Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 21 of 25
Found at i:3354554 original size:15 final size:15
Alignment explanation
Indices: 3354534--3354564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3354524 ATTTCGTTTG
*
3354534 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3354549 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3354564 G
1 G
3354565 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3356397 original size:21 final size:21
Alignment explanation
Indices: 3356368--3356412 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3356358 AAGTTTTCAT
*
3356368 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3356388 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3356410 TTT
1 TTT
3356413 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3359603 original size:19 final size:18
Alignment explanation
Indices: 3359557--3359608 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
3359547 CAAGCTTAAG
*
3359557 TGTTCATGATCTTGTATT
1 TGTTCATGATTTTGTATT
3359575 TGATTCATGATTTTGTATTT
1 TG-TTCATGATTTTGTA-TT
*
3359595 TGTTAATGATTTTG
1 TGTTCATGATTTTG
3359609 CTATATCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 24 0.80
20 4 0.13
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (18 bp):
TGTTCATGATTTTGTATT
Found at i:3363385 original size:16 final size:16
Alignment explanation
Indices: 3363364--3363396 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3363354 CTTTCACTTG
*
3363364 CTGTTTTTGTTATTCT
1 CTGTTTTTATTATTCT
3363380 CTGTTTTTATTATTCT
1 CTGTTTTTATTATTCT
3363396 C
1 C
3363397 ATCATTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.67
Consensus pattern (16 bp):
CTGTTTTTATTATTCT
Found at i:3373207 original size:2 final size:2
Alignment explanation
Indices: 3373200--3373234 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3373190 AGTAGTTTTC
3373200 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3373235 TCTATCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3373560 original size:62 final size:62
Alignment explanation
Indices: 3373493--3373614 Score: 244
Period size: 62 Copynumber: 2.0 Consensus size: 62
3373483 GTGATTTTTG
3373493 GTTTTTAAAATGTTATATCTAAAATATATGTAAAGTTATGCTATTTTTATTATTTTTCACTT
1 GTTTTTAAAATGTTATATCTAAAATATATGTAAAGTTATGCTATTTTTATTATTTTTCACTT
3373555 GTTTTTAAAATGTTATATCTAAAATATATGTAAAGTTATGCTATTTTTATTATTTTTCAC
1 GTTTTTAAAATGTTATATCTAAAATATATGTAAAGTTATGCTATTTTTATTATTTTTCAC
3373615 GCTTTCGAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (62 bp):
GTTTTTAAAATGTTATATCTAAAATATATGTAAAGTTATGCTATTTTTATTATTTTTCACTT
Found at i:3374429 original size:13 final size:13
Alignment explanation
Indices: 3374411--3374436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3374401 TACAGCAAGT
3374411 ATGTATCGATACA
1 ATGTATCGATACA
3374424 ATGTATCGATACA
1 ATGTATCGATACA
3374437 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3374958 original size:34 final size:35
Alignment explanation
Indices: 3374895--3374961 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3374885 CTAAGTGATT
3374895 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
3374931 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
3374962 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:3376629 original size:84 final size:84
Alignment explanation
Indices: 3376488--3376652 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
3376478 ACTCAAAGAA
* * * *
3376488 GAAAGTAAATCAATAAGTGTAGAGAATGATATTCTTAAAAATAAATTAAGTGAATTAGAGAAGAA
1 GAAAGTAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
3376553 TATGAAA-GAGTTGCAAAAT
66 -AAGAAATGAGTTGCAAAAT
* * * *
3376572 GAAAGTAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAGAAAGAAAATAAATGAATTAGAGGAG
1 GAAAGTAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
3376635 AAAAGAAATGAGTTGCAA
64 AAAAGAAATGAGTTGCAA
3376653 GTGGAAAATG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 59 0.86
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (84 bp):
GAAAGTAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
AAGAAATGAGTTGCAAAAT
Found at i:3377800 original size:13 final size:13
Alignment explanation
Indices: 3377782--3377806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3377772 TTTTCCAGAT
3377782 TGTATCGATACAA
1 TGTATCGATACAA
3377795 TGTATCGATACA
1 TGTATCGATACA
3377807 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3379517 original size:13 final size:13
Alignment explanation
Indices: 3379499--3379524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3379489 TACAGCAAGT
3379499 ATGTATCGATACA
1 ATGTATCGATACA
3379512 ATGTATCGATACA
1 ATGTATCGATACA
3379525 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3380046 original size:34 final size:35
Alignment explanation
Indices: 3379983--3380049 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3379973 CTAAGTGATT
3379983 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
3380019 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
3380050 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:3383905 original size:35 final size:35
Alignment explanation
Indices: 3383859--3383935 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
3383849 TACGCCAGTG
* *
3383859 CAACAACTCCAAAATATAGTTATTCCATTATTTCA
1 CAACAATTCCAAAATATAGTTATTCCATTATTGCA
3383894 CAACAATTCCAAAATATAGTTATTCCATTATTGCA
1 CAACAATTCCAAAATATAGTTATTCCATTATTGCA
3383929 CAACAAT
1 CAACAAT
3383936 CAATGTCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (35 bp):
CAACAATTCCAAAATATAGTTATTCCATTATTGCA
Found at i:3384561 original size:16 final size:17
Alignment explanation
Indices: 3384542--3384574 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3384532 TTTAATATGA
3384542 TTTA-AATTCAAAATAT
1 TTTACAATTCAAAATAT
*
3384558 TTTACATTTCAAAATAT
1 TTTACAATTCAAAATAT
3384575 CTTATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTACAATTCAAAATAT
Found at i:3384991 original size:5 final size:5
Alignment explanation
Indices: 3384983--3385041 Score: 75
Period size: 5 Copynumber: 11.6 Consensus size: 5
3384973 GAATTATAAT
* *
3384983 ATTTA ATTTGA TTTTA ATTTA ATTTA ATTT- ATTTT ATTTA ATTTA ATTTA
1 ATTTA ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
3385033 ATTTGA ATT
1 ATTT-A ATT
3385042 GAGATATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
4 4 0.08
5 36 0.75
6 8 0.17
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (5 bp):
ATTTA
Found at i:3384993 original size:24 final size:21
Alignment explanation
Indices: 3384966--3385041 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 21
3384956 AAATTAAAAA
3384966 TTGATTTGAATTATAATATTTAAT
1 TTGATTTGAATT-T-A-ATTTAAT
*
3384990 TTGATTTTAATTTAATTTAAT
1 TTGATTTGAATTTAATTTAAT
*
3385011 TT-ATTT-TATTTAATTTAAT
1 TTGATTTGAATTTAATTTAAT
*
3385030 TTAATTTGAATT
1 TTGATTTGAATT
3385042 GAGATATTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 14 0.30
20 8 0.17
21 12 0.26
22 1 0.02
23 1 0.02
24 11 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TTGATTTGAATTTAATTTAAT
Found at i:3395002 original size:53 final size:53
Alignment explanation
Indices: 3394935--3395049 Score: 214
Period size: 53 Copynumber: 2.2 Consensus size: 53
3394925 ACCAATAGGG
*
3394935 AATAGGTG-GAGAGACCCAACTTGACTATAAGACCACAAGAAACCTAAGACTT
1 AATAGATGCGAGAGACCCAACTTGACTATAAGACCACAAGAAACCTAAGACTT
3394987 AATAGATGCGAGAGACCCAACTTGACTATAAGACCACAAGAAACCTAAGACTT
1 AATAGATGCGAGAGACCCAACTTGACTATAAGACCACAAGAAACCTAAGACTT
3395040 AATAGATGCG
1 AATAGATGCG
3395050 GGTTAACACC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 7 0.11
53 54 0.89
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (53 bp):
AATAGATGCGAGAGACCCAACTTGACTATAAGACCACAAGAAACCTAAGACTT
Found at i:3400478 original size:150 final size:150
Alignment explanation
Indices: 3400207--3400505 Score: 580
Period size: 150 Copynumber: 2.0 Consensus size: 150
3400197 TTCATGATGT
3400207 AGTGGCTTCTAAATTTCCAAGCATTGAACCCCAACTGAACATTGACGTTGCACGAGCAGATATCT
1 AGTGGCTTCTAAATTTCCAAGCATTGAACCCCAACTGAACATTGACGTTGCACGAGCAGATATCT
3400272 CCAAGAGTGTGAATCGAGAAAATCTTTGGTGCACGTACTGCAAAAAGCCCAGACACACTAAAGAG
66 CCAAGAGTGTGAATCGAGAAAATCTTTGGTGCACGTACTGCAAAAAGCCCAGACACACTAAAGAG
3400337 CATTGTTGGAAGCTTCATGC
131 CATTGTTGGAAGCTTCATGC
3400357 AGTGGCTTCTAAATTTCCAAGCATTGAACCCCAACTGAACATTGACGTTGCACGAGCAGATATCT
1 AGTGGCTTCTAAATTTCCAAGCATTGAACCCCAACTGAACATTGACGTTGCACGAGCAGATATCT
*
3400422 CTAAGAGTGTGAATCGAGAAAATCTTTGGTGCACGTACTGCAAAAAGCCCAGACACACTAAAGAG
66 CCAAGAGTGTGAATCGAGAAAATCTTTGGTGCACGTACTGCAAAAAGCCCAGACACACTAAAGAG
*
3400487 CGTTGTTGGAAGCTTCATG
131 CATTGTTGGAAGCTTCATG
3400506 GTCGACCACA
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 147 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (150 bp):
AGTGGCTTCTAAATTTCCAAGCATTGAACCCCAACTGAACATTGACGTTGCACGAGCAGATATCT
CCAAGAGTGTGAATCGAGAAAATCTTTGGTGCACGTACTGCAAAAAGCCCAGACACACTAAAGAG
CATTGTTGGAAGCTTCATGC
Found at i:3404390 original size:22 final size:23
Alignment explanation
Indices: 3404360--3404404 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3404350 TACAATCTCC
*
3404360 ATTCTTTTCCACATA-TATTTCT
1 ATTCCTTTCCACATATTATTTCT
3404382 ATTCCTTTCCACATATTATTTCT
