAGATACTAAATTA-AACAAAAA
3095050 AAACTAGATACTAAATTAAACA
1 AAACTAGATACTAAATTAAACA
3095072 TTAAAACTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 8 0.20
27 27 0.66
28 5 0.12
29 1 0.02
ACGTcount: A:0.61, C:0.13, G:0.08, T:0.18
Consensus pattern (26 bp):
AAACTAGATACTAAATTAAACAAAAA
Found at i:3096996 original size:45 final size:45
Alignment explanation
Indices: 3096947--3097047 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
3096937 GTTTAACTAA
*
3096947 AAAAATAT-AAAGTTTAGAAATTGAGAA-ATTGAAAAGTAAAATTTG
1 AAAAATATGAAA-TCTAGAAATTGA-AATATTGAAAAGTAAAATTTG
* * **
3096992 AAAAATATGAAATCTAGAAATTGAAATTTTGAAATGTTCAATTTG
1 AAAAATATGAAATCTAGAAATTGAAATATTGAAAAGTAAAATTTG
3097037 AAAAAT-TGAAA
1 AAAAATATGAAA
3097048 ATAAAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 7 0.14
45 39 0.80
46 3 0.06
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (45 bp):
AAAAATATGAAATCTAGAAATTGAAATATTGAAAAGTAAAATTTG
Found at i:3099338 original size:18 final size:18
Alignment explanation
Indices: 3099315--3099349 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3099305 TTCTTCCCTG
*
3099315 AAAAAAGGGAAAAGAAAA
1 AAAAAAGAGAAAAGAAAA
*
3099333 AAAAAAGAGCAAAGAAA
1 AAAAAAGAGAAAAGAAA
3099350 CTCTTCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAGAAAA
Found at i:3103191 original size:23 final size:22
Alignment explanation
Indices: 3103143--3103193 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
3103133 TTAAAAAGAT
**
3103143 TAAGTAATTTTTTTTTGTTAAA
1 TAAGTAATTTTTTTTTGAGAAA
3103165 -AAGTAAGTTTTTTTTTGAGAAA
1 TAAGTAA-TTTTTTTTTGAGAAA
3103187 TAAGTAA
1 TAAGTAA
3103194 ATATTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (22 bp):
TAAGTAATTTTTTTTTGAGAAA
Found at i:3110655 original size:23 final size:23
Alignment explanation
Indices: 3110602--3110656 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3110592 AATTTAAATA
*
3110602 AATATTGAATTATACTTTATTAC
1 AATATTAAATTATACTTTATTAC
* *
3110625 AATATTAAATTATATTTTCATTAT
1 AATATTAAATTATACTTT-ATTAC
3110649 AAT-TTAAA
1 AATATTAAA
3110657 CTATTCAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (23 bp):
AATATTAAATTATACTTTATTAC
Found at i:3113700 original size:8 final size:8
Alignment explanation
Indices: 3113689--3113731 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
3113679 ATTAAATAAT
3113689 TAATAAAA
1 TAATAAAA
3113697 TAATAATAA
1 TAATAA-AA
*
3113706 TGAA-ATAA
1 T-AATAAAA
3113714 TAATAAAA
1 TAATAAAA
3113722 TAATAAAA
1 TAATAAAA
3113730 TA
1 TA
3113732 TCTCATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 22 0.73
9 4 0.13
10 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (8 bp):
TAATAAAA
Found at i:3113703 original size:3 final size:3
Alignment explanation
Indices: 3113683--3113731 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
3113673 TTTTATATTA
*
3113683 AAT AATT AAT AA- AAT AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3113726 AA- AAT A
1 AAT AAT A
3113732 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3113703 original size:11 final size:11
Alignment explanation
Indices: 3113682--3113727 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 11
3113672 CTTTTATATT
3113682 AAATAATTAATA
1 AAATAA-TAATA
3113694 AAATAATAATAA
1 AAATAATAAT-A
3113706 TGAAATAATAATA
1 --AAATAATAATA
3113719 AAATAATAA
1 AAATAATAA
3113728 AATATCTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 13 0.42
12 7 0.23
13 1 0.03
14 10 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AAATAATAATA
Found at i:3113711 original size:14 final size:14
Alignment explanation
Indices: 3113683--3113731 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
3113673 TTTTATATTA
3113683 AATAATTAATAAAAT
1 AATAA-TAATAAAAT
*
3113698 AATAATAATGAAAT
1 AATAATAATAAAAT
3113712 AATAATAA-AATAAT
1 AATAATAATAA-AAT
3113726 AA-AATA
1 AATAATA
3113732 TCTCATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.16
14 21 0.68
15 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:3113754 original size:20 final size:21
Alignment explanation
Indices: 3113701--3113776 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
3113691 ATAAAATAAT
* *
3113701 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
3113720 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
3113741 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
3113762 TAATCATAAAATATC
1 -AATAATAAAATATC
3113777 ATCAAAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:3117591 original size:15 final size:16
Alignment explanation
Indices: 3117573--3117605 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3117563 AAGATGTTTT
3117573 AAGAAAAGAAAAA-AA
1 AAGAAAAGAAAAAGAA
3117588 AAGAAAAGAAAAAGAA
1 AAGAAAAGAAAAAGAA
3117604 AA
1 AA
3117606 CCTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAA
