Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 87 of 120
Found at i:25159783 original size:17 final size:19
Alignment explanation
Indices: 25159763--25159803 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
25159753 TTTATATTTG
25159763 TTTTGAAAA-TATAT-AAA
1 TTTTGAAAATTATATAAAA
*
25159780 TTTTGAAAATTTTATAAAA
1 TTTTGAAAATTATATAAAA
25159799 TTTTG
1 TTTTG
25159804 TATTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 4 0.19
19 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTTGAAAATTATATAAAA
Found at i:25179440 original size:88 final size:88
Alignment explanation
Indices: 25179343--25179530 Score: 238
Period size: 88 Copynumber: 2.1 Consensus size: 88
25179333 ATATAACATA
* * *
25179343 TGGTACCTAAACTTTATACTTTTTCTT-AATTTGATACTTAAACTTTTT-GTCCAATTTGGTA-C
1 TGGTACCTAAACTTGATACTTTTT-TTAAAGTTGATACTTAAACTTTTTGGTCAAATTTGGTACC
*
25179405 TCAAACTTGACATTTTTTTCCTAATT
65 T-AAACTTGAC-TCTTTTTCCTAATT
*
25179431 TGGTACCTAAACTTGATACTTTTTTTAAAGTTGGTACTTAAACTTTTTGGGGTCAAATTTGGTAC
1 TGGTACCTAAACTTGATACTTTTTTTAAAGTTGATACTTAAACTTTTT--GGTCAAATTTGGTAC
* **
25179496 CTGAACTTGACTCTTTTTCCTTTTT
64 CTAAACTTGACTCTTTTTCCTAATT
25179521 TGGTACCTAA
1 TGGTACCTAA
25179531 TTTTTTTTAA
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
87 2 0.02
88 42 0.48
90 21 0.24
91 20 0.23
92 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.47
Consensus pattern (88 bp):
TGGTACCTAAACTTGATACTTTTTTTAAAGTTGATACTTAAACTTTTTGGTCAAATTTGGTACCT
AAACTTGACTCTTTTTCCTAATT
Found at i:25179454 original size:33 final size:32
Alignment explanation
Indices: 25179384--25179475 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 32
25179374 TGATACTTAA
*
25179384 ACTTTTTGTCCAATTTGGTACTCAAACTTGAC
1 ACTTTTTTTCCAATTTGGTACTCAAACTTGAC
*
25179416 A-TTTTTTTCCTAATTTGGTAC-CTAAACTTGAT
1 ACTTTTTTTCC-AATTTGGTACTC-AAACTTGAC
* * *
25179448 ACTTTTTTT-AAAGTTGGTACTTAAACTT
1 ACTTTTTTTCCAATTTGGTACTCAAACTT
25179476 TTTGGGGTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 24 0.47
32 20 0.39
33 7 0.14
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (32 bp):
ACTTTTTTTCCAATTTGGTACTCAAACTTGAC
Found at i:25180625 original size:48 final size:48
Alignment explanation
Indices: 25180554--25180649 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
25180544 ATCCATAAAG
25180554 ATACTGATCTATATCAAAAGGGATGCAACTGAAGATTTTCTTTCCTCT
1 ATACTGATCTATATCAAAAGGGATGCAACTGAAGATTTTCTTTCCTCT
25180602 ATACTGATCTATATCAAAAGGGATGCAACTGAAGATTTTCTTTCCTCT
1 ATACTGATCTATATCAAAAGGGATGCAACTGAAGATTTTCTTTCCTCT
25180650 TGCTTTGATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (48 bp):
ATACTGATCTATATCAAAAGGGATGCAACTGAAGATTTTCTTTCCTCT
Found at i:25182622 original size:21 final size:20
Alignment explanation
Indices: 25182584--25182622 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
25182574 GTTACCCTCA
*
25182584 TAGGATATCTTTGATCTCTT
1 TAGGATATATTTGATCTCTT
*
25182604 TAGGATAATATTTGTTCTC
1 TAGGAT-ATATTTGATCTC
25182623 CCAATATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (20 bp):
TAGGATATATTTGATCTCTT
Found at i:25183465 original size:14 final size:14
Alignment explanation
Indices: 25183446--25183472 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25183436 TACAATCAGT
25183446 AAAAATGATAAAAC
1 AAAAATGATAAAAC
25183460 AAAAATGATAAAA
1 AAAAATGATAAAA
25183473 GTTAATTGTT
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:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAATGATAAAAC
Found at i:25185527 original size:2 final size:2
Alignment explanation
Indices: 25185520--25185549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25185510 TATATTAATG
25185520 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
25185550 TAAAGTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25185695 original size:39 final size:34
Alignment explanation
Indices: 25185616--25185695 Score: 81
Period size: 39 Copynumber: 2.2 Consensus size: 34
25185606 TGTAAAATAA
*
25185616 ATAT-TAATTTATTTATTATTTAAGTAAATAGAT
1 ATATATAATTTATTTATTATTTAACTAAATAGAT
* *
25185649 ATTTATAATTTATTAATATTATTACTAACTAATATATAT
1 ATATATAATTTATT--TATTATT--TAACTAA-ATAGAT
25185688 ATATATAA
1 ATATATAA
25185696 AAGAATAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
33 3 0.08
34 9 0.24
36 7 0.19
38 6 0.16
39 12 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (34 bp):
ATATATAATTTATTTATTATTTAACTAAATAGAT
Found at i:25187502 original size:12 final size:11
Alignment explanation
Indices: 25187459--25187511 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