1 ATTCCTTTCCACATATTATTTCT
3404405 CAAATGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTCCTTTCCACATATTATTTCT
Found at i:3409057 original size:28 final size:28
Alignment explanation
Indices: 3409017--3409074 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3409007 CTGTTTTTTG
3409017 TATCTTTTCTGTACTGTTACAATGCTTT
1 TATCTTTTCTGTACTGTTACAATGCTTT
3409045 TATCTTTTCTGTACTGTTACAATGCTTT
1 TATCTTTTCTGTACTGTTACAATGCTTT
3409073 TA
1 TA
3409075 AGTACACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.53
Consensus pattern (28 bp):
TATCTTTTCTGTACTGTTACAATGCTTT
Found at i:3412622 original size:18 final size:18
Alignment explanation
Indices: 3412601--3412642 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3412591 AAACTTATTA
3412601 TTTTTTAAATAAAA-TAAT
1 TTTTTTAAA-AAAATTAAT
*
3412619 TTTTTTAAAAAAATTTAT
1 TTTTTTAAAAAAATTAAT
3412637 TTTTTT
1 TTTTTT
3412643 CATCCACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTTAAAAAAATTAAT
Found at i:3418220 original size:3 final size:3
Alignment explanation
Indices: 3418212--3418246 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3418202 ACATAAAATC
3418212 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3418247 TGACTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3418356 original size:48 final size:49
Alignment explanation
Indices: 3418284--3418377 Score: 172
Period size: 48 Copynumber: 1.9 Consensus size: 49
3418274 TACTCCTGAA
*
3418284 GAGTCGGTTTATTCGTTCAGTTTTATTGCCAAATCTTGAACCTAATGAG
1 GAGTCGGTTTATTCGATCAGTTTTATTGCCAAATCTTGAACCTAATGAG
3418333 GAGTC-GTTTATTCGATCAGTTTTATTGCCAAATCTTGAACCTAAT
1 GAGTCGGTTTATTCGATCAGTTTTATTGCCAAATCTTGAACCTAAT
3418378 TACCAATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 39 0.89
49 5 0.11
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (49 bp):
GAGTCGGTTTATTCGATCAGTTTTATTGCCAAATCTTGAACCTAATGAG
Found at i:3419022 original size:2 final size:2
Alignment explanation
Indices: 3419015--3419056 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3419005 GCGCTCCATT
3419015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3419057 AAGTCACTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3425527 original size:23 final size:23
Alignment explanation
Indices: 3425496--3425575 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
3425486 TTCTCTATCC
*
3425496 TTTTGTTTTTCGTTGCTTTCTAT
1 TTTTCTTTTTCGTTGCTTTCTAT
** **
3425519 TTTTCTTTTTATTTTTTTTTCTAT
1 TTTTCTTTTT-CGTTGCTTTCTAT
* *
3425543 TTTT-ATTTTCGTTGCTTTTTTAT
1 TTTTCTTTTTCGTTGC-TTTCTAT
3425566 TTTTCTTTTT
1 TTTTCTTTTT
3425576 ATTTAGAACT
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
22 2 0.05
23 23 0.55
24 17 0.40
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.78
Consensus pattern (23 bp):
TTTTCTTTTTCGTTGCTTTCTAT
Found at i:3425531 original size:12 final size:12
Alignment explanation
Indices: 3425511--3425579 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
3425501 TTTTTCGTTG
*
3425511 CTTTCTATTTTT
1 CTTTTTATTTTT
3425523 CTTTTTATTTTT
1 CTTTTTATTTTT
3425535 -TTTTCTATTTTT
1 CTTTT-TATTTTT
* ** **
3425547 ATTTTCGTTGCT
1 CTTTTTATTTTT
3425559 -TTTTTATTTTT
1 CTTTTTATTTTT
3425570 CTTTTTATTT
1 CTTTTTATTT
3425580 AGAACTAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 30 0.67
13 4 0.09
ACGTcount: A:0.09, C:0.10, G:0.03, T:0.78
Consensus pattern (12 bp):
CTTTTTATTTTT
Found at i:3425533 original size:6 final size:6
Alignment explanation
Indices: 3425516--3425579 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
3425506 CGTTGCTTTC
* ** **
3425516 TATTTT TCTTTT TATTTT T-TTTT CTATTTT TATTTT CGTTGC T-TTTT
1 TATTTT TATTTT TATTTT TATTTT -TATTTT TATTTT TATTTT TATTTT
*
3425563 TATTTT TCTTTT TATTT
1 TATTTT TATTTT TATTT
3425580 AGAACTAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
5 7 0.16
6 33 0.75
7 4 0.09
ACGTcount: A:0.09, C:0.08, G:0.03, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:3425539 original size:24 final size:24
Alignment explanation
Indices: 3425512--3425579 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
3425502 TTTTCGTTGC
*
3425512 TTTCTATTTTTCTTTTTATTTTTT
1 TTTCTATTTTTCTTTTTATTTCTT
* ** *
3425536 TTTCTATTTTTATTTTCGTTGCTT
1 TTTCTATTTTTCTTTTTATTTCTT
3425560 TTT-TATTTTTCTTTTTATTT
1 TTTCTATTTTTCTTTTTATTT
3425580 AGAACTAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 13 0.37
24 22 0.63
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (24 bp):
TTTCTATTTTTCTTTTTATTTCTT
Found at i:3425547 original size:18 final size:18
Alignment explanation
Indices: 3425524--3425579 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
3425514 TCTATTTTTC
3425524 TTTTTATTTTTTTTTCTA
1 TTTTTATTTTTTTTTCTA
** *
3425542 TTTTTATTTTCGTTGCT-
1 TTTTTATTTTTTTTTCTA
3425559 TTTTTATTTTTCTTTT-TA
1 TTTTTATTTTT-TTTTCTA
3425577 TTT
1 TTT
3425580 AGAACTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (18 bp):
TTTTTATTTTTTTTTCTA
Found at i:3426348 original size:13 final size:13
Alignment explanation
Indices: 3426330--3426355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3426320 CATTTTTCTG
3426330 TGTATCGATACAT
1 TGTATCGATACAT
3426343 TGTATCGATACAT
1 TGTATCGATACAT
3426356 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3426352 original size:33 final size:33
Alignment explanation
Indices: 3426310--3426376 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3426300 GCCAAGGAAA
***
3426310 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3426343 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3426376 T
1 T
3426377 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3428920 original size:31 final size:28
Alignment explanation
Indices: 3428837--3428909 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
3428827 CTTCACAATC
* * ***
3428837 GGGGACACTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
3428864 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
3428892 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3428910 ACTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.23, C:0.36, G:0.22, T:0.19
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:3428954 original size:51 final size:50
Alignment explanation
Indices: 3428892--3429061 Score: 171
Period size: 52 Copynumber: 3.3 Consensus size: 50
3428882 TTATTTCCGA
**
3428892 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGA-TTTATTTCCAAAATATCAATTTTTCATAATC
* * * * *
3428943 GGGGATACTCCAACCCCGGTTTTAATTT-CAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCC-GATTT-ATTTCCAAAATATCAATTTTTC-ATAATC
* * *
3428995 GGGGATACTCCAACACCGATTCTATTTCCCAAAATATCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATT-TATTT-CCAAAATATCAATTTTTCATAATC
**
3429047 AAGGATACTCCAACC
1 GGGGATACTCCAACC
3429062 TCGTCAATTC
Statistics
Matches: 95, Mismatches: 18, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
51 39 0.41
52 42 0.44
53 14 0.15
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTATTTCCAAAATATCAATTTTTCATAATC
Found at i:3429092 original size:211 final size:211
Alignment explanation
Indices: 3428728--3429120 Score: 574
Period size: 211 Copynumber: 1.9 Consensus size: 211
3428718 AATTCTCCAC
* * * *
3428728 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTAATTTCAAAACACCAATTTTCTATAATCAGGGATACTC
* * ** *
3428793 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTCA
* *
3428858 ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
3428923 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
* * *
3428939 AATCGGGGATACTCCAACCCCGGTTTTAATTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTAATTTCAAAACACCAATTTT-CTATAATCAGGGATACT
* * * * * *
3429004 CCAACACCGATTCTATTTCC-CAAAATATCAATTT-TTCACAATTAAGGATACTCCAACCTCGTC
65 CCAACACCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTC
3429067 AATTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAACACTCCAACCCCG
130 AA-TCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAACACTCCAACCCCG
3429121 TTATTATCTC
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
210 25 0.16
211 102 0.64
212 33 0.21
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGATTTTAATTTCAAAACACCAATTTTCTATAATCAGGGATACTC
CAACACCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTCA
ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
AATATTGATTTTTCAT
Found at i:3430317 original size:2 final size:2
Alignment explanation
Indices: 3430310--3430337 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3430300 GTGAATTGTC
3430310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3430338 TAAAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3430441 original size:51 final size:51
Alignment explanation
Indices: 3430385--3430486 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
3430375 TGTACAATAT
* *
3430385 GTACATAATTAAAGTATTATTAATGTACAAATTTACTACATAAATATTTTA
1 GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
3430436 GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
1 GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
3430487 TTACTATTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (51 bp):
GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