Found at i:3117601 original size:11 final size:10
Alignment explanation
Indices: 3117576--3117605 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3117566 ATGTTTTAAG
3117576 AAAAGAAAAA
1 AAAAGAAAAA
3117586 AAAAGAAAAGA
1 AAAAGAAAA-A
3117597 AAAAGAAAA
1 AAAAGAAAA
3117606 CCTTACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:3133718 original size:56 final size:56
Alignment explanation
Indices: 3133657--3133842 Score: 169
Period size: 56 Copynumber: 3.2 Consensus size: 56
3133647 TTGAAAATGC
*
3133657 TTTAATTATGATTCAAATTTTTTTATTATAATATCTGAATTAATAAGTTAATATAT
1 TTTAATTATGATTCAAATTTTTTTATTATAATATTTGAATTAATAAGTTAATATAT
* * * * * * *
3133713 TTTAATTAT-ATT-TAATAATTATTATAAAGTGAAATTATATTATAAGTTAAATATGTTGAAAAT
1 TTTAATTATGATTCAAAT-TTTTTTAT-TA-T--AA-TAT-TT-GAA-TTA-ATAAGTT-AATAT
*
3133776 GT
55 AT
*
3133778 TTTAATTATGATTCAAATTTTTTTATTATAATATTTGAATTGATAAGTTAATATAT
1 TTTAATTATGATTCAAATTTTTTTATTATAATATTTGAATTAATAAGTTAATATAT
3133834 TTTAATTAT
1 TTTAATTAT
3133843 ATTTAATAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
54 3 0.03
55 9 0.09
56 24 0.24
57 7 0.07
58 2 0.02
59 4 0.04
60 5 0.05
61 4 0.04
62 4 0.04
63 3 0.03
64 7 0.07
65 15 0.15
66 9 0.09
67 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (56 bp):
TTTAATTATGATTCAAATTTTTTTATTATAATATTTGAATTAATAAGTTAATATAT
Found at i:3133746 original size:121 final size:121
Alignment explanation
Indices: 3133615--3133853 Score: 424
Period size: 121 Copynumber: 2.0 Consensus size: 121
3133605 CCTTAATTAC
* * *
3133615 ATAAAGTGAAATTATATTGTAGGTTGAATATGTTGAAAATGCTTTAATTATGATTCAAATTTTTT
1 ATAAAGTGAAATTATATTATAAGTTAAATATGTTGAAAATGCTTTAATTATGATTCAAATTTTTT
3133680 TATTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAATAATTATT
66 TATTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAATAATTATT
*
3133736 ATAAAGTGAAATTATATTATAAGTTAAATATGTTGAAAATGTTTTAATTATGATTCAAATTTTTT
1 ATAAAGTGAAATTATATTATAAGTTAAATATGTTGAAAATGCTTTAATTATGATTCAAATTTTTT
* *
3133801 TATTATAATATTTGAATTGATAAGTTAATATATTTTAATTATATTTAATAATT
66 TATTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAATAATT
3133854 TAAATATAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.49
Consensus pattern (121 bp):
ATAAAGTGAAATTATATTATAAGTTAAATATGTTGAAAATGCTTTAATTATGATTCAAATTTTTT
TATTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAATAATTATT
Found at i:3134042 original size:13 final size:14
Alignment explanation
Indices: 3134011--3134041 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3134001 TCGACTAAAA
*
3134011 TTTTATTTAAATTT
1 TTTTATATAAATTT
3134025 TTTTATATAAATTT
1 TTTTATATAAATTT
3134039 TTT
1 TTT
3134042 ACTCACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATATAAATTT
Found at i:3134294 original size:14 final size:14
Alignment explanation
Indices: 3134269--3134301 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3134259 AATATTTTAT
3134269 AAATATTAAAATTGA
1 AAATATTAAAATT-A
3134284 AAATA-TAAAATTA
1 AAATATTAAAATTA
3134297 AAATA
1 AAATA
3134302 ATATTGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 7 0.39
15 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AAATATTAAAATTA
Found at i:3136971 original size:30 final size:29
Alignment explanation
Indices: 3136932--3136989 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
3136922 AGAAGAAGTA
* *
3136932 TAAACATATTGGGTCATTTATGTAAAAATT
1 TAAAAATATTGGGCCATTTAT-TAAAAATT
3136962 TAAAAATATTGGGCCATTTATTAAAAAT
1 TAAAAATATTGGGCCATTTATTAAAAAT
3136990 AAAAAAAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (29 bp):
TAAAAATATTGGGCCATTTATTAAAAATT
Found at i:3136996 original size:29 final size:30
Alignment explanation
Indices: 3136937--3136996 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3136927 AAGTATAAAC
* **
3136937 ATATTGGGTCATTTATGTAAAAATTTAAAA
1 ATATTGGGCCATTTATGTAAAAATAAAAAA
3136967 ATATTGGGCCATTTAT-TAAAAATAAAAAA
1 ATATTGGGCCATTTATGTAAAAATAAAAAA
3136996 A
1 A
3136997 GACGGAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (30 bp):
ATATTGGGCCATTTATGTAAAAATAAAAAA
Found at i:3146211 original size:57 final size:57
Alignment explanation
Indices: 3146150--3146265 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
3146140 TATAAACAAA
3146150 ATTTCATTTTCTTTTTAATAATTATGTCAAACTTCTTTATTGATATATCTTTTAGAG
1 ATTTCATTTTCTTTTTAATAATTATGTCAAACTTCTTTATTGATATATCTTTTAGAG
3146207 ATTTCATTTTCTTTTTAATAATTATGTCAAACTTCTTTATTGATATATCTTTTAGAG
1 ATTTCATTTTCTTTTTAATAATTATGTCAAACTTCTTTATTGATATATCTTTTAGAG
3146264 AT
1 AT
3146266 CGATTTGAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.54
Consensus pattern (57 bp):
ATTTCATTTTCTTTTTAATAATTATGTCAAACTTCTTTATTGATATATCTTTTAGAG
Found at i:3148342 original size:28 final size:28
Alignment explanation
Indices: 3148307--3148370 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
