Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 5 of 210
Found at i:1859305 original size:13 final size:13
Alignment explanation
Indices: 1859259--1859309 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1859249 TTTTTAAGTT
*
1859259 TTTTATTTTTCTTA
1 TTTTATTTAT-TTA
*
1859273 TTTTATTTTGTTTA
1 TTTTA-TTTATTTA
*
1859287 -TATATTTATTTA
1 TTTTATTTATTTA
1859299 TTTTATTTATT
1 TTTTATTTATT
1859310 GTTATTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 7 0.23
13 12 0.39
14 8 0.26
15 4 0.13
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:1859394 original size:11 final size:11
Alignment explanation
Indices: 1859349--1859399 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1859339 TATTTGAAAT
1859349 TTTTTATAATATA
1 TTTTTA-AAT-TA
*
1859362 TTTTTAAA-AA
1 TTTTTAAATTA
*
1859372 TTTTAAAAATTA
1 TTTT-TAAATTA
1859384 TTTTTAAATTA
1 TTTTTAAATTA
1859395 TTTTT
1 TTTTT
1859400 TAAAAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 5 0.16
11 14 0.44
12 7 0.22
13 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTAAATTA
Found at i:1859408 original size:11 final size:11
Alignment explanation
Indices: 1859345--1859408 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 11
1859335 TGTATATTTG
1859345 AAATTTTTTATA
1 AAATTTTTTA-A
*
1859357 ATATATTTTTAA
1 AAAT-TTTTTAA
1859369 AAA--TTTTAA
1 AAATTTTTTAA
1859378 AAATTATTTTTAA
1 AAA-T-TTTTTAA
*
1859391 ATTATTTTTTAA
1 A-AATTTTTTAA
1859403 AAATTT
1 AAATTT
1859409 GAATATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
9 9 0.21
11 4 0.10
12 14 0.33
13 14 0.33
14 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATTTTTTAA
Found at i:1859417 original size:33 final size:35
Alignment explanation
Indices: 1859349--1859425 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 35
1859339 TATTTGAAAT
1859349 TTTTTATAA-TATATTTTTAAAAATTTTAAAAATTA
1 TTTTTA-AATTATATTTTTAAAAATTTTAAAAATTA
* *
1859384 TTTTTAAATTAT-TTTTTAAAAA-TTTGAATATTA
1 TTTTTAAATTATATTTTTAAAAATTTTAAAAATTA
*
1859417 TTTTAAAAT
1 TTTTTAAAT
1859426 ATTAAATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 17 0.45
34 12 0.32
35 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (35 bp):
TTTTTAAATTATATTTTTAAAAATTTTAAAAATTA
Found at i:1859442 original size:22 final size:23
Alignment explanation
Indices: 1859386--1859449 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 23
1859376 AAAAATTATT
1859386 TTTAAAT-TAT-TTTTTAAAA-A
1 TTTAAATATATATTTTTAAAATA
*
1859406 TTTGAATAT-TA-TTTTAAAATA
1 TTTAAATATATATTTTTAAAATA
1859427 -TTAAATATATATTTTTAATAATA
1 TTTAAATATATATTTTTAA-AATA
1859450 GAAAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 22 0.61
21 4 0.11
22 6 0.17
23 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAATATATATTTTTAAAATA
Found at i:1859909 original size:13 final size:13
Alignment explanation
Indices: 1859891--1859946 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1859881 ATAAATTTAT
1859891 TTAAAAATATATA
1 TTAAAAATATATA
* *
1859904 TTAAAAAGTAAATT
1 TTAAAAA-TATATA
* *
1859918 TTAAAATTA-AAA
1 TTAAAAATATATA
1859930 TTTAAAAATATATA
1 -TTAAAAATATATA
1859944 TTA
1 TTA
1859947 TAAGATCACA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 1 0.03
13 20 0.61
14 12 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
TTAAAAATATATA
Found at i:1860429 original size:40 final size:41
Alignment explanation
Indices: 1860385--1860469 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 41
1860375 GTGTTGGTTA
*
1860385 TAATTTTTTAATTTTAGCACACATTTATAAATTTATATA-T
1 TAATTTTTTAATTTTAGCACACATTCATAAATTTATATACT
* *
1860425 TAATTTTTTAATTTTAGTACACATTCATAAATTTATGTACT
1 TAATTTTTTAATTTTAGCACACATTCATAAATTTATATACT
1860466 TAAT
1 TAAT
1860470 ATATATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (41 bp):
TAATTTTTTAATTTTAGCACACATTCATAAATTTATATACT
Found at i:1860480 original size:40 final size:40
Alignment explanation
Indices: 1860393--1860480 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
1860383 TATAATTTTT
* * *
1860393 TAATTTTAGCACACATTTATAAATTTATATATTAATTTTT
1 TAATTTTAGCACACATTCATAAATTTATATATTAATTATA
* *
1860433 TAATTTTAGTACACATTCATAAATTTATGTACTTAA-TATA
1 TAATTTTAGCACACATTCATAAATTTATATA-TTAATTATA
*
1860473 TATTTTTA
1 TAATTTTA
1860481 ATAGATAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (40 bp):
TAATTTTAGCACACATTCATAAATTTATATATTAATTATA
Found at i:1860618 original size:71 final size:71
Alignment explanation
Indices: 1860531--1860683 Score: 234
Period size: 71 Copynumber: 2.1 Consensus size: 71
1860521 TGTTTAAAAA
* * * * *
1860531 TTTAAAGAAATTAAATACATTAAAAAATGTTATGTATAGCCAATTTTAAAATTTTAATATATTTA
1 TTTAAA-AAATTAAATACATTAAAAAATGTTAAGTATAACCAATATTAAAATTATAATATATTCA
1860596 ATATATT
65 ATATATT
*
1860603 TTTAAAAAATTAAATATATTAAAAAATGTTAAGTATAACCAATATTAAAATTATAATATATTCAA
1 TTTAAAAAATTAAATACATTAAAAAATGTTAAGTATAACCAATATTAAAATTATAATATATTCAA
1860668 TATATT
66 TATATT
*
1860674 TTTTAAAAAT
1 TTTAAAAAAT
1860684 ATATTTTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 68 0.92
72 6 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (71 bp):
TTTAAAAAATTAAATACATTAAAAAATGTTAAGTATAACCAATATTAAAATTATAATATATTCAA
TATATT
Found at i:1863086 original size:50 final size:50
Alignment explanation
Indices: 1862976--1863322 Score: 374
Period size: 50 Copynumber: 6.8 Consensus size: 50
1862966 ATTTGGGTAA
* *
1862976 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATG
* * *
1863032 AGAGGTTCCATGTAAGACCATGTCTGGAACATGGCGTTGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
* *
1863082 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
* * *
1863132 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
** * * *
1863182 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
** * * * *
1863232 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTATAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ATATG
* ** * * *
1863281 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1863323 TGTTATTATC
Statistics
Matches: 253, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
49 36 0.14
50 176 0.70
51 2 0.01
55 1 0.00
56 38 0.15
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
Found at i:1869220 original size:13 final size:13
Alignment explanation
Indices: 1869193--1869227 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1869183 TATATTTAAA
1869193 ATTTAAAA-A-AT
1 ATTTAAAATATAT
1869204 ATTTAAAATATAT
1 ATTTAAAATATAT
1869217 ATTTAAAATAT
1 ATTTAAAATAT
1869228 TATAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTTAAAATATAT
Found at i:1869317 original size:23 final size:24
Alignment explanation
Indices: 1869262--1869341 Score: 108
Period size: 24 Copynumber: 3.3 Consensus size: 24
1869252 AGGTCATATC
* *
1869262 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATCATA-ATTTAAAATAA
1869287 TTTAAAAATCATAATTTAAAATAA
1 TTTAAAAATCATAATTTAAAATAA
*
1869311 TTTAAAAATCATAA-TTAAAAAAA
1 TTTAAAAATCATAATTTAAAATAA
1869334 TTATAAAA
1 TT-TAAAA
1869342 CAAATTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
23 10 0.20
24 29 0.57
25 12 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAAAATCATAATTTAAAATAA
Found at i:1869332 original size:14 final size:14
Alignment explanation
Indices: 1869283--1869331 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
1869273 TATATTTTAA
1869283 ATAATTTAAAAATC
1 ATAATTTAAAAATC
1869297 ATAATTT--AAA--
1 ATAATTTAAAAATC
1869307 ATAATTTAAAAATC
1 ATAATTTAAAAATC
1869321 ATAA-TTAAAAA
1 ATAATTTAAAAA
1869332 AATTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 7 0.23
12 6 0.19
13 7 0.23
14 11 0.35
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATTTAAAAATC
Found at i:1869463 original size:20 final size:19
Alignment explanation