Found at i:3436241 original size:24 final size:24
Alignment explanation
Indices: 3436213--3436279 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
3436203 TTTAATTATA
3436213 AATATATAAATATTATTATAA-AAT
1 AATATATAAATATTATTA-AATAAT
* * *
3436237 AATATTTTAATATTTTTAAATAAT
1 AATATATAAATATTATTAAATAAT
*
3436261 AAAATA-AAATATATATTAA
1 AATATATAAATAT-TATTAA
3436280 TTTAAATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 7 0.21
24 27 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AATATATAAATATTATTAAATAAT
Found at i:3437654 original size:2 final size:2
Alignment explanation
Indices: 3437649--3437673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3437639 TATATATATA
3437649 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3437674 CATTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3438435 original size:24 final size:24
Alignment explanation
Indices: 3438381--3438435 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3438371 AATTATTTTT
*
3438381 ATTTAAATTTAATTATAAATATTA
1 ATTTAAAATTAATTATAAATATTA
* * *
3438405 ATATAAAATTAATTTTTAATATTA
1 ATTTAAAATTAATTATAAATATTA
*
3438429 TTTTAAA
1 ATTTAAA
3438436 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTAAAATTAATTATAAATATTA
Found at i:3438437 original size:12 final size:13
Alignment explanation
Indices: 3438382--3438437 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 13
3438372 ATTATTTTTA
3438382 TTTAAAT-TTAAT
1 TTTAAATATTAAT
*
3438394 TATAAATATTAA-
1 TTTAAATATTAAT
*
3438406 TATAAA-ATTAAT
1 TTTAAATATTAAT
*
3438418 TTTTAATATT-AT
1 TTTAAATATTAAT
3438430 TTTAAATA
1 TTTAAATA
3438438 ATAAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 25 0.68
13 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAATATTAAT
Found at i:3439392 original size:23 final size:23
Alignment explanation
Indices: 3439323--3439392 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
3439313 TAGTTAGGAA
* *
3439323 ATATGGATATTAATATATATAATATG
1 ATATGGATATTAA-A-A-AAAATAAG
* * * *
3439349 ATATGAATATGAAGAACAATAAG
1 ATATGGATATTAAAAAAAATAAG
3439372 ATATGGATATTAAAAAAAATA
1 ATATGGATATTAAAAAAAATA
3439393 TTTTTTATAA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 23 0.66
24 1 0.03
26 11 0.31
ACGTcount: A:0.54, C:0.01, G:0.13, T:0.31
Consensus pattern (23 bp):
ATATGGATATTAAAAAAAATAAG
Found at i:3440205 original size:21 final size:21
Alignment explanation
Indices: 3440176--3440235 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
3440166 ATATCATGTC
* *
3440176 TAATAATATTTGATTATATTT
1 TAATTATATTTAATTATATTT
* *
3440197 TAATTATATATAATTTTATTT
1 TAATTATATTTAATTATATTT
*
3440218 TTATT-TATTTTAA-TATAT
1 TAATTATA-TTTAATTATAT
3440236 CTTGCATGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TAATTATATTTAATTATATTT
Found at i:3442067 original size:14 final size:14
Alignment explanation
Indices: 3442048--3442074 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3442038 GGAAGACAAA
3442048 GGGAAAGGAAAAAG
1 GGGAAAGGAAAAAG
3442062 GGGAAAGGAAAAA
1 GGGAAAGGAAAAA
3442075 AAGAAACGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
GGGAAAGGAAAAAG
Found at i:3442829 original size:21 final size:22
Alignment explanation
Indices: 3442800--3442849 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
3442790 ATTAATACTA
*
3442800 TAAATATAATA-TAATTAAATT
1 TAAAAATAATATTAATTAAATT
3442821 TAAAAATAATATTTAATTAAATT
1 TAAAAATAATA-TTAATTAAATT
3442844 TAAAAA
1 TAAAAA
3442850 AATTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.38
23 16 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATAATATTAATTAAATT
Found at i:3443151 original size:11 final size:11
Alignment explanation
Indices: 3443135--3443171 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3443125 TTATTACTTT
3443135 TTATTTATAAA
1 TTATTTATAAA
* *
3443146 TTATTTTTAAT
1 TTATTTATAAA
3443157 TTATTTATAAA
1 TTATTTATAAA
3443168 TTAT
1 TTAT
3443172 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:3443753 original size:33 final size:32
Alignment explanation
Indices: 3443711--3443773 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
3443701 CCATTGTTTG
3443711 TATCGATACATG-GCACATTGTATCGATACAATA
1 TATCGATACATGAG-A-ATTGTATCGATACAATA
3443744 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGA-GAATTGTATCGATACA
3443774 TTGCTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TATCGATACATGAGAATTGTATCGATACAATA
Found at i:3447156 original size:52 final size:52
Alignment explanation
Indices: 3447100--3447206 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
3447090 GTTGGACTCA
* * ** *
3447100 ATGTATCGATACTATTCATAATGTATCGATATGTAAGTAGTGATGAACAGTG
1 ATGTATCGATACTATTCACAATATATCGATACATAAGCAGTGATGAACAGTG
*
3447152 ATGTATCGATACTATTCACAATATATCGATACATGAGCAGTGATGAACAGTG
1 ATGTATCGATACTATTCACAATATATCGATACATAAGCAGTGATGAACAGTG
3447204 ATG
1 ATG
3447207 AATAGTGATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (52 bp):
ATGTATCGATACTATTCACAATATATCGATACATAAGCAGTGATGAACAGTG
Found at i:3447202 original size:10 final size:10
Alignment explanation
Indices: 3447184--3447224 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
3447174 ATATCGATAC
*
3447184 ATGAGCAGTG
1 ATGAACAGTG
3447194 ATGAACAGTG
1 ATGAACAGTG
*
3447204 ATGAATAGTG
1 ATGAACAGTG
3447214 ATGAACAGTG
1 ATGAACAGTG
3447224 A
1 A
3447225 AAAATGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.22
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:3447271 original size:13 final size:13
Alignment explanation
Indices: 3447253--3447277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3447243 TGCCAGTTTT
3447253 ATGTATCGATACA
1 ATGTATCGATACA
3447266 ATGTATCGATAC
1 ATGTATCGATAC
3447278 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3449232 original size:23 final size:24
Alignment explanation
Indices: 3449187--3449233 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
3449177 CAAAGGATTG
*
3449187 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
3449211 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
3449234 TTTTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:3450134 original size:21 final size:21
Alignment explanation
Indices: 3450108--3450167 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
3450098 TTTTTTTTAG
3450108 CTAACTCA-TCATTTTCATTTT
1 CTAACTCATTCATTTTC-TTTT
3450129 GC-AACTCATTTC-TTTTCTTTT
1 -CTAACTCA-TTCATTTTCTTTT
3450150 CTAACTCATTCATTTTCT
1 CTAACTCATTCATTTTCT
3450168 CCTCTAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.12
21 22 0.65
22 6 0.18
23 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.53
Consensus pattern (21 bp):
CTAACTCATTCATTTTCTTTT
Found at i:3450173 original size:21 final size:21
Alignment explanation
Indices: 3450131--3450174 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3450121 TTCATTTTGC
**
3450131 AACTCATTTCTTTTCTTTTCT
1 AACTCATTTCTTTTCTCCTCT
3450152 AACTCA-TTCATTTTCTCCTCT
1 AACTCATTTC-TTTTCTCCTCT
3450173 AA
1 AA
3450175 TTCACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.52
Consensus pattern (21 bp):
AACTCATTTCTTTTCTCCTCT
Found at i:3454894 original size:52 final size:52
Alignment explanation
Indices: 3454809--3454933 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
3454799 ATATGAAAAG
* *
3454809 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
3454861 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
3454913 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
3454934 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:3454946 original size:52 final size:51
Alignment explanation
Indices: 3454809--3454953 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
3454799 ATATGAAAAG
*
3454809 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
3454861 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
3454913 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3454954 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:3454960 original size:13 final size:13
Alignment explanation
Indices: 3454942--3454966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3454932 CAAAGATCAG
3454942 TGTATCGATACAA
1 TGTATCGATACAA
3454955 TGTATCGATACA
1 TGTATCGATACA
3454967 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3455050 original size:13 final size:13
Alignment explanation
Indices: 3455032--3455056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3455022 AAAAAAAATA
3455032 TGTATCGATACAT
1 TGTATCGATACAT
3455045 TGTATCGATACA
1 TGTATCGATACA
3455057 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3459979 original size:21 final size:22
Alignment explanation
Indices: 3459955--3460004 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3459945 ATCAAATCTT
* *
3459955 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3459976 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3459998 --TCAAAAT
1 CTTCAAAAT
3460005 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:3461782 original size:21 final size:23
Alignment explanation
Indices: 3461742--3461784 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
3461732 TTTTAACCGA
*
3461742 TTATCAAGGAGGAGAAATTTTTT
1 TTATCAAAGAGGAGAAATTTTTT
3461765 TTATCAAAG-GGA-AAATTTTT
1 TTATCAAAGAGGAGAAATTTTT
