Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
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 11 of 143
Found at i:3436581 original size:76 final size:76
Alignment explanation
Indices: 3436280--3437034 Score: 1149
Period size: 76 Copynumber: 10.0 Consensus size: 76
3436270 ATCAGACCGC
* * *
3436280 AGCAAGATCATTCCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3436345 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3436356 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3436420 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * *
3436431 ACCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTTTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3436495 ATTGAAGTAAG
66 ATTGAAGTAAG
*
3436506 AGCAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
1 AGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGA
3436570 AATTGAAGTAAG
65 AATTGAAGTAAG
* * * * * *
3436582 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTTATCTCTAAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3436647 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * *
3436658 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
*
3436723 ATTGAAGTCAG
66 ATTGAAGTAAG
* * *
3436734 AGCAAGATCGTCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3436799 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3436810 AGCAACG-TCATTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
1 AGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGA
*
3436874 AATTAAAGTAAG
65 AATTGAAGTAAG
* * * *
3436886 AGCAACATCAATTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3436951 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * *
3436962 AGCAACATCATTTCCTATTCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
3437027 ATTGAAGT
66 ATTGAAGT
3437035 CTTTATCTCT
Statistics
Matches: 637, Mismatches: 37, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
75 145 0.23
76 491 0.77
77 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (76 bp):
AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:3437347 original size:6 final size:6
Alignment explanation
Indices: 3437336--3437404 Score: 79
Period size: 6 Copynumber: 11.5 Consensus size: 6
3437326 ATTTTGAATT
* *
3437336 AATTTA AATTTA AATTT- ATTTTA AATTTA AATTCA ACTATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA A--ATTTA AATTTA
*
3437384 ATTTTA AATTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AAT
3437405 CAAATTATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.15
6 40 0.75
8 5 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:3437358 original size:17 final size:17
Alignment explanation
Indices: 3437320--3437401 Score: 82
Period size: 17 Copynumber: 5.0 Consensus size: 17
3437310 AACTTTTATG
*
3437320 TTTTAAATTTTGAA-TTA
1 TTTTAAA-TTTAAATTTA
*
3437337 ATTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
3437354 TTTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
**
3437371 -ACT--ATTTAAATTTA
1 TTTTAAATTTAAATTTA
3437385 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
3437402 AATCAAATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 6 0.12
17 35 0.67
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:3437409 original size:11 final size:12
Alignment explanation
Indices: 3437336--3437410 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
3437326 ATTTTGAATT
*
3437336 AATTTAAATTTA
1 AATTTAAATTCA
* *
3437348 AATTT-ATTTTA
1 AATTTAAATTCA
3437359 AATTTAAATTCA
1 AATTTAAATTCA
*
3437371 ACTATTTAAATT-T
1 A--ATTTAAATTCA
* *
3437384 ATTTTAAATTTA
1 AATTTAAATTCA
3437396 AATTTAAA-TCA
1 AATTTAAATTCA
3437407 AATT
1 AATT
3437411 ATGAAAATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
11 24 0.47
12 17 0.33
13 1 0.02
14 9 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTTAAATTCA
Found at i:3438125 original size:22 final size:20
Alignment explanation
Indices: 3438086--3438136 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
3438076 CTCATTGAAT
3438086 ATTTTAAAT-GCATTAATTA
1 ATTTTAAATAGCATTAATTA
*
3438105 ATGTTTTAAATAGTATTAATTA
1 A--TTTTAAATAGCATTAATTA
3438127 ATTTTAAATA
1 ATTTTAAATA
3438137 AAAGCATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
21 8 0.29
22 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (20 bp):
ATTTTAAATAGCATTAATTA
Found at i:3438156 original size:18 final size:19
Alignment explanation
Indices: 3438133--3438175 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3438123 ATTAATTTTA
3438133 AATAAAAGCATTAAT-AAT
1 AATAAAAGCATTAATAAAT
* **
3438151 AATAAATGTTTTAATAAAT
1 AATAAAAGCATTAATAAAT
3438170 AATAAA
1 AATAAA
3438176 TAAAAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
AATAAAAGCATTAATAAAT
Found at i:3439382 original size:29 final size:29
Alignment explanation
Indices: 3439317--3439596 Score: 163
Period size: 29 Copynumber: 9.6 Consensus size: 29
3439307 CTCCAAACAG
* *
3439317 TCCAAAAATTGCATTTTGA-CCCTAAAAT
1 TCCAAAAATTACATTTTGACCCCTAAACT
* * *
3439345 TCTAGAAAATTATATTTTGACCCCGAAACT
1 TCCA-AAAATTACATTTTGACCCCTAAACT
3439375 TCCAAAAATTAACATTTT-ACCCCTAAACT
1 TCCAAAAATT-ACATTTTGACCCCTAAACT
* * * * *
3439404 TTCGAAAATTCCATTTTTAACCCC--AATT
1 TCCAAAAATTACA-TTTTGACCCCTAAACT
*
3439432 TCACCAAAAATTACCATTTT-ACCCCCAAACTT
1 T--CCAAAAATTA-CATTTTGACCCCTAAAC-T
* *
3439464 TCC-AAAATTCCATTTTTGACCCCT--ATT
1 TCCAAAAATTACA-TTTTGACCCCTAAACT
3439491 TCACCAAAAATTACCATTTT-ACCCCTAAACTT
1 T--CCAAAAATTA-CATTTTGACCCCTAAAC-T
* * **
3439523 TCC-AAAATTCCATTTTAACCCC-AATTT
1 TCCAAAAATTACATTTTGACCCCTAAACT
*
3439550 TACCAAAAATTACCATTTT-ACCCCCAAACTT
1 T-CCAAAAATTA-CATTTTGACCCCTAAAC-T
*
3439581 TCC-AAAATTCCATTTT
1 TCCAAAAATTACATTTT
3439597 TAACCTCGAT
Statistics
Matches: 198, Mismatches: 28, Indels: 52
0.71 0.10 0.19
Matches are distributed among these distances:
27 4 0.02
28 28 0.14
29 92 0.46
30 61 0.31
31 9 0.05
32 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTACATTTTGACCCCTAAACT
Found at i:3439571 original size:117 final size:118
Alignment explanation
Indices: 3439376--3439632 Score: 417
Period size: 117 Copynumber: 2.2 Consensus size: 118
3439366 CCCGAAACTT
* *
3439376 CCAAAAATTAACATTTTACCCCTAAACTTTCGAAAATTCCATTTTTAACCCCAATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAA
* *
3439441 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCTATTTCA
66 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
3439494 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCCAATTTTACCAAAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAA
*
3439558 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
66 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
** * *
3439611 CTGAAATTTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
3439633 CGAGAGTCCA
Statistics
Matches: 129, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 90 0.70
118 39 0.30
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAA
ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:3439618 original size:58 final size:59
Alignment explanation
Indices: 3439376--3439633 Score: 392
Period size: 59 Copynumber: 4.4 Consensus size: 59
3439366 CCCGAAACTT
* * *
3439376 CCAAAAATTAACATTTTACCCCTAAACTTTCGAAAATTCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* *
3439435 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCTATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* *
3439494 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCCAATTTTA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* *
3439552 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
** * *
3439611 CTGAAATTTACCATTTTGCCCCC
1 CCAAAAATTACCATTTTACCCCC
3439634 GAGAGTCCAA
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 54 0.30
59 127 0.70
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
Found at i:3439683 original size:28 final size:28
Alignment explanation
Indices: 3439619--3439675 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3439609 CACTGAAATT
*
3439619 TACCATTTTGCCCCCGAGAGTCCAAAAT
1 TACCATTTTGCCCCCGAGAGTCCAAAAG
*
3439647 TACCATTTTGCCCCCGGGTA-TCCAAAAG
1 TACCATTTTGCCCCCGAG-AGTCCAAAAG
3439675 T
1 T
3439676 CCCGTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (28 bp):
TACCATTTTGCCCCCGAGAGTCCAAAAG
Found at i:3441019 original size:16 final size:16
Alignment explanation
Indices: 3440990--3441031 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3440980 TTTAACCCTT
*
3440990 TAAATATTATAAATTA
1 TAAATATTATAAATAA
3441006 TAAACTATTA-AAATAA
1 TAAA-TATTATAAATAA
3441022 TAAA-ATTATA
1 TAAATATTATA
3441032 TTTTTACGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 1 0.04
16 13 0.57
17 5 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATTATAAATAA
Found at i:3441117 original size:14 final size:14
Alignment explanation
Indices: 3441089--3441123 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3441079 ACACTTTGCG
3441089 AATAAAACAAGACA
1 AATAAAACAAGACA
3441103 AATAATAACAA-ACA
1 AATAA-AACAAGACA
3441117 AATAAAA
1 AATAAAA
3441124 ACCAATAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 13 0.65
15 5 0.25
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.11
Consensus pattern (14 bp):
AATAAAACAAGACA
Found at i:3442321 original size:21 final size:18
Alignment explanation
Indices: 3442306--3442376 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
3442296 TTTGGTGCTA
3442306 TTTTTTACTGTTTTGGTTG
1 TTTTTTACTGTTTTGG-TG
3442325 CTTTTTTTGA-TGTTTTGGTG
1 --TTTTTT-ACTGTTTTGGTG
*
3442345 TTTTTTACTGTTTTGATG
1 TTTTTTACTGTTTTGGTG
3442363 TTTTTTACTGTTTT
1 TTTTTTACTGTTTT
3442377 AGTTGTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
17 1 0.02
18 29 0.62
20 2 0.04
21 14 0.30
22 1 0.02
ACGTcount: A:0.07, C:0.06, G:0.18, T:0.69
Consensus pattern (18 bp):
TTTTTTACTGTTTTGGTG
Found at i:3442348 original size:18 final size:19
Alignment explanation
Indices: 3442295--3442376 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 19
3442285 TATATTGTTA
3442295 TTTTGGTGCTATTTTTTACTG
1 TTTTGGTGC--TTTTTTACTG
3442316 TTTTGGTTGCTTTTTTTGA-TG
1 TTTTGG-TGC-TTTTTT-ACTG
3442337 TTTTGGTG-TTTTTTACTG
1 TTTTGGTGCTTTTTTACTG
*
3442355 TTTTGATG-TTTTTTACTG
1 TTTTGGTGCTTTTTTACTG
3442373 TTTT
1 TTTT
3442377 AGTTGTTGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.02
18 29 0.52
20 2 0.04
21 20 0.36
22 4 0.07
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.67
Consensus pattern (19 bp):
TTTTGGTGCTTTTTTACTG
Found at i:3442430 original size:48 final size:48
Alignment explanation
Indices: 3442335--3442433 Score: 134
Period size: 49 Copynumber: 2.1 Consensus size: 48
3442325 CTTTTTTTGA
* * *
3442335 TGTTTTGGTGTTTTTTACTGTTTTGATGTTTTTTACTGTTTTAGTTGT
1 TGTTTTGGTATTTTTTACTGTTTTGATGTCTGTTACTGTTTTAGTTGT
3442383 TGTTTTGGTACTTTTTTACTGTTTTGATG-CTGTTA-T-TTTT-GTTGT
1 TGTTTTGGTA-TTTTTTACTGTTTTGATGTCTGTTACTGTTTTAGTTGT
3442428 TGTTTT
1 TGTTTT
3442434 TTTGCTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
45 11 0.23
46 4 0.09
47 1 0.02
48 13 0.28
49 18 0.38
ACGTcount: A:0.08, C:0.05, G:0.20, T:0.67
Consensus pattern (48 bp):
TGTTTTGGTATTTTTTACTGTTTTGATGTCTGTTACTGTTTTAGTTGT
Found at i:3442437 original size:48 final size:47
Alignment explanation
Indices: 3442337--3442481 Score: 125
Period size: 48 Copynumber: 3.0 Consensus size: 47
3442327 TTTTTTGATG
* * * * *
3442337 TTTTGGT-GTTTTTTACTGTTTTGATGTTTTTTACTGTTTTAGTTGTTG
1 TTTTGGTACTTTTTTACTGTTTTGATG-TTGTTA-TTTTTTTGTTGTTT