Indices: 1869414--1869464 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1869404 TAAAATATTT
*
1869414 AAAT-TTTTTATATTTTTAA
1 AAATATTTTTA-ATATTTAA
*
1869433 AAATATATTTAATATTTAA
1 AAATATTTTTAATATTTAA
1869452 AAATAATTTTTAA
1 AAAT-ATTTTTAA
1869465 ANNNNNNNNN
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTTTTAATATTTAA
Found at i:1870370 original size:55 final size:55
Alignment explanation
Indices: 1870302--1870411 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
1870292 GTTTCAACAG
*
1870302 AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGTTTTATATCCTCTCCAGAC
1 AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGCTTTATATCCTCTCCAGAC
*
1870357 AAAGAAAAGGAAAAAGTTGATGGTCTTTTCAATAGGCTTTATATCCTCTCCAGAC
1 AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGCTTTATATCCTCTCCAGAC
1870412 TCCTTATACA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (55 bp):
AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGCTTTATATCCTCTCCAGAC
Found at i:1871275 original size:12 final size:12
Alignment explanation
Indices: 1871258--1871314 Score: 87
Period size: 12 Copynumber: 4.8 Consensus size: 12
1871248 GATATCGCAA
1871258 AGTGGCGGCTGC
1 AGTGGCGGCTGC
1871270 AGTGGCGGCTGC
1 AGTGGCGGCTGC
* *
1871282 AGTGACAGCTGC
1 AGTGGCGGCTGC
*
1871294 AATGGCGGCTGC
1 AGTGGCGGCTGC
1871306 AGTGGCGGC
1 AGTGGCGGC
1871315 GTAGGTGGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.14, C:0.25, G:0.46, T:0.16
Consensus pattern (12 bp):
AGTGGCGGCTGC
Found at i:1875550 original size:29 final size:28
Alignment explanation
Indices: 1875520--1875582 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1875510 TGTTTGTTAT
*
1875520 TTTTTATATTT-AGAATTTAGTCCTTCTA
1 TTTTTA-ATTTAAGAATTTAGTCCCTCTA
1875548 TTTTTAATTTAAAGAATTTAGTCCCTCTA
1 TTTTTAATTT-AAGAATTTAGTCCCTCTA
1875577 CTTTTT
1 -TTTTT
1875583 GGATTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 4 0.13
28 6 0.19
29 16 0.52
30 5 0.16
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTTTAATTTAAGAATTTAGTCCCTCTA
Found at i:1878554 original size:30 final size:30
Alignment explanation
Indices: 1878518--1878685 Score: 179
Period size: 30 Copynumber: 5.8 Consensus size: 30
1878508 CATCACCACT
*
1878518 ATCAGCATCCCTATTGCCGTCACCGTCACC
1 ATCAGCATCCCTATTGCCATCACCGTCACC
* * * *
1878548 ATCAGCATCACAATTGTCATCA-C--CACT
1 ATCAGCATCCCTATTGCCATCACCGTCACC
*
1878575 ATCAACATCCCTATTGCCATCACCGTCACC
1 ATCAGCATCCCTATTGCCATCACCGTCACC
* * *
1878605 ATCAGCATCACAATTGCCATCA-C--CACT
1 ATCAGCATCCCTATTGCCATCACCGTCACC
*
1878632 ATCAACATCCCTATTGCCATCACCGTCACC
1 ATCAGCATCCCTATTGCCATCACCGTCACC
*
1878662 TTCAGCATCACC-ATTGCCATCACC
1 ATCAGCATC-CCTATTGCCATCACC
1878686 ATCAGCGTCA
Statistics
Matches: 111, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
27 43 0.39
28 2 0.02
29 2 0.02
30 62 0.56
31 2 0.02
ACGTcount: A:0.27, C:0.40, G:0.08, T:0.24
Consensus pattern (30 bp):
ATCAGCATCCCTATTGCCATCACCGTCACC
Found at i:1878584 original size:57 final size:57
Alignment explanation
Indices: 1878507--1878686 Score: 315
Period size: 57 Copynumber: 3.2 Consensus size: 57
1878497 ATCACCATCA
* *
1878507 CCATCACCACTATCAGCATCCCTATTGCCGTCACCGTCACCATCAGCATCACAATTG
1 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
*
1878564 TCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
1 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
* *
1878621 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCTTCAGCATCACCATTG
1 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
1878678 CCATCACCA
1 CCATCACCA
1878687 TCAGCGTCAC
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 117 1.00
ACGTcount: A:0.28, C:0.41, G:0.08, T:0.23
Consensus pattern (57 bp):
CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
Found at i:1878627 original size:24 final size:24
Alignment explanation
Indices: 1878600--1878709 Score: 85
Period size: 27 Copynumber: 4.2 Consensus size: 24
1878590 GCCATCACCG
1878600 TCACCATCAGCATCACAATTGCCA
1 TCACCATCAGCATCACAATTGCCA
* * *
1878624 TCACCACTATCAACATCCCTATTGCCA
1 TCA-C-C-ATCAGCATCACAATTGCCA
*
1878651 TCACCGTCACCTTCAGCATCACCATTGCCA
1 TCA-C--CA---TCAGCATCACAATTGCCA
* *
1878681 TCACCATCAGCGTCACAATTACCA
1 TCACCATCAGCATCACAATTGCCA
1878705 TCACC
1 TCACC
1878710 GTCACCACTA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
24 23 0.33
25 1 0.01
26 1 0.01
27 24 0.35
28 1 0.01
29 1 0.01
30 18 0.26
ACGTcount: A:0.29, C:0.41, G:0.07, T:0.23
Consensus pattern (24 bp):
TCACCATCAGCATCACAATTGCCA
Found at i:1881428 original size:2 final size:2
Alignment explanation
Indices: 1881421--1881451 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1881411 AATAATTCAT
*
1881421 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1881452 GTCTTGAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1884763 original size:31 final size:31
Alignment explanation
Indices: 1884723--1884785 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1884713 TTCTATTACA
* *
1884723 TTTAGTTTAAT-TTATTAAATTCATTTTATTT
1 TTTAATTTAATATAATTAAATTC-TTTTATTT
*
1884754 TTTAATTTAATATAATTAATTTCTTTTATTT
1 TTTAATTTAATATAATTAAATTCTTTTATTT
1884785 T
1 T
1884786 GATTATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (31 bp):
TTTAATTTAATATAATTAAATTCTTTTATTT
Found at i:1884780 original size:26 final size:26
Alignment explanation
Indices: 1884728--1884780 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1884718 TTACATTTAG
* *
1884728 TTTAATTTATTAAATTCATTTTATTT
1 TTTAATTTAATAAATTCAATTTATTT
*
1884754 TTTAATTTAATATAATT-AATTTCTTT
1 TTTAATTTAATA-AATTCAATTTATTT
1884780 T
1 T
1884781 ATTTTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTAATTTAATAAATTCAATTTATTT
Found at i:1891857 original size:30 final size:31
Alignment explanation
Indices: 1891823--1891880 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1891813 AGATGATACT
*
1891823 TGTGATGATG-ATCTTATGGGCC-TATGTACA
1 TGTGATGATGCA-CCTATGGGCCTTATGTACA
*
1891853 TGTGATTATGCACCTATGGGCCTTATGT
1 TGTGATGATGCACCTATGGGCCTTATGT
1891881 GTGAAGATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (31 bp):
TGTGATGATGCACCTATGGGCCTTATGTACA
Found at i:1899723 original size:7 final size:7
Alignment explanation
Indices: 1899711--1899739 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1899701 ATAATGATTG
1899711 ATTTATA
1 ATTTATA
1899718 ATTTATA
1 ATTTATA
1899725 ATTTATA
1 ATTTATA
1899732 ATTTATA
1 ATTTATA
1899739 A
1 A
1899740 ATAATAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTATA
Found at i:1900798 original size:22 final size:23
Alignment explanation
Indices: 1900761--1900809 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1900751 AAATTTAAAA
1900761 TTATTTAAATAATAAAAAATAATT
1 TTATTTAAAT-ATAAAAAATAATT
* *
1900785 TTATTTAAAT-TAAATAATATTT
1 TTATTTAAATATAAAAAATAATT
1900807 TTA
1 TTA
1900810 ATTATTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTAAATATAAAAAATAATT
Found at i:1902868 original size:29 final size:29
Alignment explanation
Indices: 1902810--1902872 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
1902800 TATTCGATAA
*
1902810 TTTTTATTTAAGTCACTGAACTATTCAAG
1 TTTTTATTTAAATCACTGAACTATTCAAG
* * *
1902839 TTTTTCATTTAAATCATTGAATTGTT-AAG
1 TTTTT-ATTTAAATCACTGAACTATTCAAG
1902868 TTTTT
1 TTTTT
1902873 TTTCTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
TTTTTATTTAAATCACTGAACTATTCAAG
Found at i:1904539 original size:31 final size:31
Alignment explanation
Indices: 1904491--1904559 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1904481 TTAAACTTTT
*
1904491 TTTATCC-ATGTTAATCCTCAAACTTATAAC
1 TTTATCCAATATTAATCCTCAAACTTATAAC
1904521 TTTATCCAATATTAATCCTCAAACTTATAAC
1 TTTATCCAATATTAATCCTCAAACTTATAAC
1904552 TTTATCCA
1 TTTATCCA