25187449 TTTTACTTTG
*
25187459 AAATTAAATTT
1 AAATTAATTTT
**
25187470 ATTTTAATTTT
1 AAATTAATTTT
*
25187481 AAATTTATTTT
1 AAATTAATTTT
25187492 AAATTCAATTTT
1 AAATT-AATTTT
25187504 AAAATTAA
1 -AAATTAA
25187512 ATTTGAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 21 0.64
12 7 0.21
13 5 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:25187504 original size:17 final size:16
Alignment explanation
Indices: 25187459--25187502 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
25187449 TTTTACTTTG
25187459 AAATTAAATTTATTTT
1 AAATTAAATTTATTTT
*
25187475 AATTTTAAATTTATTTT
1 AA-ATTAAATTTATTTT
*
25187492 AAATTCAATTT
1 AAATTAAATTT
25187503 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTAAATTTATTTT
Found at i:25187539 original size:29 final size:29
Alignment explanation
Indices: 25187462--25187539 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
25187452 TACTTTGAAA
* * *
25187462 TTAAATT-TATTTTAATTTTAAATTTATT
1 TTAAATTCAATTTTAATATTAAATTTAAT
*
25187490 TTAAATTCAATTTTAAAATTAAATTTGAAT
1 TTAAATTCAATTTTAATATTAAATTT-AAT
* *
25187520 TTAACTTGAA-TTTAATATTA
1 TTAAATTCAATTTTAATATTA
25187540 TTATAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 7 0.17
29 24 0.59
30 10 0.24
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
TTAAATTCAATTTTAATATTAAATTTAAT
Found at i:25188284 original size:13 final size:13
Alignment explanation
Indices: 25188255--25188309 Score: 78
Period size: 13 Copynumber: 4.4 Consensus size: 13
25188245 ATATTGAATG
25188255 TTAATAATATT--
1 TTAATAATATTAA
25188266 TTAATAATATTAA
1 TTAATAATATTAA
25188279 TTAATAATATTAA
1 TTAATAATATTAA
* *
25188292 TTAATATTAATAA
1 TTAATAATATTAA
25188305 TTAAT
1 TTAAT
25188310 TTTTTTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.28
13 29 0.73
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATAATATTAA
Found at i:25188652 original size:19 final size:19
Alignment explanation
Indices: 25188628--25188664 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
25188618 TGTTTTAAAA
25188628 TTTTCCAGATCTGGGTTTC
1 TTTTCCAGATCTGGGTTTC
25188647 TTTTCCAGATCTGGGTTT
1 TTTTCCAGATCTGGGTTT
25188665 AGTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.49
Consensus pattern (19 bp):
TTTTCCAGATCTGGGTTTC
Found at i:25189391 original size:30 final size:30
Alignment explanation
Indices: 25189357--25189577 Score: 236
Period size: 30 Copynumber: 7.4 Consensus size: 30
25189347 AACTGTTCAG
* *
25189357 AAATTATATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTGACCCTAAAACTTTCTAA
** *
25189387 AAATTACATTTCAACCCTAAAATTTTCCT-A
1 AAATTACATTTTGACCCTAAAACTTT-CTAA
* * *
25189417 AAATTATATTTTAACTCTAAAACTTTCTAA
1 AAATTACATTTTGACCCTAAAACTTTCTAA
*
25189447 AAATTACATTTTGACCCTAAAACTTT-TCCA
1 AAATTACATTTTGACCCTAAAACTTTCT-AA
*
25189477 AAATTACATTTTGACCCTAAAACTTT-TCCA
1 AAATTACATTTTGACCCTAAAACTTTCT-AA
* *
25189507 AAATTATATTTTAACCCTAAAACTTT-TCAA
1 AAATTACATTTTGACCCTAAAACTTTCT-AA
* *
25189537 AAATTGCATTTTGACCCCAAAACTTTC-AA
1 AAATTACATTTTGACCCTAAAACTTTCTAA
25189566 AAATTACCATTT
1 AAATTA-CATTT
25189578 ACCCCCGAAT
Statistics
Matches: 165, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
29 10 0.06
30 153 0.93
31 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTGACCCTAAAACTTTCTAA
Found at i:25189439 original size:60 final size:60
Alignment explanation
Indices: 25189357--25189577 Score: 286
Period size: 60 Copynumber: 3.7 Consensus size: 60
25189347 AACTGTTCAG
* *
25189357 AAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTCAACCCTAAAA-TTTTCCTA
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCC-A
* * * * *
25189417 AAATTATATTTTAACTCTAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCA
* * * *
25189477 AAATTACATTTTGACCCTAAAACTTT-TCCAAAATTATATTTTAACCCTAAAACTTTTCAA
1 AAATTACATTTTGACCCCAAAACTTTCT-AAAAATTACATTTTAACCCTAAAACTTTTCCA
*
25189537 AAATTGCATTTTGACCCCAAAACTTTC-AAAAATTACCATTT
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTA-CATTT
25189578 ACCCCCGAAT
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
59 8 0.06
60 127 0.90
61 6 0.04
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (60 bp):
AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCA
Found at i:25189510 original size:90 final size:89
Alignment explanation
Indices: 25189342--25189577 Score: 325
Period size: 90 Copynumber: 2.6 Consensus size: 89
25189332 GCTGCCAAGT
* * *
25189342 CCCT-AAACTGTTCAGAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTCAACCCTA
1 CCCTAAAACTTTTCAAAAATTACATTTTGACCCCAAAACTTTC-AAAAATTACATTTCAACCCTA