*
3442385 TTTTGGTACTTTTTTACTGTTTTGATGCTGTTATTTTTGTTGTTGTTT
1 TTTTGGTACTTTTTTACTGTTTTGATGTTGTTATTTTT-TTGTTGTTT
* * * * *
3442433 TTTTGCTATTTTTGTTATTATTTT--TGTTGTTATTTTTATTGTTATTT
1 TTTTGGTACTTTT-TTACTGTTTTGATGTTGTTATTTTT-TTGTTGTTT
3442480 TT
1 TT
3442482 GTTGTTTTGC
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
47 26 0.32
48 29 0.36
49 26 0.32
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.70
Consensus pattern (47 bp):
TTTTGGTACTTTTTTACTGTTTTGATGTTGTTATTTTTTTGTTGTTT
Found at i:3442501 original size:12 final size:12
Alignment explanation
Indices: 3442413--3442487 Score: 107
Period size: 12 Copynumber: 6.3 Consensus size: 12
3442403 GTTTTGATGC
3442413 TGTTATTTTTGT
1 TGTTATTTTTGT
*
3442425 TGTTGTTTTT-T
1 TGTTATTTTTGT
*
3442436 TGCTATTTTTGT
1 TGTTATTTTTGT
*
3442448 TATTATTTTTGT
1 TGTTATTTTTGT
*
3442460 TGTTATTTTTAT
1 TGTTATTTTTGT
3442472 TGTTATTTTTGT
1 TGTTATTTTTGT
3442484 TGTT
1 TGTT
3442488 TTGCTGTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
11 9 0.17
12 45 0.83
ACGTcount: A:0.09, C:0.01, G:0.15, T:0.75
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:3446235 original size:47 final size:47
Alignment explanation
Indices: 3446164--3446264 Score: 168
Period size: 47 Copynumber: 2.1 Consensus size: 47
3446154 TTGAAATGTC
*
3446164 TCGAAATAATAAATTCAAATCTAAAAATTTATATTCCTTAACTAAAT
1 TCGAAATAATAAATTCAAATCTAAAAACTTATATTCCTTAACTAAAT
*
3446211 TCGAAATAATAAATTCAGGA-CTAAAAACTTATATTCCTTAACTAAAT
1 TCGAAATAATAAATTCA-AATCTAAAAACTTATATTCCTTAACTAAAT
3446258 TCGAAAT
1 TCGAAAT
3446265 TGAGCTGGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
47 50 0.98
48 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (47 bp):
TCGAAATAATAAATTCAAATCTAAAAACTTATATTCCTTAACTAAAT
Found at i:3446631 original size:19 final size:19
Alignment explanation
Indices: 3446589--3446649 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
3446579 TCTCAACAAA
*
3446589 AAAAATATAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
3446608 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
* *
3446627 AAAAATTTTAAAAAATATAT
1 AAAAA-TTTAAAATATTTAT
3446647 AAA
1 AAA
3446650 GACGTTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 4 0.11
19 16 0.46
20 15 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:3450908 original size:16 final size:15
Alignment explanation
Indices: 3450887--3450925 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3450877 TTTAGAGTGA
*
3450887 AGAAAATTGGAAGGAT
1 AGAAAATTGAAAGG-T
3450903 AGAAAATTGAAAGGT
1 AGAAAATTGAAAGGT
*
3450918 AAAAAATT
1 AGAAAATT
3450926 AAATGGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (15 bp):
AGAAAATTGAAAGGT
Found at i:3454182 original size:19 final size:22
Alignment explanation
Indices: 3454158--3454197 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
3454148 TTTATTATTT
3454158 TATAAT-T-TAAAAA-AAATTA
1 TATAATCTCTAAAAATAAATTA
3454177 TATAATCTCTAAAAATAAATT
1 TATAATCTCTAAAAATAAATT
3454198 CAAACCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAATCTCTAAAAATAAATTA
Found at i:3456929 original size:13 final size:13
Alignment explanation
Indices: 3456913--3456958 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
3456903 ATAATTAATA
3456913 AAATCAATTGATC
1 AAATCAATTGATC
* *
3456926 AAATCAATTAATA
1 AAATCAATTGATC
*
3456939 AAATCAATTGGTC
1 AAATCAATTGATC
3456952 AAATCAA
1 AAATCAA
3456959 CCACTACAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (13 bp):
AAATCAATTGATC
Found at i:3456934 original size:26 final size:26
Alignment explanation
Indices: 3456901--3456958 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
3456891 AATTTTAAAT
3456901 AAAT-AATTAATAAAATCAATTGATC
1 AAATCAATTAATAAAATCAATTGATC
*
3456926 AAATCAATTAATAAAATCAATTGGTC
1 AAATCAATTAATAAAATCAATTGATC
3456952 AAATCAA
1 AAATCAA
3456959 CCACTACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (26 bp):
AAATCAATTAATAAAATCAATTGATC
Found at i:3456969 original size:26 final size:26
Alignment explanation
Indices: 3456909--3456971 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
3456899 ATAAATAATT
**
3456909 AATAAAATCAATTGATCAAATCAATT
1 AATAAAATCAATTGATCAAATCAACC
*
3456935 AATAAAATCAATTGGTCAAATCAACC
1 AATAAAATCAATTGATCAAATCAACC
* *
3456961 ACTACAATCAA
1 AATAAAATCAA
3456972 CTATTAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.25
Consensus pattern (26 bp):
AATAAAATCAATTGATCAAATCAACC
Found at i:3457707 original size:8 final size:7
Alignment explanation
Indices: 3457677--3457726 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
3457667 ATAAACAATA
3457677 AATATTT
1 AATATTT
3457684 AATAATTT
1 AAT-ATTT
*
3457692 AATTTTT
1 AATATTT
3457699 ATATATTT
1 A-ATATTT
3457707 -ATATTT
1 AATATTT
3457713 AA-ATTT
1 AATATTT
3457719 AAATATTT
1 -AATATTT
3457727 TTTATTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 10 0.28
7 10 0.28
8 16 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATATTT
Found at i:3457712 original size:21 final size:21
Alignment explanation
Indices: 3457675--3457739 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 21
3457665 TAATAAACAA
3457675 TAAATATTTAATAATTTAATTTT
1 TAAATATTT-AT-ATTTAATTTT
* *
3457698 TATATATTTATATTTAA-ATT
1 TAAATATTTATATTTAATTTT
*
3457718 TAAATATTT-TTTATTAATTTT
1 TAAATATTTATAT-TTAATTTT
3457739 T
1 T
3457740 GAACATTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.06
20 14 0.40
21 9 0.26
22 2 0.06
23 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAAATATTTATATTTAATTTT
Found at i:3465454 original size:16 final size:17
Alignment explanation
Indices: 3465425--3465470 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3465415 TAAAATATGC
3465425 ATTATATA-TCTAATTA-
1 ATTATATACT-TAATTAT
3465441 ATTATATACTTAA-TAT
1 ATTATATACTTAATTAT
*
3465457 ATTTTATACTTAAT
1 ATTATATACTTAAT
3465471 GTCGTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 23 0.88
17 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATATACTTAATTAT
Found at i:3482871 original size:19 final size:18
Alignment explanation
Indices: 3482829--3482871 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3482819 TTTAATATAA
*
3482829 AATAAACATTAAAGTTAT
1 AATAAACATTAAAATTAT
*
3482847 ATATAAACTTTAAAAATTAT
1 A-ATAAACATT-AAAATTAT
3482867 AATAA
1 AATAA
3482872 TGCTTGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (18 bp):
AATAAACATTAAAATTAT
Found at i:3482968 original size:16 final size:17
Alignment explanation
Indices: 3482942--3482987 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
3482932 ATTTGTGTAT
3482942 ATAAT-ATATTAATTTA
1 ATAATAATATTAATTTA
3482958 A-AATAATATTAATTTA
1 ATAATAATATTAATTTA
*
3482974 ATAATATTATTAAT
1 ATAATAATATTAAT
3482988 GATTTATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 3 0.11
16 13 0.48
17 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATAATATTAATTTA
Found at i:3482978 original size:14 final size:14
Alignment explanation
Indices: 3482943--3482982 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
3482933 TTTGTGTATA
3482943 TAAT-ATATTAATT
1 TAATAATATTAATT
3482956 TAAAATAATATTAATT
1 T--AATAATATTAATT
3482972 TAATAATATTA
1 TAATAATATTA
3482983 TTAATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 3 0.12
16 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATAATATTAATT
Found at i:3489953 original size:29 final size:30
Alignment explanation
Indices: 3489895--3489964 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
3489885 ATTCCAAAAC
* *
3489895 TATACATGAACTATGGTTTAATGTGTAATTA
1 TATACATGAACTATGATTT-ATGTGCAATTA
* *
3489926 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTATGATTTATGTGCAATTA
3489955 TATACATGAA
1 TATACATGAA
3489965 ATTTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGCAATTA
Found at i:3489975 original size:29 final size:29
Alignment explanation
Indices: 3489916--3489985 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3489906 TATGGTTTAA
* * * *
3489916 TGTGTAATTATATACATGAACTTTGATTT
1 TGTGCAATTTTATACATGAAATTTGAATT
*
3489945 TGTGCAATTTTATACATGAAATTTTAATT
1 TGTGCAATTTTATACATGAAATTTGAATT
*
3489974 TGATCCAATTTT
1 TG-TGCAATTTT
3489986 TATAAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (29 bp):
TGTGCAATTTTATACATGAAATTTGAATT
Found at i:3494548 original size:84 final size:84
Alignment explanation
Indices: 3494413--3495121 Score: 986
Period size: 84 Copynumber: 8.4 Consensus size: 84
3494403 AGTTATCTTC
* * * * * * * *
3494413 TCAAGTTGCTAAGCAACTGGAAGATATATATTCTAGAACTGCTGCCTGGAAACCTTTTATTAATA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
* * **
3494478 AAGCTCCCCAATCATCTTC
66 AAACTCCCCAATCCTCTGA
* * * *
3494497 TCAACTTGTTAAGGAGCTGGAGGATAAATATTTTAGAACTGCTGTCTGGAAATCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
*
3494562 AAACTCCTCAATCCTCTGA
66 AAACTCCCCAATCCTCTGA
* *
3494581 TCAACTTGCTAAAGAGCTGGAGGATAAATATTCTAGAACTGTTGCCTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
*
3494646 AAACTTCCCAATCCTCTGA
66 AAACTCCCCAATCCTCTGA
* * * * *
3494665 TCAATTTGCTAAGGTGCTGGAGGATAAATATTTTAGAACTGCTACCTGGAAATCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
*
3494730 AAACTCCTCAATCCTCTGA
66 AAACTCCCCAATCCTCTGA
* *
3494749 TCAACTTGCTAAAGAGCTGGAGGATAAATATTCTAGAACTGCTGTCTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
*
3494814 AAACTTCCCAATCCTCTGA
66 AAACTCCCCAATCCTCTGA
* * * * *
3494833 TCAATTTGCTAAGGTGCTGGAGGATAAATATTTTAGAACTGTTGCTTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
* *
3494898 AAACTCCTCAATCCTCTGG
66 AAACTCCCCAATCCTCTGA
*
3494917 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
*
3494982 AAACTCTCCAATCCTCTGA
66 AAACTCCCCAATCCTCTGA
* * * * * * *
3495001 TCAACTTACTAAAGAGTTGGAGGATAAATATTTTAGAATTGTTGCCTGAAAAACCTTTTGTTGAC
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTG-GAAACCTTTTGTTGAC
* *
3495066 AAAACTCCCTAATCCTCTTA
65 AAAACTCCCCAATCCTCTGA
3495086 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAG
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAG
3495122 TTTATCTGAT
Statistics
Matches: 549, Mismatches: 75, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
84 485 0.88
85 64 0.12
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (84 bp):
TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAACTGCTGCCTGGAAACCTTTTGTTGACA
AAACTCCCCAATCCTCTGA
Found at i:3499489 original size:8 final size:8
Alignment explanation
Indices: 3499476--3499501 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3499466 TAATAAATAT
3499476 AAAAAAGA
1 AAAAAAGA
3499484 AAAAAAGA
1 AAAAAAGA
3499492 AAAAAAGA
1 AAAAAAGA
3499500 AA
1 AA
3499502 GAGAGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:3509278 original size:20 final size:20
Alignment explanation
Indices: 3509253--3509292 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3509243 TCGTTGTGAC
3509253 ATTTGGATCTTTAGCATATT
1 ATTTGGATCTTTAGCATATT
*
3509273 ATTTGGATCTTTAGCTTATT
1 ATTTGGATCTTTAGCATATT
3509293 TTAGACGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (20 bp):
ATTTGGATCTTTAGCATATT
Found at i:3510487 original size:15 final size:14
Alignment explanation
Indices: 3510455--3510492 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3510445 TGAAATTTTT
3510455 AAATATT-ATTAAA
1 AAATATTAATTAAA
*
3510468 AAATATTAATCTACA
1 AAATATTAAT-TAAA
3510483 AAATATTAAT
1 AAATATTAAT
3510493 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 13 0.59