1904560 GTTTTGATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 7 0.19
31 30 0.81
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.41
Consensus pattern (31 bp):
TTTATCCAATATTAATCCTCAAACTTATAAC
Found at i:1908742 original size:20 final size:20
Alignment explanation
Indices: 1908707--1908745 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1908697 TCTTAAGAAC
*
1908707 AATATTCCAACCGAAAAAAA
1 AATATTCCAACAGAAAAAAA
*
1908727 AATATTCCAATAGAAAAAA
1 AATATTCCAACAGAAAAAA
1908746 TGATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.15, G:0.05, T:0.18
Consensus pattern (20 bp):
AATATTCCAACAGAAAAAAA
Found at i:1909304 original size:28 final size:28
Alignment explanation
Indices: 1909255--1909310 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1909245 TTTAATTAAA
*
1909255 AAAATTAAAGTTGATCGGAAAATTCAAT
1 AAAATTAAAGTTGATCGCAAAATTCAAT
*
1909283 AAAATTAAAGTTTAGT-GCAAAATTCAAT
1 AAAATTAAAGTTGA-TCGCAAAATTCAAT
1909311 CACATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTAAAGTTGATCGCAAAATTCAAT
Found at i:1909809 original size:70 final size:70
Alignment explanation
Indices: 1909731--1909865 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 70
1909721 GTGAAGAGTA
* * *
1909731 ATGAATGATTCATCAAAAAGAATACATTGACCGTACGTGGATGTACGATCGTTCATTAAAAAGTA
1 ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
1909796 CTGTT
66 CTGTT
1909801 ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
1 ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
1909866 ATGTGAGCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (70 bp):
ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
CTGTT
Found at i:1921734 original size:18 final size:18
Alignment explanation
Indices: 1921711--1921749 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1921701 CCGCTCCAGC
1921711 AAAGGACACTAAAGATGG
1 AAAGGACACTAAAGATGG
**
1921729 AAAGGATGCTAAAGATGG
1 AAAGGACACTAAAGATGG
1921747 AAA
1 AAA
1921750 AGACTCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.28, T:0.13
Consensus pattern (18 bp):
AAAGGACACTAAAGATGG
Found at i:1922260 original size:38 final size:38
Alignment explanation
Indices: 1922218--1922299 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1922208 TTTGCTTATT
* * *
1922218 ATCAT-TTTCGTGGTTTTATCTATGATTGTGTTTAAAAC
1 ATCATATTT-GTGGTTATATCGATGATTGTGCTTAAAAC
* *
1922256 ATCATATTTGTGGTTATATCGATGATTGTGCTTAACAT
1 ATCATATTTGTGGTTATATCGATGATTGTGCTTAAAAC
1922294 ATCATA
1 ATCATA
1922300 AAAATGACCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 35 0.92
39 3 0.08
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (38 bp):
ATCATATTTGTGGTTATATCGATGATTGTGCTTAAAAC
Found at i:1931597 original size:30 final size:31
Alignment explanation
Indices: 1931559--1931626 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1931549 TACAAAATGA
*
1931559 TCATTAAATTA-TTGAAAAGTTTAATTTAAG
1 TCATTAAATTATTTAAAAAGTTTAATTTAAG
* * *
1931589 TTATTAAATTATTTAAAAATTTTTATTTAAG
1 TCATTAAATTATTTAAAAAGTTTAATTTAAG
1931620 TCATTAA
1 TCATTAA
1931627 GTTGTGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
TCATTAAATTATTTAAAAAGTTTAATTTAAG
Found at i:1935345 original size:5 final size:5
Alignment explanation
Indices: 1935326--1935416 Score: 75
Period size: 5 Copynumber: 18.6 Consensus size: 5
1935316 TTAGTTTATT
*
1935326 TAATA T-ATAA TAATA TAATA TAATA TAATA TAAT- TAATA TTATA TTATATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA -TA-ATA
* * * *
1935377 TTATA TTATA TTATA TTATA TAATA -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
1935417 AACATAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
3 1 0.01
4 14 0.19
5 52 0.70
6 4 0.05
7 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
TAATA
Found at i:1935374 original size:17 final size:17
Alignment explanation
Indices: 1935329--1935391 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
1935319 GTTTATTTAA
*
1935329 TATATAATAATATAATAT
1 TATATTATAAT-TAATAT
*
1935347 AATATAATATAATTAATAT
1 --TATATTATAATTAATAT
1935366 TATATTATATATT-ATAT
1 TATATTATA-ATTAATAT
1935383 TATATTATA
1 TATATTATA
1935392 TTATATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 21 0.54
18 3 0.08
19 6 0.15
20 9 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTATAATTAATAT
Found at i:1935398 original size:17 final size:17
Alignment explanation
Indices: 1935338--1935392 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
1935328 ATATATAATA
* * *
1935338 ATATAATATAATATAAT
1 ATATATTATATTATATT
1935355 ATA-ATTAATATTATATT
1 ATATATT-ATATTATATT
1935372 ATATATTATATTATATT
1 ATATATTATATTATATT
1935389 ATAT
1 ATAT
1935393 TATATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 28 0.85
18 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATTATATTATATT
Found at i:1941656 original size:15 final size:15
Alignment explanation
Indices: 1941636--1941671 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1941626 GTTTGGATGA
1941636 GCGGTGAGGTACAGT
1 GCGGTGAGGTACAGT
1941651 GCGGTGAGGTACAGT
1 GCGGTGAGGTACAGT
1941666 GCGGTG
1 GCGGTG
1941672 CGTTTAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.50, T:0.19
Consensus pattern (15 bp):
GCGGTGAGGTACAGT
Found at i:1954736 original size:13 final size:14
Alignment explanation
Indices: 1954700--1954738 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1954690 TTATGTTAAA
1954700 TTAAAATAAAATTG
1 TTAAAATAAAATTG
1954714 TTAAATATAAAATT-
1 TTAAA-ATAAAATTG
*
1954728 TTAACATAAAA
1 TTAAAATAAAA
1954739 GTAGGACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
TTAAAATAAAATTG
Found at i:1955478 original size:31 final size:30
Alignment explanation
Indices: 1955443--1955505 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
1955433 TACAAAATGA
1955443 TCATTGAACTATTC-AAAAGTTTTCATTTAAG
1 TCATTGAACTATTCGAAAA-TTTT-ATTTAAG
**
1955474 TCATTGAGTTATTCTGAAAATTTTATTTAAG
1 TCATTGAACTATTC-GAAAATTTTATTTAAG
1955505 T
1 T
1955506 TACCGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 20 0.71
32 4 0.14
33 4 0.14
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (30 bp):
TCATTGAACTATTCGAAAATTTTATTTAAG
Found at i:1956072 original size:11 final size:11
Alignment explanation
Indices: 1956056--1956088 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1956046 CTTTTAAATA
1956056 ATTTAATAATT
1 ATTTAATAATT
1956067 ATTTAATAATT
1 ATTTAATAATT
*
1956078 TTTTAA-AATT
1 ATTTAATAATT
1956088 A
1 A
1956089 AACGATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:1962146 original size:20 final size:21
Alignment explanation
Indices: 1962121--1962159 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1962111 TATATTTGAG
1962121 ATGTTA-CGTTTTAGTTACTT
1 ATGTTATCGTTTTAGTTACTT
*
1962141 ATGTTATCGTTTTCGTTAC
1 ATGTTATCGTTTTAGTTAC
1962160 AAAATGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (21 bp):
ATGTTATCGTTTTAGTTACTT
Found at i:1963828 original size:33 final size:34
Alignment explanation
Indices: 1963791--1963855 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
1963781 TAAACGGAGA
1963791 TCTGGGCCTTGAATT-TTTTTTT-TCTGTTTTGGT
1 TCTGGGCC-TGAATTATTTTTTTCTCTGTTTTGGT
** *
1963824 TCTGGTTCTGATTTATTTTTTTCTCTGTTTTG
1 TCTGGGCCTGAATTATTTTTTTCTCTGTTTTG
1963856 TTCATACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 5 0.19
33 13 0.48
34 9 0.33
ACGTcount: A:0.06, C:0.12, G:0.18, T:0.63
Consensus pattern (34 bp):
TCTGGGCCTGAATTATTTTTTTCTCTGTTTTGGT
Found at i:1974557 original size:21 final size:22
Alignment explanation
Indices: 1974522--1974564 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1974512 AACTTCTTTT
* *
1974522 TTTATTTCTAATATTATATTAA
1 TTTATTTCAAATATTAAATTAA
1974544 TTTA-TTCAAATATTAAATTAA
1 TTTATTTCAAATATTAAATTAA