3148297 TATTTAAAAT
3148307 AATATAAAT-CTAAATATTTTTATAATTA
1 AATATAAATAC-AAATATTTTTATAATTA
* *
3148335 AATTTAAATACAAATATTTTTATTATTA
1 AATATAAATACAAATATTTTTATAATTA
3148363 AATATAAA
1 AATATAAA
3148371 ATTAAGTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATAAATACAAATATTTTTATAATTA
Found at i:3152822 original size:54 final size:57
Alignment explanation
Indices: 3152727--3152832 Score: 148
Period size: 54 Copynumber: 1.9 Consensus size: 57
3152717 CTATGTCATA
* *
3152727 ATTATTACTTATCTCTTAATTAAATTAAATATTAAGCGATAAATAATAAATAAATAT
1 ATTATTACTTATCTCTTAATTAAATTAAATAATAAGAGATAAATAATAAATAAATAT
*
3152784 ATTATTA-TT-TCTC-TAATT-AATTAAATTAATATGAGATAAATAATAAATA
1 ATTATTACTTATCTCTTAATTAAATTAAA-TAATAAGAGATAAATAATAAATA
3152833 GATGAGAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 7 0.16
54 25 0.56
55 4 0.09
56 2 0.04
57 7 0.16
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (57 bp):
ATTATTACTTATCTCTTAATTAAATTAAATAATAAGAGATAAATAATAAATAAATAT
Found at i:3157571 original size:17 final size:16
Alignment explanation
Indices: 3157531--3157574 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3157521 CAGATAATTT
3157531 AAAAT-TTATAAATTCA
1 AAAATATTA-AAATTCA
3157547 AAAA-ATTAAAATTCAA
1 AAAATATTAAAATTC-A
3157563 AAAATATTAAAA
1 AAAATATTAAAA
3157575 AACTCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAAATTCA
Found at i:3161313 original size:17 final size:17
Alignment explanation
Indices: 3161280--3161314 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3161270 TAACCAATTC
* *
3161280 AATTAAAAATTATTAAA
1 AATTAAAAATAAATAAA
3161297 AATTAAAAATAAATAAA
1 AATTAAAAATAAATAAA
3161314 A
1 A
3161315 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAAAATAAATAAA
Found at i:3164669 original size:157 final size:157
Alignment explanation
Indices: 3164383--3164695 Score: 617
Period size: 157 Copynumber: 2.0 Consensus size: 157
3164373 TTTTGAAATA
3164383 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
1 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
3164448 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAATATCAAAACAAATATA
66 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAATATCAAAACAAATATA
3164513 TGCTATGTGAAGGAGAGGCCACATATT
131 TGCTATGTGAAGGAGAGGCCACATATT
3164540 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
1 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
*
3164605 GCAGGGGTGCCTAAAAAGATACATCATAGTCCCTAACACATCAAAAAAATATCAAAACAAATATA
66 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAATATCAAAACAAATATA
3164670 TGCTATGTGAAGGAGAGGCCACATAT
131 TGCTATGTGAAGGAGAGGCCACATAT
3164696 GACAATTATT
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (157 bp):
CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAATATCAAAACAAATATA
TGCTATGTGAAGGAGAGGCCACATATT
Found at i:3175377 original size:20 final size:20
Alignment explanation
Indices: 3175352--3175391 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3175342 TATTGGAGAA
3175352 AGGGAGAAAAATAAACAGAG
1 AGGGAGAAAAATAAACAGAG
3175372 AGGGAGAAAAATAAACAGAG
1 AGGGAGAAAAATAAACAGAG
3175392 GAAGAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.30, T:0.05
Consensus pattern (20 bp):
AGGGAGAAAAATAAACAGAG
Found at i:3175398 original size:20 final size:20
Alignment explanation
Indices: 3175355--3175400 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3175345 TGGAGAAAGG
*
3175355 GAGAAAAATAAACAGAGAGG
1 GAGAAAAATAAACAGAGAGA
3175375 GAGAAAAATAAACAGAG-GAA
1 GAGAAAAATAAACAGAGAG-A
3175395 GAGAAA
1 GAGAAA
3175401 TAACCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.63, C:0.04, G:0.28, T:0.04
Consensus pattern (20 bp):
GAGAAAAATAAACAGAGAGA
Found at i:3175401 original size:18 final size:19
Alignment explanation
Indices: 3175356--3175403 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
3175346 GGAGAAAGGG
*
3175356 AGAAAAATAAACAGAGAGGG
1 AGAAAAATAAACA-AGAGGA
3175376 AGAAAAATAAAC-AGAGGA
1 AGAAAAATAAACAAGAGGA
*
3175394 AGAGAAATAA
1 AGAAAAATAA
3175404 CCAAAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
20 12 0.46
ACGTcount: A:0.65, C:0.04, G:0.25, T:0.06
Consensus pattern (19 bp):
AGAAAAATAAACAAGAGGA
Found at i:3177727 original size:11 final size:11
Alignment explanation
Indices: 3177705--3177739 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3177695 TAAAATCTTA
3177705 AAAAAAC-A-T
1 AAAAAACTATT
3177714 AAAAAACTATT
1 AAAAAACTATT
3177725 AAAAAACTATT
1 AAAAAACTATT
3177736 AAAA
1 AAAA
3177740 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.29
10 1 0.04
11 16 0.67
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAACTATT
Found at i:3177739 original size:21 final size:20
Alignment explanation
Indices: 3177686--3177749 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
3177676 TAAAAAAATG
* *