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATTAATTAAA
Found at i:3510585 original size:19 final size:21
Alignment explanation
Indices: 3510541--3510585 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
3510531 AGAAATATTA
*
3510541 AATAAGTTAATATATTTTAAT
1 AATAAGTTAATATATTTAAAT
*
3510562 TATAA-TTAATA-ATTTAAAT
1 AATAAGTTAATATATTTAAAT
3510581 AATAA
1 AATAA
3510586 ATTACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 11 0.52
20 6 0.29
21 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAAGTTAATATATTTAAAT
Found at i:3510588 original size:20 final size:21
Alignment explanation
Indices: 3510541--3510589 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3510531 AGAAATATTA
* *
3510541 AATAAGTTAATATATTTTAAT
1 AATAAATTAATATATTTAAAT
*
3510562 TAT-AATTAATA-ATTTAAAT
1 AATAAATTAATATATTTAAAT
3510581 AATAAATTA
1 AATAAATTA
3510590 CAAAATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATAAATTAATATATTTAAAT
Found at i:3511122 original size:3 final size:3
Alignment explanation
Indices: 3511114--3511149 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3511104 ATTTCATTAA
3511114 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3511150 TTGGTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3514563 original size:23 final size:23
Alignment explanation
Indices: 3514537--3514643 Score: 124
Period size: 23 Copynumber: 4.7 Consensus size: 23
3514527 TACTGTTCAA
* *
3514537 CACTGTGTATGCTTACTGATTCG
1 CACTGTGTGTGCTTACTGATTTG
* ** *
3514560 CACTATACGTGCTTACTAATTTG
1 CACTGTGTGTGCTTACTGATTTG
* *
3514583 AACTGTGTGTGCTTACTGTTTTG
1 CACTGTGTGTGCTTACTGATTTG
* *
3514606 CACTGCGTGTGCCTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTG
3514629 CACTGTGTGTGCTTA
1 CACTGTGTGTGCTTA
3514644 TTGTTTCCCC
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (23 bp):
CACTGTGTGTGCTTACTGATTTG
Found at i:3517309 original size:23 final size:23
Alignment explanation
Indices: 3517283--3517344 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
3517273 AAAAATGGAA
3517283 ACTAGAGCTTGGAAACACTGTTC
1 ACTAGAGCTTGGAAACACTGTTC
3517306 ACTAGAGCTTGGAAACACTGTTC
1 ACTAGAGCTTGGAAACACTGTTC
*
3517329 ATTAGAGCTTGGAAAC
1 ACTAGAGCTTGGAAAC
3517345 TAGAAGGTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (23 bp):
ACTAGAGCTTGGAAACACTGTTC
Found at i:3521898 original size:22 final size:21
Alignment explanation
Indices: 3521873--3521917 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3521863 CTAATTACAC
3521873 TTTTAATCTCTATATTTTTTAA
1 TTTTAATCTCTATA-TTTTTAA
* *
3521895 TTTTAATCTTTCTATTTTTAA
1 TTTTAATCTCTATATTTTTAA
3521916 TT
1 TT
3521918 CTAAAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTAATCTCTATATTTTTAA
Found at i:3521914 original size:21 final size:21
Alignment explanation
Indices: 3521873--3521935 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
3521863 CTAATTACAC
* *
3521873 TTTTAATCTCTATATTTTTTAA
1 TTTTAATCTTTCTA-TTTTTAA
3521895 TTTTAATCTTTCTATTTTTAA
1 TTTTAATCTTTCTATTTTTAA
* **
3521916 TTCTAA-AATTCTATTTTTAA
1 TTTTAATCTTTCTATTTTTAA
3521936 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 12 0.33
21 12 0.33
22 12 0.33
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATCTTTCTATTTTTAA
Found at i:3533363 original size:11 final size:11
Alignment explanation
Indices: 3533342--3533382 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
3533332 CCCATAAAAA
*
3533342 ACCCTAAATTC
1 ACCCCAAATTC
*
3533353 ACGCCAAATTC
1 ACCCCAAATTC
3533364 ACCCCAAATTC
1 ACCCCAAATTC
3533375 ACCCCAAA
1 ACCCCAAA
3533383 CCTAAACCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.39, C:0.41, G:0.02, T:0.17
Consensus pattern (11 bp):
ACCCCAAATTC
Found at i:3543509 original size:32 final size:33
Alignment explanation
Indices: 3543468--3543539 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
3543458 TTATTTGAGA
3543468 AAATAATAATCATAAAAA-AATATTGATCAAAT
1 AAATAATAATCATAAAAATAATATTGATCAAAT
* * *
3543500 AAATAATAATCATAAAAATTATTTTTATCAAAT
1 AAATAATAATCATAAAAATAATATTGATCAAAT
3543533 -AATAATA
1 AAATAATA
3543540 TAGTTTGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (33 bp):
AAATAATAATCATAAAAATAATATTGATCAAAT
Found at i:3543511 original size:15 final size:15
Alignment explanation
Indices: 3543467--3543518 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3543457 ATTATTTGAG
3543467 AAAATAATAATCATAAA
1 AAAATAATAATC--AAA
* *
3543484 AAAATATTGATCAAA
1 AAAATAATAATCAAA
* *
3543499 TAAATAATAATCATA
1 AAAATAATAATCAAA
3543514 AAAAT
1 AAAAT
3543519 TATTTTTATC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 18 0.64
17 10 0.36
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAATAATAATCAAA
Found at i:3553537 original size:136 final size:134
Alignment explanation
Indices: 3553119--3553825 Score: 669
Period size: 136 Copynumber: 5.3 Consensus size: 134
3553109 TGATGAATGT
*
3553119 ATCCTAAATCTAAAAGATAAACCACTCGAGACAAAGATTTAGGGAAGAGAGACACCATATAAGCC
1 ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAGCC
* * * * *
3553184 AAATGGAAAAAAGCGGACTTCATGCA-ATTCGCATGATCATATCCGTAACTCAGAGAGTGACCAT
66 AAATGGAAAAAAGCAGACTCCATG-AGATTCGTATGATCATATCTGTAACTCAAAGAGTGA-CAT
3553248 T-G-GG
129 TGGAGG
* * *** * *
3553252 ATCCTAAATCTAAAAGGTAAACCATTTGTGACAAAAGATTTGGGGAAGAGAGCCACAACATATAA
1 ATCCTAAATCTAAAAGATAAACCACTCAAGAC-AAAGATTTAGGGAAGAGAG--ACACCATATAA
* * ** * ** * *
3553317 GTCAAATGGATAAAATG--GACTCCATGCCATTCGTGTGATTGTATCCGTAATTCAGAA-A--G-
63 GCCAAATGGA-AAAAAGCAGACTCCATGAGATTCGTATGATCATATCTGTAACTCA-AAGAGTGA
* *
3553376 CAATGAACGG
126 CATTGGA-GG
3553386 ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAGCC
1 ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAGCC
* *
3553451 AAATGGAAAAAAGCAGACTCCATGAGTTTCGTATGATCATATCTATAACTCAAAGAGTGATCATT
66 AAATGGAAAAAAGCAGACTCCATGAGATTCGTATGATCATATCTGTAACTCAAAGAGTGA-CATT
3553516 GGATGG
130 GGA-GG
** * *
3553522 ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTACTGAAGAGAGGCACCATATAAGGC
1 ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAGCC
* * * *
3553587 ACATGGAAAAAAGCAAACTCCATGCA-ATTTGTATGATCATATCTGTAACTCAAAGAGTAATCAT
66 AAATGGAAAAAAGCAGACTCCATG-AGATTCGTATGATCATATCTGTAACTCAAAGAGTGA-CAT
3553651 T-G-GG
129 TGGAGG
* * * ** *
3553655 ATCCTAAATCTAGAAGGTAAACTACTCCTGACAAAAGATTTGGGGAAGAGAGACACAACATATAA
1 ATCCTAAATCTAAAAGATAAACCACTCAAGAC-AAAGATTTAGGGAAGAGAGACAC--CATATAA
* * * * * * *
3553720 GTCAAATGGATAAAA-CGGACTCCATGTGATTCATATGATCATATCTGAAATTCAGAA-AGT-A-
63 GCCAAATGGAAAAAAGCAGACTCCATGAGATTCGTATGATCATATCTGTAACTCA-AAGAGTGAC
*
3553781 A-TGAATGGG
127 ATTGGA--GG
*
3553790 ATCCT-AATCTCAAAAG-TAAACCACTCATGACAAAGA
1 ATCCTAAATCT-AAAAGATAAACCACTCAAGACAAAGA
3553826 AAGGATATCT
Statistics
Matches: 475, Mismatches: 72, Indels: 54
0.79 0.12 0.09
Matches are distributed among these distances:
130 5 0.01
131 25 0.05
132 30 0.06
133 81 0.17
134 86 0.18
135 76 0.16
136 166 0.35
137 6 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (134 bp):
ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAGCC
AAATGGAAAAAAGCAGACTCCATGAGATTCGTATGATCATATCTGTAACTCAAAGAGTGACATTG
GAGG
Found at i:3553583 original size:267 final size:266
Alignment explanation
Indices: 3553046--3553825 Score: 868
Period size: 267 Copynumber: 2.9 Consensus size: 266
3553036 TGGGGAAGAG
* * *
3553046 ATAAGTCAAATGGATAAAATGGACTCCATGCTATTTGTGTGATCGTATCCATAATTCAGAAAGTG
1 ATAAGTCAAATGGATAAAATGGACTCCATGCAATTTGTGTGATCGTATCCGTAATTCAGAAAGTA
* * *
3553111 ATGAATGTATCCTAAATCTAAAAGATAAACCACTCGAGACAAAGATTTAGGGAAGAGAGACACCA
66 ATGAACGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCA
* * ** *
3553176 TATAAGCCAAATGGAAAAAAGCGGACTTCATGCA-ATTCGCATGATCATATCCGTAACTCAGAGA
131 TATAAGCCAAATGGAAAAAAGCGGACTCCATG-AGATTCGTATGATCATATCTATAACTCAAAGA
* ** **
3553240 GTGACCATT-G--GGATCCTAAATCTAAAAGGTAAACCATTTGTGACAAAAGATTTGGGGAAGAG
195 GTGA-CATTGGATGGATCCTAAATCTAAAA-GTAAACCACTCATGAC-AAAGATTTACGGAAGAG
3553302 AGCCACAACAT
257 AGCCAC-ACAT
* * * *
3553313 ATAAGTCAAATGGATAAAATGGACTCCATGCCATTCGTGTGATTGTATCCGTAATTCAGAAAGCA
1 ATAAGTCAAATGGATAAAATGGACTCCATGCAATTTGTGTGATCGTATCCGTAATTCAGAAAGTA
3553378 ATGAACGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCA
66 ATGAACGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCA
* *
3553443 TATAAGCCAAATGGAAAAAAGCAGACTCCATGAGTTTCGTATGATCATATCTATAACTCAAAGAG
131 TATAAGCCAAATGGAAAAAAGCGGACTCCATGAGATTCGTATGATCATATCTATAACTCAAAGAG
* *
3553508 TGATCATTGGATGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTACTGAAGAGAG
196 TGA-CATTGGATGGATCCTAAATCTAAAAG-TAAACCACTCATGACAAAGATTTACGGAAGAGAG
*
3553573 GCAC-CAT
259 CCACACAT
* * * * * * * *
3553580 ATAAGGCACATGGA-AAAAAGCAAACTCCATGCAATTTGTATGATCATATCTGTAACTCA-AAGA
1 ATAAGTCAAATGGATAAAATG--GACTCCATGCAATTTGTGTGATCGTATCCGTAATTCAGAA-A
* ** * * * ** *
3553643 GTAATCATTGGGATCCTAAATCTAGAAGGTAAACTACTCCTGACAAAAGATTTGGGGAAGAGAGA
63 GTAATGA-ACGGATCCTAAATCTAAAAGATAAACCACTCAAGAC-AAAGATTTAGGGAAGAGAGA
* * * * *
3553708 CACAACATATAAGTCAAATGGATAAAA-CGGACTCCATGTGATTCATATGATCATATCTGA-AAT
126 CAC--CATATAAGCCAAATGGAAAAAAGCGGACTCCATGAGATTCGTATGATCATATCT-ATAAC
*
3553771 TCAGAA-AGT-A-A-TGAATGGGATCCT-AATCTCAAAAGTAAACCACTCATGACAAAGA
188 TCA-AAGAGTGACATTGGAT-GGATCCTAAATCT-AAAAGTAAACCACTCATGACAAAGA
3553826 AAGGATATCT
Statistics
Matches: 442, Mismatches: 55, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
266 6 0.01
267 229 0.52
268 49 0.11
269 49 0.11
270 51 0.12
271 35 0.08
272 23 0.05
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (266 bp):
ATAAGTCAAATGGATAAAATGGACTCCATGCAATTTGTGTGATCGTATCCGTAATTCAGAAAGTA
ATGAACGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCA
TATAAGCCAAATGGAAAAAAGCGGACTCCATGAGATTCGTATGATCATATCTATAACTCAAAGAG
TGACATTGGATGGATCCTAAATCTAAAAGTAAACCACTCATGACAAAGATTTACGGAAGAGAGCC
ACACAT
Found at i:3558425 original size:18 final size:18
Alignment explanation
Indices: 3558402--3558451 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
3558392 ATAATTCATA
3558402 TCACTTTCAATTTTAATT
1 TCACTTTCAATTTTAATT
* * *
3558420 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTTAATT
*
3558438 TCATTTTCAATTTT
1 TCACTTTCAATTTT
3558452 GATCACAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (18 bp):
TCACTTTCAATTTTAATT
Found at i:3558427 original size:6 final size:6
Alignment explanation
Indices: 3558402--3558446 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
3558392 ATAATTCATA
* * * *
3558402 TCACTT TCAATT TTAATT TCACTT TCACTT TCACTT TCATTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
3558447 ATTTTGATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (6 bp):
TCACTT
Found at i:3561807 original size:459 final size:459
Alignment explanation
Indices: 3561001--3561839 Score: 1279
Period size: 459 Copynumber: 1.8 Consensus size: 459
3560991 GGTTCGTCAC
* ** *
3561001 CTCAAGACTTCTTGAATGTACACAACGCAGCTCGTGCGGTGGTTGGTGTTAGCCCCATCACTTGG
1 CTCAAGACTACTTGAATGTACACAACGCAGCTCGTGCGGCAGTTGGTGTTAGACCCATCACTTGG
* * * *
3561066 AACAATGTGGTGGCCAGGTACGCAGCAGACTATGCCGAAAAGAGGATATCAGACTGTGAACTTGT
66 AACAATGTCGTGGCCAGGTACGCAGCAGACTATGCCAAAAACAGGATATCAGACTGTGAACTCGT
*
3561131 GCATTCAGGAGGGCCTTATGGTGAGAATCTTGCATGGAGTAGCGGTGATCTTTCTGGACCCGATG
131 GCATTCAGGAGGGCCTTATGGTGAGAATCTTGCATGGAGTAGCGCTGATCTTTCTGGACCCGATG
* * * *
3561196 CTGTGAGCTTGTGGACTGATGAGAAGGACTATTATAATTTGAAATCCGGTGTATGTGATTCAGGC
196 CTGTGAGATTGTGGACTAATGAAAAGGACGATTATAATTTGAAATCCGGTGTATGTGATTCAGGC
* * * * * *