1974565 AATATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATTTCAAATATTAAATTAA
Found at i:1982903 original size:22 final size:20
Alignment explanation
Indices: 1982855--1982894 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1982845 ATTGATGTCC
1982855 TTTCATTGATTCTTCCTAAA
1 TTTCATTGATTCTTCCTAAA
*
1982875 TTGCATTGATT-TATCCTAAA
1 TTTCATTGATTCT-TCCTAAA
1982895 AATTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTCATTGATTCTTCCTAAA
Found at i:1984076 original size:24 final size:24
Alignment explanation
Indices: 1984041--1984094 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1984031 TATTTTAATA
*
1984041 TATAAA-ATATAAATTTTAAGTATT
1 TATAAACA-ATAAATATTAAGTATT
* *
1984065 TTTAAACAATAAATATTAATTATT
1 TATAAACAATAAATATTAAGTATT
1984089 TATAAA
1 TATAAA
1984095 ATTTAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TATAAACAATAAATATTAAGTATT
Found at i:1990983 original size:34 final size:34
Alignment explanation
Indices: 1990945--1991011 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1990935 CCACCAAAAT
1990945 GATAATATTTTGATTTAATCTTTTAAAAAATCAA
1 GATAATATTTTGATTTAATCTTTTAAAAAATCAA
1990979 GATAATATTTTGATTTAATCTTTTAAAAAATCA
1 GATAATATTTTGATTTAATCTTTTAAAAAATCA
1991012 TAAAGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (34 bp):
GATAATATTTTGATTTAATCTTTTAAAAAATCAA
Found at i:1994080 original size:135 final size:135
Alignment explanation
Indices: 1993919--1994213 Score: 509
Period size: 135 Copynumber: 2.2 Consensus size: 135
1993909 TACAGCCCCT
* * * * *
1993919 AAGCAAATATGGCGACTGGTTTCAGCTTCTAGTAATGCAACTAATAGCGAGCTGAAAAAGGATGA
1 AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACAACTAAGAGCGAGCTGAAAAAGGATAA
*
1993984 ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAA
66 ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
1994049 CTGTA
131 CTGTA
*
1994054 AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACGACTAAGAGCGAGCTGAAAAAGGATAA
1 AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACAACTAAGAGCGAGCTGAAAAAGGATAA
*
1994119 ACCTTTGGAATCATCTAGTAGTGATGGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
66 ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
1994184 CTGTA
131 CTGTA
*
1994189 AAGCAAAAATGGAGACCGGTTTCAG
1 AAGCAAAAATGGAGACTGGTTTCAG
1994214 GAGGCATGGT
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 151 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (135 bp):
AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACAACTAAGAGCGAGCTGAAAAAGGATAA
ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
CTGTA
Found at i:1996360 original size:29 final size:29
Alignment explanation
Indices: 1996309--1996364 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1996299 CTTTGGACCT
* *
1996309 GATCAAATTAGTCCTTCTACTATTAAATG
1 GATCAAATTAGTCCCTATACTATTAAATG
* *
1996338 GATCAATTTAGTCCCTATTCTATTAAA
1 GATCAAATTAGTCCCTATACTATTAAA
1996365 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (29 bp):
GATCAAATTAGTCCCTATACTATTAAATG
Found at i:2007231 original size:31 final size:29
Alignment explanation
Indices: 2007196--2007267 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2007186 CGCTCCGTGT
* * *
2007196 CTAAAATATTACAATTTGATAACATAAGTGA
1 CTAAAATATAAC-ATTTCA-AACATAAATGA
*
2007227 CTAAAACATAACATTTCAAACATAAATGA
1 CTAAAATATAACATTTCAAACATAAATGA
*
2007256 CTAAAATGTAAC
1 CTAAAATATAAC
2007268 CCGAGACAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 20 0.57
30 5 0.14
31 10 0.29
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (29 bp):
CTAAAATATAACATTTCAAACATAAATGA
Found at i:2010827 original size:16 final size:16
Alignment explanation
Indices: 2010803--2010843 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2010793 TAGTAAAAAT
2010803 ATAATTTTATTATTTTA
1 ATAATTTTA-TATTTTA
*
2010820 AT-ATTTTATATTTTT
1 ATAATTTTATATTTTA
2010835 ATAATTTTA
1 ATAATTTTA
2010844 AAGATTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 12 0.55
17 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATAATTTTATATTTTA
Found at i:2011391 original size:25 final size:26
Alignment explanation
Indices: 2011363--2011416 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
2011353 TTTCTACTAT
* *
2011363 ATAAAATAATA-TTGGAATTAAAAAA
1 ATAAAATAATACATGAAATTAAAAAA
*
2011388 AT-AAATCATACATGAAATTAAAAAA
1 ATAAAATAATACATGAAATTAAAAAA
2011413 ATAA
1 ATAA
2011417 TTCTTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.29
25 16 0.67
26 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.26
Consensus pattern (26 bp):
ATAAAATAATACATGAAATTAAAAAA
Found at i:2013164 original size:25 final size:24
Alignment explanation
Indices: 2013128--2013180 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
2013118 CACAAACGCA
2013128 GCTCTTTATGAGCGTCCTAATATAG
1 GCTCTTTATGAGCGTCCTAATAT-G
* * *
2013153 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTAATATG
2013177 GCTC
1 GCTC
2013181 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTAATATG
Found at i:2041277 original size:2 final size:2
Alignment explanation
Indices: 2041270--2041294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2041260 TTGCATACAA
2041270 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2041295 ACGAAGAATA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2042803 original size:16 final size:16
Alignment explanation
Indices: 2042784--2042816 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2042774 TATCAAACAT
2042784 TTGTTGGATCATGATG
1 TTGTTGGATCATGATG
2042800 TTGTTGGATCATGATG
1 TTGTTGGATCATGATG
2042816 T
1 T
2042817 ACCAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.30, T:0.45
Consensus pattern (16 bp):
TTGTTGGATCATGATG
Found at i:2046986 original size:22 final size:23
Alignment explanation
Indices: 2046961--2047005 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2046951 ACACGATACT
* *
2046961 AATA-CTTTAAGGACTTAATTAA
1 AATATCTTTAAAGACTAAATTAA
*
2046983 AATATTTTTAAAGACTAAATTAA
1 AATATCTTTAAAGACTAAATTAA
2047006 TATTATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (23 bp):
AATATCTTTAAAGACTAAATTAA
Found at i:2048177 original size:33 final size:35
Alignment explanation
Indices: 2048140--2048236 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
2048130 CTGGTTGTAT
2048140 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
2048173 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
2048208 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
2048237 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:2051572 original size:16 final size:16
Alignment explanation
Indices: 2051551--2051613 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 16
2051541 TTAAGGAATT
2051551 ATCAAATATATATTTA
1 ATCAAATATATATTTA
2051567 ATC-AA-ATATA-TTA
1 ATCAAATATATATTTA
*
2051580 A--AAAGATATATTATA
1 ATCAAATATATATT-TA
*
2051595 TATTAAATATATATTTA
1 -ATCAAATATATATTTA
2051612 AT
1 AT
2051614 ATGGGTTGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
12 2 0.05
13 9 0.23
14 6 0.15
15 4 0.10
16 6 0.15
17 2 0.05
18 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (16 bp):
ATCAAATATATATTTA
Found at i:2051615 original size:20 final size:21
Alignment explanation
Indices: 2051571--2051615 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2051561 TATTTAATCA
2051571 AATATATTAAAAAGATATATT
1 AATATATTAAAAAGATATATT
* *
2051592 -ATATATTAAATATATAT-TT
1 AATATATTAAAAAGATATATT
2051611 AATAT
1 AATAT
2051616 GGGTTGGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATTAAAAAGATATATT
Found at i:2060861 original size:23 final size:23
Alignment explanation
Indices: 2060834--2060888 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2060824 TAATTTGATC
2060834 ATTTTAGTCCCTATACTTTTT-GA
1 ATTTTAGTCCCTATA-TTTTTCGA