25189406 AAATTTTCCTAAAATTATATTTTAA
65 AAATTTTCCTAAAATTATATTTTAA
* * * **
25189431 CTCTAAAAC-TTTCTAAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCT
1 CCCTAAAACTTTTC-AAAAATTACATTTTGACCCCAAAAC-TTTCAAAAATTACATTTCAACCCT
25189495 AAAACTTTTCC-AAAATTATATTTTAA
64 AAAA-TTTTCCTAAAATTATATTTTAA
*
25189521 CCCTAAAACTTTTCAAAAATTGCATTTTGACCCCAAAACTTTCAAAAATTACCATTT
1 CCCTAAAACTTTTCAAAAATTACATTTTGACCCCAAAACTTTCAAAAATTA-CATTT
25189578 ACCCCCGAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
89 17 0.13
90 98 0.76
91 14 0.11
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (89 bp):
CCCTAAAACTTTTCAAAAATTACATTTTGACCCCAAAACTTTCAAAAATTACATTTCAACCCTAA
AATTTTCCTAAAATTATATTTTAA
Found at i:25189609 original size:90 final size:87
Alignment explanation
Indices: 25189342--25189605 Score: 318
Period size: 90 Copynumber: 3.0 Consensus size: 87
25189332 GCTGCCAAGT
* * *
25189342 CCCT-AAACTGTTCAGAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTCAACCCTA
1 CCCTAAAACTTTTCAAAAATTACATTTTGACCCCAAAACTTTC-AAAAATTACATTT-AACCCTA
25189406 AAATTTTCCTAAAATTATATTTTAA
64 AAATTTTCC-AAAATTATATTTTAA
* * * *
25189431 CTCTAAAAC-TTTCTAAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCT
1 CCCTAAAACTTTTC-AAAAATTACATTTTGACCCCAAAAC-TTTCAAAAATTACA-TTTAACCCT
25189495 AAAACTTTTCCAAAATTATATTTTAA
63 AAAA-TTTTCCAAAATTATATTTTAA
* ***
25189521 CCCTAAAACTTTTCAAAAATTGCATTTTGACCCCAAAACTTTCAAAAATTACCATTT-ACCCCCG
1 CCCTAAAACTTTTCAAAAATTACATTTTGACCCCAAAACTTTCAAAAATTA-CATTTAACCCTAA
* *
25189585 AATCTTCCAAAATTCTATTTT
65 AATTTTCCAAAATTATATTTT
25189606 TTTACCCTAA
Statistics
Matches: 152, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
87 17 0.11
88 6 0.04
89 20 0.13
90 92 0.61
91 17 0.11
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (87 bp):
CCCTAAAACTTTTCAAAAATTACATTTTGACCCCAAAACTTTCAAAAATTACATTTAACCCTAAA
ATTTTCCAAAATTATATTTTAA
Found at i:25189661 original size:28 final size:27
Alignment explanation
Indices: 25189630--25189721 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 27
25189620 ACCAAAATTA
*
25189630 CCATTTTACCCCCAAACTTCCCTAAATC
1 CCATTTTA-CCCCAAACTTACCTAAATC
* ** * * *
25189658 CCATTTTTAACCCTAATTTTATCAAAATTA
1 CCA-TTTT-ACCCCAAACTTACCTAAA-TC
*
25189688 CCATTTTACCCCAAACTTTCCTAAATC
1 CCATTTTACCCCAAACTTACCTAAATC
25189715 CCATTTT
1 CCATTTT
25189722 TAACCTCGAT
Statistics
Matches: 47, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
27 8 0.17
28 15 0.32
29 19 0.40
30 5 0.11
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (27 bp):
CCATTTTACCCCAAACTTACCTAAATC
Found at i:25189759 original size:30 final size:29
Alignment explanation
Indices: 25189719--25189810 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 29
25189709 TAAATCCCAT
* *
25189719 TTTTAACCTCGATTTTACCAAAATTTACCG
1 TTTTGACCTCGATTTT-CCAAAATTTACCA
* *
25189749 TTTTGCCCTCGAACTTTCCAAAATTT--CA
1 TTTTGACCTCG-ATTTTCCAAAATTTACCA
25189777 TTTTGACCTCGATTTTGCCAAAATTTACCA
1 TTTTGACCTCGATTTT-CCAAAATTTACCA
25189807 TTTT
1 TTTT
25189811 ACCCCCCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.08
28 20 0.38
30 24 0.46
31 4 0.08
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (29 bp):
TTTTGACCTCGATTTTCCAAAATTTACCA
Found at i:25189859 original size:59 final size:58
Alignment explanation
Indices: 25189565--25189873 Score: 283
Period size: 58 Copynumber: 5.3 Consensus size: 58
25189555 AAAACTTTCA
* * * * *
25189565 AAAATTACCA-TTTACCCCCGAATC-TTCCAAAATTCTATTTTTTTACCCTAATTTCACC
1 AAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCA--TTTTTACCCTGATTTTACC
* * * * *
25189623 AAAATTACCATTTTA-CCCCCAAACTTCCCTAAATCCCATTTTTAACCCTAATTTTATC
1 AAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTT-ACCCTGATTTTACC
* * *
25189681 AAAATTACCATTTTA--CCCCAAACTTTCCTAAATCCCATTTTTAACCTCGATTTTACC
1 AAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTTACCCT-GATTTTACC
* * * * * * *
25189738 AAAATTTACCGTTTT-GCCCTCGAACTTTCCAAAATTTCATTTTGA-CCTCGATTTTGCC
1 AAAA-TTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTTACCCT-GATTTTACC
* *
25189796 AAAATTTACCATTTTACCCCCCAAACTTTCC-AAATTCCATTTTTAGCCCTGATTTCACA
1 AAAA-TTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTTA-CCCTGATTTTACC
*
25189855 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
25189874 AAAAAGCCCA
Statistics
Matches: 211, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
56 4 0.02
57 42 0.20
58 105 0.50
59 57 0.27
60 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTTACCCTGATTTTACC
Found at i:25201653 original size:46 final size:46
Alignment explanation