3561261 CACGTATGTAGGCAATATACTCAAGTGATTGGGCGCAACTCAAGTCGTCTTGGATGTGCAAAAGT
261 AAAGTATGTAGGCAATATACTCAAGTGATTGGGCACAACTCAAGTCATCTAGGATGTGCAAAAGC
* * * * * *
3561326 TAGGTGCAATAACGGTGGAACTTTTGTTATTTGTAACTATGACCCTCCAAGTAACGATCCGATAG
326 GAGATGCAACAAAGGGGGAACTTTTATTATTTGTAACTATGACCCTCCAAGTAACGATCCGATAG
3561391 GTAGGAACCAATCCAACATCTCCGTAGCAACCGCGCCAAACCCTAGTTCTGCTGCAGAAGGTTCA
391 GTAGGAACCAATCCAACATCTCCGTAGCAACCGCGCCAAACCCTAGTTCTGCTGCAGAAGGTTCA
3561456 TTAT
456 TTAT
** *
3561460 CTCAAGACTACTTGAATGTACACAACGTGGCTCGTGCGGCAGTTGGTGTTCGACCCATCACTTGG
1 CTCAAGACTACTTGAATGTACACAACGCAGCTCGTGCGGCAGTTGGTGTTAGACCCATCACTTGG
* * * *
3561525 GACAATGTCGTGGCTAGGTACGCAGCAGAGTATGCCAAAAACAGGATATCAGACTGTGAGCTCGT
66 AACAATGTCGTGGCCAGGTACGCAGCAGACTATGCCAAAAACAGGATATCAGACTGTGAACTCGT
3561590 GCATTCAGGAGGGCCTTATGGTGAGAATCTTGCATGGAGTAGCGCTGATCTTTCTGGACCCGATG
131 GCATTCAGGAGGGCCTTATGGTGAGAATCTTGCATGGAGTAGCGCTGATCTTTCTGGACCCGATG
* *
3561655 CTGTGAGATTGTGGATTAATGAAAAGTACGATTATAATTTGAAATCCGGTGTATGTGATTTC-GG
196 CTGTGAGATTGTGGACTAATGAAAAGGACGATTATAATTTGAAATCCGGTGTATGTGA-TTCAGG
* * *
3561719 CAAAGTATGT-GGCCATTATACTCAAGTGATTTGGCACAATTC-AGTTCATCTAGGATGTGCAAA
260 CAAAGTATGTAGG-CAATATACTCAAGTGATTGGGCACAACTCAAG-TCATCTAGGATGTGCAAA
* *
3561782 AGCGAGATGCAACAAAGGGGGAACTTTTATTGTTTGTAACTATGACCCTCCAGGTAAC
323 AGCGAGATGCAACAAAGGGGGAACTTTTATTATTTGTAACTATGACCCTCCAAGTAAC
3561840 ATTGTCGGTG
Statistics
Matches: 338, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
458 4 0.01
459 331 0.98
460 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (459 bp):
CTCAAGACTACTTGAATGTACACAACGCAGCTCGTGCGGCAGTTGGTGTTAGACCCATCACTTGG
AACAATGTCGTGGCCAGGTACGCAGCAGACTATGCCAAAAACAGGATATCAGACTGTGAACTCGT
GCATTCAGGAGGGCCTTATGGTGAGAATCTTGCATGGAGTAGCGCTGATCTTTCTGGACCCGATG
CTGTGAGATTGTGGACTAATGAAAAGGACGATTATAATTTGAAATCCGGTGTATGTGATTCAGGC
AAAGTATGTAGGCAATATACTCAAGTGATTGGGCACAACTCAAGTCATCTAGGATGTGCAAAAGC
GAGATGCAACAAAGGGGGAACTTTTATTATTTGTAACTATGACCCTCCAAGTAACGATCCGATAG
GTAGGAACCAATCCAACATCTCCGTAGCAACCGCGCCAAACCCTAGTTCTGCTGCAGAAGGTTCA
TTAT
Found at i:3561929 original size:12 final size:12
Alignment explanation
Indices: 3561912--3561937 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3561902 TGCTCCTTCA
3561912 CCATATTTCTTT
1 CCATATTTCTTT
3561924 CCATATTTCTTT
1 CCATATTTCTTT
3561936 CC
1 CC
3561938 TTCGGAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (12 bp):
CCATATTTCTTT
Found at i:3563783 original size:22 final size:21
Alignment explanation
Indices: 3563727--3563785 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3563717 ATAATTTATA
*
3563727 AATTC-TATA-AAATTTTAAT
1 AATTCTTATATAATTTTTAAT
3563746 AATTCTTATATAATTTTTAAT
1 AATTCTTATATAATTTTTAAT
*
3563767 ATATT-TTTTGATAATTTTT
1 A-ATTCTTAT-ATAATTTTT
3563786 GAAAACCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 13 0.38
22 12 0.35
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (21 bp):
AATTCTTATATAATTTTTAAT
Found at i:3566295 original size:54 final size:54
Alignment explanation
Indices: 3566208--3566312 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
3566198 CATTAGAGGA
*
3566208 TTAGTGGTGGAGCTAATTGTTGGAGCTTGTGGTTTGATTCTTAGCCTAGGTTTG
1 TTAGTGGTGGAGCTAATTGTTGGAGCTTCTGGTTTGATTCTTAGCCTAGGTTTG
* * * * *
3566262 TTAGTGGTGGGGTTAATTGTTGGAGTTTCTGGTTTGATTTTTGGCCTAGGT
1 TTAGTGGTGGAGCTAATTGTTGGAGCTTCTGGTTTGATTCTTAGCCTAGGT
3566313 GTGTCCTTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.13, C:0.08, G:0.34, T:0.45
Consensus pattern (54 bp):
TTAGTGGTGGAGCTAATTGTTGGAGCTTCTGGTTTGATTCTTAGCCTAGGTTTG
Found at i:3569266 original size:23 final size:23
Alignment explanation
Indices: 3569240--3569285 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3569230 AAATTATAAA
3569240 ATATAAT-ATAATAAAATAAAAAT
1 ATATAATAATAATAAAA-AAAAAT
*
3569263 ATATACTAATAATAAAAAAAAAT
1 ATATAATAATAATAAAAAAAAAT
3569286 TGGAGTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
ATATAATAATAATAAAAAAAAAT
Found at i:3576396 original size:302 final size:302
Alignment explanation
Indices: 3575844--3576447 Score: 1102
Period size: 302 Copynumber: 2.0 Consensus size: 302
3575834 TAGGTAACAA
*
3575844 ATTCAGCAAGTATACTGAGGTGTTCACAGCCTCAGCCCAAAATACTTTTGGAAGATCCTTTTCAA
1 ATTCAGCAAGTATACTGAGGTGTTCACAGCCTCAGCCCAAAATACTTTTGGAAGAGCCTTTTCAA
*
3575909 ACAACAAACATCTAGCCATCTCCATAATTGTTCTATTTTTCCTTTCACTCACTCCATTTTGTTGA
66 ACAACAAACATCTAGCCATCTCCATAATTGTTCTATTTTTCCTTTCACTCACTCCATTTTCTTGA
* *
3575974 GGAGTGTAAAGAACAGTAAATTGTTGCTGAATTCCAACTTGTTGACAAAAACTAGCAAATTCTCT
131 GGAATGTAAAGAACAGTAAATTGTTGCTGAATTCCAACTTGTTGACAAAAACTAGCAAATTCCCT
*
3576039 TGAGTTGTACTCAGTCCCATTATCAGATCTCAATTTTTTCATTAAACTACCTGATTCAACTTCAA
196 TGAGTTGTACTCAGTCCCATTATCAGATCTCAATTTCTTCATTAAACTACCTGATTCAACTTCAA
3576104 CCATGCTCTTGAACCTTTGGAATGCCTCAAATACTTCTAATT
261 CCATGCTCTTGAACCTTTGGAATGCCTCAAATACTTCTAATT
3576146 ATTCAGCAAGTATACTGAGGTGTTCACAGCCTCAGCCCAAAATACTTTTGGAAGAGCCTTTTCAA
1 ATTCAGCAAGTATACTGAGGTGTTCACAGCCTCAGCCCAAAATACTTTTGGAAGAGCCTTTTCAA
**
3576211 ACAGTAAACATCTAGCCATCTCCATAATTGTTCTATTTTTCCTTTCACTCACTCCATTTTCTTGA
66 ACAACAAACATCTAGCCATCTCCATAATTGTTCTATTTTTCCTTTCACTCACTCCATTTTCTTGA
* *
3576276 GGAATGTAAGGAATAGTAAATTGTTGCTGAATTCCAACTTGTTGACAAAAACTAGCAAATTCCCT
131 GGAATGTAAAGAACAGTAAATTGTTGCTGAATTCCAACTTGTTGACAAAAACTAGCAAATTCCCT
3576341 TGAGTTGTACTCAGTCCCATTATCAGATCTCAATTTCTTCATTAAAC-AGCCTGATTCAACTTCA
196 TGAGTTGTACTCAGTCCCATTATCAGATCTCAATTTCTTCATTAAACTA-CCTGATTCAACTTCA
*
3576405 ACCATGCTTTTGAACCTTTGGAATGCCTCAAATACTTCTAATT
260 ACCATGCTCTTGAACCTTTGGAATGCCTCAAATACTTCTAATT
3576448 TTTGTTTGAG
Statistics
Matches: 291, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
301 1 0.00
302 290 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (302 bp):
ATTCAGCAAGTATACTGAGGTGTTCACAGCCTCAGCCCAAAATACTTTTGGAAGAGCCTTTTCAA
ACAACAAACATCTAGCCATCTCCATAATTGTTCTATTTTTCCTTTCACTCACTCCATTTTCTTGA
GGAATGTAAAGAACAGTAAATTGTTGCTGAATTCCAACTTGTTGACAAAAACTAGCAAATTCCCT
TGAGTTGTACTCAGTCCCATTATCAGATCTCAATTTCTTCATTAAACTACCTGATTCAACTTCAA
CCATGCTCTTGAACCTTTGGAATGCCTCAAATACTTCTAATT
Found at i:3582923 original size:222 final size:222
Alignment explanation
Indices: 3582512--3582952 Score: 749
Period size: 222 Copynumber: 2.0 Consensus size: 222
3582502 TGAAACAAGG
* * * *
3582512 GAACCGTCTGAAAATACGCCATAATCTCTTCGTGTATTAACACAACGAAAATGACAATAATAATA
1 GAACCGCCTGAAAATACACCATAACCTCTTCGTATATTAACACAACGAAAATGACAATAATAATA
3582577 TAAAATCCTTCCTTTGAACCCACTCTTAATCATAAATATGGATGATTGAAAGAGGCATTTTTTTA
66 TAAAATCCTTCCTTTGAACCCACTCTTAATCATAAATATGGATGATTGAAAGAGGCATTTTTTTA
3582642 AATACAATTAAGGTTGGAATAGGAAATTAACATGAACCTTCCCTTCCACAAGGAAAGTTCAATAC
131 AATACAATTAAGGTTGGAATAGGAAATTAACATGAACCTTCCCTTCCACAAGGAAAGTTCAATAC
*
3582707 GATGAAAACAATGTAATAAATTAACAT
196 GATGAAAACAATGCAATAAATTAACAT
* *
3582734 GAACCGCCTGAAGATACACCATAACCTCTTCGTATATTAACACAACGAAAATGACAATAATAGTA
1 GAACCGCCTGAAAATACACCATAACCTCTTCGTATATTAACACAACGAAAATGACAATAATAATA
** * *
3582799 TAAAATTTTTCCTTTGAACCCACTCTTAATCATAAATATGGATGATTGGAAGAGGTA-TTTTTTA
66 TAAAATCCTTCCTTTGAACCCACTCTTAATCATAAATATGGATGATTGAAAGAGGCATTTTTTTA
* *
3582863 ACATGCAGTTAAGGTTGGAATAGGAAATTAACATGAACCTTCCCTTCCACAAGGAAAGTTCAATA
131 A-ATACAATTAAGGTTGGAATAGGAAATTAACATGAACCTTCCCTTCCACAAGGAAAGTTCAATA
3582928 CGATGAAAACAATGCAATAAATTAA
195 CGATGAAAACAATGCAATAAATTAA
3582953 TGGGTATTGT
Statistics
Matches: 205, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
221 8 0.04
222 197 0.96
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (222 bp):
GAACCGCCTGAAAATACACCATAACCTCTTCGTATATTAACACAACGAAAATGACAATAATAATA
TAAAATCCTTCCTTTGAACCCACTCTTAATCATAAATATGGATGATTGAAAGAGGCATTTTTTTA
AATACAATTAAGGTTGGAATAGGAAATTAACATGAACCTTCCCTTCCACAAGGAAAGTTCAATAC
GATGAAAACAATGCAATAAATTAACAT
Found at i:3586510 original size:36 final size:36
Alignment explanation
Indices: 3586470--3586542 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3586460 CAAGAACAAG
*
3586470 AACAAAAGCAAAAACATAAATATTTTTCATTCAGCC
1 AACAAAAACAAAAACATAAATATTTTTCATTCAGCC
3586506 AACAAAAACAAAAACATAAATATTTTTCATTCAGCC
1 AACAAAAACAAAAACATAAATATTTTTCATTCAGCC
3586542 A
1 A
3586543 TCATCGAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (36 bp):
AACAAAAACAAAAACATAAATATTTTTCATTCAGCC
Found at i:3610058 original size:17 final size:17
Alignment explanation
Indices: 3610036--3610074 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3610026 AATTTAGATG
*
3610036 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
3610053 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
3610070 TAAAA
1 TAAAA
3610075 ATGGAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:3610195 original size:24 final size:25
Alignment explanation
Indices: 3610137--3610195 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
3610127 CTAATAATTA
*
3610137 ATATAGAATATAAAAGAAATATAACT
1 ATATAG-ATAAAAAAGAAATATAACT
* * *
3610163 A-AGATATAAAAAAGAAATTTAA-T
1 ATATAGATAAAAAAGAAATATAACT
3610186 ATATAGATAA
1 ATATAGATAA
3610196 GTAATATATC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
23 2 0.08
24 21 0.81
25 2 0.08
26 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (25 bp):
ATATAGATAAAAAAGAAATATAACT
Found at i:3628280 original size:32 final size:31
Alignment explanation
Indices: 3628230--3628334 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 31
3628220 TTGCTGTCCT
* *
3628230 AAAATAGAAAATTTTATATTTAAATC-TTTA
1 AAAATAAAAAAATTTATATTTAAATCTTTTA
*
3628260 AATTAATAAAAAAATTTATATTTTAATCTTTTA
1 AA--AATAAAAAAATTTATATTTAAATCTTTTA
*
3628293 AAAATAATAAAAA-TT-TATTT-AATTTTTTA
1 AAAATAA-AAAAATTTATATTTAAATCTTTTA
* *
3628322 AAATTATAAAAAT
1 AAAATAAAAAAAT
3628335 ATAAACTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
28 5 0.08
29 13 0.20
30 7 0.11
31 7 0.11
32 26 0.41
33 6 0.09
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (31 bp):
AAAATAAAAAAATTTATATTTAAATCTTTTA
Found at i:3628935 original size:1 final size:1
Alignment explanation
Indices: 3628925--3628958 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
3628915 GGACAAATTA
*
3628925 CCCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3628959 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:3636392 original size:470 final size:469
Alignment explanation
Indices: 3635463--3636662 Score: 1701
Period size: 470 Copynumber: 2.5 Consensus size: 469
3635453 ATCTACAAAT
* * *
3635463 ATAAACAAGGGAACAA-AAAGTAACGTTTCTACTTAAGTTTAACATTCAAAAGCGTTAGAAAATG
1 ATAAACAAGGGAACAAGAAA-TAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATG
* *
3635527 AGATAGTTGGCCAATGCTAAATTGCATCAGAACTTTCAAC-AAA-TCCACTTTCAGAATCTTTTG
65 AGATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTG
* * * * *
3635590 ACATTAAATACAGTGGTTGATTGTTAATGCAATGATTTGTGACAAACCAACACAATCTAATTATT
130 ACATTAAATACAGTAGTTTATTGTTAATGCAATGATTCGCGACAAACCAACAGAATCTAATTATT
*
3635655 ATACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTTACAA
195 ATACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAA
* *
3635720 AAAAAGGATTCCATTTTTGTTAATAGCTACAAAATCTAGAATCGAATTGTGCCAATGGAATATAA
260 AAAAAGGATTCC--------T-ATAGCTACAAAATCTAGAATCGAATTGTGCAAATGGAAGATAA
* * * ** *
3635785 AAAGTCATCGAATTGTAAAACCCAGAAATCTTCATTCACTTGGGTTTCACAAGTAGCCAAAGGGC
316 AAAGTCAACGAATCGAAAAACCCAGAAATCTTCATTCACTCAGGTTTCACAAGAAGCCAAAGGGC
*
3635850 ACTTCTTACGACTTCTCGTGACATTGACTAGAGAAAATTCCTTAAATAATAACCATATAAGGAAC
381 ACTTCTTACGACTTCTCGTGACATTAACTAGAGAAAATTCCTTAAATAATAACCATATAAGGAAC
*
3635915 ATGTTACTTGTAG-TCAACACTCTA
446 ATGTTACTTGTAGCTC-ACACCCTA