3177686 AAAAATTATTAAAATCTTAA
1 AAAAACTATTAAAAACTTAA
* *
3177706 AAAAAC-ATAAAAAACTATTA
1 AAAAACTATTAAAAACT-TAA
*
3177726 AAAAACTATT-AAAATTTAA
1 AAAAACTATTAAAAACTTAA
3177745 AAAAA
1 AAAAA
3177750 TATATATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 15 0.43
20 18 0.51
21 2 0.06
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAACTATTAAAAACTTAA
Found at i:3179745 original size:15 final size:15
Alignment explanation
Indices: 3179722--3179770 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3179712 GGTTAAACGG
*
3179722 TTATGATTTTTTATA
1 TTATTATTTTTTATA
3179737 TTATTATTTTTTATGA
1 TTATTATTTTTTAT-A
3179753 TT-TT-TTTATTTA-A
1 TTATTATTT-TTTATA
3179766 TTATT
1 TTATT
3179771 TTTGAACTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 19 0.63
16 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (15 bp):
TTATTATTTTTTATA
Found at i:3179756 original size:25 final size:26
Alignment explanation
Indices: 3179722--3179773 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
3179712 GGTTAAACGG
3179722 TTATGA-TTTTTTATATT-ATTATTTT
1 TTATGATTTTTTTAT-TTAATTATTTT
3179747 TTATGATTTTTTTATTTAATTATTTT
1 TTATGATTTTTTTATTTAATTATTTT
3179773 T
1 T
3179774 GAACTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (26 bp):
TTATGATTTTTTTATTTAATTATTTT
Found at i:3179768 original size:26 final size:25
Alignment explanation
Indices: 3179722--3179773 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
3179712 GGTTAAACGG
3179722 TTATGATTTTTTATATTATTATTTT
1 TTATGATTTTTTATATTATTATTTT
3179747 TTATGATTTTTT-TATTTAATTATTTT
1 TTATGATTTTTTATA-TT-ATTATTTT
3179773 T
1 T
3179774 GAACTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 2 0.08
25 14 0.56
26 9 0.36
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATGATTTTTTATATTATTATTTT
Found at i:3184354 original size:94 final size:94
Alignment explanation
Indices: 3184250--3184433 Score: 287
Period size: 94 Copynumber: 2.0 Consensus size: 94
3184240 TAATTGAGAA
* * *
3184250 AAAAAAGTACCTGCTGCAAGAATGGTATCACCAACTCTAGAATTTCAAAAACAAAAAGGGAAGCG
1 AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCA
3184315 CACAGAGGCAACGAAAGAGGAAGCATGAG
66 CACAGAGGCAACGAAAGAGGAAGCATGAG
* ** *
3184344 AAAAAGGTACCTACTGCAAGAATGGTATTGCCAGCTCTAGAACTTCAAAAACAAAAAGGGAAGCA
1 AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCA
* *
3184409 CGCAGAGGCAATGAAAGAGGAAGCA
66 CACAGAGGCAACGAAAGAGGAAGCA
3184434 CTCAGGCTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (94 bp):
AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCA
CACAGAGGCAACGAAAGAGGAAGCATGAG
Found at i:3186582 original size:21 final size:22
Alignment explanation
Indices: 3186534--3186582 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
3186524 CCTCAAAAGT
*
3186534 AGATGCTTTTTTGTTGGCTTCA
1 AGATGTTTTTTTGTTGGCTTCA
3186556 AGATGTTTTTTTGTTGGCTTCA
1 AGATGTTTTTTTGTTGGCTTCA
3186578 A-ATGT
1 AGATGT
3186583 AGTTGAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.16, C:0.10, G:0.22, T:0.51
Consensus pattern (22 bp):
AGATGTTTTTTTGTTGGCTTCA
Found at i:3197083 original size:28 final size:28
Alignment explanation
Indices: 3197043--3197100 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3197033 TAATGATTTG
3197043 CTTATTAATGTGATGCAACTCACAGAAT
1 CTTATTAATGTGATGCAACTCACAGAAT
3197071 CTTATTAATGTGATGCAACTCACAGAAT
1 CTTATTAATGTGATGCAACTCACAGAAT
3197099 CT
1 CT
3197101 CTAAAGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (28 bp):
CTTATTAATGTGATGCAACTCACAGAAT
Found at i:3199281 original size:13 final size:15
Alignment explanation
Indices: 3199263--3199300 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
3199253 TTTAATCAAA
3199263 ATTTTAAATT-TAT-
1 ATTTTAAATTATATC
3199276 ATTTTAAATTATATC
1 ATTTTAAATTATATC
3199291 ATATTTAAAT
1 AT-TTTAAAT
3199301 AAATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.45
14 3 0.14
15 2 0.09
16 7 0.32
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAAATTATATC
Found at i:3201121 original size:28 final size:28
Alignment explanation
Indices: 3201081--3201138 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3201071 TAATGATTTG
3201081 CTTATTAATGTGATGCAACTCACAGAAT
1 CTTATTAATGTGATGCAACTCACAGAAT
3201109 CTTATTAATGTGATGCAACTCACAGAAT
1 CTTATTAATGTGATGCAACTCACAGAAT
3201137 CT
1 CT
3201139 CTAAAGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (28 bp):
CTTATTAATGTGATGCAACTCACAGAAT
Found at i:3204224 original size:28 final size:28
Alignment explanation
Indices: 3204193--3204248 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3204183 TTGTAATCAA
3204193 ATTTGAAAGGAGACCTTTATTTATTTAC
1 ATTTGAAAGGAGACCTTTATTTATTTAC
3204221 ATTTGAAAGGAGACCTTTATTTATTTAC
1 ATTTGAAAGGAGACCTTTATTTATTTAC
3204249 TTATCATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (28 bp):