*
2060857 ATTTTAGTCCCTGTATTTTTCGA
1 ATTTTAGTCCCTATATTTTTCGA
2060880 ATTTTAGTC
1 ATTTTAGTC
2060889 ATGACCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTTTAGTCCCTATATTTTTCGA
Found at i:2065713 original size:38 final size:38
Alignment explanation
Indices: 2065671--2065783 Score: 208
Period size: 38 Copynumber: 3.0 Consensus size: 38
2065661 AAGAGAAGAC
* *
2065671 TATTCTAAAAGAAAGTTTATGCGGAATTTACAAGATCG
1 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
2065709 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
1 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
2065747 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATC
1 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATC
2065784 CTATACAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (38 bp):
TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
Found at i:2068865 original size:2 final size:2
Alignment explanation
Indices: 2068858--2068893 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2068848 AAACACATCA
2068858 AT AT AT AT 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 AT AT AT AT
2068894 CTTATCTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2079345 original size:15 final size:15
Alignment explanation
Indices: 2079325--2079362 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2079315 GGTAGCAATA
2079325 CAAATAACAACCCT-C
1 CAAATAA-AACCCTAC
*
2079340 CAAATAAAATCCTAC
1 CAAATAAAACCCTAC
2079355 CAAATAAA
1 CAAATAAA
2079363 CTTTCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (15 bp):
CAAATAAAACCCTAC
Found at i:2080894 original size:27 final size:26
Alignment explanation
Indices: 2080859--2080910 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2080849 CTTTGAATAA
*
2080859 TATTCATTTTAATATTTCAATATATTT
1 TATTCATTTTAATATTTAAAT-TATTT
* *
2080886 TATTTATTTTAGTATTTAAATTATT
1 TATTCATTTTAATATTTAAATTATT
2080911 ATCTTGTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTCATTTTAATATTTAAATTATTT
Found at i:2081207 original size:28 final size:28
Alignment explanation
Indices: 2081174--2081240 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
2081164 AAGCCCATTC
* *
2081174 ATATTATTTTTATTTTTAAAAAATATTT
1 ATATTATTTTTATATTTAAAAAATATAT
* * * *
2081202 ATATTATATTCATATTTAATAATTATAT
1 ATATTATTTTTATATTTAAAAAATATAT
2081230 ATATTATTTTT
1 ATATTATTTTT
2081241 TAAAATTTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTATTTTTATATTTAAAAAATATAT
Found at i:2086577 original size:2 final size:2
Alignment explanation
Indices: 2086570--2086605 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2086560 TAATTTAAAC
2086570 AT AT AT AT 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 AT AT AT AT
2086606 TTGGGGTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2088795 original size:26 final size:26
Alignment explanation
Indices: 2088755--2088829 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
2088745 GGATGACGAG
* * *
2088755 GTAAGTTCACGGGCCCAGCTCGCGAT
1 GTAAGTTCGCAGGCCCAGCTCGCAAT
*
2088781 GTAAGTTCGCAGGCCTAGCTCGCAAT
1 GTAAGTTCGCAGGCCCAGCTCGCAAT
**
2088807 GTAAGCTT-GCAGATCCAGCTCGC
1 GTAAG-TTCGCAGGCCCAGCTCGC
2088830 CACAGTCTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 39 0.95
27 2 0.05
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.21
Consensus pattern (26 bp):
GTAAGTTCGCAGGCCCAGCTCGCAAT
Found at i:2098582 original size:34 final size:34
Alignment explanation
Indices: 2098543--2098613 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2098533 TACTTTTATT
2098543 TTCATTCAATTTGCTATCAATTTTACGATTAATG
1 TTCATTCAATTTGCTATCAATTTTACGATTAATG
2098577 TTCATTCAATTTGCTATCAATTTTACGATTAATG
1 TTCATTCAATTTGCTATCAATTTTACGATTAATG
2098611 TTC
1 TTC
2098614 GAAGTTGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (34 bp):
TTCATTCAATTTGCTATCAATTTTACGATTAATG
Found at i:2100997 original size:23 final size:23
Alignment explanation
Indices: 2100954--2100997 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2100944 TTCAACATTT
*
2100954 ATCAATAAATCATGTTTAAACTA
1 ATCAATAAATCATGTTGAAACTA
2100977 ATCACATAAATCATG-TGAAAC
1 ATCA-ATAAATCATGTTGAAAC
2100998 AAGAGGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (23 bp):
ATCAATAAATCATGTTGAAACTA
Found at i:2109024 original size:27 final size:26
Alignment explanation
Indices: 2108966--2109024 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2108956 ACAAATAAAT
* *
2108966 TAAAATTATAAAAATATTTAAAAAAT
1 TAAAATTATAAAAAAATTTAAAAAAC
*
2108992 TCAAAATTATAAAAAAAGTTTATAAAAC
1 T-AAAATTATAAAAAAA-TTTAAAAAAC
2109020 TAAAA
1 TAAAA
2109025 AATGAATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.64
28 9 0.32
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAAATTATAAAAAAATTTAAAAAAC
Found at i:2121687 original size:72 final size:72
Alignment explanation
Indices: 2121570--2121714 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
2121560 ACTTCCACGA
*
2121570 TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCTCAAGTGCTGGAGAGAT
1 TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCACAAGTGCTGGAGAGAT
2121635 ACAAAGC
66 ACAAAGC
* * *
2121642 TGCTAAATTTCATTTAAGTAAAGAATCCCTTTCCATTCAATAAAAATCACAAGTGCTGGAGGGAT
1 TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCACAAGTGCTGGAGAGAT
*
2121707 ACAGAGC
66 ACAAAGC
2121714 T
1 T
2121715 TGCTTGACAC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (72 bp):
TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCACAAGTGCTGGAGAGAT
ACAAAGC
Found at i:2133487 original size:22 final size:21
Alignment explanation
Indices: 2133432--2133487 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2133422 TAAAAAAATA
*
2133432 TAAATTTAAA-AGTTTTATAT
1 TAAATTTAAATAATTTTATAT
* *
2133452 TCAAGTTTATATAATTTTATAAT
1 T-AAATTTAAATAATTTTAT-AT
2133475 TAAATTTAAATAA
1 TAAATTTAAATAA
2133488 AATAATCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 7 0.25
22 17 0.61
23 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (21 bp):
TAAATTTAAATAATTTTATAT
Found at i:2133788 original size:2 final size:2
Alignment explanation
Indices: 2133783--2133807 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2133773 TGAATTAGTG
2133783 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 T
2133808 TAGAAAAAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2137021 original size:3 final size:3
Alignment explanation
Indices: 2137013--2137039 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2137003 TACGCAACAT
2137013 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2137040 CCTCAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2147025 original size:7 final size:7
Alignment explanation
Indices: 2147013--2147038 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2147003 GGGGAGTATA
2147013 TGAGATT
1 TGAGATT
2147020 TGAGATT
1 TGAGATT
2147027 TGAGATT
1 TGAGATT
2147034 TGAGA
1 TGAGA
2147039 ACAGATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (7 bp):
TGAGATT
Found at i:2147414 original size:31 final size:31
Alignment explanation
Indices: 2147331--2147429 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
2147321 AAGAGTCTTC
* *
2147331 AAAAATATTGAAGGGTCTAATTAAAAATTTT
1 AAAAATTTTGAAGGGACTAATTAAAAATTTT
* ** * **
2147362 AAAACTTTT-AAATGACTTAATTAGACTTTTT
1 AAAAATTTTGAAGGGAC-TAATTAAAAATTTT
*
2147393 AAAAATTTTGAAGGGACTAATT-CAAATTTT
1 AAAAATTTTGAAGGGACTAATTAAAAATTTT
*
2147423 CAAAATT
1 AAAAATT
2147430 ATGCATAATA
Statistics
Matches: 51, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
30 15 0.29
31 31 0.61
32 5 0.10
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.38
Consensus pattern (31 bp):
AAAAATTTTGAAGGGACTAATTAAAAATTTT
Found at i:2153518 original size:46 final size:45
Alignment explanation