* * *
3635939 ATAAACAAAGGAACAAGGAATAACATTTCTACTTGAGTATAACATTCAAAAGCTTTAGAAAATGA
1 ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
*
3636004 GATGGTTGGCCAATGCTAGATTGCATCCA-AACTTTCAACAAAATTCCACTTTCAAAATCTTTTG
66 GATGGTTGGCCAATGCTAGATTGCAT-CAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTG
* * * *
3636068 ACATTAAATACAGTAGTTTATTATTAATGCAATGATTCACGACAACCCAACAGAATCTATTTATT
130 ACATTAAATACAGTAGTTTATTGTTAATGCAATGATTCGCGACAAACCAACAGAATCTAATTATT
* * *
3636133 ATACATCATAACGAACTGACCAACTTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAA
195 ATACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAA
* *
3636198 AGAAACGGATTCC-ATAGCTACAAAATCTAGAATCTAATTGTGCAAATGGAAAGATAAAAAGTCA
260 A-AAAAGGATTCCTATAGCTACAAAATCTAGAATCGAATTGTGCAAATGG-AAGATAAAAAGTCA
* * *
3636262 ACGAATCGAAAAACCCAGAAATCTTCGTTCACTCAGGTTTCACGAGAAGCCAAAGGGCAGTTCTT
323 ACGAATCGAAAAACCCAGAAATCTTCATTCACTCAGGTTTCACAAGAAGCCAAAGGGCACTTCTT
* * * * *
3636327 ATGATTTTTCGTGACATTAACTGGAGAAAATTCCTTAAATAATAACCATATAAGGCACATGTTAC
388 ACGACTTCTCGTGACATTAACTAGAGAAAATTCCTTAAATAATAACCATATAAGGAACATGTTAC
3636392 TTGTAGCTCACACCCTA
453 TTGTAGCTCACACCCTA
* *
3636409 ATAAACAAGGGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGTTTTAGAAAATGA
1 ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
* * *
3636474 GATGGTTGCCCAATGCTAGACTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCATTTGA
66 GATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTGA
* * * * * *
3636539 CATTAGATACAATTGTTTATTGTTAATGCAATGAGTCGCAAAAAACCAACAGAATCTAATTATTA
131 CATTAAATACAGTAGTTTATTGTTAATGCAATGATTCGCGACAAACCAACAGAATCTAATTATTA
* * * * * *
3636604 TATATCATAACAAACCAACAAAATTTTCCAAAAGAAGTTATCAACTACAGGTGGCAAGT
196 TACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGT
3636663 TTGCAACTCA
Statistics
Matches: 646, Mismatches: 70, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
469 36 0.06
470 364 0.56
471 2 0.00
476 90 0.14
477 7 0.01
478 137 0.21
479 10 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (469 bp):
ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
GATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTGA
CATTAAATACAGTAGTTTATTGTTAATGCAATGATTCGCGACAAACCAACAGAATCTAATTATTA
TACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAAA
AAAAGGATTCCTATAGCTACAAAATCTAGAATCGAATTGTGCAAATGGAAGATAAAAAGTCAACG
AATCGAAAAACCCAGAAATCTTCATTCACTCAGGTTTCACAAGAAGCCAAAGGGCACTTCTTACG
ACTTCTCGTGACATTAACTAGAGAAAATTCCTTAAATAATAACCATATAAGGAACATGTTACTTG
TAGCTCACACCCTA
Found at i:3637263 original size:516 final size:517
Alignment explanation
Indices: 3636211--3637288 Score: 1552
Period size: 516 Copynumber: 2.1 Consensus size: 517
3636201 AACGGATTCC
*
3636211 ATAGCTACAAAATCTAGAATCTAATTGTGCAAATGGAAAGATAAAAAGTCAACGAATCGAAAAAC
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCAACGAATCGAAAAAC
* * * * *
3636276 CCAGAAATCTTCGTTCACTCAGGTTTCACGAGAAGCCAAAGGGCAGTTCTTATGATTTTTCGTGA
66 CCAGAAATCTTCATTCACTCAGGTTTAACGAGAAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
* * *
3636341 CATTAACTGGAGAAAATTCCTTAAATAATAACCATATAAGGCACATGTTACTTGTAGCTCACACC
131 CACTAACTGGAGAAAATTCCTTAAATAATAACCATATAAGGCACATGTTACTAGTAGATCACACC
* *
3636406 CTAATAAACAAGGGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGTTTTAGAAAA
196 CTAATAAACAAGAGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGCTTTAGAAAA
* *
3636471 TGAGATGGTTGCCCAATGCTAGACTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCATT
261 TGAGATGGTTGCCCAATGCTAGACTGCATCAGAACTTTCAACAAAAGTCCACTTCCAGAATCATT
* ** * *
3636536 TGACATTAGATACAATTGTTTATTGTTAATGCAATGAGTCGCAAAAAACCAACAGAATCTAATTA
326 TGACATTAAATACAACGGTTGATTGTTAATGCAATGAGTCACAAAAAACCAACAGAATCTAATTA
* * * *
3636601 TTATATATCATAACAAACCAACAAAATTTTCCAAAAGAAGTTATCAACTACAGGTGGCAAGTTTG
391 TTATACATCATAACAAACCAACAAAATTTGCCAAAAGAACTTATCAACTACACGTGGCAAGTTTG
* * *
3636666 CAACTCAGAATCAGGCATGAGCTAACTAAACTGGTACAACGAAATGGATTCCATTTTTGTTA
456 CAACTCAGAATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
* * *
3636728 ATAGCTACAAAATCTAGAATCTAAATGTGCCAATGGAAAGATAAAAAGTCATCGAATCGTAAAAC
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCAACGAATCGAAAAAC
* *
3636793 CCAGAAATCTTCATTCACTTAGGTTTAAC-AGTAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
66 CCAGAAATCTTCATTCACTCAGGTTTAACGAGAAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
* * * * * *
3636857 TACTGACTGGAGAAAATTCCTTTAATAATGATCA-AGTAAGGTACATGTTACTAGTA-ATCAACA
131 CACTAACTGGAGAAAATTCCTTAAATAATAACCATA-TAAGGCACATGTTACTAGTAGATC-ACA
* * *
3636920 CCCTAATAAACAAGAGAATAAGAAATAGCATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAA
194 CCCTAATAAACAAGAGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGCTTTAGAA
* *** * *
3636985 AATGAGATGGTTGCCCAATGCTAGATTGCATCAGAACTTTCAATGTAGGTCCACTTCCAGAATCT
259 AATGAGATGGTTGCCCAATGCTAGACTGCATCAGAACTTTCAACAAAAGTCCACTTCCAGAATCA
* * * * **
3637050 TTTGACATTAAATACAGCGGTTGATTGTTAATGCAATGATTCACGATAAACTGACAGAATCTAAT
324 TTTGACATTAAATACAACGGTTGATTGTTAATGCAATGAGTCACAAAAAACCAACAGAATCTAAT
* * * * * *
3637115 TATTATGCATCCTAACGAACTAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGGCAGGTT
389 TATTATACATCATAACAAACCAACAAAATTTGCCAAAAGAACTTATCAACTACACGTGGCAAGTT
* * * *
3637180 TGCCAAGTTAGAATCTGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGTTTCCATTTTTGTTA
454 TG-CAACTCAGAATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
3637245 ATAGCTACAAAA-CTAGAATCTAATTGTGCCAATGGAAAGATAAA
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAA
3637289 CAAAGAAACA
Statistics
Matches: 496, Mismatches: 62, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
515 3 0.01
516 339 0.68
517 154 0.31
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (517 bp):
ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCAACGAATCGAAAAAC
CCAGAAATCTTCATTCACTCAGGTTTAACGAGAAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
CACTAACTGGAGAAAATTCCTTAAATAATAACCATATAAGGCACATGTTACTAGTAGATCACACC
CTAATAAACAAGAGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGCTTTAGAAAA
TGAGATGGTTGCCCAATGCTAGACTGCATCAGAACTTTCAACAAAAGTCCACTTCCAGAATCATT
TGACATTAAATACAACGGTTGATTGTTAATGCAATGAGTCACAAAAAACCAACAGAATCTAATTA
TTATACATCATAACAAACCAACAAAATTTGCCAAAAGAACTTATCAACTACACGTGGCAAGTTTG
CAACTCAGAATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
Found at i:3637292 original size:70 final size:70
Alignment explanation
Indices: 3637218--3637356 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
3637208 CTAAACTGGT
* * *
3637218 ACAAAGAAACGGTTTCCATTTTTGTTAATAGCTACAAAA-CTAGAATCTAATTGTGCCAATGGAA
1 ACAAAGAAACAGATTCCA-CTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAA
3637282 AGATAA
65 AGATAA
3637288 ACAAAGAAACAGATTCCACTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAA
1 ACAAAGAAACAGATTCCACTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAA
3637353 GATA
66 GATA
3637357 CAAAGTCATC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 19 0.29
70 46 0.71
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (70 bp):
ACAAAGAAACAGATTCCACTTTGTTAATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAA
GATAA
Found at i:3637843 original size:127 final size:132
Alignment explanation
Indices: 3637597--3637852 Score: 326
Period size: 127 Copynumber: 2.0 Consensus size: 132
3637587 GAAAGAAAGC
* ***
3637597 CAATGAATGTAGTGATAAAGAAATCAATGTGCCAAGCTCTCGGGTTCATAGTTTCCGTTTAGGGG
1 CAATGAATGTAGTGATAAAGAAATCAATGTGCCAAGCTCTCGGGTTCATAGTTTACGACAAGGGG
*
3637662 ATCAATTCCAGATTTAGTCATACCGAATGTAACTACCAAATTGCCAAGGGTTTTAGTAAAAAACC
66 ATCAATT-C--ATTTAGTCATACCGAATGTAACAACCAAATTGCCAAGGGTTTTAGTAAAAAACC
3637727 CTTGG
128 CTTGG
* *
3637732 CAATGAATGTAG-GA-AATA-AAA-CGATGTGCCAAGCTCTTGGGTTCATAGTTTACGACAAGGG
1 CAATGAATGTAGTGATAA-AGAAATCAATGTGCCAAGCTCTCGGGTTCATAGTTTACGACAAGGG
* ** * *
3637793 GCTCAA-T-ATTTAGTCATATTGAATGTAACAACCGAATTGCCAAGGGTTTTAGTCAAAAAC
65 GATCAATTCATTTAGTCATACCGAATGTAACAACCAAATTGCCAAGGGTTTTAGTAAAAAAC
3637853 ACTAGGAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
127 48 0.44
131 1 0.01
132 39 0.36
133 5 0.05
134 3 0.03
135 12 0.11
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (132 bp):
CAATGAATGTAGTGATAAAGAAATCAATGTGCCAAGCTCTCGGGTTCATAGTTTACGACAAGGGG
ATCAATTCATTTAGTCATACCGAATGTAACAACCAAATTGCCAAGGGTTTTAGTAAAAAACCCTT
GG
Found at i:3643016 original size:21 final size:21
Alignment explanation
Indices: 3642986--3643038 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3642976 CTTGCAACTT
* *
3642986 CTACCTATACAATCATTTTTA
1 CTACCGATACAATCATTCTTA
3643007 CTACCGATACAATCATTCTTA
1 CTACCGATACAATCATTCTTA
*
3643028 CTATCGATACA
1 CTACCGATACA
3643039 TAAATACCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (21 bp):
CTACCGATACAATCATTCTTA
Found at i:3643059 original size:24 final size:21
Alignment explanation
Indices: 3643027--3643083 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
3643017 AATCATTCTT
*
3643027 ACTATCGATACATAAATACCATAA
1 ACTACCGATACATAAAT--C-TAA
* *
3643051 ACTACCGATACTTACATCTAA
1 ACTACCGATACATAAATCTAA
3643072 ACTACCGATACA
1 ACTACCGATACA
3643084 ACCCAAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.48
22 1 0.03
24 14 0.48
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.25
Consensus pattern (21 bp):
ACTACCGATACATAAATCTAA
Found at i:3643729 original size:24 final size:24
Alignment explanation
Indices: 3643676--3643730 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
3643666 GCCAACACGG
*
3643676 ACCCAAAATAATTAGCTCTTACGA
1 ACCCAGAATAATTAGCTCTTACGA
*
3643700 ACCCAGAATGATTAGCTCTTACGA
1 ACCCAGAATAATTAGCTCTTACGA
*
3643724 GCCCAGA
1 ACCCAGA
3643731 TGGAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (24 bp):
ACCCAGAATAATTAGCTCTTACGA
Found at i:3647543 original size:23 final size:23
Alignment explanation
Indices: 3647513--3647575 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
3647503 ACGCTAGCGC
*
3647513 GCTTACTGTTTCG-TACTTTGTGT
1 GCTTACTGTTTCGCT-CCTTGTGT
3647536 GCTTACTGTTTCGCTCCTTGTGT
1 GCTTACTGTTTCGCTCCTTGTGT
*
3647559 GCCTACTGATTTGCGCT
1 GCTTACTG-TTT-CGCT
3647576 GTGTGCGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 27 0.77
24 4 0.11
25 4 0.11
ACGTcount: A:0.08, C:0.24, G:0.22, T:0.46
Consensus pattern (23 bp):
GCTTACTGTTTCGCTCCTTGTGT
Found at i:3647580 original size:23 final size:22
Alignment explanation
Indices: 3647554--3647634 Score: 117
Period size: 23 Copynumber: 3.6 Consensus size: 22
3647544 TTTCGCTCCT
*
3647554 TGTGTGCCTACTGATTTGCGCTG
1 TGTGTGCCTACTGA-TTGCACTG
* *
3647577 TGTGCGCCTACTGATTACACTG
1 TGTGTGCCTACTGATTGCACTG
3647599 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTG
3647622 TGTGTGCCTACTG
1 TGTGTGCCTACTG
3647635 TTTCCCCTGC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
22 18 0.35
23 34 0.65
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.36
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTG
Found at i:3649599 original size:29 final size:29
Alignment explanation
Indices: 3649469--3649688 Score: 108
Period size: 30 Copynumber: 7.5 Consensus size: 29
3649459 ACCCGGGGGC
*
3649469 AAAATGGTAATTTTAGGAAAATTCG-GGGTT
1 AAAATGGTAATTTT-GGAAAGTTCGAGGG-T
* * *
3649499 AAGAATGG-GATTTTGGAAGGTTCGAGGAT
1 AA-AATGGTAATTTTGGAAAGTTCGAGGGT
*
3649528 AAAACGGTAATTTTCGGTGAAA--TC-AGGGTT
1 AAAATGGTAATTTT--G-GAAAGTTCGAGGG-T
3649558 AAAAATGG-AATTTTGGAAAGTTCGAGGGT
1 -AAAATGGTAATTTTGGAAAGTTCGAGGGT
3649587 AAAATGGTAATTTTTGGTGAAA--TCG-GGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTCGAGGG-T