ATTTGAAAGGAGACCTTTATTTATTTAC
Found at i:3205211 original size:117 final size:117
Alignment explanation
Indices: 3205005--3205245 Score: 473
Period size: 117 Copynumber: 2.1 Consensus size: 117
3204995 TGATAGCATG
*
3205005 CTTGCCTTGGCTCATATTTTTAACCTCTCCCTTCAATTAATTTTGAAAGATGTCAAAAGATATTA
1 CTTGCCTTGGCTCATATTTTCAACCTCTCCCTTCAATTAATTTTGAAAGATGTCAAAAGATATTA
3205070 AATCCTGTGGTTGGGATCAGTAACTGATTGAGAAGCTTTATAAGTATTTCCT
66 AATCCTGTGGTTGGGATCAGTAACTGATTGAGAAGCTTTATAAGTATTTCCT
3205122 CTTGCCTTGGCTCATATTTTCAACCTCTCCCTTCAATTAATTTTGAAAGATGTCAAAAGATATTA
1 CTTGCCTTGGCTCATATTTTCAACCTCTCCCTTCAATTAATTTTGAAAGATGTCAAAAGATATTA
3205187 AATCCTGTGGTTGGGATCAGTAACTGATTGAGAAGCTTTATAAGTATTTCCT
66 AATCCTGTGGTTGGGATCAGTAACTGATTGAGAAGCTTTATAAGTATTTCCT
3205239 CTTGCCT
1 CTTGCCT
3205246 AGCATGTAAT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 123 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (117 bp):
CTTGCCTTGGCTCATATTTTCAACCTCTCCCTTCAATTAATTTTGAAAGATGTCAAAAGATATTA
AATCCTGTGGTTGGGATCAGTAACTGATTGAGAAGCTTTATAAGTATTTCCT
Found at i:3217917 original size:33 final size:33
Alignment explanation
Indices: 3217879--3217977 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
3217869 GATTGAGTGG
*
3217879 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
*
3217912 GAGTGTTTTGCTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
*
3217945 GGGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
3217978 CAAGAAGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.17, C:0.10, G:0.41, T:0.31
Consensus pattern (33 bp):
GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
Found at i:3222710 original size:26 final size:28
Alignment explanation
Indices: 3222651--3222712 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
3222641 AAAATATTTT
*
3222651 TATAAATTAATCTATTTTTATTTTCATGCA
1 TATAAATTAATCTA--TATATTTTCATGCA
*
3222681 TATAAATTAATCTA-ATATTTTTAT-CA
1 TATAAATTAATCTATATATTTTCATGCA
3222707 TATAAA
1 TATAAA
3222713 GATTCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.27
27 8 0.27
30 14 0.47
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (28 bp):
TATAAATTAATCTATATATTTTCATGCA
Found at i:3225807 original size:24 final size:24
Alignment explanation
Indices: 3225780--3225830 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3225770 ACTAAGCTAT
*
3225780 GATGTTTCGTACAAAAAATACGAA
1 GATGTTTCATACAAAAAATACGAA
* *
3225804 GATGTTTCATACAAGAAATGCGAA
1 GATGTTTCATACAAAAAATACGAA
3225828 GAT
1 GAT
3225831 TGCAAGCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (24 bp):
GATGTTTCATACAAAAAATACGAA
Found at i:3228010 original size:20 final size:20
Alignment explanation
Indices: 3227960--3228018 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 20
3227950 GAATTAAAAA
*
3227960 AAATCTTAATAAAA-ATATT
1 AAATTTTAATAAAATATATT
3227979 --ATTTTAATAAAATAT-TT
1 AAATTTTAATAAAATATATT
3227996 AAATTTTATATAAAATATATT
1 AAATTTTA-ATAAAATATATT
3228017 AA
1 AA
3228019 TTATATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 13 0.38
18 2 0.06
19 6 0.18
20 9 0.26
21 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTTAATAAAATATATT
Found at i:3228020 original size:20 final size:19
Alignment explanation
Indices: 3227965--3228020 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
3227955 AAAAAAAATC
3227965 TTAATAAAA-ATATT-ATT
1 TTAATAAAATATATTAATT
3227982 TTAATAAAATAT-TTAAATT
1 TTAATAAAATATATT-AATT
3228001 TTATATAAAATATATTAATT
1 TTA-ATAAAATATATTAATT
3228021 ATATTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 6 0.18
20 13 0.38
21 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAAAATATATTAATT
Found at i:3235897 original size:33 final size:30
Alignment explanation
Indices: 3235831--3235898 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
3235821 AAATGATATT
*
3235831 TTTTGATTAAATAAAAAAAGAAGAAGCTAG
1 TTTTGATTAAATAAAAAAAGAAGAAGATAG
*
3235861 TTTTGATTAAAGTAATGAAAGAGAAGAGAGAT-G
1 TTTTGATTAAA-TAA--AAAAAGAAGA-AGATAG
3235894 TTTTG
1 TTTTG
3235899 TGTTTTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 11 0.34
31 3 0.09
33 15 0.47
34 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.31
Consensus pattern (30 bp):
TTTTGATTAAATAAAAAAAGAAGAAGATAG
Found at i:3239456 original size:20 final size:19
Alignment explanation
Indices: 3239431--3239502 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
3239421 TTTTTTACTA
3239431 TTATAATCAAATATCTGTTT
1 TTATAA-CAAATATCTGTTT
* *
3239451 TTATAACAAAT-TTTAATTACT
1 TTATAACAAATATCT-GTT--T
*
3239472 ATTATAGTCAAATATCTGTTT
1 -TTATA-ACAAATATCTGTTT
3239493 TTATAACAAA
1 TTATAACAAA
3239503 ATTTAATACC
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 2 0.05
19 11 0.28
20 11 0.28
21 2 0.05
22 5 0.12
23 7 0.17
24 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (19 bp):