Indices: 25201603--25201745 Score: 109
Period size: 46 Copynumber: 3.1 Consensus size: 46
25201593 TTGAAGTAAG
25201603 AGTAAGATGAAGCATCAACGTCATTTTCCTATCCTCTTGAAATTGA
1 AGTAAGATGAAGCATCAACGTCATTTTCCTATCCTCTTGAAATTGA
* * * * * * * * *
25201649 AGTAAAGCTGGA-TAACAA-G-CCTTCGTCCT-T-CTGAAATTG-AAGTAA
1 AGT-AAGATGAAGCATCAACGTCATT-TTCCTATCCT---CTTGAAATTGA
25201694 GAGTAAGATGAAGCATCAACGTCATTTTCCTATCCTCTTGAAATTGA
1 -AGTAAGATGAAGCATCAACGTCATTTTCCTATCCTCTTGAAATTGA
25201741 AGTAA
1 AGTAA
25201746 AGCTGGATAA
Statistics
Matches: 67, Mismatches: 18, Indels: 24
0.61 0.17 0.22
Matches are distributed among these distances:
43 2 0.03
44 4 0.06
45 15 0.22
46 25 0.37
47 15 0.22
48 4 0.06
49 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (46 bp):
AGTAAGATGAAGCATCAACGTCATTTTCCTATCCTCTTGAAATTGA
Found at i:25201684 original size:40 final size:40
Alignment explanation
Indices: 25201640--25201785 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
25201630 CCTATCCTCT
25201640 TGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTC
1 TGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTC
* * *
25201680 TGAAATTGAAGTAAGAG-TAAGATGAAGCATCAACGTCATT-TTCCTATCCTC
1 TGAAATTGAAGTAA-AGCT-GGAT--A--A-CAA-G-CCTTCGTCC--T--TC
25201731 TTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTC
1 -TGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTC
25201772 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
25201786 GAGTAAGATG
Statistics
Matches: 84, Mismatches: 6, Indels: 32
0.69 0.05 0.26
Matches are distributed among these distances:
40 29 0.35
41 7 0.08
43 2 0.02
44 3 0.04
45 5 0.06
46 6 0.07
47 5 0.06
48 3 0.04
49 2 0.02
51 7 0.08
52 15 0.18
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (40 bp):
TGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTC
Found at i:25201689 original size:92 final size:92
Alignment explanation
Indices: 25201527--25202159 Score: 904
Period size: 92 Copynumber: 6.9 Consensus size: 92
25201517 AGATCAATCA
*
25201527 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATAACAAGCCTTCGTCCTTCTGAA
1 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
*
25201592 GTTGAAGTAAGAGTAAGATGAAGCATC
66 ATTGAAGTAAGAGTAAGATGAAGCATC
25201619 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
1 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
25201684 ATTGAAGTAAGAGTAAGATGAAGCATC
66 ATTGAAGTAAGAGTAAGATGAAGCATC
25201711 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
1 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
25201776 ATTGAAGTAAGAGTAAGATGAAGCATC
66 ATTGAAGTAAGAGTAAGATGAAGCATC
* * **
25201803 AATGTCATTTTCTTATCCTCTTGAAATTGAAGTAAAGCTATATAACAAGCCTTCGTCCTTCTGAA
1 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
25201868 ATTGAAGTAAGAGTAAGATGAAGCATC
66 ATTGAAGTAAGAGTAAGATGAAGCATC
** **
25201895 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAATCTTTAT-CTCTCTGA
1 AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCT-TCTGA
* *
25201959 AATTGAAGTAAGAGCAAGATGAAACA-C
65 AATTGAAGTAAGAGTAAGATGAAGCATC
* * * * * * *
25201986 TGACATC-TTTTCCTAACCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCTTTTGTCCCTCTGA
1 -AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGA
*
25202050 AATTGAAGTAAGAGCAAGATGAAGCA-C
65 AATTGAAGTAAGAGTAAGATGAAGCATC
* * * * * **
25202077 --CGACATCTTTCCTATCCTCTTGAAGTT-ATAGTAAAGATGGATATCAAGTCTTTAT-CTCTCT
1 AACGTCAT-TTTCCTATCCTCTTGAAATTGA-AGTAAAGCTGGATAACAAGCCTTCGTCCT-TCT
* *
25202138 AAAATTGAAGTAAGAGGAAGAT
63 GAAATTGAAGTAAGAGTAAGAT
25202160 AAACCCCGAC
Statistics
Matches: 495, Mismatches: 39, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
88 2 0.00
89 3 0.01
90 61 0.12
91 77 0.16
92 352 0.71
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (92 bp):
AACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAA
ATTGAAGTAAGAGTAAGATGAAGCATC
Found at i:25202465 original size:6 final size:6
Alignment explanation
Indices: 25202444--25202504 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
25202434 TACTTTGAAA
* * * *
25202444 TTAAAT TT-ATT TTAAAT TTAAAT TT-ATT TTAAA- TTCAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
25202489 TTAAAT TTGAAT TTAA
1 TTAAAT TTAAAT TTAA
25202505 CTTGAATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
5 12 0.29
6 30 0.71
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:25202485 original size:11 final size:11
Alignment explanation
Indices: 25202441--25202501 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
25202431 TTTTACTTTG
25202441 AAATTAAATTT