* *
3649617 AAAAATGG-AATTTTAGAAAGTT-TAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTCGA-GGGT
* *
3649646 AATATGGTAATTTTTGG-AAGTTTC-AAGGT
1 AAAATGGTAA-TTTTGGAAAG-TTCGAGGGT
3649675 CAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
3649689 CCAAAATTTT
Statistics
Matches: 149, Mismatches: 15, Indels: 54
0.68 0.07 0.25
Matches are distributed among these distances:
27 8 0.05
28 22 0.15
29 45 0.30
30 47 0.32
31 20 0.13
32 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTCGAGGGT
Found at i:3649646 original size:59 final size:58
Alignment explanation
Indices: 3649469--3649662 Score: 230
Period size: 59 Copynumber: 3.3 Consensus size: 58
3649459 ACCCGGGGGC
* * * * * *
3649469 AAAATGGTAATTTTAGG-AAAATTCGGGGTTAAGAATGGGATTTTGGAAGGTTCGAGGAT
1 AAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGAATTTT-GAAAGTTCGAGGGT
* * *
3649528 AAAACGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAGTTCGAGGGT
*
3649587 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAGTTCGA-GGGT
*
3649646 AATATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
3649663 AAGTTTCAAG
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 1 0.01
59 115 0.97
60 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTCGAGGGT
Found at i:3650362 original size:14 final size:14
Alignment explanation
Indices: 3650340--3650369 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3650330 TACTCAAAAC
*
3650340 GAAACCCAGATCTG
1 GAAAACCAGATCTG
3650354 GAAAACCAGATCTG
1 GAAAACCAGATCTG
3650368 GA
1 GA
3650370 TTTTCCCAAA
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:0.40, C:0.23, G:0.23, T:0.13
Consensus pattern (14 bp):
GAAAACCAGATCTG
Found at i:3650699 original size:3 final size:3
Alignment explanation
Indices: 3650693--3650781 Score: 61
Period size: 3 Copynumber: 28.0 Consensus size: 3
3650683 TTTCATTTTT
* * * * *
3650693 TTA TTA TCA TTA TTG TTAA TTA ATA TTAA TTAA TTA TAA ATA TTTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TT-A TT-A TTA TTA TTA -TTA TTA
* * *
3650742 TTA TTA TTTA TTA TTA TGA TTA TTA CTA ATA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3650782 ATAATATTTA
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
3 53 0.79
4 14 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:3651475 original size:6 final size:6
Alignment explanation
Indices: 3651458--3651554 Score: 80
Period size: 6 Copynumber: 17.0 Consensus size: 6
3651448 CTTGGACTTT
* * * * *
3651458 AATTTA AA-TTA ATTTTA AATTTA AA-ATA AATTTA GACTCA AA-TTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
3651503 AATTCA AATTTAA AATTT- AATTTA AATTTA AATTTA AA--TA AATCTA
1 AATTTA AATTT-A AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
3651549 AATTTA
1 AATTTA
3651555 TATCAAATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
4 4 0.06
5 17 0.24
6 45 0.62
7 6 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:3651480 original size:17 final size:17
Alignment explanation
Indices: 3651458--3651541 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
3651448 CTTGGACTTT
*
3651458 AATTTAAATTAATTTTA
1 AATTTAAATTAAATTTA
*
3651475 AATTTAAAATAAATTTA
1 AATTTAAATTAAATTTA
* * * *
3651492 GACTCAAATTAAATTCA
1 AATTTAAATTAAATTTA
*
3651509 AATTTAAAATTTAATTTA
1 AATTT-AAATTAAATTTA
3651527 AATTTAAATTTAAAT
1 AATTTAAA-TTAAAT
3651542 AAATCTAAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
17 32 0.62
18 20 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:3653991 original size:14 final size:15
Alignment explanation
Indices: 3653963--3653991 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3653953 TTAACTACCC
3653963 TTTTTCTTTTATATT
1 TTTTTCTTTTATATT
3653978 TTTTTCTTTT-TATT
1 TTTTTCTTTTATATT
3653992 AAAAAGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTATATT
Found at i:3665993 original size:27 final size:27
Alignment explanation
Indices: 3665963--3666038 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
3665953 TAACTCCTAA
* *
3665963 ATTGATATTTAAACTATATTTTTTCAT
1 ATTGATATCTAAACTATATTTTTTCAC
**
3665990 ATTGATGCCTAAA-T-T-TTTTTTCAC
1 ATTGATATCTAAACTATATTTTTTCAC
*
3666014 ATATGGTATCTAAACTATATTTTTT
1 AT-TGATATCTAAACTATATTTTTT
3666039 TCTTGAATTG
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
24 10 0.26
25 9 0.24
26 2 0.05
27 11 0.29
28 6 0.16
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (27 bp):
ATTGATATCTAAACTATATTTTTTCAC
Found at i:3668619 original size:24 final size:24
Alignment explanation
Indices: 3668587--3668633 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3668577 TGAAGTTTTT
3668587 TGTTTGTTTCTCGAGAAAATACTC
1 TGTTTGTTTCTCGAGAAAATACTC
*
3668611 TGTTTGTTTCTCGGGAAAATACT
1 TGTTTGTTTCTCGAGAAAATACT
3668634 GAACCCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGTTTGTTTCTCGAGAAAATACTC
Found at i:3669012 original size:30 final size:29
Alignment explanation
Indices: 3668977--3669103 Score: 158
Period size: 30 Copynumber: 4.5 Consensus size: 29
3668967 GATGATGATG
*
3668977 ATTTTAATAATTATATATTTTAAAAAATA
1 ATTTTAATAATTTTATATTTTAAAAAATA
*
3669006 ATTTT--TAA-ATTA-ATTTT--AAAATA
1 ATTTTAATAATTTTATATTTTAAAAAATA
3669029 ATTTTAATAATTTTATATTTTTAAAAAATA
1 ATTTTAATAATTTTATA-TTTTAAAAAATA
*
3669059 AGTTTAATAATTTTATATTTTAAAAAAATA
1 ATTTTAATAATTTTATATTTT-AAAAAATA
*
3669089 AGTTTAATAATTTTA
1 ATTTTAATAATTTTA
3669104 AAATCATTTG
Statistics
Matches: 86, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
23 11 0.13
25 8 0.09
26 5 0.06
27 4 0.05
28 4 0.05
29 9 0.10
30 45 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
ATTTTAATAATTTTATATTTTAAAAAATA
Found at i:3669022 original size:11 final size:10
Alignment explanation
Indices: 3669001--3669043 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
3668991 ATATTTTAAA
3669001 AAATAATTTTT
1 AAATAA-TTTT
3669012 AAATTAATTTT
1 AAA-TAATTTT
3669023 AAAATAATTTT
1 -AAATAATTTT
3669034 -AATAATTTT
1 AAATAATTTT
3669043 A
1 A
3669044 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.31
11 14 0.48
12 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AAATAATTTT
Found at i:3669065 original size:52 final size:50
Alignment explanation
Indices: 3668977--3669073 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 50
3668967 GATGATGATG
*
3668977 ATTTTAATAATTATATATTTTAAAAAATAATTTTTAAATTAATTTTAAAATA
1 ATTTTAATAATTATATATTTTAAAAAATAATGTTT-AA-TAATTTTAAAATA
*
3669029 ATTTTAATAATTTTATATTTTTAAAAAATAA-GTTTAATAATTTTA
1 ATTTTAATAATTATATA-TTTTAAAAAATAATGTTTAATAATTTTA
3669074 TATTTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 8 0.19
51 2 0.05
52 19 0.45
53 13 0.31
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (50 bp):
ATTTTAATAATTATATATTTTAAAAAATAATGTTTAATAATTTTAAAATA
Found at i:3671092 original size:18 final size:19
Alignment explanation
Indices: 3671060--3671098 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3671050 TATTTCTTTT
3671060 TTATTAATTTAAAATT-TA
1 TTATTAATTTAAAATTATA
3671078 TTATTAAATTT-AAATTATA
1 TTATT-AATTTAAAATTATA
3671097 TT
1 TT
3671099 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTAATTTAAAATTATA
Found at i:3679157 original size:47 final size:47
Alignment explanation
Indices: 3679104--3679197 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
3679094 TGATTTTCAA
3679104 AAATTTGAAAACAAGGTTACTCAAATTGAGCTTCAAGTCACACATTT
1 AAATTTGAAAACAAGGTTACTCAAATTGAGCTTCAAGTCACACATTT
*
3679151 AAATTTGAAAATAAGGTTACTCAAATTGAGCTTCAAGTCACACATTT
1 AAATTTGAAAACAAGGTTACTCAAATTGAGCTTCAAGTCACACATTT
3679198 CATTTCAAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (47 bp):
AAATTTGAAAACAAGGTTACTCAAATTGAGCTTCAAGTCACACATTT
Found at i:3683291 original size:18 final size:18
Alignment explanation
Indices: 3683268--3683305 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3683258 TAGATTAATA
*
3683268 AAATTAACTAATAATTAT
1 AAATTAAATAATAATTAT
*
3683286 AAATTAAATTATAATTAT
1 AAATTAAATAATAATTAT
3683304 AA
1 AA
3683306 TTACACATTT
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTAAATAATAATTAT
Found at i:3683416 original size:21 final size:24
Alignment explanation
Indices: 3683382--3683436 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
3683372 GCATAATATT
3683382 TTAACTAATAA-TTTT-AAATTAAA
1 TTAA-TAATAATTTTTAAAATTAAA
* *
3683405 TT-ATAATTATTTTTAAAATTAAT
1 TTAATAATAATTTTTAAAATTAAA
3683428 TTAATAATA
1 TTAATAATA
3683437 TGATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 11 0.42
24 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATAATAATTTTTAAAATTAAA
Found at i:3689408 original size:47 final size:47
Alignment explanation
Indices: 3689319--3689408 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
3689309 TGATGTAAAA
* *
3689319 ATAAATATTTTATATTTAAAATAATGAAAATAATTTAAAATTTTTAT
1 ATAAAAATTGTATATTTAAAATAATGAAAATAATTTAAAATTTTTAT
3689366 ATAAAAATTGTAT-TTTAAAA-AAT-AAAATAGAATTTCAAAATTT
1 ATAAAAATTGTATATTTAAAATAATGAAAAT--AATTT-AAAATTT
3689409 GAAAACTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 5 0.13
45 3 0.08
46 12 0.32
47 18 0.47
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (47 bp):
ATAAAAATTGTATATTTAAAATAATGAAAATAATTTAAAATTTTTAT
Found at i:3692302 original size:42 final size:41
Alignment explanation
Indices: 3692241--3692327 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
3692231 TTATGTATTT
* * * *
3692241 AATTAGATAACTTTTTCAATTTTCGTAAAGCAGAAGAATCA
1 AATTAGATAACTTTCTCAATATTCATAAAACAGAAGAATCA
* * *
3692282 AATTATGATAAGTTTCTCAATATTCATAAAACAGAAGGATGA
1 AATTA-GATAACTTTCTCAATATTCATAAAACAGAAGAATCA
3692324 AATT
1 AATT
3692328 TTCAATTAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 5 0.13
42 33 0.87
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (41 bp):
AATTAGATAACTTTCTCAATATTCATAAAACAGAAGAATCA
Found at i:3694988 original size:47 final size:47
Alignment explanation
Indices: 3694934--3695030 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
3694924 ATTCTTATCA
3694934 AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
1 AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
*
3694981 AATAATCCAACAAGTCACAGGTTATTGATTTAACTGATGTCCAAACC
1 AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
3695028 AAT
1 AAT
3695031 TAGTGTTTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (47 bp):
AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
Found at i:3698824 original size:19 final size:19
Alignment explanation
Indices: 3698800--3698838 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3698790 TATTAGTATT
3698800 AGTTAATTATAATTAATTA
1 AGTTAATTATAATTAATTA
*
3698819 AGTTAATTTTAATTAATTA
1 AGTTAATTATAATTAATTA
3698838 A
1 A
3698839 TAAACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
AGTTAATTATAATTAATTA
Found at i:3701855 original size:11 final size:11
Alignment explanation
Indices: 3701832--3701864 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3701822 TAAATGAACA
3701832 GAAC-GTTCGGT
1 GAACTGTTC-GT
3701843 GAACTGTTCGT
1 GAACTGTTCGT
3701854 GAACTGTTCGT
1 GAACTGTTCGT
3701865 ATAATGTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (11 bp):
GAACTGTTCGT
Found at i:3703663 original size:19 final size:20
Alignment explanation
Indices: 3703627--3703668 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3703617 TAACTAAGTT
*
3703627 TTTTATTT-AGTTGGTTTTG
1 TTTTATTTAATTTGGTTTTG
**
3703646 TTTTATTTAATTTTTTTTTG
1 TTTTATTTAATTTGGTTTTG
3703666 TTT
1 TTT