Indices: 2153412--2153606 Score: 230
Period size: 46 Copynumber: 4.5 Consensus size: 45
2153402 CATATGACCT
*
2153412 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2153455 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
2153501 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** * *
2153538 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
2153584 CTTATCACTTTGTCACTTGATCA
1 CTTATCACTTTGTCACTTGATCA
2153607 AAAGTACTCA
Statistics
Matches: 129, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
37 28 0.22
39 2 0.02
40 3 0.02
41 1 0.01
42 1 0.01
43 10 0.08
44 5 0.04
45 21 0.16
46 58 0.45
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2153539 original size:37 final size:37
Alignment explanation
Indices: 2153498--2153572 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
2153488 GCTGAAGCTA
2153498 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* **
2153535 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
2153572 C
1 C
2153573 TAAAACTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:2153558 original size:83 final size:83
Alignment explanation
Indices: 2153452--2153606 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 83
2153442 AGCTAGGCTA
* *
2153452 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
2153517 TTGATCAGATAAGTGTAG
66 TTGATCAGATAAGTGTAG
**** * *
2153535 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTATCACTTATCACTTTGTCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
2153600 TTGATCA
66 TTGATCA
2153607 AAAGTACTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (83 bp):
CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
TTGATCAGATAAGTGTAG
Found at i:2158715 original size:24 final size:25
Alignment explanation
Indices: 2158679--2158725 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2158669 TCACAATATA
**
2158679 AAAAATTTTAATAA-ATAAAAAATT
1 AAAAATTAAAATAATATAAAAAATT
2158703 AAAAATTAAAATAATATAAAAAA
1 AAAAATTAAAATAATATAAAAAA
2158726 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAATTAAAATAATATAAAAAATT
Found at i:2158736 original size:23 final size:21
Alignment explanation
Indices: 2158678--2158738 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
2158668 ATCACAATAT
*
2158678 AAAAAATTTTAATAAATAAAAA
1 AAAAAAATTTAA-AAATAAAAA
*
2158700 ATTAAAAA-TT-AAAATAATATAA
1 A-AAAAAATTTAAAAATAA-A-AA
2158722 AAAAAAATTTAAAAATA
1 AAAAAAATTTAAAAATA
2158739 TGGACGGGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 6 0.19
21 7 0.23
22 8 0.26
23 10 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAAATTTAAAAATAAAAA
Found at i:2167814 original size:2 final size:2
Alignment explanation
Indices: 2167807--2167834 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2167797 CCAACCTTCA
2167807 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
2167835 TAATGGAAAC
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:2169988 original size:19 final size:21
Alignment explanation
Indices: 2169950--2169990 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
2169940 TTAGTCCACT
*
2169950 ATTTTTATTTTAGAAGATTTA
1 ATTTTTATTTTAGAAAATTTA
2169971 ATTTTT-TTTTA-AAAATTTA
1 ATTTTTATTTTAGAAAATTTA
2169990 A
1 A
2169991 GTCCAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTATTTTAGAAAATTTA
Found at i:2171290 original size:14 final size:14
Alignment explanation
Indices: 2171245--2171295 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2171235 AATCAACCTG
* *
2171245 AACCTTGAATCCTA
1 AACCTCGAACCCTA
* * *
2171259 AACCTCAAACTCTT
1 AACCTCGAACCCTA
2171273 AACCTCGAACCCTA
1 AACCTCGAACCCTA
2171287 AACCT-GAAC
1 AACCTCGAAC
2171296 TTGAACTCCA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.37, C:0.35, G:0.06, T:0.22
Consensus pattern (14 bp):
AACCTCGAACCCTA
Found at i:2174827 original size:154 final size:154
Alignment explanation
Indices: 2174538--2175163 Score: 918
Period size: 154 Copynumber: 4.0 Consensus size: 154
2174528 ATATATTTGA
* * * *
2174538 TGTGTGAATTACATTTGTTTTTATTAAGCTTCTTGTAAACGAGTCTTGTTTTTTTTATAATTCAG
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTG-TTTTTTTATAATTCAG
* *
2174603 TTTACGATTCGTTTTTTCTCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAG
65 TTTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAG
*
2174668 AGTTTTGTGTTGATTTTCAGTGAGT
130 TGTTTTGTGTTGATTTTCAGTGAGT
* *
2174693 TGTGAGAATTACATTTATTTTGATTAAACTTCTTATAAACGAGGCTTGTTTTTTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
*
2174758 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGT
66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
2174823 GTTTTGTGTTGATTTTCAGTGAGT
131 GTTTTGTGTTGATTTTCAGTGAGT
**
2174847 TGTGAGAATTACATTTATTTTTTTTAAGCTTCTTATAAACGAGTCTTG-TTTTTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
*
2174911 TTACGATTCGTTTTTTTCGCTTTGGTGATTTGGTCGATTGGCTGGTTTTTGAAATGTGAATTTAG
66 TTACGATTCG-TTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAG
* * * *
2174976 TGTTTTGTATTGATGTTAAGTGGGT
130 TGTTTTGTGTTGATTTTCAGTGAGT
**
2175001 TGTGAGAATTACATTTCATTTTGATTAAGCTTCTTATAAACGTTTCTTGTTTTTTTATAATTCAG
1 TGTGAGAATTACATTT-ATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAG
* * * * * *
2175066 TTTAGGATTCAATTTTTT-GCTTTGGTTTG-TTTGGTCGATTGGCTGTTTTTTTAAACGTGAATT
65 TTTACGATTC-GTTTTTTCGCTTTGG--TGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATT
* *
2175129 GAGTGTTTCGTGTTG-TTGTTCAGTGAGT
127 TAGTGTTTTGTGTTGATT-TTCAGTGAGT
2175157 TGTGAGA
1 TGTGAGA
2175164 TTGAGTCAAA
Statistics
Matches: 431, Mismatches: 33, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
153 26 0.06
154 237 0.55
155 78 0.18
156 88 0.20
157 2 0.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.50
Consensus pattern (154 bp):
TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
GTTTTGTGTTGATTTTCAGTGAGT
Found at i:2179839 original size:18 final size:17
Alignment explanation
Indices: 2179809--2179850 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2179799 TTATTGTTTG
2179809 TAATGTTTTTATATTATA
1 TAAT-TTTTTATATTATA
*
2179827 TTATTTTTATATATTATA
1 TAATTTTT-TATATTATA
2179845 TAATTT
1 TAATTT
2179851 GTAACCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TAATTTTTTATATTATA
Found at i:2187022 original size:2 final size:2
Alignment explanation
Indices: 2187017--2187057 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2187007 ATTTTTTCAT
2187017 TA TA TA 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 TA TA TA T
2187058 NNNNNNNNNN
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2197719 original size:14 final size:14
Alignment explanation
Indices: 2197697--2197738 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2197687 AACATTCGGT
*
2197697 GTTTCAAAATTTAA
1 GTTTTAAAATTTAA
2197711 GTTTTAAAATTTAA
1 GTTTTAAAATTTAA
* *
2197725 GGTTTAGAATTTAA
1 GTTTTAAAATTTAA
2197739 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (14 bp):
GTTTTAAAATTTAA
Found at i:2197898 original size:14 final size:14
Alignment explanation
Indices: 2197865--2197900 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2197855 AAGGTATAGT
2197865 GGTTCAAAATTCAA
1 GGTTCAAAATTCAA
* *
2197879 GCTTCAAAATTCAG
1 GGTTCAAAATTCAA
2197893 GGTTCAAA
1 GGTTCAAA
2197901 GCTTCATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (14 bp):
GGTTCAAAATTCAA
Found at i:2208921 original size:32 final size:32
Alignment explanation
Indices: 2208868--2208933 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2208858 AGTCTCTGTA
*
2208868 TTTTGATAGAATTTAAGATTTAATCCTTATAC
1 TTTTGATAGAATTGAAGATTTAATCCTTATAC
* * *
2208900 TTTTTATAGAATATGAA-ATTTAGTCCTTGTAC
1 TTTTGATAGAAT-TGAAGATTTAATCCTTATAC
2208932 TT
1 TT
2208934 GAAAGGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 26 0.90