TTATAACAAATATCTGTTT
Found at i:3239476 original size:42 final size:42
Alignment explanation
Indices: 3239425--3239509 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
3239415 CTTTAATTTT
*
3239425 TTACTATTATAATCAAATATCTGTTTTTATAACAAATTTTAA
1 TTACTATTATAATCAAATATCTGTTTTTATAACAAAATTTAA
*
3239467 TTACTATTATAGTCAAATATCTGTTTTTATAACAAAATTTAA
1 TTACTATTATAATCAAATATCTGTTTTTATAACAAAATTTAA
3239509 T
1 T
3239510 ACCCAGAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (42 bp):
TTACTATTATAATCAAATATCTGTTTTTATAACAAAATTTAA
Found at i:3241628 original size:46 final size:46
Alignment explanation
Indices: 3241561--3241735 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
3241551 TGTAACCCGC
3241561 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
3241607 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
3241657 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
3241700 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
3241736 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 63 0.58
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:3241681 original size:93 final size:93
Alignment explanation
Indices: 3241569--3241739 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3241559 GCCCATAAGT
** *
3241569 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3241634 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
3241662 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3241727 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3241740 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:3244799 original size:33 final size:30
Alignment explanation
Indices: 3244733--3244800 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
3244723 AAATGATATT
*
3244733 TTTTGATTAAATAAAAAAAGAAGAAGCTAG
1 TTTTGATTAAATAAAAAAAGAAGAAGATAG
*
3244763 TTTTGATTAAAGTAATGAAAGAGAAGAGAGAT-G
1 TTTTGATTAAA-TAA--AAAAAGAAGA-AGATAG
3244796 TTTTG
1 TTTTG
3244801 TGTTTTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 11 0.34
31 3 0.09
33 15 0.47
34 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.31
Consensus pattern (30 bp):
TTTTGATTAAATAAAAAAAGAAGAAGATAG
Found at i:3247008 original size:15 final size:15
Alignment explanation
Indices: 3246985--3247074 Score: 62
Period size: 15 Copynumber: 6.1 Consensus size: 15
3246975 TAATTAAATA
*
3246985 TATTATTATTATTAT
1 TATTATTACTATTAT
* *
3247000 TACTGTTATCT-TTAT
1 TATTATTA-CTATTAT
* *
3247015 TACTATTACTATTTT
1 TATTATTACTATTAT
3247030 TATTATTA-TATTAT
1 TATTATTACTATTAT
*
3247044 TA-TACTAACATATTAT
1 TATTA-TTAC-TATTAT
*
3247060 CATTATTA-TATTAT
1 TATTATTACTATTAT
3247074 T
1 T
3247075 TTTACCTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
13 2 0.03
14 17 0.29
15 27 0.47
16 10 0.17
17 2 0.03
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:3247087 original size:3 final size:3
Alignment explanation
Indices: 3246985--3247046 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
3246975 TAATTAAATA
* * * * *
3246985 TAT TAT TAT TAT TAT TAC TGT TAT CT-T TAT TAC TAT TAC TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
3247030 TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
3247047 ACTAACATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 3 0.07
3 42 0.91
4 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3247141 original size:16 final size:17
Alignment explanation
Indices: 3247122--3247171 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
3247112 TATTTCTCAC
*
3247122 TTATATTATATGT-TAT
1 TTATATTATATGTACAT
*
3247138 TTAT-TTACATGTACAT
1 TTATATTATATGTACAT
*
3247154 TTATA-TATATATACAT
1 TTATATTATATGTACAT
3247170 TT
1 TT
3247172 GTATATATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (17 bp):
TTATATTATATGTACAT
Found at i:3247176 original size:16 final size:16
Alignment explanation
Indices: 3247149--3247179 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3247139 TATTTACATG
3247149 TACATTTATATATATA
1 TACATTTATATATATA
*
3247165 TACATTTGTATATAT
1 TACATTTATATATAT
3247180 CGTTCCAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
TACATTTATATATATA
Found at i:3247311 original size:3 final size:3
Alignment explanation
Indices: 3247303--3247451 Score: 79
Period size: 3 Copynumber: 48.7 Consensus size: 3
3247293 TATTTCTAAC
* *
3247303 TAT TAT TAT TTT TAT GTAT ATAT TAT TAT T-T ATAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * * * * * * *
3247350 TAC TAT TACT AAA TAT TTT TAT TAT TAC TAT TAT TTT TGT TCCT T-T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
* * * **
3247396 TAT TAT TGTT TAT TAT CAT TA- TAT TAT TAT TAT TAC TCC TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3247441 TAT TAT CAT TA
1 TAT TAT TAT TA
3247452 CTGCTTTTTT
Statistics
Matches: 110, Mismatches: 28, Indels: 16
0.71 0.18 0.10