3461785 GACAAGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
TTATCAAAGAGGAGAAATTTTTT
Found at i:3462376 original size:13 final size:13
Alignment explanation
Indices: 3462358--3462382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3462348 CATTATGCTT
3462358 TGTATCGATACAA
1 TGTATCGATACAA
3462371 TGTATCGATACA
1 TGTATCGATACA
3462383 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3462379 original size:33 final size:32
Alignment explanation
Indices: 3462337--3462401 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
3462327 ACACACCTAG
*
3462337 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
3462370 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
3462402 TGAACAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:3462413 original size:20 final size:20
Alignment explanation
Indices: 3462367--3462425 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3462357 TTGTATCGAT
*
3462367 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGA
*
3462386 TC-ATTGTATCGATACATGA
1 ACAATTGTATCGATACATGA
*
3462405 ACAATTGTATTGATACATGA
1 ACAATTGTATCGATACATGA
3462425 A
1 A
3462426 ACTGGCAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 17 0.50
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (20 bp):
ACAATTGTATCGATACATGA
Found at i:3466573 original size:89 final size:90
Alignment explanation
Indices: 3466320--3467420 Score: 1109
Period size: 95 Copynumber: 12.1 Consensus size: 90
3466310 CAACTGTGAT
* * * *
3466320 ATTTACAATCAATCAACTTTTTAACTTTTCTATCAAAAAGAATCTGATTCTCAAATATAATTTAT
1 ATTTACAATCAATCAACTTTTT--TTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCAT
** * * * *
3466385 GCATTAGTCTAATATTTGCAGTGTCAT
64 GCATTAGTCTAATCCTTACAGTCTGAC
* * * * * * * * *
3466412 ACTTATAATTAACCAACTTTTCTTTTTTTTTTACCAAAAAAAATCCGATTCTCATG-TACAATTC
1 ATTTACAATCAATCAACTTTT-TTTTTTCTATA--AAAAAGAATCTGATTCTCA-GATATAATTC
* * *
3466476 ATGCATTAGTCTAATCATTGCAGTTTGAC
62 ATGCATTAGTCTAATCCTTACAGTCTGAC
* **
3466505 ATTTACAATCAGTCAAC-TTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATAT
1 ATTTACAATCAATCAACTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
3466569 ATTAGTCTAATCCTTACAGTCTGAC
66 ATTAGTCTAATCCTTACAGTCTGAC
* * * *
3466594 ATTTACAGTCAGTCAAC---TTTTTTTCTATAAAAAAGAAT-TCGATTTTCATATATAATTCATG
1 ATTTACAATCAATCAACTTTTTTTTTTCTATAAAAAAGAATCT-GATTCTCAGATATAATTCATG
** * *
3466655 CATTAGTCTAATCCTTGTAATCTAAC
65 CATTAGTCTAATCCTTACAGTCTGAC
* *
3466681 ATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAA-AAT-TAATTCTCATATATAATTCAT
1 ATTTACAATCAATCAAC-TTT-TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCAT
* * *
3466744 GCATTAGTTTAATCCTTACTGTCTGAT
64 GCATTAGTCTAATCCTTACAGTCTGAC
*
3466771 ATTTACAATCAATCAATCTTTCTTTTTTTTTTCTATAAAAGAGAATCTGATTCTCAGATATAATT
1 ATTTACAATCAATCAA-----CTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATT
* * * ** *
3466836 CATGTATTAGTTTAATCTTTACAACCTGAT
61 CATGCATTAGTCTAATCCTTACAGTCTGAC
* *
3466866 GTTTACAATCAGTCAACTTTTCTTTTTTTTTTCTATAAAAAAGAATAC-GATTCTCAGATATAAT
1 ATTTACAATCAATCAA-----CTTTTTTTTTTCTATAAAAAAGAAT-CTGATTCTCAGATATAAT
** *
3466930 TCATGCATTAGTCTAATCCTTGTAGTTTGAC
60 TCATGCATTAGTCTAATCCTTACAGTCTGAC
* * *
3466961 ATTTATAATCAATCAACTTTTTTTTTTCTATAAAAAAGAAT-TGATTCTCAAATATAATTTATGC
1 ATTTACAATCAATCAACTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
* *
3467025 ATTAGTCTAATTCTTACAGTCTGAT
66 ATTAGTCTAATCCTTACAGTCTGAC
* * ** *
3467050 ATTTACAATCATTCAAATTTTCTTTTTTTCTATAAAAAAGAATCCAATTCTCAAATATAATTCAT
1 ATTTACAATCAATC-AACTTT-TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCAT
*
3467115 GCATTAGTCTAATCCTTGCAGTCTGAC
64 GCATTAGTCTAATCCTTACAGTCTGAC
* * * *
3467142 ATTTATAATCAATCAAC-TTTTTTTTTCTATAAAAAAAAAT-TGATTCTCAGATATAATTTATGT
1 ATTTACAATCAATCAACTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
* * *
3467205 ATTGGTCTAATCCTTGCAGTCTGAT
66 ATTAGTCTAATCCTTACAGTCTGAC
* * * * *
3467230 ATTTACAATTAGTCAAC--TTTTTTTT-TGTAAAAAAGAATCTGATTTTCAGATATAATTCATGT
1 ATTTACAATCAATCAACTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
* * *
3467292 ATTAGTTTAATCTTTATAGTCTGAC
66 ATTAGTCTAATCCTTACAGTCTGAC
* * *
3467317 ATTTACAATCAGTCAACTTTTCTTTTTTTTTTTCTATAAAAAA-AATCCGATTCTTAGATATAAT
1 ATTTACAATCAATCAA-----C-TTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAAT
* *
3467381 TCATGTATTAGTCTATTCCTTACAGTCTGAC
60 TCATGCATTAGTCTAATCCTTACAGTCTGAC
3467412 ATTTACAAT
1 ATTTACAAT
3467421 TTATACATTA
Statistics
Matches: 849, Mismatches: 127, Indels: 63
0.82 0.12 0.06
Matches are distributed among these distances:
86 12 0.01
87 138 0.16
88 56 0.07
89 136 0.16
90 86 0.10
91 42 0.05
92 92 0.11
93 76 0.09
94 6 0.01
95 196 0.23
96 9 0.01
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (90 bp):
ATTTACAATCAATCAACTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
ATTAGTCTAATCCTTACAGTCTGAC
Found at i:3468024 original size:121 final size:121
Alignment explanation
Indices: 3467899--3468220 Score: 372
Period size: 120 Copynumber: 2.6 Consensus size: 121
3467889 AATAATAATG
* *
3467899 TATTAATTATTATTTTAATAAAAATAATATTTAATTAAATTTAAAAAAATTTATATTAACAAATT
1 TATTAATTATTATTTTAATAAAAATAATATTTAATTAAGTTT-AAAAAATTTACATTAACAAATT
3467964 AAAATATTAATTT-T-TTAAAATAAAAA-AAAATTAA-ATAAAAATAAAAAATGATTTAT
65 AAAATATTAATTTATGTTAAAATAAAAATAAAA--AATATAAAAATAAAAAA-GATTTAT
*
3468020 TATT-ATTATTATTTTAATAAAATTAAAAATAATATTTAATTAGGTTTAAAAAA-TTACATTAAC
1 TATTAATTATTA-TTT--T--AA-TAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAAC
*** * * *
3468083 AAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAAATTTTAAAATAAAAAAGTTTTAT
60 AAATTAAAATATTAA-T-TTATGTTAAAATAAAAATAAAAAATATAAAAATAAAAAAGATTTAT
* * *
3468147 TA-TAATTTTTA-ATAAATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTA
1 TATTAATTATTATTTTAATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTA
3468210 AAATATTAATT
66 AAATATTAATT
3468221 ATTATGTTTT
Statistics
Matches: 174, Mismatches: 13, Indels: 30
0.80 0.06 0.14
Matches are distributed among these distances:
119 1 0.01
120 37 0.21
121 34 0.20
123 1 0.01
124 24 0.14
125 10 0.06
126 25 0.14
127 17 0.10
128 21 0.12
129 4 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (121 bp):
TATTAATTATTATTTTAATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTA
AAATATTAATTTATGTTAAAATAAAAATAAAAAATATAAAAATAAAAAAGATTTAT
Found at i:3468134 original size:15 final size:16
Alignment explanation
Indices: 3468114--3468145 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3468104 TGTTTTTATA
3468114 AAAATAAAAAA-TTTT
1 AAAATAAAAAAGTTTT
3468129 AAAATAAAAAAGTTTT
1 AAAATAAAAAAGTTTT
3468145 A
1 A
3468146 TTATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATAAAAAAGTTTT
Found at i:3468221 original size:121 final size:127
Alignment explanation
Indices: 3467915--3468255 Score: 435
Period size: 121 Copynumber: 2.8 Consensus size: 127
3467905 TTATTATTTT
* *
3467915 AATAAAAATAATATTTAATTAAATTTAAAAAAATTTATATTAACAAATTAAAATATTAA-T-TT-
1 AATAAAAATAATATTTAATTAAGTTT-AAAAAATTTACATTAACAAATTAAAATATTAATTATTA
*** * * *
3467977 T-TTAAAATAAAAA-AAAATTAA-ATAAAAATAAAAAATGATTTATTATTATTATTATTTTAATA
65 TGTTTTTATAAAAATAAAA--AATTTTAAAATAAAAAATGA-TTATTATTATTAATATTTTAATA
3468039 A
127 A
*
3468040 AATTAAAAATAATATTTAATTAGGTTTAAAAAA-TTACATTAACAAATTAAAATATTAATTATTA
1 AA-TAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTA
3468104 TGTTTTTATAAAAATAAAAAATTTTAAAATAAAAAA-G-TT-TTATTA-TAAT-TTTTAAT-A
65 TGTTTTTATAAAAATAAAAAATTTTAAAATAAAAAATGATTATTATTATTAATATTTTAATAA
3468161 AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
1 AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
*
3468226 GTTTTT-T-AAAAT-AAAAATTTTAAATTAAAA
66 GTTTTTATAAAAATAAAAAATTTTAAAATAAAA
3468256 TTTTTTTTTA
Statistics
Matches: 197, Mismatches: 11, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
118 17 0.09
119 5 0.03
120 30 0.15
121 41 0.21
122 7 0.04
123 3 0.02
124 30 0.15
125 11 0.06
126 24 0.12
127 4 0.02
128 21 0.11
129 4 0.02
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (127 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
GTTTTTATAAAAATAAAAAATTTTAAAATAAAAAATGATTATTATTATTAATATTTTAATAA
Found at i:3468282 original size:19 final size:19
Alignment explanation
Indices: 3468250--3468302 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3468240 AAATTTTAAA
*
3468250 TTAAAATTTTTTTTTA-TT
1 TTAAAATATTTTTTTATTT
3468268 TTAATAATATTTTTTTATTT
1 TTAA-AATATTTTTTTATTT
*
3468288 TTAAAATATGTTTTT
1 TTAAAATATTTTTTT
3468303 GAGAAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 4 0.13
19 21 0.68
20 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTAAAATATTTTTTTATTT
Found at i:3468295 original size:22 final size:21
Alignment explanation
Indices: 3468243--3468295 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3468233 AAAATAAAAA
*
3468243 TTTTAAATTAAAATTTTTTTT
1 TTTTAAAATAAAATTTTTTTT
* *
3468264 TATTT-TAATAATATTTTTTTAT
1 T-TTTAAAATAAAATTTTTTT-T
3468286 TTTTAAAATA
1 TTTTAAAATA
3468296 TGTTTTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAAAATAAAATTTTTTTT
Found at i:3468766 original size:106 final size:106
Alignment explanation
Indices: 3468575--3468767 Score: 257