3703669 GTTTGGTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (20 bp):
TTTTATTTAATTTGGTTTTG
Found at i:3703760 original size:23 final size:23
Alignment explanation
Indices: 3703682--3703907 Score: 211
Period size: 23 Copynumber: 9.7 Consensus size: 23
3703672 TGGTTAGTTA
* *
3703682 TAAACGAACATGTTCGCGAACACA
1 TAAACGAACATGTTCACGAACA-T
* *
3703706 TAAATGAACATGTTCATGAACGCA-
1 TAAACGAACATGTTCACGAA--CAT
* *
3703730 TAAACGAACATGTTCGCGAATAT
1 TAAACGAACATGTTCACGAACAT
* ** *
3703753 TAAACGAACATATAAATGAACAT
1 TAAACGAACATGTTCACGAACAT
*
3703776 ATAAACGAACATGTTCATGAACAT
1 -TAAACGAACATGTTCACGAACAT
* * * * *
3703800 ATAAACAAATATATTCATGAACGT
1 -TAAACGAACATGTTCACGAACAT
* *
3703824 TAAACGAACATGTTCTCGAACGT
1 TAAACGAACATGTTCACGAACAT
* *
3703847 TAAACGAACATGTTCTCGAACGT
1 TAAACGAACATGTTCACGAACAT
*
3703870 TAAACGAACATGTTCACGAACGT
1 TAAACGAACATGTTCACGAACAT
3703893 TAAACGAACATGTTC
1 TAAACGAACATGTTC
3703908 GTGAATGATA
Statistics
Matches: 172, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
22 1 0.01
23 95 0.55
24 74 0.43
26 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCACGAACAT
Found at i:3703768 original size:12 final size:12
Alignment explanation
Indices: 3703753--3703787 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3703743 TCGCGAATAT
3703753 TAAACGAACATA
1 TAAACGAACATA
*
3703765 TAAATGAACATA
1 TAAACGAACATA
3703777 TAAACGAACAT
1 TAAACGAACAT
3703788 GTTCATGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (12 bp):
TAAACGAACATA
Found at i:3703871 original size:46 final size:46
Alignment explanation
Indices: 3703682--3703924 Score: 254
Period size: 46 Copynumber: 5.2 Consensus size: 46
3703672 TGGTTAGTTA
* * *
3703682 TAAACGAACATGTTCGCGAACACATAAATGAACATGTTCATGAACGCA
1 TAAACGAACATGTTCGCGAACA-TTAAACGAACATGTTCATGAACG-T
* * ** *
3703730 TAAACGAACATGTTCGCGAATATTAAACGAACATATAAATGAACAT
1 TAAACGAACATGTTCGCGAACATTAAACGAACATGTTCATGAACGT
** * * *
3703776 ATAAACGAACATGTTCATGAACATATAAACAAATATATTCATGAACGT
1 -TAAACGAACATGTTCGCGAACAT-TAAACGAACATGTTCATGAACGT
* *
3703824 TAAACGAACATGTTCTCGAACGTTAAACGAACATGTTC-TCGAACGT
1 TAAACGAACATGTTCGCGAACATTAAACGAACATGTTCAT-GAACGT
* * * * *
3703870 TAAACGAACATGTTCACGAACGTTAAACGAACATGTTCGTGAATGA
1 TAAACGAACATGTTCGCGAACATTAAACGAACATGTTCATGAACGT
3703916 TAAACGAAC
1 TAAACGAAC
3703925 GAGCTCGAAC
Statistics
Matches: 166, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.01
46 68 0.41
47 58 0.35
48 39 0.23
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (46 bp):
TAAACGAACATGTTCGCGAACATTAAACGAACATGTTCATGAACGT
Found at i:3704370 original size:91 final size:89
Alignment explanation
Indices: 3704275--3704483 Score: 226
Period size: 91 Copynumber: 2.3 Consensus size: 89
3704265 TGTAAAAAGT
* ** ** * *
3704275 CCTCAATTTTTTTCAAAAAAAGCAATTAAACCTTTTTTTTTTTTTTTCACTCAATTGAGCAT-TT
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAACCCCTGCTTTTTTCTCTCACTCAATTG-G-ATATT
*
3704339 GAACTTTCAAAAT-ACATAAAAAAAGGC
64 GAACTTTCAAAATGA-AT-AAAAAAGAC
* * * *
3704366 CCTCAAACTTCTTCAAAAAAAGCAATGAAGCCCCTGCTTTTTTCTCTCACTCAATTGGATACTTG
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAACCCCTGCTTTTTTCTCTCACTCAATTGGATA-TTG
*
3704431 AACTTTCAAAATGAATCAAAAAGAC
65 AACTTTCAAAATGAATAAAAAAGAC
*
3704456 CCTAAAATTTTTTC-AAAAAAGCAATTAA
1 CCTCAAATTTTTTCAAAAAAAGCAATTAA
3704484 GCCATTGCTC
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
89 15 0.15
90 19 0.19
91 63 0.64
92 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.34
Consensus pattern (89 bp):
CCTCAAATTTTTTCAAAAAAAGCAATTAAACCCCTGCTTTTTTCTCTCACTCAATTGGATATTGA
ACTTTCAAAATGAATAAAAAAGAC
Found at i:3704591 original size:18 final size:20
Alignment explanation
Indices: 3704560--3704608 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3704550 TTTAATAAAA
3704560 ATATAAAAACTTTAAA-TTTT
1 ATATAAAAA-TTTAAACTTTT
3704580 AT-TAAAAATTTAAACTTTT
1 ATATAAAAATTTAAACTTTT
*
3704599 TTATAAAAAT
1 ATATAAAAAT
3704609 CATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 6 0.23
19 11 0.42
20 9 0.35
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAAAAATTTAAACTTTT
Found at i:3704658 original size:19 final size:19
Alignment explanation
Indices: 3704636--3704674 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3704626 TGTAAAATTT
3704636 TATAGAAAT-CATAAAAAAA
1 TATA-AAATGCATAAAAAAA
*
3704655 TATAAAATGCATTAAAAAA
1 TATAAAATGCATAAAAAAA
3704674 T
1 T
3704675 TTCTTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
TATAAAATGCATAAAAAAA
Found at i:3704903 original size:20 final size:19
Alignment explanation
Indices: 3704846--3704903 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
3704836 TGGTATGGTA
* *
3704846 ATTTTTATAATTTTTTTACG
1 ATTTTTATAATTTTCTTA-T
3704866 ATTTTTAT-A-TTTCTTTAT
1 ATTTTTATAATTTTC-TTAT
3704884 ATTTTGTATAATTTTCTTAT
1 ATTTT-TATAATTTTCTTAT
3704904 GACTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 13 0.41
21 4 0.12
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTTTATAATTTTCTTAT
Found at i:3704928 original size:58 final size:55
Alignment explanation
Indices: 3704866--3704992 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 55
3704856 TTTTTTTACG
* * *
3704866 ATTTTTATATTTCTTTATATTTTGTATAATTTTCTTATGACTTTATAAAAAATTATATA
1 ATTTTTATATTTCTATATA-TTT-TATAATTTT-TTACGA-TTTATAAAAAATTATACA
* * * *
3704925 TTTTTTTATATTTCTATATATTTTATAATTTTTTACGATTTTTATAAAATTTTACA
1 -ATTTTTATATTTCTATATATTTTATAATTTTTTACGATTTATAAAAAATTATACA
3704981 ATTTTTATATTT
1 ATTTTTATATTT
3704993 TTGACAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
55 11 0.19
56 14 0.24
57 5 0.08
58 9 0.15
59 3 0.05
60 17 0.29
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.61
Consensus pattern (55 bp):
ATTTTTATATTTCTATATATTTTATAATTTTTTACGATTTATAAAAAATTATACA
Found at i:3704967 original size:19 final size:19
Alignment explanation
Indices: 3704945--3705023 Score: 92
Period size: 18 Copynumber: 4.3 Consensus size: 19
3704935 TTTCTATATA
*
3704945 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACAAT
**
3704964 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
*
3704983 TTTTAT-ATTTTTGACAAT
1 TTTTATAATTTTTTACAAT
3705001 TTTTAT-ATTTTTT-CTAAT
1 TTTTATAATTTTTTAC-AAT
3705019 TTTTA
1 TTTTA
3705024 ATTTTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.02
18 29 0.56
19 22 0.42
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:3705030 original size:8 final size:9
Alignment explanation
Indices: 3704844--3705023 Score: 73
Period size: 9 Copynumber: 19.0 Consensus size: 9
3704834 TTTGGTATGG
3704844 TAATTTTTA
1 TAATTTTTA
*
3704853 TAATTTTTT
1 TAATTTTTA
3704862 TACGATTTTTA
1 TA--ATTTTTA
*
3704873 TATTTCTTTA
1 TAATT-TTTA
3704883 T-ATTTTGTA
1 TAATTTT-TA
3704892 TAATTTTCTTA
1 TAA-TTT-TTA
* *
3704903 TGA-CTTTA
1 TAATTTTTA
***
3704911 TAAAAAATTA
1 T-AATTTTTA
*
3704921 TATATTTTTT
1 TA-ATTTTTA
*
3704931 TATATTTCTA
1 TA-ATTTTTA
3704941 T-ATATTTTA
1 TAAT-TTTTA
3704950 TAATTTTT-
1 TAATTTTTA
3704958 TACGATTTTTA
1 TA--ATTTTTA
*
3704969 TAAAATTTTA
1 T-AATTTTTA
*
3704979 CAATTTTTA
1 TAATTTTTA
3704988 T-ATTTTTGA
1 TAATTTTT-A
*
3704997 CAATTTTTA
1 TAATTTTTA
* *
3705006 TATTTTTTC
1 TAATTTTTA
3705015 TAATTTTTA
1 TAATTTTTA
3705024 ATTTTTTTTA
Statistics
Matches: 127, Mismatches: 26, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
8 16 0.13
9 51 0.40
10 42 0.33
11 16 0.13
12 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (9 bp):
TAATTTTTA
Found at i:3705031 original size:18 final size:17
Alignment explanation
Indices: 3704974--3705031 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
3704964 TTTTATAAAA
*
3704974 TTTTACAATTTTTATATT
1 TTTTTCAATTTTTA-ATT
**
3704992 TTTGACAATTTTT-ATAT
1 TTTTTCAATTTTTAAT-T
3705009 TTTTTCTAATTTTTAATT
1 TTTTTC-AATTTTTAATT
3705027 TTTTT
1 TTTTT
3705032 TATTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 25 0.74
19 2 0.06
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTCAATTTTTAATT
Found at i:3705192 original size:91 final size:92
Alignment explanation
Indices: 3705097--3705329 Score: 231
Period size: 91 Copynumber: 2.5 Consensus size: 92
3705087 TTTTGTTAAT
* * *
3705097 AAAAGTAGGGGTTTAATTACTTTTTTTGAAAAAAGTTTGAGACTTTTTTTTTATGCATTTTAAAA
1 AAAAGTAGGGGCTTAATTGCTTTTTTTG-AAAAAGTTTGAGACTTTTTTTTGATGCATTTTAAAA
3705162 ATTCAAG-CCC-AATTGAGTGC-AAAAAA
65 ATTCAAGACCCTAA-TGAGTGCAAAAAAA
** * * * ** * *
3705188 AAAAGTAAAGACTTAATTGCTTTTTTTGAAAACGTTTAAG-GGTTTTTTTGATGCATTTTGAAAG
1 AAAAGTAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGACTTTTTTTTGATGCATTTTAAAAA
*
3705252 TTGAAGTACCCTAATGAGTGCAAAAAAA
66 TTCAAG-ACCCTAATGAGTGCAAAAAAA
* * * *
3705280 AAAAGAAGGGGCTTAATTGGGTTTTTTTTTAGAAAGTTTGAGAGCTTTTT
1 AAAAGTAGGGGCTTAATT--GCTTTTTTTGAAAAAGTTTGAGA-CTTTTT
3705330 ATACCCTTAA
Statistics
Matches: 110, Mismatches: 24, Indels: 11
0.76 0.17 0.08
Matches are distributed among these distances:
89 24 0.22
90 10 0.09
91 33 0.30
92 22 0.20
94 17 0.15
96 4 0.04
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (92 bp):
AAAAGTAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGACTTTTTTTTGATGCATTTTAAAAA
TTCAAGACCCTAATGAGTGCAAAAAAA
Found at i:3707250 original size:66 final size:70
Alignment explanation
Indices: 3707168--3707313 Score: 246
Period size: 72 Copynumber: 2.1 Consensus size: 70
3707158 AGCTCCAACC
3707168 GCAAACGCAGCCGCTTTTCATGCAA-C-C-GCCGCCG-CCGCCGCCGAAAGAAACGCAAACGTTG
1 GCAAACGCAGCCGCTTTTCATGCAACCGCAGCCGCCGCCCGCCGCCGAAAGAAACGCAAACGTTG
3707229 TTCAT
66 TTCAT
3707234 GCAAACGCAGCCGCTTTTCATGCAACCGCAGCCGCCGCCTCCGCCGCCGAAAGAAACGCAAACGT
1 GCAAACGCAGCCGCTTTTCATGCAACCGCAGCCGCCG-C-CCGCCGCCGAAAGAAACGCAAACGT
3707299 TGTTCAT
64 TGTTCAT
3707306 GCAAACGC
1 GCAAACGC
3707314 CGCCACAGAA
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
66 25 0.34
67 1 0.01
68 1 0.01
69 7 0.09
72 40 0.54
ACGTcount: A:0.26, C:0.37, G:0.23, T:0.14
Consensus pattern (70 bp):
GCAAACGCAGCCGCTTTTCATGCAACCGCAGCCGCCGCCCGCCGCCGAAAGAAACGCAAACGTTG
TTCAT
Found at i:3707253 original size:21 final size:21
Alignment explanation
Indices: 3707229--3707268 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3707219 GCAAACGTTG
3707229 TTCATGCAAACGCAGCCGCTT
1 TTCATGCAAACGCAGCCGCTT
*
3707250 TTCATGCAACCGCAGCCGC
1 TTCATGCAAACGCAGCCGC
3707269 CGCCTCCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
TTCATGCAAACGCAGCCGCTT
Found at i:3717744 original size:8 final size:7
Alignment explanation
Indices: 3717733--3717795 Score: 58
Period size: 8 Copynumber: 8.7 Consensus size: 7
3717723 CAAAAATTAA
3717733 AAAAAAGG
1 AAAAAA-G
3717741 AAAAAAG
1 AAAAAAG
*
3717748 AGAAAAAA
1 A-AAAAAG
3717756 AGAAAAAG
1 A-AAAAAG
*
3717764 -AAAAGG
1 AAAAAAG
3717770 AAAAAAG
1 AAAAAAG
3717777 AAGAAAAG
1 AA-AAAAG
3717785 -AAAAAG
1 AAAAAAG
3717791 AAAAA
1 AAAAA
3717796 TGAGAGGTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
6 10 0.21
7 14 0.30
8 23 0.49
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3717753 original size:16 final size:16
Alignment explanation
Indices: 3717734--3717783 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
3717724 AAAAATTAAA
3717734 AAAAAGGAAAAAAGAG
1 AAAAAGGAAAAAAGAG
3717750 AAAAA--AAGAAAA-AG
1 AAAAAGGAA-AAAAGAG
3717764 -AAAAGGAAAAAAGAAG
1 AAAAAGGAAAAAAG-AG
3717780 AAAA
1 AAAA
3717784 GAAAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 6 0.21
16 7 0.25
17 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGGAAAAAAGAG
Found at i:3717761 original size:6 final size:6