Matches are distributed among these distances:
2 5 0.05
3 92 0.84
4 13 0.12
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3247522 original size:22 final size:20
Alignment explanation
Indices: 3247492--3247538 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
3247482 TCATATACGT
3247492 TATTGTTTATTATTATTACTA
1 TATT-TTTATTATTATTACTA
3247513 TATTTTT-TTATTATTACTA
1 TATTTTTATTATTATTACTA
3247532 TATTTTT
1 TATTTTT
3247539 GTATTCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.73
20 3 0.12
21 4 0.15
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTTTATTATTATTACTA
Found at i:3250270 original size:25 final size:25
Alignment explanation
Indices: 3250233--3250288 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3250223 GGATAAAAAA
* *
3250233 AATAAATTAACATACACACAATAGT
1 AATAAATTAACATACAAACAATAAT
* * *
3250258 AATAAGTTCACATCCAAACAATAAT
1 AATAAATTAACATACAAACAATAAT
3250283 AATAAA
1 AATAAA
3250289 AAATATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.23
Consensus pattern (25 bp):
AATAAATTAACATACAAACAATAAT
Found at i:3250599 original size:25 final size:25
Alignment explanation
Indices: 3250504--3250618 Score: 92
Period size: 25 Copynumber: 4.5 Consensus size: 25
3250494 AAATAATATA
* *
3250504 AAAATAAATAATATA-ACAAGGTTT
1 AAAATAAATAATATATAAAAAGTTT
* *
3250528 AAAATAAATGATAAATGAAACCAA--TT
1 AAAATAAATAATATAT-AAA--AAGTTT
* * *
3250554 AAAGTAAAAAAAATACATAAAAAGTTT
1 AAA--ATAAATAATATATAAAAAGTTT
*
3250581 AAAATAAATAATATATAAAAATTTT
1 AAAATAAATAATATATAAAAAGTTT
3250606 AAAATAAATAATA
1 AAAATAAATAATA
3250619 AATGAAATGA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
24 13 0.18
25 33 0.46
26 7 0.10
27 8 0.11
28 10 0.14
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.27
Consensus pattern (25 bp):
AAAATAAATAATATATAAAAAGTTT
Found at i:3250992 original size:22 final size:21
Alignment explanation
Indices: 3250926--3250992 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
3250916 AAAGTAATAA
*
3250926 AATAAACAAGTTTAATACAAAT
1 AATAAATAAG-TTAATACAAAT
* * * *
3250948 AATATATGAGATATTA-AAA-
1 AATAAATAAGTTAATACAAAT
3250967 AATAAATAAGCTTAATACAAAT
1 AATAAATAAG-TTAATACAAAT
3250989 AATA
1 AATA
3250993 TATGTAAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 8 0.24
20 7 0.21
21 7 0.21
22 11 0.33
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (21 bp):
AATAAATAAGTTAATACAAAT
Found at i:3253616 original size:17 final size:18
Alignment explanation
Indices: 3253591--3253628 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
3253581 TAACTACATG
3253591 ATATATAAAAA-TTTTAA
1 ATATATAAAAACTTTTAA
*
3253608 ATATGTAAAAACTTTTAA
1 ATATATAAAAACTTTTAA
3253626 ATA
1 ATA
3253629 CATGTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
ATATATAAAAACTTTTAA
Found at i:3255355 original size:6 final size:6
Alignment explanation
Indices: 3255344--3255368 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3255334 TATGTGCTGT
3255344 TGTGGG TGTGGG TGTGGG TGTGGG T
1 TGTGGG TGTGGG TGTGGG TGTGGG T
3255369 TTGAAGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TGTGGG
Found at i:3256207 original size:18 final size:20
Alignment explanation
Indices: 3256175--3256219 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
3256165 AAAAATTAAT
*
3256175 ATTTTATTTATATTTT-T-TA
1 ATTTT-TTTAGATTTTATATA
3256194 ATTTTTTTAGATTTTATATA
1 ATTTTTTTAGATTTTATATA
3256214 ATTTTT
1 ATTTTT
3256220 AAAATTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 8 0.35
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTTTAGATTTTATATA
Found at i:3256544 original size:20 final size:21
Alignment explanation
Indices: 3256516--3256559 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
3256506 AAGCCTATGG
3256516 AAATATATA-AAAATATTATAA
1 AAATATATATAAAAT-TTATAA
*
3256537 AAAT-TATATGAAATTTATAA
1 AAATATATATAAAATTTATAA
3256557 AAA
1 AAA
3256560 AAATCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATATATATAAAATTTATAA
Found at i:3261810 original size:25 final size:25
Alignment explanation
Indices: 3261761--3261813 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
3261751 AGATAAAATA
3261761 TTTAAATTATATTTATTTAACTTAAT
1 TTTAAATTATATTTA-TTAACTTAAT
*
3261787 TTTAAATTATATTTCA-TAATTTAAT
1 TTTAAATTATATTT-ATTAACTTAAT
3261812 TT
1 TT
3261814 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 10 0.40
26 14 0.56
27 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAAATTATATTTATTAACTTAAT
Found at i:3266902 original size:21 final size:22
Alignment explanation
Indices: 3266873--3266919 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3266863 CAGAAGGAGT
*
3266873 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3266895 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3266916 GAGT
1 GAGT