Period size: 106 Copynumber: 1.8 Consensus size: 106
3468565 AAATGTTATT
* *
3468575 TTTTAATTTGTTAATGTAAATTTTTTAAAATTTAATTAAATATCATTTTTATTTTATTAAAAAAA
1 TTTTAATTTGTTAATATAAATTTTTTAAAACTTAATTAAATATCATTTTTATTTTATTAAAAAAA
** *
3468640 TAAAAAATACTTTTTATTTTTATAAAAATATAATAGTTAATA
66 TAAAAAATAC-AATCATTTTTATAAAAATATAATAGTTAATA
* *
3468682 TTTTAATTTGTTAATAT-AATTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATT-AAAAA
1 TTTTAATTTGTTAATATAAATTTTTTAAAACTTAATTAAATATCATTTTT-ATTTTATTAAAAAA
*
3468745 ATAATAATAATA-AATCCTTTTTA
65 ATAA-AA-AATACAATCATTTTTA
3468768 ATTTAATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
106 45 0.60
107 26 0.35
108 4 0.05
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (106 bp):
TTTTAATTTGTTAATATAAATTTTTTAAAACTTAATTAAATATCATTTTTATTTTATTAAAAAAA
TAAAAAATACAATCATTTTTATAAAAATATAATAGTTAATA
Found at i:3468890 original size:9 final size:9
Alignment explanation
Indices: 3468876--3468908 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3468866 ATACATTATT
3468876 ATTTATTAA
1 ATTTATTAA
3468885 ATTTATTAA
1 ATTTATTAA
3468894 ATTTAATT-A
1 ATTT-ATTAA
3468903 ATTTAT
1 ATTTAT
3468909 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 18 0.78
10 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTTATTAA
Found at i:3469032 original size:15 final size:15
Alignment explanation
Indices: 3469012--3469060 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3469002 AGTATTCATA
3469012 AAAAAATCTTATTTT
1 AAAAAATCTTATTTT
* *
3469027 AAAAAATATT-TTAT
1 AAAAAATCTTATTTT
3469041 AAAAAA-CTTATTTAT
1 AAAAAATCTTATTT-T
3469056 AAAAA
1 AAAAA
3469061 TAAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAAATCTTATTTT
Found at i:3469383 original size:14 final size:15
Alignment explanation
Indices: 3469360--3469398 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3469350 GTATTATGTT
3469360 TAAATT-ATTTTTTA
1 TAAATTAATTTTTTA
3469374 -AAATTAATTTTTTA
1 TAAATTAATTTTTTA
*
3469388 TATATTAATTT
1 TAAATTAATTT
3469399 ATTTTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAAATTAATTTTTTA
Found at i:3469394 original size:15 final size:15
Alignment explanation
Indices: 3469366--3469407 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3469356 TGTTTAAATT
*
3469366 ATTTTTTA-AAATTA
1 ATTTTTTATATATTA
3469380 ATTTTTTATATATTA
1 ATTTTTTATATATTA
3469395 ATTTATTT-TATAT
1 ATTT-TTTATATAT
3469408 CTTACATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 14 0.56
16 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTTTATATATTA
Found at i:3469801 original size:20 final size:19
Alignment explanation
Indices: 3469754--3469805 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
3469744 ATAAATTATT
*
3469754 AATATATTAAAATTTAAATA
1 AATATA-TAATATTTAAATA
3469774 AATATATAATATTTAAAATA
1 AATATATAATATTT-AAATA
3469794 AA-ATTATAATAT
1 AATA-TATAATAT
3469806 ATTTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATATAATATTTAAATA
Found at i:3469804 original size:27 final size:27
Alignment explanation
Indices: 3469721--3469807 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
3469711 ATTAATTAAG
3469721 TAATATATTAAAATTTATATAACATAAAT-TA
1 TAATATATTAAAA--T-TA-AA-ATAAATATA
*
3469752 TTAATATATTAAAATTTAAATAAATATA
1 -TAATATATTAAAATTAAAATAAATATA
3469780 TAATAT-TTAAAA-TAAAATTATAATATA
1 TAATATATTAAAATTAAAA-TA-AATATA
3469807 T
1 T
3469808 TTTTAAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
25 4 0.08
26 8 0.16
27 19 0.38
28 4 0.08
29 1 0.02
30 1 0.02
32 13 0.26
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATATATTAAAATTAAAATAAATATA
Found at i:3471244 original size:3 final size:3
Alignment explanation
Indices: 3471236--3471269 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3471226 ATACCGTTCT
3471236 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
3471270 GCCGCTGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:3472803 original size:21 final size:21
Alignment explanation
Indices: 3472756--3472825 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
3472746 TACTGTATTT
* *
3472756 TTTTATTATAATTTTATTTAAA
1 TTTT-TTATAAATTTATATAAA
*
3472778 -ATTTTATAAATTTATATAAA
1 TTTTTTATAAATTTATATAAA
3472798 TTTTTTATAAA-TTA-AT-AA
1 TTTTTTATAAATTTATATAAA
3472816 TTTATTTATA
1 TTT-TTTATA
3472826 TTAATTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 8 0.19
20 18 0.43
21 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTATAAATTTATATAAA
Found at i:3472832 original size:14 final size:14
Alignment explanation
Indices: 3472813--3472864 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
3472803 TATAAATTAA
3472813 TAATTTATTTATAT
1 TAATTTATTTATAT
*
3472827 TAATTTAATTATAT
1 TAATTTATTTATAT
* * *
3472841 TTATATGTTTATAT
1 TAATTTATTTATAT
3472855 TATATTTATT
1 TA-ATTTATT
3472865 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TAATTTATTTATAT
Found at i:3473259 original size:34 final size:34
Alignment explanation
Indices: 3473216--3473299 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
3473206 TTATTATTTA
* * *
3473216 TTTATTTATTTATACTATATTA-TATTTTTTATAT
1 TTTAATTATTTATA-TATATTATTAATTTATATAT
* * *
3473250 TTTAATTATTTTTATATTTTATTAATTTATATTT
1 TTTAATTATTTATATATATTATTAATTTATATAT
*
3473284 TTTAATTA-ATATATAT
1 TTTAATTATTTATATAT
3473300 TTAAAAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 12 0.29
34 29 0.71
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (34 bp):
TTTAATTATTTATATATATTATTAATTTATATAT
Found at i:3473263 original size:17 final size:17
Alignment explanation
Indices: 3473241--3473291 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
3473231 TATATTATAT
3473241 TTTTTATATTTTAATTA
1 TTTTTATATTTTAATTA
3473258 TTTTTATATTTT-ATTAA
1 TTTTTATATTTTAATT-A
* *
3473275 TTTATATTTTTTAATTA
1 TTTTTATATTTTAATTA
3473292 ATATATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 3 0.10
17 24 0.80
18 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATATTTTAATTA
Found at i:3473285 original size:16 final size:16
Alignment explanation
Indices: 3473243--3473301 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
3473233 TATTATATTT
*
3473243 TTTATATTTTAATT-A
1 TTTATATTTTTATTAA
*
3473258 TTTTTATATTTTATTAA
1 TTTATAT-TTTTATTAA
3473275 TTTATATTTTTTAATTAA
1 TTTATA-TTTTT-ATTAA
*
3473293 TATATATTT
1 TTTATATTT
3473302 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 6 0.17
16 6 0.17
17 13 0.36
18 11 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTTTTATTAA
Found at i:3473293 original size:18 final size:18
Alignment explanation
Indices: 3473249--3473301 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
3473239 ATTTTTTATA
* *
3473249 TTTTAATT-ATTTTTATA
1 TTTTAATTAATTTATATT
3473266 TTTT-ATTAATTTATATT
1 TTTTAATTAATTTATATT
*
3473283 TTTTAATTAATATATATT
1 TTTTAATTAATTTATATT
3473301 T
1 T
3473302 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 15 0.48
18 13 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAATTAATTTATATT
Found at i:3473295 original size:14 final size:15
Alignment explanation
Indices: 3473263--3473295 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3473253 AATTATTTTT
*
3473263 ATATTTTATTAATTT
1 ATATTTTATTAATTA
3473278 ATATTTT-TTAATTA
1 ATATTTTATTAATTA
3473292 ATAT
1 ATAT
3473296 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTTTATTAATTA
Found at i:3475513 original size:24 final size:22
Alignment explanation
Indices: 3475486--3475545 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
3475476 AAAATTAAAA
3475486 TAATAAATTATATTAAAAATATT
1 TAATAAATTATATTAAAAA-ATT
** *
3475509 CTAATAAAAAATATTTAAAAATT
1 -TAATAAATTATATTAAAAAATT
3475532 TAATAAATTATATT
1 TAATAAATTATATT
3475546 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 12 0.39
23 3 0.10
24 16 0.52
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAAATTATATTAAAAAATT
Found at i:3475538 original size:22 final size:23
Alignment explanation
Indices: 3475486--3475552 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
3475476 AAAATTAAAA
*
3475486 TAATAAATTATATTAAAAATATTC
1 TAATAAATTATATTTAAAA-ATTC
**
3475510 TAATAAAAAATATTTAAAAATT-
1 TAATAAATTATATTTAAAAATTC
*
3475532 TAATAAATTATATTTTAAAAT
1 TAATAAATTATATTTAAAAAT
3475553 AAAATTTAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 18 0.49
23 3 0.08
24 16 0.43
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAATTATATTTAAAAATTC
Found at i:3475588 original size:13 final size:13
Alignment explanation
Indices: 3475570--3475612 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3475560 AGATATATTG
3475570 AAAATAAGATTTA
1 AAAATAAGATTTA
**
3475583 AAAATATTATTTA
1 AAAATAAGATTTA
3475596 AAAAT-AGCATTTA
1 AAAATAAG-ATTTA
3475609 AAAA
1 AAAA
3475613 ATATTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (13 bp):
AAAATAAGATTTA
Found at i:3475589 original size:22 final size:22
Alignment explanation
Indices: 3475548--3475590 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3475538 ATTATATTTT
* *
3475548 AAAATAAAATTTAGATATATTG
1 AAAATAAAATTTAAAAATATTG
*
3475570 AAAATAAGATTTAAAAATATT
1 AAAATAAAATTTAAAAATATT
3475591 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (22 bp):
AAAATAAAATTTAAAAATATTG
Found at i:3475607 original size:26 final size:26