1 AAATTAAATTT
**
25202452 ATTTTAAATTT
1 AAATTAAATTT
* *
25202463 AAATTTATTTT
1 AAATTAAATTT
*
25202474 AAATTCAATTT
1 AAATTAAATTT
25202485 AAAATTAAATTT
1 -AAATTAAATTT
*
25202497 GAATT
1 AAATT
25202502 TAACTTGAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 29 0.74
12 10 0.26
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:25202485 original size:16 final size:16
Alignment explanation
Indices: 25202441--25202485 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
25202431 TTTTACTTTG
25202441 AAATTAAATTTATTTT
1 AAATTAAATTTATTTT
25202457 AAATTTAAATTTATTTT
1 AAA-TTAAATTTATTTT
*
25202474 AAATTCAATTTA
1 AAATTAAATTTA
25202486 AAATTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTAAATTTATTTT
Found at i:25203263 original size:13 final size:13
Alignment explanation
Indices: 25203245--25203288 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
25203235 TAATAATGTT
25203245 TTAATAATATTAA
1 TTAATAATATTAA
*
25203258 TTAATAGTATTAA
1 TTAATAATATTAA
* *
25203271 TTAATATTAATAA
1 TTAATAATATTAA
25203284 TTAAT
1 TTAAT
25203289 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAATAATATTAA
Found at i:25204123 original size:60 final size:59
Alignment explanation
Indices: 25204024--25204247 Score: 258
Period size: 60 Copynumber: 3.8 Consensus size: 59
25204014 CCCTAAACTG
* * * *
25204024 TTCAAAAATTATATTTTGACCCTAAAAACTTTCTAAAAATTACATTTCGACCCTAAAATT
1 TTCAAAAATTATATTTTAACCCCAAAAA-TTTCTAAAAATTACATTTTGACCCCAAAATT
*
25204084 TTCTTAAAATTATATTTTAACCCCAAAAATTTCTAAAAATTACATTTTGACCCCAAAACTT
1 TTC-AAAAATTATATTTTAACCCCAAAAATTTCTAAAAATTACATTTTGACCCCAAAA-TT
* * * *
25204145 TTCCAAAATTATATTTTGACCCCAAAACTTT-TCCAAAATTACATTTTGACCCCAAAATT
1 TTCAAAAATTATATTTTAACCCCAAAAATTTCT-AAAAATTACATTTTGACCCCAAAATT
* ** *
25204204 TCCAAAAATTGCATTTTAA-CCCAAAACTTTC--AAAATTACCATTT
1 TTCAAAAATTATATTTTAACCCCAAAAATTTCTAAAAATTA-CATTT
25204248 ACCCCCGAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
56 7 0.05
57 5 0.03
58 11 0.08
59 17 0.12
60 78 0.54
61 27 0.19
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (59 bp):
TTCAAAAATTATATTTTAACCCCAAAAATTTCTAAAAATTACATTTTGACCCCAAAATT
Found at i:25204141 original size:29 final size:30
Alignment explanation
Indices: 25204018--25204247 Score: 231
Period size: 30 Copynumber: 7.7 Consensus size: 30
25204008 GTAGGTCCCT
* *
25204018 AAACTGTTC-AAAAATTATATTTTGACCCTAA
1 AAACT-TTCTAAAAATTACATTTTGACCC-CA
* *
25204049 AAACTTTCTAAAAATTACATTTCGACCCTA
1 AAACTTTCTAAAAATTACATTTTGACCCCA
* * * *
25204079 AAATTTTCTTAAAATTATATTTTAACCCCA
1 AAACTTTCTAAAAATTACATTTTGACCCCA
*
25204109 AAAATTTCTAAAAATTACATTTTGACCCCA
1 AAACTTTCTAAAAATTACATTTTGACCCCA
* *
25204139 AAACTTT-TCCAAAATTATATTTTGACCCCA
1 AAACTTTCT-AAAAATTACATTTTGACCCCA
*
25204169 AAACTTT-TCCAAAATTACATTTTGACCCCA
1 AAACTTTCT-AAAAATTACATTTTGACCCCA
* * *
25204199 AAA-TTTCCAAAAATTGCATTTT-AACCCA
1 AAACTTTCTAAAAATTACATTTTGACCCCA
25204227 AAACTTTC--AAAATTACCATTT
1 AAACTTTCTAAAAATTA-CATTT
25204248 ACCCCCGAAT
Statistics
Matches: 172, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.03
28 13 0.08
29 20 0.12
30 111 0.65
31 22 0.13
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTTCTAAAAATTACATTTTGACCCCA
Found at i:25204246 original size:28 final size:27
Alignment explanation
Indices: 25204018--25204376 Score: 172
Period size: 30 Copynumber: 12.3 Consensus size: 27
25204008 GTAGGTCCCT
* *
25204018 AAACTGTTCAAAAATTATATTTTGACCCTAA
1 AAACT-TTC-AAAATTACATTTT-ACCC-CA
* *
25204049 AAACTTTCTAAAAATTACATTTCGACCCTA
1 AAACTTTC--AAAATTACATTT-TACCCCA
* *
25204079 AAATTTTCTTAAAATTATATTTTAACCCCA
1 AAACTTTC--AAAATTACATTTT-ACCCCA
*
25204109 AAAATTTCTAAAAATTACATTTTGACCCCA
1 AAACTTTC--AAAATTACATTTT-ACCCCA
*
25204139 AAACTTTTCCAAAATTATATTTTGACCCCA
1 AAAC-TTT-CAAAATTACATTTT-ACCCCA
25204169 AAACTTTTCCAAAATTACATTTTGACCCCA
1 AAAC-TTT-CAAAATTACATTTT-ACCCCA
* *
25204199 AAA-TTTCCAAAAATTGCATTTTAACCCA
1 AAACTTT-C-AAAATTACATTTTACCCCA
*
25204227 AAACTTTCAAAATTACCA-TTTACCCCCG
1 AAACTTTCAAAATTA-CATTTTA-CCCCA
* *
25204255 AATCTTCCAAAATT-CTATTTTTTA-CCC-
1 AAACTTTCAAAATTAC-A--TTTTACCCCA
* *
25204282 TAA-TTTCACCAAAATTACCATTTTACCCCT
1 AAACTTT---CAAAATTA-CATTTTACCCCA
* ** * *
25204312 AAACTTTCCTAAATCCCATTTTAACCCT
1 AAACTTT-CAAAATTACATTTTACCCCA
** *
25204340 AATTTTATCAAAATTACCATTTTACCCCC
1 AAACTT-TCAAAATTA-CATTTTACCCCA
25204369 AAACTTTC
1 AAACTTTC
25204377 CTAAATCCCA
Statistics
Matches: 266, Mismatches: 39, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.01
27 12 0.05
28 61 0.23
29 46 0.17
30 115 0.43
31 28 0.11