3266920 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3271351 original size:16 final size:16
Alignment explanation
Indices: 3271330--3271362 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3271320 AGGAGTCAAA
3271330 TATTTGTAGTACTTAT
1 TATTTGTAGTACTTAT
3271346 TATTTGTAGTACTTAT
1 TATTTGTAGTACTTAT
3271362 T
1 T
3271363 TCCAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (16 bp):
TATTTGTAGTACTTAT
Found at i:3272907 original size:10 final size:10
Alignment explanation
Indices: 3272887--3272920 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3272877 GTTTTAATAC
3272887 TTTTA-TATT
1 TTTTACTATT
3272896 TTTTACTATT
1 TTTTACTATT
*
3272906 TTTTACTATG
1 TTTTACTATT
3272916 TTTTA
1 TTTTA
3272921 ATTTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTTACTATT
Found at i:3273695 original size:22 final size:22
Alignment explanation
Indices: 3273645--3273696 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3273635 CATCAATACT
*
3273645 AATATTGTAGGAATATTCTGTA
1 AATATTTTAGGAATATTCTGTA
*
3273667 AATATTTTAGGAATATTTTGTA
1 AATATTTTAGGAATATTCTGTA
*
3273689 GATATTTT
1 AATATTTT
3273697 CTTTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (22 bp):
AATATTTTAGGAATATTCTGTA
Found at i:3274771 original size:22 final size:22
Alignment explanation
Indices: 3274743--3274787 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3274733 AGGAGGAGTG
3274743 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
3274765 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
3274787 T
1 T
3274788 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:3286576 original size:21 final size:21
Alignment explanation
Indices: 3286550--3286590 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3286540 ATCTGCTCAA
* *
3286550 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3286571 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3286591 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3292104 original size:24 final size:24
Alignment explanation
Indices: 3292065--3292112 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3292055 AAAAAAACAT
3292065 AAAATTTTAAATATATATATTTTA
1 AAAATTTTAAATATATATATTTTA
*
3292089 AAAATATTTAAA-ATATATTTTTTA
1 AAAAT-TTTAAATATATATATTTTA
3292113 GTCTAGTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATTTTAAATATATATATTTTA
Found at i:3292329 original size:12 final size:13
Alignment explanation
Indices: 3292300--3292330 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3292290 ATCAGTTCAA
3292300 TCGATTTTTTACC
1 TCGATTTTTTACC
3292313 TCGATTTTTTACC
1 TCGATTTTTTACC
3292326 -CGATT
1 TCGATT
3292331 CAACCAGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.16, C:0.23, G:0.10, T:0.52
Consensus pattern (13 bp):
TCGATTTTTTACC
Found at i:3294470 original size:27 final size:24
Alignment explanation
Indices: 3294429--3294483 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
3294419 TGTAAATTGT
3294429 AAATATCATTTATC-TATTGTTATA
1 AAATATCATTTATCTTA-TGTTATA
3294453 AAATATGCAATTTCATCTTATGTTATA
1 AAATAT-C-ATTT-ATCTTATGTTATA
3294480 AAAT
1 AAAT
3294484 CTTGATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.22
25 1 0.04
26 4 0.15
27 14 0.52
28 2 0.07
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (24 bp):
AAATATCATTTATCTTATGTTATA
Found at i:3294797 original size:16 final size:15
Alignment explanation
Indices: 3294773--3294802 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3294763 GAGAACAGTA
3294773 AAATATTAAAAAAAT
1 AAATATTAAAAAAAT
3294788 AAATACTTAAAAAAA
1 AAATA-TTAAAAAAA
3294803 ATAGACTTAT
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:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:3298122 original size:21 final size:21
Alignment explanation
Indices: 3298096--3298139 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3298086 AAAAAATCCT
*
3298096 AAAATTTCAAAAAT-ATCAGAA
1 AAAATTTAAAAAATCATCA-AA
3298117 AAAATTTAAAAAATCATCAAA
1 AAAATTTAAAAAATCATCAAA
3298138 AA
1 AA
3298140 TGAAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAATTTAAAAAATCATCAAA
Found at i:3301856 original size:28 final size:28
Alignment explanation
Indices: 3301816--3301872 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3301806 ACACGAGAAA
3301816 AAGATAGTTTATATTTTTTAACCATTGT
1 AAGATAGTTTATATTTTTTAACCATTGT
3301844 AAGATAGTTTATATTTTTTAACCATTGT
1 AAGATAGTTTATATTTTTTAACCATTGT
3301872 A
1 A
3301873 GTTAAAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (28 bp):
AAGATAGTTTATATTTTTTAACCATTGT
Found at i:3308849 original size:5 final size:5
Alignment explanation
Indices: 3308841--3308866 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3308831 AACAGATACA
3308841 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
3308867 GATGGTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Done.