33 3 0.10
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (32 bp):
TTTTGATAGAATTGAAGATTTAATCCTTATAC
Found at i:2220120 original size:75 final size:76
Alignment explanation
Indices: 2219983--2220153 Score: 272
Period size: 75 Copynumber: 2.2 Consensus size: 76
2219973 CATTGTTGTA
* * *
2219983 CTCATTGTTACCATTGTAATAGTTGTTGTTGTTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCT
1 CTCATTGTTACCATTGTAATA--TGTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCT
*
2220048 CAGTGAACATGGC
64 CAGTGAACAAGGC
2220061 CTCATTGTTACCATTGTAATA-GTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
1 CTCATTGTTACCATTGTAATATGTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
2220125 GTGAACAAGGC
66 GTGAACAAGGC
*
2220136 CTCGTTGTTACCATTGTA
1 CTCATTGTTACCATTGTA
2220154 GTTGTTGGTT
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 67 0.76
78 21 0.24
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (76 bp):
CTCATTGTTACCATTGTAATATGTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
GTGAACAAGGC
Found at i:2231714 original size:53 final size:56
Alignment explanation
Indices: 2231653--2231863 Score: 200
Period size: 64 Copynumber: 3.6 Consensus size: 56
2231643 TTACAAGCTG
*
2231653 TTTTATTTTATTATTATTTACTTTTTTATTTATTTT-C-A-A-CCTTTCAT-AATTTT
1 TTTTATTTT-TTATTATTTACTTATTTATTTATTTTCCAATAGCCTTTCATGAA-TTT
2231706 TTTTATTTTTTTATTATTTACTTATTTATTTATTATTCCAATTTCAGCCTTTCATGAATTT
1 TTTTA-TTTTTTATTATTTACTTATTTATTTATT-TTCCAA--T-AGCCTTTCATGAATTT
* *
2231767 TTTTATTTTTTATTATTTACTCATTTATTTATTTATTATTGCAATTTTAGCCTTTCATGAATCT
1 TTTTATTTTTTATTATTTA--C--TTATTTATTTATT-TTCCAA---TAGCCTTTCATGAATTT
*
2231831 TTTTA-TTTTTACTCATTTACTTATTTATTTATT
1 TTTTATTTTTTA-TTATTTACTTATTTATTTATT
2231864 ATTGCCCTAC
Statistics
Matches: 138, Mismatches: 4, Indels: 25
0.83 0.02 0.15
Matches are distributed among these distances:
53 28 0.20
54 6 0.04
55 1 0.01
56 1 0.01
60 28 0.20
61 16 0.12
62 4 0.03
63 6 0.04
64 45 0.33
65 3 0.02
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.64
Consensus pattern (56 bp):
TTTTATTTTTTATTATTTACTTATTTATTTATTTTCCAATAGCCTTTCATGAATTT
Found at i:2231779 original size:60 final size:60
Alignment explanation
Indices: 2231686--2231866 Score: 240
Period size: 64 Copynumber: 2.9 Consensus size: 60
2231676 TTTTATTTAT
*
2231686 TTTCAACCTTTCAT-AATTTTTTTTATTTTTTTATTATTTACTTATTTATTTATTATTCCAA
1 TTTCAGCCTTTCATGAA-TTTTTTTA-TTTTTTATTATTTACTTATTTATTTATTATTCCAA
*
2231747 TTTCAGCCTTTCATGAATTTTTTTATTTTTTATTATTTACTCATTTATTTATTTATTATTGCAA
1 TTTCAGCCTTTCATGAATTTTTTTATTTTTTATTATTTA--C--TTATTTATTTATTATTCCAA
* * *
2231811 TTTTAGCCTTTCATGAATCTTTTTA-TTTTTACTCATTTACTTATTTATTTATTATT
1 TTTCAGCCTTTCATGAATTTTTTTATTTTTTA-TTATTTACTTATTTATTTATTATT
2231867 GCCCTACCTT
Statistics
Matches: 109, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
60 30 0.28
61 21 0.19
62 4 0.04
63 6 0.06
64 48 0.44
ACGTcount: A:0.23, C:0.12, G:0.03, T:0.62
Consensus pattern (60 bp):
TTTCAGCCTTTCATGAATTTTTTTATTTTTTATTATTTACTTATTTATTTATTATTCCAA
Found at i:2232051 original size:19 final size:19
Alignment explanation
Indices: 2232027--2232093 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
2232017 AATTTTTATT
2232027 TTTATTTTAAGTTAACTTA
1 TTTATTTTAAGTTAACTTA
**
2232046 TTTATTTT-A-TTATTTTTA
1 TTTATTTTAAGTTA-ACTTA
2232064 TTTTTATTTTAAGTTAACTTA
1 --TTTATTTTAAGTTAACTTA
*
2232085 TCTATTTTA
1 TTTATTTTA
2232094 TTATTATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 16 0.42
20 8 0.21
21 4 0.11
22 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTATTTTAAGTTAACTTA
Found at i:2232061 original size:39 final size:39
Alignment explanation
Indices: 2232018--2232098 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
2232008 ACATCTTCTA
*
2232018 ATTTTTATTTTTATTTTAAGTTAACTTATTTATTTTATT
1 ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
2232057 ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
1 ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
2232096 ATT
1 ATT
2232099 ATGATTACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (39 bp):
ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
Found at i:2240266 original size:18 final size:18
Alignment explanation
Indices: 2240230--2240274 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2240220 CAAAGTTGTT
*
2240230 TTATAAAAAAAAATTAAA
1 TTATAAAAAAAAATAAAA
2240248 TTATAAAAAATAAA-AAAA
1 TTATAAAAAA-AAATAAAA
*
2240266 TAATAAAAA
1 TTATAAAAA
2240275 TGCAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TTATAAAAAAAAATAAAA
Found at i:2246056 original size:10 final size:10
Alignment explanation
Indices: 2246041--2246078 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2246031 AAAAAAATTC
2246041 TGTTGTTGTT
1 TGTTGTTGTT
2246051 TGTTGTTGTT
1 TGTTGTTGTT
*
2246061 TATTGTTGTT
1 TGTTGTTGTT
2246071 ATGTTGTT
1 -TGTTGTT
2246079 TTGCTACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.05, C:0.00, G:0.26, T:0.68
Consensus pattern (10 bp):
TGTTGTTGTT
Found at i:2246162 original size:18 final size:19
Alignment explanation
Indices: 2246134--2246174 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
2246124 ATTGTTTGGA
2246134 TATTGTATAATTTTTG-TTT
1 TATTGTATAA-TTTTGCTTT
2246153 TATTGT-TAATTTTGCTTT
1 TATTGTATAATTTTGCTTT
2246171 TATT
1 TATT
2246175 TTAGAGGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (19 bp):
TATTGTATAATTTTGCTTT
Found at i:2250342 original size:20 final size:21
Alignment explanation
Indices: 2250317--2250378 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 21
2250307 TAAAATATAA
2250317 ATTTTGAAATTTTT-ACAAA-T
1 ATTTTGAAATTTTTGA-AAATT
2250337 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
2250357 ATTTTGAATTATTTTTAGAAAA
1 ATTTTGAA--ATTTTT-GAAAA
2250379 AGATAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.28
20 14 0.39
21 1 0.03
23 6 0.17
24 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:2250348 original size:19 final size:20
Alignment explanation
Indices: 2250317--2250366 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2250307 TAAAATATAA
2250317 ATTTTGAAATTTTT-ACAAA-T
1 ATTTTG-AATTTTTGA-AAATT
2250337 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
2250357 ATTTTGAATT
1 ATTTTGAATT
2250367 ATTTTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:2250957 original size:21 final size:21
Alignment explanation
Indices: 2250931--2250971 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2250921 CTTAACAGGA
2250931 TAGCTGACGTGGCCAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
*
2250952 TAGCTGATGTGGCCAGTTAA
1 TAGCTGACGTGGCCAGTTAA
2250972 TTTGCCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
TAGCTGACGTGGCCAGTTAAC
Found at i:2251078 original size:21 final size:21
Alignment explanation
Indices: 2251040--2251079 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2251030 CTTCTCTATG
*
2251040 TCTTTCTTCTTTTTCTTCTCA
1 TCTTTCTTCTTTTGCTTCTCA
2251061 TCTTTC-TCTTTATGCTTCT
1 TCTTTCTTCTTT-TGCTTCT
2251080 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.05, C:0.28, G:0.03, T:0.65
Consensus pattern (21 bp):
TCTTTCTTCTTTTGCTTCTCA
Found at i:2251941 original size:11 final size:11
Alignment explanation
Indices: 2251921--2252029 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
2251911 TAAAAATTAA
2251921 AAAAAGTATTTT
1 AAAAA-TATTTT
2251933 AAAAATATTTT
1 AAAAATATTTT
2251944 --AAA-A--TT
1 AAAAATATTTT
* **
2251950 AAAAAAATTAA
1 AAAAATATTTT
2251961 AAAAAGTATTTT
1 AAAAA-TATTTT
* *
2251973 AAAAAGATTTA
1 AAAAATATTTT
*
2251984 AAAAAAATTTT
1 AAAAATATTTT
*
2251995 AAAAATA---A
1 AAAAATATTTT
2252003 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2252015 AAAAGTATTTT
1 AAAAATATTTT
2252026 AAAA