Alignment explanation
Indices: 3717752--3717795 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
3717742 AAAAAGAGAA
*
3717752 AAAAAG AAAAAG AAAAGG AAAAAAG AAGAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG -A-AAAAG AAAAAG AAAAA
3717796 TGAGAGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 21 0.62
7 8 0.24
8 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3717767 original size:21 final size:23
Alignment explanation
Indices: 3717743--3717795 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
3717733 AAAAAAGGAA
3717743 AAAAGAGAAAAAAAG-A-AAAAG
1 AAAAGAGAAAAAAAGAAGAAAAG
3717764 AAAAG-G-AAAAAAGAAGAAAAG
1 AAAAGAGAAAAAAAGAAGAAAAG
3717785 AAAA-AGAAAAA
1 AAAAGAGAAAAA
3717796 TGAGAGGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 7 0.25
20 2 0.07
21 15 0.54
22 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAAGAGAAAAAAAGAAGAAAAG
Found at i:3717784 original size:16 final size:15
Alignment explanation
Indices: 3717735--3717789 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
3717725 AAAATTAAAA
3717735 AAAAGGAAAAAAG-AG
1 AAAA-GAAAAAAGAAG
3717750 AAAA-AAAGAAA-AAG
1 AAAAGAAA-AAAGAAG
3717764 AAAAGGAAAAAAGAAG
1 AAAA-GAAAAAAGAAG
3717780 AAAAGAAAAA
1 AAAAGAAAAA
3717790 GAAAAATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.09
14 9 0.26
15 13 0.37
16 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAG
Found at i:3717784 original size:27 final size:29
Alignment explanation
Indices: 3717735--3717794 Score: 97
Period size: 27 Copynumber: 2.1 Consensus size: 29
3717725 AAAATTAAAA
3717735 AAAAGGAAAAAAGAGAAAAAAAGAAAAAG
1 AAAAGGAAAAAAGAGAAAAAAAGAAAAAG
*
3717764 AAAAGG-AAAAA-AGAAGAAAAGAAAAAG
1 AAAAGGAAAAAAGAGAAAAAAAGAAAAAG
3717791 AAAA
1 AAAA
3717795 ATGAGAGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 19 0.63
28 5 0.17
29 6 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAGGAAAAAAGAGAAAAAAAGAAAAAG
Found at i:3718767 original size:49 final size:48
Alignment explanation
Indices: 3718679--3718879 Score: 125
Period size: 49 Copynumber: 4.1 Consensus size: 48
3718669 TCTACAGGTT
* * ** * *
3718679 TGAAGGGAAAGATTGAAGCCGCAACGGCAAATCTAATACCCTAGAGATA
1 TGAA-GGAAAGGTTGAAGCCACAACGGTGAACCTTATACCCTAGAGATA
* * * **
3718728 TGAAGAGAAAGGTTGAAGCCACAATGGTGAACCTTATACCTTAGGGACG
1 TGAAG-GAAAGGTTGAAGCCACAACGGTGAACCTTATACCCTAGAGATA
* *** * * * *
3718777 TGATAGGAAAGATTGAAGCCGTGACGGTGAATCTTGTTCCCTAGAGTTA
1 TGA-AGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCCTAGAGATA
* ** ** * *
3718826 TGGAGGGAAAGGTTGAAGCTGCAAC-ACGAACCTTGTACCCTAGAGATG
1 T-GAAGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCCTAGAGATA
3718874 TGAAGG
1 TGAAGG
3718880 GAAAAATTGG
Statistics
Matches: 113, Mismatches: 36, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
47 4 0.04
48 19 0.17
49 86 0.76
50 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (48 bp):
TGAAGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCCTAGAGATA
Found at i:3719354 original size:38 final size:39
Alignment explanation
Indices: 3719247--3719473 Score: 146
Period size: 39 Copynumber: 5.8 Consensus size: 39
3719237 CCTAATCAGA
* * *
3719247 GGGCAGATTGAAGATCATCTAATCTTTTA-CCCTAACCA-G
1 GGGCAGATTGAAG-TCATCCAATATTTTACCCCGAA-CATG
* ** * *
3719286 AGGGCAAATTGAAAACCATCCAATCTTTTACCCCGATCATG
1 -GGGCAGATTG-AAGTCATCCAATATTTTACCCCGAACATG
* *
3719327 GGGCAGATTGAAGT-ATCCATTATTTTA-CCCTAAC-TAG
1 GGGCAGATTGAAGTCATCCAATATTTTACCCCGAACAT-G
* * *
3719364 AGGGCAGATTGAAGTCATCCAATCTCTTACCCCGACCATG
1 -GGGCAGATTGAAGTCATCCAATATTTTACCCCGAACATG
* **
3719404 GGGCAGATTGAAG-CAATCCAATCTTTTA-CCTTAACCA-G
1 GGGCAGATTGAAGTC-ATCCAATATTTTACCCCGAA-CATG
* * *
3719442 AGGGCAAATTGAAATCATCCAATCTTTTACCC
1 -GGGCAGATTGAAGTCATCCAATATTTTACCC
3719474 TAATCAGAGG
Statistics
Matches: 150, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
36 1 0.01
37 6 0.04
38 30 0.20
39 63 0.42
40 42 0.28
41 8 0.05
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (39 bp):
GGGCAGATTGAAGTCATCCAATATTTTACCCCGAACATG
Found at i:3719395 original size:39 final size:39
Alignment explanation
Indices: 3719181--3719534 Score: 367
Period size: 40 Copynumber: 9.0 Consensus size: 39
3719171 CAAGTTACAA
** *
3719181 TCATCCAATCTTTTACCCTAATCAGAGGATAGATTGAAAA
1 TCATCCAATCTTTTACCCTAATCAGAGGGCAGATTG-AAG
* *
3719221 CCATTCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
1 TCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
* * * *
3719260 ATCATCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAAA
1 -TCATCCAATCTTTTACCCTAATCAGAGGGCAGATTG-AAG
* **
3719301 CCATCCAATCTTTTACCCCGATCATG-GGGCAGATTGAAG
1 TCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAG
* *
3719340 T-ATCCATTATTTTACCCTAA-CTAGAGGGCAGATTGAAG
1 TCATCCAATCTTTTACCCTAATC-AGAGGGCAGATTGAAG
* ** *
3719378 TCATCCAATCTCTTACCCCGACCATG-GGGCAGATTGAAG
1 TCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAG
* * * *
3719417 -CAATCCAATCTTTTACCTTAACCAGAGGGCAAATTGAAA
1 TC-ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
*
3719456 TCATCCAATCTTTTACCCTAATCAGAGGACAGATTGAAG
1 TCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
* * *
3719495 ACCATTCAATCTTTTACTCTAATCAGAGGGCAGATTGAAG
1 -TCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
3719535 GCCATCAGAT
Statistics
Matches: 259, Mismatches: 43, Indels: 24
0.79 0.13 0.07
Matches are distributed among these distances:
37 2 0.01
38 32 0.12
39 93 0.36
40 129 0.50
41 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (39 bp):
TCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
Found at i:3719415 original size:117 final size:118
Alignment explanation
Indices: 3719183--3719533 Score: 343
Period size: 117 Copynumber: 3.0 Consensus size: 118
3719173 AGTTACAATC
* * ** * * * *
3719183 ATCCAATCTTTTACCCTAATCAGAGGATAGATTGAAAACCATTCAATCTTTTACCCTAATCAGAG
1 ATCCAATCTTTTACCCCAACCAGAGGGCAAATTG-AAATCATCCAATATTTTACCCTAATCAGAG
* * * *
3719248 GGCAGATTGAAGATCATCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAAACC
65 GGCAGATTGAAGATCATCCAATCTCTTACCCCAACCAGAGGGCAAATTG-AAACA
* * * * *
3719303 ATCCAATCTTTTACCCCGATCATG-GGGCAGATTGAAGT-ATCCATTATTTTACCCTAA-CTAGA
1 ATCCAATCTTTTACCCCAACCA-GAGGGCAAATTGAAATCATCCAATATTTTACCCTAATC-AGA
* * *
3719365 GGGCAGATTGAAG-TCATCCAATCTCTTACCCCGACCATG-GGGCAGATTGAAGCA
64 GGGCAGATTGAAGATCATCCAATCTCTTACCCCAACCA-GAGGGCAAATTGAAACA
** *
3719419 ATCCAATCTTTTACCTTAACCAGAGGGCAAATTGAAATCATCCAATCTTTTACCCTAATCAGAGG
1 ATCCAATCTTTTACCCCAACCAGAGGGCAAATTGAAATCATCCAATATTTTACCCTAATCAGAGG
* * * * * * * *
3719484 ACAGATTGAAGACCATTCAATCTTTTACTCTAATCAGAGGGCAGATTGAA
66 GCAGATTGAAGATCATCCAATCTCTTACCCCAACCAGAGGGCAAATTGAA
3719534 GGCCATCAGA
Statistics
Matches: 191, Mismatches: 32, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
115 1 0.01
116 33 0.17
117 63 0.33
118 63 0.33
119 2 0.01
120 28 0.15
121 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (118 bp):
ATCCAATCTTTTACCCCAACCAGAGGGCAAATTGAAATCATCCAATATTTTACCCTAATCAGAGG
GCAGATTGAAGATCATCCAATCTCTTACCCCAACCAGAGGGCAAATTGAAACA
Found at i:3719423 original size:78 final size:78
Alignment explanation
Indices: 3719183--3719533 Score: 368
Period size: 78 Copynumber: 4.5 Consensus size: 78
3719173 AGTTACAATC
* ** * * * **
3719183 ATCCAATCTTTTACCCTAATCAGAGGATAGATTGAAAACCATTCAATCTTTTACCCTAATCA-GA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTG-AAATCATCCAATCTTTTACCCCGATCATG-
3719247 GGGCAGATTGAAG-A
64 GGGCAGATTGAAGCA
* *
3719261 TCATCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAAACCATCCAATCTTTTACCCCGATCAT
1 --ATCCAATCTTTTACCCTAACCAGAGGGCAAATTG-AAATCATCCAATCTTTTACCCCGATCAT
*
3719326 GGGGCAGATTGAAG-T
63 GGGGCAGATTGAAGCA
* * * * * * *
3719341 ATCCATTATTTTACCCTAACTAGAGGGCAGATTGAAGTCATCCAATCTCTTACCCCGACCATGGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAATCATCCAATCTTTTACCCCGATCATGGG
3719406 GCAGATTGAAGCA
66 GCAGATTGAAGCA
* **
3719419 ATCCAATCTTTTACCTTAACCAGAGGGCAAATTGAAATCATCCAATCTTTTACCCTAATCA-GAG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAATCATCCAATCTTTTACCCCGATCATG-G
* *
3719483 GACAGATTGAAGACC
65 GGCAGATTGAAG-CA
* * * *
3719498 ATTCAATCTTTTACTCTAATCAGAGGGCAGATTGAA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAA
3719534 GGCCATCAGA
Statistics
Matches: 231, Mismatches: 36, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
77 39 0.17
78 92 0.40
79 32 0.14
80 67 0.29
81 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (78 bp):
ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAATCATCCAATCTTTTACCCCGATCATGGG
GCAGATTGAAGCA
Found at i:3719554 original size:20 final size:20
Alignment explanation
Indices: 3719529--3719569 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3719519 AGAGGGCAGA
*
3719529 TTGAAGGCCA-TCAGATCTTT
1 TTGAAGACCATTCA-ATCTTT
3719549 TTGAAGACCATTCAATCTTT
1 TTGAAGACCATTCAATCTTT
3719569 T
1 T
3719570 ACCCTAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGAAGACCATTCAATCTTT
Found at i:3719928 original size:79 final size:78
Alignment explanation
Indices: 3719561--3720266 Score: 708
Period size: 79 Copynumber: 8.9 Consensus size: 78
3719551 GAAGACCATT
* *
3719561 CAATCTTTTACCCTAACTAGAGGGTAGATTGAAGACCATCCAAT-TTCTTACCCCGACCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGA-CATCCAATCTT-TTACCCCGACCATGGGG
* * *
3719625 CAGATTAAAGCAGTC
64 CAGATTGAAGTAATC
* ** * *
3719640 CAATCTTTTACCCTAACTAGAGGGCAGATTGAAGTTATCCAATCTCTTACCCTGACCATGGGGCA
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACATCCAATCTTTTACCCCGACCATGGGGCA
*
3719705 GATTGAAGTAATT
66 GATTGAAGTAATC
* **
3719718 TAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGG
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGA-CATCCAATCTTTTACCCCGACCATG-GGG
*
3719782 CAAATTGAAG-ACTAT-
64 CAGATTGAAGTA--ATC
* ** * * *
3719797 CAGATCTTTTACCCTAATCAGAGGATAAATTGAAGACCATCCAATCTCTTACCCCGATCATGGGG
1 CA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGA-CATCCAATCTTTTACCCCGACCATGGGG
*
3719862 CAGATTAAAGTAATC
64 CAGATTGAAGTAATC
* * ** *
3719877 CAATCTTTTACCCTAACCATG-GGGTAGATTGAAGTA-ATTCAAATCTTTTACCCTAACTA-GAG
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG-ACA-TCCAATCTTTTACCCCGACCATG-G
*
3719939 GGCAGATTAAAGTAATC
62 GGCAGATTGAAGTAATC
* * *
3719956 CAATCTTTTACCCTAACCAGATGGCAGATTAAAGCCATCCAATCTTTTACCCCGACCATGGGGGC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACATCCAATCTTTTACCCCGACCAT-GGGGC
*
3720021 AGATTGAAGCAATC
65 AGATTGAAGTAATC
* * * * * *
3720035 TAATCTTTTACCCTAACCAGAGGGCAGATTAAAGACTATCCGATCTCTTACCCCAACCATGAGGC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC-ATCCAATCTTTTACCCCGACCATGGGGC
* *
3720100 AAATTGAAGCAATC
65 AGATTGAAGTAATC
* ** * *
3720114 CAATCTTTTACCCTAACCAGAGGGCAGATTAAAGACCATCTGATCTTTTACCCCAACCATGGGAC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGA-CATCCAATCTTTTACCCCGACCATGGGGC
*
3720179 AGATTGAAGTAATT
65 AGATTGAAGTAATC
* * * * * * *
3720193 TAGATCTTTTACCCTAACTAGAGGGCAAATTAAAGTA-ATCCAGATCTCTTACCTCGACTATGGG
1 CA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAG-ACATCCA-ATCTTTTACCCCGACCATGGG
*
3720257 GCAAATTGAA
63 GCAGATTGAA
3720267 ACCATCAGAT
Statistics
Matches: 532, Mismatches: 73, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
78 88 0.17
79 298 0.56
80 143 0.27
81 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (78 bp):
CAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACATCCAATCTTTTACCCCGACCATGGGGCA
GATTGAAGTAATC
Done.