32 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (27 bp):
AAACTTTCAAAATTACATTTTACCCCA
Found at i:25204297 original size:57 final size:58
Alignment explanation
Indices: 25204234--25204542 Score: 301
Period size: 58 Copynumber: 5.3 Consensus size: 58
25204224 CCAAAACTTT
* *
25204234 CAAAATTACCA-TTTACCCCCGAATC-TTCCAAAATTCTATTTTTTACCCTAATTTCAC
1 CAAAATTACCATTTTACCCCCGAAACTTTCCAAAATTCTA-TTTTTACCCTGATTTCAC
* * * * * * * *
25204291 CAAAATTACCATTTTA-CCCCTAAACTTTCCTAAATCCCATTTTAACCCTAATTTTAT
1 CAAAATTACCATTTTACCCCCGAAACTTTCCAAAATTCTATTTTTACCCTGATTTCAC
* * * *
25204348 CAAAATTACCATTTTACCCCC-AAACTTTCCTAAATCCCATTTTTAACCTCGATTTCAC
1 CAAAATTACCATTTTACCCCCGAAACTTTCCAAAATTCTATTTTTACCCT-GATTTCAC
* * **
25204406 CAAAATTTACCATTTTACCCCCG-AACTTTTCAAAATT-TCATTTTGA-CCTCGATTTTGC
1 CAAAA-TTACCATTTTACCCCCGAAACTTTCCAAAATTCT-ATTTTTACCCT-GATTTCAC
* *
25204464 CAAAATTTACCATTTTACCCCCCAAACTTTCC-AAATTCTATTTTTAGCCTTGATTTCAC
1 CAAAA-TTACCATTTTACCCCCGAAACTTTCCAAAATTCTATTTTTA-CCCTGATTTCAC
* *
25204523 AAAAATTACCATTTTGCCCC
1 CAAAATTACCATTTTACCCC
25204543 AAAAAGCCCA
Statistics
Matches: 213, Mismatches: 28, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
57 75 0.35
58 85 0.40
59 51 0.24
60 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (58 bp):
CAAAATTACCATTTTACCCCCGAAACTTTCCAAAATTCTATTTTTACCCTGATTTCAC
Found at i:25204305 original size:29 final size:27
Alignment explanation
Indices: 25204274--25204366 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 27
25204264 AAATTCTATT
25204274 TTTTACCCTAATTTCACCAAAATTACCA
1 TTTTACCCTAATTT-ACCAAAATTACCA
* *
25204302 TTTTACCCCTAAACTTT-CCTAAA-TCCCA
1 TTTTA-CCCT-AA-TTTACCAAAATTACCA
*
25204330 TTTTAACCCTAATTTTATCAAAATTACCA
1 TTTT-ACCCTAA-TTTACCAAAATTACCA
25204359 TTTTACCC
1 TTTTACCC
25204367 CCAAACTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 5 0.09
28 25 0.47
29 18 0.34
30 2 0.04
31 3 0.06
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (27 bp):
TTTTACCCTAATTTACCAAAATTACCA
Found at i:25204382 original size:29 final size:29
Alignment explanation
Indices: 25204119--25204498 Score: 193
Period size: 30 Copynumber: 13.1 Consensus size: 29
25204109 AAAATTTCTA
*
25204119 AAAATTA-CATTTTGACCCCAAAACTTTTCC
1 AAAATTACCATTTT-ACCCCCAAAC-TTTCC
* *
25204149 AAAATTA-TATTTTGACCCCAAAACTTTTCC
1 AAAATTACCATTTT-ACCCCCAAAC-TTTCC
*
25204179 AAAATTA-CATTTTGA-CCCCAAAATTTCC
1 AAAATTACCATTTT-ACCCCCAAACTTTCC
* * *
25204207 AAAAATT-GCATTTTAACCCAAAACTTT-C
1 -AAAATTACCATTTTACCCCCAAACTTTCC
*
25204235 AAAATTACCA-TTTACCCCCGAA-TCTTCC
1 AAAATTACCATTTTACCCCCAAACT-TTCC
* *** *
25204263 AAAATT-CTATTTTTTACCCTAA-TTTCACC
1 AAAATTACCATTTTACCCCCAAACTTT--CC
*
25204292 AAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTACCATTTTACCCCCAAACTTTCC
* * * * * *
25204321 TAAA-TCCCATTTTA-ACCCTAATTTTATC
1 AAAATTACCATTTTACCCCCAAACTTT-CC
25204349 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCCCAAACTTTCC
* * * * *
25204378 TAAA-TCCCATTTTTAACCTC-GA-TTTCACC
1 AAAATTACCA-TTTTACCCCCAAACTTT--CC
* *
25204407 AAAATTTACCATTTTACCCCCGAACTTTTC
1 AAAA-TTACCATTTTACCCCCAAACTTTCC
* * * *
25204437 AAAATT-TCATTTTGA-CCTC-GATTTTGCC
1 AAAATTACCATTTT-ACCCCCAAACTTT-CC
25204465 AAAATTTACCATTTTACCCCCCAAACTTTCC
1 AAAA-TTACCATTTTA-CCCCCAAACTTTCC
25204496 AAA
1 AAA
25204499 TTCTATTTTT
Statistics
Matches: 268, Mismatches: 54, Indels: 55
0.71 0.14 0.15
Matches are distributed among these distances:
26 1 0.00
27 35 0.13
28 57 0.21
29 72 0.27
30 80 0.30
31 16 0.06
32 7 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACTTTCC
Found at i:25204388 original size:28 final size:28
Alignment explanation
Indices: 25204299--25204390 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
25204289 ACCAAAATTA
*
25204299 CCATTTTACCCCTAAACTTTCCTAAATC
1 CCATTTTACCCCCAAACTTTCCTAAATC
* * * * * *
25204327 CCATTTTA-ACCCTAATTTTATCAAAATTA
1 CCATTTTACCCCCAAACTTT-CCTAAA-TC
25204356 CCATTTTACCCCCAAACTTTCCTAAATC
1 CCATTTTACCCCCAAACTTTCCTAAATC
25204384 CCATTTT
1 CCATTTT
25204391 TAACCTCGAT
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
27 7 0.15
28 20 0.42
29 13 0.27
30 8 0.17
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (28 bp):
CCATTTTACCCCCAAACTTTCCTAAATC
Found at i:25204461 original size:116 final size:114
Alignment explanation
Indices: 25204177--25204542 Score: 368
Period size: 116 Copynumber: 3.2 Consensus size: 114
25204167 CAAAACTTTT
* ** * **
25204177 CCAAAATTA-CATTTTGA-CCCCAAAATTTCCAAAAATTGCATTTTAACCCAAAACTT-TCAAAA
1 CCAAAATTACCATTTT-ACCCCCAAACTTTCC-AAAATCCCATTTTAACCCTAATTTTATCAAAA
* * *