Alignment explanation
Indices: 3475570--3475635 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
3475560 AGATATATTG
3475570 AAAATAAGATTT-AAAAATATTATTTA
1 AAAATAAGATTTAAAAAATATT-TTTA
3475596 AAAAT-AGCATTTAAAAAATATTTTTA
1 AAAATAAG-ATTTAAAAAATATTTTTA
* * *
3475622 TATATAATATTTAA
1 AAAATAAGATTTAA
3475636 TATTAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.06
26 22 0.65
27 10 0.29
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (26 bp):
AAAATAAGATTTAAAAAATATTTTTA
Found at i:3477061 original size:20 final size:19
Alignment explanation
Indices: 3477025--3477066 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3477015 TTCTTTGGTA
*
3477025 TTATAATTATATTTAAAATT
1 TTATAATTATATAT-AAATT
3477045 TTATATATT-TATATAAATT
1 TTATA-ATTATATATAAATT
3477064 TTA
1 TTA
3477067 ATAAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 9 0.45
21 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAATTATATATAAATT
Found at i:3480595 original size:18 final size:18
Alignment explanation
Indices: 3480581--3480620 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3480571 CAAAAAAGAA
*
3480581 AAAGGAAAAACAAAAAAT
1 AAAGAAAAAACAAAAAAT
3480599 AAAGAAAAAACAAAAAAT
1 AAAGAAAAAACAAAAAAT
3480617 AAAG
1 AAAG
3480621 TAAGAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAACAAAAAAT
Found at i:3481657 original size:48 final size:49
Alignment explanation
Indices: 3481599--3481698 Score: 121
Period size: 49 Copynumber: 2.1 Consensus size: 49
3481589 TCAAATAGAC
** * *
3481599 CAAAATTAAGTCTTTTGGGGTTAA-CTCATGCTTTCAGTCAAAATTGAT
1 CAAAATTAAGTCTTTTAAGGTAAATCTCATGCTTTCAGTCAAAACTGAT
* * * *
3481647 CAAAATTAAGTTTTTTAAGGTAAATTTTATGCTTTCTGTCAAAACTGAT
1 CAAAATTAAGTCTTTTAAGGTAAATCTCATGCTTTCAGTCAAAACTGAT
3481696 CAA
1 CAA
3481699 GAATCTAGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (49 bp):
CAAAATTAAGTCTTTTAAGGTAAATCTCATGCTTTCAGTCAAAACTGAT
Found at i:3481770 original size:50 final size:50
Alignment explanation
Indices: 3481630--3481774 Score: 134
Period size: 50 Copynumber: 2.9 Consensus size: 50
3481620 TAACTCATGC
* * * * *
3481630 TTTCAGTCAAAATTGATCAAAATTAAGTTTTTTAAGGTAAATTTTATGCTT
1 TTTCA-TCAAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTTATGATT
* * * * *
3481681 TCT-GTCAAAACTGATCAAGAATCTAGTCTCTT-AGAGTTAGTTTT-TGTATT
1 TTTCATCAAAATTGATCAA-AATCAAGTCTTTTAAG-GTTAGTTTTATG-ATT
*
3481731 TTTCATCGAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTT
1 TTTCATCAAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTT
3481775 GCACTTACTA
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
49 17 0.23
50 40 0.55
51 16 0.22
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (50 bp):
TTTCATCAAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTTATGATT
Found at i:3491584 original size:13 final size:13
Alignment explanation
Indices: 3491566--3491592 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3491556 ACATTATGCT
3491566 TTGTATCGATACA
1 TTGTATCGATACA
3491579 TTGTATCGATACA
1 TTGTATCGATACA
3491592 T
1 T
3491593 AATTATATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3493133 original size:20 final size:21
Alignment explanation
Indices: 3493108--3493159 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3493098 AGGCCAAATG
*
3493108 TATCGATACAATTCAAGC-TA
1 TATCGATACAATTCAAACATA
* * *
3493128 TATCGATAAAATTTAAACATT
1 TATCGATACAATTCAAACATA
3493149 TATCGATACAA
1 TATCGATACAA
3493160 ACACAGGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (21 bp):
TATCGATACAATTCAAACATA
Found at i:3493271 original size:33 final size:33
Alignment explanation
Indices: 3493229--3493293 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
3493219 AATTTCATAG
3493229 TGTATCGATACAAAGCAATTTGTATCGATACAA
1 TGTATCGATACAAAGCAATTTGTATCGATACAA
** *
3493262 TGTATCGATACTTAGTAATTTGTATCGATACA
1 TGTATCGATACAAAGCAATTTGTATCGATACA
3493294 TCTACATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATTTGTATCGATACAA
Found at i:3499943 original size:40 final size:39
Alignment explanation
Indices: 3499899--3500025 Score: 114
Period size: 42 Copynumber: 3.2 Consensus size: 39
3499889 GAAAGTAAAG
3499899 ACCTAAGACTAAAAGACTTGGTTTCTACAAAAAGTATGAA
1 ACCTAAG-CTAAAAGACTTGGTTTCTACAAAAAGTATGAA
* * * * *
3499939 ACCTAAGCTAAACTAGAACTTGATCTCGACAAAATGTAT-AG
1 ACCTAAGCTAAA--AG-ACTTGGTTTCTACAAAAAGTATGAA
* * *
3499980 ATCTAAGCTTAAAAGATTTGGTTT-TCATAAAAAGTATGAA
1 ACCTAAGC-TAAAAGACTTGGTTTCT-ACAAAAAGTATGAA
3500020 ACCTAA
1 ACCTAA
3500026 AGTAAACTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
39 20 0.30
40 15 0.22
41 10 0.15
42 22 0.33
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (39 bp):
ACCTAAGCTAAAAGACTTGGTTTCTACAAAAAGTATGAA
Found at i:3499950 original size:81 final size:81
Alignment explanation
Indices: 3499861--3500062 Score: 236
Period size: 81 Copynumber: 2.5 Consensus size: 81
3499851 AGAAAAAAAT
*
3499861 TAAA-CTAAACTAAACTTGATCTCTAACAGAAAGTAAAGACCTAAGAC-TAAAAGACTTGG-TTT
1 TAAAGCTAAACTAAACTTGATCTC-AACAGAAAGTATAGACCTAAG-CTTAAAAGACTTGGTTTT
3499923 CTACAAAAAGTATGAAACC
64 C-ACAAAAAGTATGAAACC
* * *
3499942 T-AAGCTAAACTAGAACTTGATCTCGACA-AAATGTATAGATCTAAGCTTAAAAGATTTGGTTTT
1 TAAAGCTAAACTA-AACTTGATCTCAACAGAAA-GTATAGACCTAAGCTTAAAAGACTTGGTTTT
*
3500005 CATAAAAAGTATGAAACC
64 CACAAAAAGTATGAAACC
** *
3500023 TAAAG-TAAACTCAAACTCAATCTCAACAGAAGGTATAGAC
1 TAAAGCTAAACT-AAACTTGATCTCAACAGAAAGTATAGAC
3500063 TTAGGCTTGT
Statistics
Matches: 103, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
80 6 0.06
81 76 0.74
82 21 0.20
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (81 bp):
TAAAGCTAAACTAAACTTGATCTCAACAGAAAGTATAGACCTAAGCTTAAAAGACTTGGTTTTCA
CAAAAAGTATGAAACC
Found at i:3499972 original size:42 final size:43
Alignment explanation
Indices: 3499864--3499986 Score: 109
Period size: 42 Copynumber: 3.0 Consensus size: 43
3499854 AAAAAATTAA
*
3499864 ACTAAACTA-AACTTGATCTCTAACAGAAAGTA-AAGACCTAAG
1 ACTAAACTAGAACTTGATCTC-AACAAAAAGTATAAGACCTAAG
* * *
3499906 ACTAAA--AG-ACTTGGTTTCTACAAAAAGTATGAA-ACCTAAG
1 ACTAAACTAGAACTTGATCTCAACAAAAAGTAT-AAGACCTAAG
* * *
3499946 -CTAAACTAGAACTTGATCTCGACAAAATGTAT-AGATCTAAG
1 ACTAAACTAGAACTTGATCTCAACAAAAAGTATAAGACCTAAG
3499987 CTTAAAAGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
39 14 0.22
40 17 0.26
41 10 0.15
42 24 0.37
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (43 bp):
ACTAAACTAGAACTTGATCTCAACAAAAAGTATAAGACCTAAG
Found at i:3502148 original size:26 final size:27
Alignment explanation
Indices: 3502100--3502156 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
3502090 GTAAGAAAAT
*
3502100 AATTAAAATTAAAAATTAGTATGTGAA
1 AATTAAAATTAAAAATTAGTATGTAAA
* **
3502127 AATTAAAA-TAAAAGTTTTTATGTAAA
1 AATTAAAATTAAAAATTAGTATGTAAA
3502153 AATT
1 AATT
3502157 TCAAGTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (27 bp):
AATTAAAATTAAAAATTAGTATGTAAA
Found at i:3503315 original size:2 final size:2
Alignment explanation
Indices: 3503308--3503348 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3503298 AAACATTAAA
3503308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3503349 AAAGTGTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3504209 original size:19 final size:19
Alignment explanation
Indices: 3504185--3504222 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3504175 CAATTACGAA
3504185 TATGTTAAAATCTATATAT
1 TATGTTAAAATCTATATAT
* *
3504204 TATGTTAAAGTTTATATAT
1 TATGTTAAAATCTATATAT
3504223 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TATGTTAAAATCTATATAT
Found at i:3504715 original size:14 final size:14
Alignment explanation
Indices: 3504677--3504717 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 14
3504667 TTAATTCCGT
3504677 AAATAGGTTTTTTCTA
1 AAATAGG-TTTTT-TA
3504693 AAATA--TTTTTTA
1 AAATAGGTTTTTTA
3504705 AAATAGGTTTTTT
1 AAATAGGTTTTTT
3504718 TTTTTACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
14 6 0.26
16 5 0.22
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (14 bp):
AAATAGGTTTTTTA
Found at i:3505052 original size:116 final size:117
Alignment explanation
Indices: 3504927--3505322 Score: 472
Period size: 116 Copynumber: 3.4 Consensus size: 117
3504917 TATTTTCTAA
* *
3504927 TAAAAATAATATTTAATTAAGTTTAAAAAAAATTACATTAATAAATTAAAATATTAATTATTTTT
1 TAAAAATAATATTTAATTAAATTTAAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTT
*
3504992 TTAAAATAAAAAATTAAATTAAAAAATGT-TTATTATTATTTTTAATAAAAT
66 TTAAAATAAAAAATTAAATTAAAAAATTTATTATTATTATTTTTAATAAAAT
* * ** * * *
3505043 TAAAAATAATGTTTAATTAATTTTTTAAAAAATTATATTAATAAATTAAAATATTAATTATTTTG
1 TAAAAATAATATTTAATTAAATTTAAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTT
* * *
3505108 TAAAAATAAAAAATTAAATTAAAAAGGGTTTATTATTATTATTTTTAAATAAATT
66 TTAAAATAAAAAATTAAATTAAAAA--ATTTATTATTATTATTTTT-AATAAAAT
* *
3505163 TAAAAATAATATTTAATTAAATTT-TAAAAAATTACATTAACAAATTAAAATGTTAATTATTATG
1 TAAAAATAATATTTAATTAAATTTAAAAAAAATTACATTAACAAATTAAAATATTAATTATT-T-
* **
3505227 TTTT--TAT-AAAAA-T--A--AAAGTATTTATTATTATT-TTTTTAATAAAAT
64 TTTTAAAATAAAAAATTAAATTAAAAAATTTATTATTATTATTTTTAATAAAAT
* * **
3505272 AAAAAATGATATTTAATTAAATTTAAAAAAGTTTACATTAACAAATTAAAA
1 TAAAAATAATATTTAATTAAATTTAAAAAAAATTACATTAACAAATTAAAA