1 AAAA
2252030 TTTAAAAATA
Statistics
Matches: 74, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
6 2 0.03
8 9 0.12
9 6 0.08
11 40 0.54
12 17 0.23
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2251961 original size:52 final size:51
Alignment explanation
Indices: 2251900--2252007 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
2251890 AATTTATTTT
* * *
2251900 AAAAATTAAAATAAA-AATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAA-AAAGAATTAAAAAAAG-ATTTAAAAAAAATTTTAAAAATAA
* **
2251952 AAAAATTAAAAAAAGTATTTTAAAAAGATTTAAAAAAAATTTTAAAAATAA
1 AAAAATTAAAAAAAGAATTAAAAAAAGATTTAAAAAAAATTTTAAAAATAA
2252003 AAAAA
1 AAAAA
2252008 GTATTTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
51 29 0.59
52 20 0.41
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (51 bp):
AAAAATTAAAAAAAGAATTAAAAAAAGATTTAAAAAAAATTTTAAAAATAA
Found at i:2252533 original size:17 final size:17
Alignment explanation
Indices: 2252511--2252550 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2252501 TTCCATTTTC
2252511 TCTTCTTCTTATCTTAT
1 TCTTCTTCTTATCTTAT
* * *
2252528 TCTTCTTTTTCTCTTCT
1 TCTTCTTCTTATCTTAT
2252545 TCTTCT
1 TCTTCT
2252551 ACTGCCCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.68
Consensus pattern (17 bp):
TCTTCTTCTTATCTTAT
Found at i:2253984 original size:14 final size:15
Alignment explanation
Indices: 2253962--2254038 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2253952 CAATCAAACA
2253962 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2253976 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2253991 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2254011 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
2254025 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
2254039 ACTGGAATCA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2254003 original size:20 final size:20
Alignment explanation
Indices: 2253978--2254017 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2253968 AATATTTTCC
*
2253978 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2253998 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2254018 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2254023 original size:34 final size:35
Alignment explanation
Indices: 2253966--2254032 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2253956 CAAACACCAG
*
2253966 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2254001 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2254033 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2263011 original size:21 final size:21
Alignment explanation
Indices: 2262985--2263029 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2262975 AGCTACTTGT
*
2262985 ATAGCAAGT-ATGAGATTTGAA
1 ATAGCAAGTGATGAGAATT-AA
2263006 ATAGCAAGTGATGAGAATTAA
1 ATAGCAAGTGATGAGAATTAA
2263027 ATA
1 ATA
2263030 TGTTATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (21 bp):
ATAGCAAGTGATGAGAATTAA
Found at i:2263564 original size:20 final size:22
Alignment explanation
Indices: 2263539--2263578 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2263529 GAATTATCGT
2263539 TTTGA-TATGTTTT-AATTGTA
1 TTTGATTATGTTTTGAATTGTA
*
2263559 TTTGATTGTGTTTTGAATTG
1 TTTGATTATGTTTTGAATTG
2263579 GTTGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTGATTATGTTTTGAATTGTA
Found at i:2271744 original size:3 final size:3
Alignment explanation
Indices: 2271736--2271768 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2271726 AAACTGTGGG
*
2271736 TCT TCT TCT TCT TCT TCT TC- TCT TCC TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2271769 GCGTGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:2272870 original size:34 final size:34
Alignment explanation
Indices: 2272822--2272886 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2272812 TTACTATTCA
2272822 ATTTAAAACAAAATAATAAT-ATTAATTTAAAATG
1 ATTTAAAACAAAATAA-AATAATTAATTTAAAATG
** *
2272856 ATTTAAAAGTAAATAAAATAATTAGTTTAAA
1 ATTTAAAACAAAATAAAATAATTAATTTAAA
2272887 TATATAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 24 0.89
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (34 bp):
ATTTAAAACAAAATAAAATAATTAATTTAAAATG
Found at i:2289077 original size:19 final size:20
Alignment explanation
Indices: 2289036--2289077 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2289026 ATTTCTATGC
* *
2289036 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
2289056 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
2289075 CAT
1 CAT
2289078 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:2289905 original size:14 final size:15
Alignment explanation
Indices: 2289888--2289916 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2289878 ATATAGTAGC
2289888 AAAACAG-AAGAAAA
1 AAAACAGCAAGAAAA
2289902 AAAACAGCAAGAAAA
1 AAAACAGCAAGAAAA
2289917 CAACAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAACAGCAAGAAAA
Found at i:2296139 original size:9 final size:9
Alignment explanation
Indices: 2296125--2296200 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
2296115 AAATAAAATT
2296125 AAAATTATA
1 AAAATTATA
2296134 AAAATT-TA
1 AAAATTATA
2296142 AAAA-TATTA
1 AAAATTA-TA
2296151 TAAAA-TATA
1 -AAAATTATA
* *
2296160 AAAAATCTA
1 AAAATTATA
*
2296169 ATAAATTGTAA
1 A-AAATTAT-A
*
2296180 AAAAATATA
1 AAAATTATA
*
2296189 AAAATAATA
1 AAAATTATA
2296198 AAA
1 AAA
2296201 CTTGTTTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
7 1 0.02
8 10 0.19
9 25 0.46
10 16 0.30
11 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:2296150 original size:19 final size:18
Alignment explanation
Indices: 2296125--2296193 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
2296115 AAATAAAATT
2296125 AAAATTATAAAAATTTAA
1 AAAATTATAAAAATTTAA
*
2296143 AAATATTAT-AAAATATAA
1 AAA-ATTATAAAAATTTAA
*
2296161 AAAATCTA-ATAAATTGTAA
1 AAAAT-TATAAAAATT-TAA
*
2296180 AAAAATATAAAAAT
1 AAAATTATAAAAAT
2296194 AATAAAACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 2 0.05
18 22 0.54
19 17 0.41
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAATTTAA
Found at i:2296180 original size:26 final size:25
Alignment explanation
Indices: 2296116--2296181 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
2296106 CTCCTACAAA
* *
2296116 AATAAAATTAAAATTATAAAAATTT
1 AATAAATTTAAAATTATAAAAATCT
*
2296141 AA-AAATATTATAAAATATAAAAAATCT
1 AATAAAT-TTA-AAATTAT-AAAAATCT
2296168 AATAAATTGTAAAA
1 AATAAATT-TAAAA
2296182 AAATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 6 0.18
27 13 0.39
28 6 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
AATAAATTTAAAATTATAAAAATCT
Found at i:2298215 original size:16 final size:18
Alignment explanation
Indices: 2298196--2298233 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2298186 TTAATTTTTT
2298196 TAAATTA-TAAAA-AATA
1 TAAATTATTAAAATAATA
2298212 TAAATTATTAAAATAATA
1 TAAATTATTAAAATAATA
2298230 -AAAT
1 TAAAT
2298234 CATATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATTATTAAAATAATA
Found at i:2302096 original size:2 final size:2
Alignment explanation
Indices: 2302089--2302116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2302079 TGCATACATA
2302089 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
2302117 TGTTTTGATA
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:2314354 original size:19 final size:19
Alignment explanation
Indices: 2314309--2314355 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
2314299 TTTTCTTTTT
2314309 CATAGTTTCTGCTTTGAGTA
1 CATAGTTT-TGCTTTGAGTA
2314329 -A-AGTTTTGACTTTGA-TA
1 CATAGTTTTG-CTTTGAGTA
2314346 CATAGTTTTG
1 CATAGTTTTG
2314356 TAGGCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (19 bp):
CATAGTTTTGCTTTGAGTA
Done.