25204239 TTACCA-TTTACCCCCGAA-TCTTCCAAAATTCTATTTTTTACC-CTAATTTCA
64 TTACCATTTTACCCCCAAACT-TTCC-AAATTCTATTTTTAACCTC-GATTTCA
* *
25204290 CCAAAATTACCATTTTACCCCTAAACTTTCCTAAATCCCATTTTAACCCTAATTTTATCAAAATT
1 CCAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAACCCTAATTTTATCAAAATT
* *
25204355 ACCATTTTACCCCCAAACTTTCCTAAATCCCATTTTTAACCTCGATTTCA
66 ACCATTTTACCCCCAAACTTTCC-AAATTCTATTTTTAACCTCGATTTCA
* * ** * * **
25204405 CCAAAATTTACCATTTTACCCCCGAACTTTTCAAAATTTCATTTTGA-CCTCGATTTTGCCAAAA
1 CCAAAA-TTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAACCCT-AATTTTATCAAAA
* *
25204469 TTTACCATTTTACCCCCCAAACTTTCCAAATTCTATTTTTAGCCTTGATTTCA
64 -TTACCATTTTA-CCCCCAAACTTTCCAAATTCTATTTTTAACCTCGATTTCA
* *
25204522 CAAAAATTACCATTTTGCCCC
1 CCAAAATTACCATTTTACCCC
25204543 AAAAAGCCCA
Statistics
Matches: 213, Mismatches: 30, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
113 29 0.14
114 29 0.14
115 44 0.21
116 59 0.28
117 38 0.18
118 14 0.07
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (114 bp):
CCAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAACCCTAATTTTATCAAAATT
ACCATTTTACCCCCAAACTTTCCAAATTCTATTTTTAACCTCGATTTCA
Found at i:25213883 original size:30 final size:32
Alignment explanation
Indices: 25213831--25213891 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
25213821 TGTTAGTTAT
*
25213831 TTATAAAAATTAAACTAAAATTAAATTATCAG
1 TTATAAAAATTAAACTAAAATTAAAATATCAG
*
25213863 TTAT-AAAATTATAC-AAAATTAAAATATCA
1 TTATAAAAATTAAACTAAAATTAAAATATCA
25213892 AAATTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 14 0.52
31 9 0.33
32 4 0.15
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (32 bp):
TTATAAAAATTAAACTAAAATTAAAATATCAG
Found at i:25218135 original size:30 final size:31
Alignment explanation
Indices: 25218072--25218136 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
25218062 TACATATGAC
*
25218072 CATGCTTGCTCAAAAATTACTCTTTTTGCCA
1 CATGCTTGCTCAAAAATTACTCTATTTGCCA
*
25218103 CATGCTTGCT-AAAAATTACT-TCATTTGTCA
1 CATGCTTGCTCAAAAATTACTCT-ATTTGCCA
25218133 CATG
1 CATG
25218137 TATCTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 1 0.03
30 20 0.65
31 10 0.32
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (31 bp):
CATGCTTGCTCAAAAATTACTCTATTTGCCA
Found at i:25218754 original size:13 final size:13
Alignment explanation
Indices: 25218736--25218761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25218726 AGAATTCCTT
25218736 GATTCTTACTCAA
1 GATTCTTACTCAA
25218749 GATTCTTACTCAA
1 GATTCTTACTCAA
25218762 TCTGCCTCAA
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:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
GATTCTTACTCAA
Found at i:25234050 original size:16 final size:16
Alignment explanation
Indices: 25234029--25234071 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
25234019 GATGTCCCAT
25234029 CACCACTTGCTTCTGC
1 CACCACTTGCTTCTGC
*
25234045 CACCACTTGCCTCTGC
1 CACCACTTGCTTCTGC
*
25234061 CACCACATGCT
1 CACCACTTGCT
25234072 ATCACCATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.16, C:0.47, G:0.12, T:0.26
Consensus pattern (16 bp):
CACCACTTGCTTCTGC
Found at i:25235362 original size:60 final size:58
Alignment explanation
Indices: 25235267--25235656 Score: 342
Period size: 59 Copynumber: 6.6 Consensus size: 58
25235257 AATAGGTCCT
* * * *
25235267 TAAACTTTACATAAATTACATTTTGACCCTCAAACTTCTCTAAAATCATATTTTTACCC
1 TAAACTTTTCA-AAATTACATTTTGACCCTTAAACTTCTCTAAAATCACATTTTGACCC
* * * **
25235326 TAAAACTTCTTCAAAATTACATTGTGACCCTTAAACTTCTCCAAAAAT-ATATTTTGACAAT
1 T-AAACTT-TTCAAAATTACATTTTGACCCTTAAACTTCT-CTAAAATCACATTTTGAC-CC
* * * * *
25235387 TAAACTTTCCAAAATTACATTTTGACCCCTAAACTTTTC-AAAATTATATTTTGACCCC
1 TAAACTTTTCAAAATTACATTTTGACCCTTAAACTTCTCTAAAATCACATTTTGA-CCC
* *
25235445 TAAACTTTTCAAAATTATATTTTGACTCC-TAAACTT-TTTCAAAATCACATTTTGACCCC
1 TAAACTTTTCAAAATTACATTTTGAC-CCTTAAACTTCTCT-AAAATCACATTTTGA-CCC
* * * * *
25235504 TCAAACTTTTCCAAAATCATATTTTCACCCCTAAACTTCTCAAAAATCACATTTTGACCAC
1 T-AAACTTTT-CAAAATTACATTTTGACCCTTAAACTTCTCTAAAATCACATTTTGACC-C
* * * * * *
25235565 CAAACCTTCTT-AAAATCACATTTTGA-CCTTAAATTTCTTTAAAATAACATTTTAACCC
1 TAAA-CTT-TTCAAAATTACATTTTGACCCTTAAACTTCTCTAAAATCACATTTTGACCC
* *
25235623 TAAACTTTTCTAAAATTACATTTTTACCCCTAAA
1 TAAACTTTTC-AAAATTACATTTTGACCCTTAAA
25235657 TTTTTCCAAA
Statistics
Matches: 277, Mismatches: 35, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
56 2 0.01
57 9 0.03
58 58 0.21
59 80 0.29
60 74 0.27
61 51 0.18
62 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (58 bp):
TAAACTTTTCAAAATTACATTTTGACCCTTAAACTTCTCTAAAATCACATTTTGACCC