3505323 AAAAATTAAG
Statistics
Matches: 246, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
109 29 0.12
110 28 0.11
111 12 0.05
113 3 0.01
115 1 0.00
116 83 0.34
117 1 0.00
118 7 0.03
119 50 0.20
120 30 0.12
121 2 0.01
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (117 bp):
TAAAAATAATATTTAATTAAATTTAAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTT
TTAAAATAAAAAATTAAATTAAAAAATTTATTATTATTATTTTTAATAAAAT
Found at i:3505068 original size:34 final size:32
Alignment explanation
Indices: 3505007--3505077 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 32
3504997 ATAAAAAATT
*
3505007 AAATT-AAAAAATGTTTATTATTATTTTTAATA
1 AAATTAAAAAAATGTTTATTAATATTTTTAA-A
3505039 AAATTAAAAATAATGTTTAATTAAT-TTTTTAAA
1 AAATTAAAAA-AATGTTT-ATTAATATTTTTAAA
3505072 AAATTA
1 AAATTA
3505078 TATTAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 5 0.14
33 11 0.31
34 14 0.40
35 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
AAATTAAAAAAATGTTTATTAATATTTTTAAA
Found at i:3505072 original size:31 final size:30
Alignment explanation
Indices: 3505007--3505072 Score: 73
Period size: 33 Copynumber: 2.1 Consensus size: 30
3504997 ATAAAAAATT
3505007 AAATTAAAAAATGTTTATTATTATTTTTAATA
1 AAATTAAAAAATGTTTATTA-TATTTTT-ATA
3505039 AAATTAAAAATAATGTTTAATTA-ATTTTT-TA
1 AAATT-AAAA-AATGTTT-ATTATATTTTTATA
3505070 AAA
1 AAA
3505073 AATTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
31 5 0.16
32 5 0.16
33 10 0.32
34 7 0.23
35 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (30 bp):
AAATTAAAAAATGTTTATTATATTTTTATA
Found at i:3505128 original size:38 final size:38
Alignment explanation
Indices: 3504968--3505131 Score: 126
Period size: 38 Copynumber: 4.3 Consensus size: 38
3504958 ATTACATTAA
*
3504968 TAAATTAAAATATTAATTATTTTTTTAAAATAAAAAAT
1 TAAATTAAAATATTAATTATTTTTTAAAAATAAAAAAT
* * *
3505006 TAAATTAAAAAATGTTTATTATTATTTT--TAAT--AAAAT
1 TAAATT--AAAATATTAATTATT-TTTTAAAAATAAAAAAT
* **
3505043 TAAA--AATAATGTTTAATTAATTTTTTAAAAAATTATATTAA-
1 TAAATTAA-AAT-ATTAATT-ATTTTTT-AAAAA-TA-AAAAAT
*
3505084 TAAATTAAAATATTAATTATTTTGTAAAAATAAAAAAT
1 TAAATTAAAATATTAATTATTTTTTAAAAATAAAAAAT
3505122 TAAATTAAAA
1 TAAATTAAAA
3505132 AGGGTTTATT
Statistics
Matches: 98, Mismatches: 12, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
33 2 0.02
34 3 0.03
35 9 0.09
36 3 0.03
37 12 0.12
38 20 0.20
39 9 0.09
40 19 0.19
41 14 0.14
42 5 0.05
43 2 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (38 bp):
TAAATTAAAATATTAATTATTTTTTAAAAATAAAAAAT
Found at i:3505612 original size:15 final size:15
Alignment explanation
Indices: 3505592--3505621 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3505582 TTATAATAAT
3505592 TTTTTTAATTTAAAA
1 TTTTTTAATTTAAAA
*
3505607 TTTTTTATTTTAAAA
1 TTTTTTAATTTAAAA
3505622 AACATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:3505766 original size:126 final size:124
Alignment explanation
Indices: 3505592--3505921 Score: 406
Period size: 126 Copynumber: 2.8 Consensus size: 124
3505582 TTATAATAAT
*
3505592 TTTTTTAATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTAA
1 TTTTTTATTTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGT--
* * *
3505657 AATTTT-TAAACTTAATTAAATATTAATTTT-TATTTTATT-AAAAATTATAATAAAAAATC
64 AATTTTATAAACTTAATTAAATATT-ATTTTAAATTTTATTAAAAAATAATAATAAAAAACC
3505716 TTTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGT
1 TTTTTTATTTTAAAATTTTTTA-TTTTA-AAAAACATAATAATTAATATTTTAATTTGTTAATGT
*
3505781 AATTTTATAAACTTAATTAAATATTATTTTAAATTTTATTAAAAAATAATAATAATAAACC
64 AATTTTATAAACTTAATTAAATATTATTTTAAATTTTATTAAAAAATAATAATAAAAAACC
* *
3505842 ----CT-TTTT---A-TTTTTATTTT---AAA-A-AATAATTAATATTTTAATTTGTTAATATAA
1 TTTTTTATTTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGT-A
* *
3505893 ATTTTTTAAAGTTAATTAAATATTATTTT
65 ATTTTATAAACTTAATTAAATATTATTTT
3505922 TTATTAAAAA
Statistics
Matches: 191, Mismatches: 9, Indels: 25
0.85 0.04 0.11
Matches are distributed among these distances:
110 27 0.14
111 29 0.15
112 3 0.02
116 4 0.02
117 6 0.03
118 1 0.01
121 4 0.02
122 1 0.01
124 32 0.17
125 31 0.16
126 53 0.28
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (124 bp):
TTTTTTATTTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTAA
TTTTATAAACTTAATTAAATATTATTTTAAATTTTATTAAAAAATAATAATAAAAAACC
Found at i:3506568 original size:92 final size:91
Alignment explanation
Indices: 3506402--3506568 Score: 264
Period size: 92 Copynumber: 1.8 Consensus size: 91
3506392 CTGTAAGAAA
3506402 TAGACTAATGCATGATTATATCTAAGAATCAGATTCTTTTTTATGAAAAAAAAGAAAAGTTGATT
1 TAGACTAATGCATGATTATATCTAAGAATCAGATTCTTTTTTATGAAAAAAAAGAAAAGTTGATT
***
3506467 GATTGTAAATATCAAACTACAAGGAT
66 GACCCTAAATATCAAACTACAAGGAT
* *
3506493 TAGAGTAATGCATGAATTATATCTGAGAATCA-ATTCTTTTTTATAGAAAAAAAAGAAAAGTTGA
1 TAGACTAATGCATG-ATTATATCTAAGAATCAGATTCTTTTTTAT-GAAAAAAAAGAAAAGTTGA
3506557 TTGACCCTAAAT
64 TTGACCCTAAAT
3506569 GTGAGACTGC
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 25 0.36
92 44 0.64
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (91 bp):
TAGACTAATGCATGATTATATCTAAGAATCAGATTCTTTTTTATGAAAAAAAAGAAAAGTTGATT
GACCCTAAATATCAAACTACAAGGAT
Found at i:3506761 original size:18 final size:17
Alignment explanation
Indices: 3506734--3506768 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3506724 TATAATAAAT
3506734 GAATAGATTCTTACTGA
1 GAATAGATTCTTACTGA
*
3506751 GAATCAGATTCTTTCTGA
1 GAAT-AGATTCTTACTGA
3506769 TTTGAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (17 bp):
GAATAGATTCTTACTGA
Found at i:3506955 original size:90 final size:91
Alignment explanation
Indices: 3506800--3507580 Score: 452
Period size: 92 Copynumber: 8.9 Consensus size: 91
3506790 TAATGTATAA
* * * *
3506800 ATTGTAAATGTTAGACTG-TAAGAAATAGACTAATGCATG-ATTATATCTGAGAATCGGATTCTT
1 ATTGTAAATGTCAGACTGCAAAG-ATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTT
3506863 TTTTATTAAAAAAAGAAAAGTTGATTG
65 TTTTATTAAAAAAAGAAAAGTTGATTG
* * * * *
3506890 ATTGTAAATATCAAACTACAAAGATTAGAGTAATGCATGAATTATATCTGAGAATC-AATTTTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
** * *
3506954 TTTAGAAAAAAAAGAGAAGTTGATTA
66 TTTATTAAAAAAAGAAAAGTTGATTG
*** * * * *
3506980 ACCCTAAATGTCAGACTGCAAATATTAGACTAATGCATAAATTATATTTGAGAATCAAATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
*
3507045 TTTATGGAAAAAAAGAAAAGTTGATTG
66 TTTAT-TAAAAAAAGAAAAGTTGATTG
* * * * *
3507072 ATTGTAAATGTCAGACTGTAAGGATTGGACTAATACATGAATTATATCTGAGAATCGGATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
*
3507137 TTTATT---AAAA-AAAAGTTAGACTG
66 TTTATTAAAAAAAGAAAAGTT-GATTG
* * * * * * * *
3507160 ACTGCAAGGAT-T-AGACT--AATGCATGA-ATTATAT--TTG-A-GA-ATC-G-GATTC---TT
1 ATTGTAA--ATGTCAGACTGCAAAG-ATTAGACTA-ATGCATGAATTATATCTGAGAATCGAATT
* * *
3507210 -TTTTTATA-GAAAAAAAG-GAAGACTGATTG
62 CTTTTT-TATTAAAAAAAGAAAAG-TTGATTG
* * * * * *
3507239 ATTATAAATGTCAGACTGTAAGGATTAGACTAATGTATAAATTATA--T----AT--AAGTC--T
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
** ** **
3507294 TAGAAAAAAAGAAAGGCTAA-TTGATTG
66 TTTATTAAAA-AAA-GAAAAGTTGATTG
* * * **
3507321 ----TAAATGTCAGACTGCAAATATTAGACTAATGCATGAAATATATCTAAGAATTAAATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
3507382 TTTATGTAAAAAAAGAAAAGTTGATTG
66 TTTAT-TAAAAAAAGAAAAGTTGATTG
* * * ** *
3507409 ATTGTAAATGTCAAATTGTATGGATTAGACTAATGCATAAATTATATCTGAGAATC-AGA-T-TT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGA-ATTCTT
* * *
3507471 TTTT-TTATAAAAAG-AAAGACTAATTG
65 TTTTATTAAAAAAAGAAAAG-TTGATTG
* * * *
3507497 ATTGTAAATGTTAGA-TAGTAAAGATTAGACTAATGCATGAATTATATGTGAGGATC-AGATTCT
1 ATTGTAAATGTCAGACT-GCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGA-ATTCT
3507560 TTTTTA-TAGGAAAAAAGAAAA
64 TTTTTATTA--AAAAAAGAAAA
3507581 ACTATAAGGA
Statistics
Matches: 528, Mismatches: 105, Indels: 113
0.71 0.14 0.15
Matches are distributed among these distances:
76 5 0.01
77 6 0.01
78 37 0.07
79 20 0.04
80 12 0.02
81 14 0.03
82 14 0.03
83 3 0.01
84 6 0.01
85 3 0.01
86 10 0.02
87 19 0.04
88 94 0.18
89 7 0.01
90 118 0.22
91 32 0.06
92 125 0.24
93 3 0.01
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (91 bp):
ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
TTTATTAAAAAAAGAAAAGTTGATTG
Found at i:3507103 original size:92 final size:92
Alignment explanation
Indices: 3506800--3507151 Score: 426
Period size: 90 Copynumber: 3.9 Consensus size: 92
3506790 TAATGTATAA
* * * *
3506800 ATTGTAAATGTTAGACTG-TAAGAAATAGACTAATGCATG-ATTATATCTGAGAATCGGATTCTT
1 ATTGTAAATGTCAGACTGCAAAG-ATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTT
*
3506863 TTTTAT-TAAAAAAAGAAAAGTTGATTG
65 TTTTATGAAAAAAAAGAAAAGTTGATTG
* * * * *
3506890 ATTGTAAATATCAAACTACAAAGATTAGAGTAATGCATGAATTATATCTGAGAATC-AATTTTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
* *
3506954 TTTA-GAAAAAAAAGAGAAGTTGATTA
66 TTTATGAAAAAAAAGAAAAGTTGATTG
*** * * * *
3506980 ACCCTAAATGTCAGACTGCAAATATTAGACTAATGCATAAATTATATTTGAGAATCAAATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
*
3507045 TTTATGGAAAAAAAGAAAAGTTGATTG
66 TTTATGAAAAAAAAGAAAAGTTGATTG
* * * * *
3507072 ATTGTAAATGTCAGACTGTAAGGATTGGACTAATACATGAATTATATCTGAGAATCGGATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
*
3507137 TTTATTAAAAAAAAG
66 TTTATGAAAAAAAAG
3507152 TTAGACTGAC
Statistics
Matches: 217, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
90 102 0.47
91 30 0.14
92 85 0.39
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (92 bp):
ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
TTTATGAAAAAAAAGAAAAGTTGATTG
Found at i:3507206 original size:74 final size:75
Alignment explanation
Indices: 3507085--3507235 Score: 225
Period size: 74 Copynumber: 2.0 Consensus size: 75
3507075 GTAAATGTCA
* *
3507085 GACTGTAAGGATTGGACTAATACATGAATTATATCTGAGAATCGGATTC-TTTTTTATTA-AAAA
1 GACTGCAAGGATTAGACTAATACATGAATTATATCTGAGAATCGGATTCTTTTTTTA-TAGAAAA
**
3507148 AAAGTTAGACT
65 AAAGGAAGACT
* *
3507159 GACTGCAAGGATTAGACTAATGCATGAATTATATTTGAGAATCGGATTCTTTTTTTATAGAAAAA
1 GACTGCAAGGATTAGACTAATACATGAATTATATCTGAGAATCGGATTCTTTTTTTATAGAAAAA
3507224 AAGGAAGACT
66 AAGGAAGACT
3507234 GA
1 GA
3507236 TTGATTATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 47 0.68
75 22 0.32
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (75 bp):
GACTGCAAGGATTAGACTAATACATGAATTATATCTGAGAATCGGATTCTTTTTTTATAGAAAAA
AAGGAAGACT
Found at i:3507301 original size:78 final size:78
Alignment explanation
Indices: 3507216--3507368 Score: 209
Period size: 78 Copynumber: 2.0 Consensus size: 78
3507206 TCTTTTTTTA
* * * * *
3507216 TAGAAAAAAAGGAAGACTGATTGATTATAAATGTCAGACTGTAAGGATTAGACTAATGTAT-AAA
1 TAGAAAAAAAGAAAGACTAATTGATTATAAATGTCAGACTGCAAAGATTAGACTAATGCATGAAA
3507280 TTATATATAAGTCT
66 -TATATATAAGTCT
* * *
3507294 TAGAAAAAAAGAAAGGCTAATTGATTGTAAATGTCAGACTGCAAATATTAGACTAATGCATGAAA
1 TAGAAAAAAAGAAAGACTAATTGATTATAAATGTCAGACTGCAAAGATTAGACTAATGCATGAAA
*
3507359 TATATCTAAG
66 TATATATAAG
3507369 AATTAAATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 62 0.95
79 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.29
Consensus pattern (78 bp):
TAGAAAAAAAGAAAGACTAATTGATTATAAATGTCAGACTGCAAAGATTAGACTAATGCATGAAA
TATATATAAGTCT
Found at i:3507577 original size:88 final size:87
Alignment explanation
Indices: 3507300--3507577 Score: 290
Period size: 88 Copynumber: 3.1 Consensus size: 87
3507290 GTCTTAGAAA
* * * *
3507300 AAAAGAAAGGCTAATTGATTGTAAATGTCAGACTGCAAATATTAGACTAATGCATGAAATATATC
1 AAAA-AAAGACTAATTGATTGTAAATGTCAGA-TGTAAAGATTAGACTAATGCATGAATTATATC
* * *
3507365 TAAGAATTAAATTCTTTTTTAT-G
64 TGAGAATCAGATTCTTTTTTATAG
* * * ** *
3507388 TAAAAAAAGAAAAGTTGATTGATTGTAAATGTCAAATTGTATGGATTAGACTAATGCATAAATTA
1 -AAAAAAAG---A-CTAATTGATTGTAAATGTCAGA-TGTAAAGATTAGACTAATGCATGAATTA
*
3507453 TATCTGAGAATCAGATTTTTTTTTATA-
60 TATCTGAGAATCAGATTCTTTTTTATAG
* *
3507480 AAAAGAAAGACTAATTGATTGTAAATGTTAGATAGTAAAGATTAGACTAATGCATGAATTATATG
1 AAAA-AAAGACTAATTGATTGTAAATGTCAGAT-GTAAAGATTAGACTAATGCATGAATTATATC
*
3507545 TGAGGATCAGATTCTTTTTTATAG
64 TGAGAATCAGATTCTTTTTTATAG
*
3507569 GAAAAAAGA
1 AAAAAAAGA
3507578 AAAACTATAA
Statistics
Matches: 155, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
87 1 0.01
88 75 0.48
89 8 0.05
91 4 0.03
92 67 0.43
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (87 bp):
AAAAAAAGACTAATTGATTGTAAATGTCAGATGTAAAGATTAGACTAATGCATGAATTATATCTG
AGAATCAGATTCTTTTTTATAG
Found at i:3511623 original size:298 final size:291
Alignment explanation
Indices: 3511054--3511697 Score: 970
Period size: 298 Copynumber: 2.2 Consensus size: 291
3511044 GAAAATATTT
* * * *
3511054 TTGGTCATTTTACAGATAAAGAAAAGCTCGTATGTAAGTCGTTACCGAAAAATGAAATGTGTGCA
1 TTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTATCAAAAAATAAAATGTGTGCA
* * ** * *
3511119 TTTGTAAATCTGAAATAAGTCGTTATCGAAAAATGTAATTTATTGTTGGCTAACATAAATTTAAG
66 TCTGTAAATCTGAAATAAGTCGTTATCGAAAAAAGTAAAATATTATTGACTAACATAAATTTAAG
* * *
3511184 TTCTATCAATTATAAACATGTACAATATTAATTAATTTTTTAAAAAATAAATTTGTATAATTTAT
131 TTCTATCAATTATAAACATGTACAACATTAATTAATTTTATAAAAAATAAATTTGCATAATTTAT
* *
3511249 TAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATTCATGCACAATATTAATTAATTTTAA
196 AAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTAATTAATTTTAA
*
3511314 TAAAAATAATACATGTACAATAAATTTTTTC
261 TAAAAATAATACATGTAAAATAAATTTTTTC
*
3511345 TTGGTCATTTTACAGATAAA-AGAAAGCTTGTATTTAAGTCGTTATCAAAAAATAAAATGTGTGC
1 TTGGTCATTTTACAGATAAAGA-AAAGCTCGTATTTAAGTCGTTATCAAAAAATAAAATGTGTGC
3511409 ATCTGTAAAT-TCGAAATAAGTCGTTATCGAAAAAAGTAAAATATTATTGACTAACATAAATTTA
65 ATCTGTAAATCT-GAAATAAGTCGTTATCGAAAAAAGTAAAATATTATTGACTAACATAAATTTA
* *
3511473 AGTTTTATCAATTATAAAAATAATACATGTACAACATTAATTAATTTTA-ATAAAAATGAATTTG
129 AGTTCTATCAA-T-T----ATAA-ACATGTACAACATTAATTAATTTTATA-AAAAATAAATTTG
*
3511537 CATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATATTAA
186 CATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTAA
3511602 TTAATTTTAATAAAAATAATACATGTAAAATAAATTTTTTC
251 TTAATTTTAATAAAAATAATACATGTAAAATAAATTTTTTC
* * *
3511643 TTAGTCATTTTACAAATAAAGAAAAACTCGTATTTAAGTCGTTATCAAAAAATAA
1 TTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTATCAAAAAATAA
3511698 TACATGTAAA
Statistics
Matches: 318, Mismatches: 24, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
290 2 0.01
291 123 0.39
292 1 0.00
293 1 0.00
297 5 0.02
298 185 0.58
299 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (291 bp):
TTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTATCAAAAAATAAAATGTGTGCA
TCTGTAAATCTGAAATAAGTCGTTATCGAAAAAAGTAAAATATTATTGACTAACATAAATTTAAG
TTCTATCAATTATAAACATGTACAACATTAATTAATTTTATAAAAAATAAATTTGCATAATTTAT
AAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTAATTAATTTTAA
TAAAAATAATACATGTAAAATAAATTTTTTC
Found at i:3511890 original size:31 final size:32
Alignment explanation
Indices: 3511854--3511951 Score: 92
Period size: 36 Copynumber: 2.9 Consensus size: 32
3511844 AAATCATAGC
3511854 TTAATTTTTTAAATTTAATTATATATTATTT-
1 TTAATTTTTTAAATTTAATTATATATTATTTA
* *
3511885 TTAATTTTATAAAAAATAATAATTAATATATTATTTA
1 TTAATTTT-T--TAAAT-TTAATT-ATATATTATTTA
* *
3511922 TTAAAATTTTTAAATTTAATTA-ATTTTATT
1 TT-AATTTTTTAAATTTAATTATATATTATT
3511952 AAAAAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
31 8 0.15
32 8 0.15
33 1 0.02
34 9 0.17
35 9 0.17
36 11 0.20
37 3 0.06
38 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TTAATTTTTTAAATTTAATTATATATTATTTA
Found at i:3511990 original size:13 final size:13
Alignment explanation
Indices: 3511972--3511996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3511962 TAATAAATGC
3511972 TTTTTATTTTAAT
1 TTTTTATTTTAAT
3511985 TTTTTATTTTAA
1 TTTTTATTTTAA
3511997 AAAATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:3512092 original size:116 final size:114
Alignment explanation
Indices: 3511941--3512172 Score: 394
Period size: 116 Copynumber: 2.0 Consensus size: 114
3511931 TTAAATTTAA
*
3511941 TTAATTTTATTAAAAAAATAATAATAAATGCTTTTTATTTTAATTTTTTATTTTAAAAAATAATT
1 TTAATTTTATTAAAAAAATAATAATAAATGCTTTTTAATTTAATTTTTTATTTTAAAAAATAATT
* *
3512006 TATATTTTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAAATATTATTT
66 AATATTTTAATTTATTAATGT-AA-TTTTTT-AAGTTAAGTAAATATTATTT
*
3512058 TTAATTTTATT-AAAAAATAATAATAAATGTTTTTTAATTTAATTTTTTATTTTAAAAAATAATT
1 TTAATTTTATTAAAAAAATAATAATAAATGCTTTTTAATTTAATTTTTTATTTTAAAAAATAATT
3512122 AATATTTTAATTTATTAATGTAATTTTTTAAGTTAAGTAAATATTATTT
66 AATATTTTAATTTATTAATGTAATTTTTTAAGTTAAGTAAATATTATTT
3512171 TT
1 TT
3512173 TATTAAAAAT
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
113 21 0.19
114 6 0.05
115 2 0.02
116 71 0.64
117 11 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (114 bp):
TTAATTTTATTAAAAAAATAATAATAAATGCTTTTTAATTTAATTTTTTATTTTAAAAAATAATT
AATATTTTAATTTATTAATGTAATTTTTTAAGTTAAGTAAATATTATTT
Found at i:3512120 original size:42 final size:41
Alignment explanation
Indices: 3511923--3512125 Score: 110
Period size: 42 Copynumber: 5.0 Consensus size: 41
3511913 TATTATTTAT
* * *
3511923 TAAAATTTTTAAATTTAATTAATTTTA-TTAAAAAAATAATAA
1 TAAATTTTTTTAATTTAATT--TTTTATTTTAAAAAATAATAA
* * *
3511965 TAAATGCTTTTTATTTTAATTTTTTATTTTAAAAAATAAT-T
1 TAAAT-TTTTTTAATTTAATTTTTTATTTTAAAAAATAATAA
* * **
3512006 TATATTTTAATTT-A-TTAATGTAAATTT-TTTT-AAAGTTAAT--
1 TAAATTTT--TTTAATTTAAT-T--TTTTATTTTAAAAAATAATAA
* *
3512046 TAAATATTATT--TTTAA--TTTTA--TTAAAAAATAATAA
1 TAAATTTTTTTAATTTAATTTTTTATTTTAAAAAATAATAA
3512081 TAAATGTTTTTTAATTTAATTTTTTATTTTAAAAAATAATTAA
1 TAAAT-TTTTTTAATTTAATTTTTTATTTTAAAAAATAA-TAA
3512124 TA
1 TA
3512126 TTTTAATTTA
Statistics
Matches: 121, Mismatches: 20, Indels: 39
0.67 0.11 0.22
Matches are distributed among these distances:
32 2 0.02
33 10 0.08
35 5 0.04
36 4 0.03
38 11 0.09
40 18 0.15
41 17 0.14
42 34 0.28
43 20 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
TAAATTTTTTTAATTTAATTTTTTATTTTAAAAAATAATAA
Found at i:3512348 original size:29 final size:29
Alignment explanation
Indices: 3512286--3512349 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
3512276 TTTCTCAATA
*
3512286 AATTTGTAAAAAAAACTTATTTTAAAAAAT
1 AATTT-TAAAAAAAACCTATTTTAAAAAAT
* *
3512316 -ATTTTATAAAAAACCTA-TTTACAAAATT
1 AATTTTAAAAAAAACCTATTTTA-AAAAAT
3512344 AATTTT
1 AATTTT
3512350 TTTTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 4 0.14
28 16 0.55
29 9 0.31
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (29 bp):
AATTTTAAAAAAAACCTATTTTAAAAAAT
Done.