Found at i:25235408 original size:29 final size:29
Alignment explanation
Indices: 25235264--25235667 Score: 323
Period size: 30 Copynumber: 13.6 Consensus size: 29
25235254 CCTAATAGGT
*
25235264 CCTTAAACTTTACATAAATTACATTTTGAC
1 CCTTAAACTTTTCA-AAATTACATTTTGAC
* * * * *
25235294 CCTCAAACTTCTCTAAAATCATATTTTTAC
1 CCTTAAACTTTTC-AAAATTACATTTTGAC
* *
25235324 CCTAAAACTTCTTCAAAATTACATTGTGAC
1 CCTTAAACTT-TTCAAAATTACATTTTGAC
* * *
25235354 CCTTAAACTTCTCCAAAAATATATTTTGAC
1 CCTTAAACTT-TTCAAAATTACATTTTGAC
** *
25235384 AATTAAACTTTCCAAAATTACATTTTGAC
1 CCTTAAACTTTTCAAAATTACATTTTGAC
* *
25235413 CCCTAAACTTTTCAAAATTATATTTTGAC
1 CCTTAAACTTTTCAAAATTACATTTTGAC
* *
25235442 CCCTAAACTTTTCAAAATTATATTTTGAC
1 CCTTAAACTTTTCAAAATTACATTTTGAC
*
25235471 TCC-TAAACTTTTTCAAAATCACATTTTGACC
1 -CCTTAAAC-TTTTCAAAATTACATTTTGA-C
* * * *
25235502 CCTCAAACTTTTCCAAAATCATATTTTCAC
1 CCTTAAACTTTT-CAAAATTACATTTTGAC
* * *
25235532 CCCTAAACTTCTCAAAAATCACATTTTGAC
1 CCTTAAACTTTTC-AAAATTACATTTTGAC
* *
25235562 CAC-CAAACCTTCTT-AAAATCACATTTTGA-
1 C-CTTAAA-CTT-TTCAAAATTACATTTTGAC
* * * *
25235591 CCTTAAATTTCTTTAAAATAACATTTTAAC
1 CCTTAAACTT-TTCAAAATTACATTTTGAC
*
25235621 CC-TAAACTTTTCTAAAATTACATTTTTAC
1 CCTTAAACTTTTC-AAAATTACATTTTGAC
* *
25235650 CCCTAAATTTTTCCAAAA
1 CCTTAAACTTTT-CAAAA
25235668 ATATGTTTTA
Statistics
Matches: 310, Mismatches: 47, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.03
29 115 0.37
30 159 0.51
31 27 0.09
32 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
CCTTAAACTTTTCAAAATTACATTTTGAC
Found at i:25241169 original size:14 final size:13
Alignment explanation
Indices: 25241149--25241244 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 13
25241139 CAGATTCGAT
25241149 GAAAAAAAATAAAA
1 GAAAAAAAA-AAAA
* *
25241163 -TAAAAAAAGAAA
1 GAAAAAAAAAAAA
25241175 GAAAAAAAAAAAAA
1 G-AAAAAAAAAAAA
25241189 GAAAGAAAAAAAAA
1 GAAA-AAAAAAAAA
25241203 GAAAAAGAAAAAAA
1 GAAAAA-AAAAAAA
25241217 GGAAAAAAGAAAAAAA
1 -G-AAAAA-AAAAAAA
25241233 GAAAAGAAAAAA
1 GAAAA-AAAAAA
25241245 GAGGAAAAGG
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
12 3 0.04
13 12 0.17
14 40 0.56
15 3 0.04
16 13 0.18
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:25241183 original size:16 final size:15
Alignment explanation
Indices: 25241150--25241244 Score: 104
Period size: 15 Copynumber: 6.3 Consensus size: 15
25241140 AGATTCGATG
*
25241150 AAAAAAAATAAAATAA
1 AAAAAAAAGAAAA-AA
25241166 AAAAAGAAAG-AAAAA
1 AAAAA-AAAGAAAAAA
*
25241181 AAAAAAAAG-AAAGA
1 AAAAAAAAGAAAAAA
*
25241195 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAA
*
25241210 AAAAAAAGGAAAAAA
1 AAAAAAAAGAAAAAA
*
25241225 GAAAAAAAGAAAAGAA
1 AAAAAAAAGAAAA-AA
25241241 AAAA
1 AAAA
25241245 GAGGAAAAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
14 17 0.25
15 34 0.51
16 13 0.19
17 3 0.04
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:25241197 original size:29 final size:27
Alignment explanation
Indices: 25241149--25241244 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 27
25241139 CAGATTCGAT
* * *
25241149 GAAAAAAAATAAAA-TAAAAAAAGAAA
1 GAAAAAAAAAAAAAGAAAAAAAAAAAA
25241175 GAAAAAAAAAAAAAGAAAGAAAAAAAAA
1 GAAAAAAAAAAAAAGAAA-AAAAAAAAA
*
25241203 GAAAAAGAAAAAAAGGAAAAAAGAAAAAAA
1 GAAAAA-AAAAAAAAG-AAAAA-AAAAAAA
*
25241233 GAAAAGAAAAAA
1 GAAAAAAAAAAA
25241245 GAGGAAAAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.22
27 2 0.03
28 14 0.23
29 16 0.27
30 15 0.25
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (27 bp):
GAAAAAAAAAAAAAGAAAAAAAAAAAA
Found at i:25241214 original size:45 final size:46
Alignment explanation
Indices: 25241150--25241259 Score: 129
Period size: 45 Copynumber: 2.4 Consensus size: 46
25241140 AGATTCGATG
*
25241150 AAAAAAAATAAAATA-AAAAAAGAAAGAAAAAA-AAAAAAAG-AAAGA
1 AAAAAAAAGAAAA-AGAAAAAA-AAAGAAAAAAGAAAAAAAGAAAAGA
*
25241195 AAAAAAAAGAAAAAG-AAAAAAAGGAAAAAAGAAAAAAAGAAAAGA
1 AAAAAAAAGAAAAAGAAAAAAAAAGAAAAAAGAAAAAAAGAAAAGA
* * *
25241240 AAAAAGAGGAAAAGGAAAAA
1 AAAAAAAAGAAAAAGAAAAA
25241260 TGAGAGGTCG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
43 9 0.16
44 14 0.25
45 29 0.52
46 4 0.07
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (46 bp):
AAAAAAAAGAAAAAGAAAAAAAAAGAAAAAAGAAAAAAAGAAAAGA
Found at i:25241251 original size:15 final size:14
Alignment explanation
Indices: 25241175--25241259 Score: 82
Period size: 15 Copynumber: 5.8 Consensus size: 14
25241165 AAAAAAGAAA
* *
25241175 GAAAAAAAAAAAAA
1 GAAAAGAAAAAAAG
*
25241189 GAAAGAAAAAAAAAG
1 GAAA-AGAAAAAAAG
*
25241204 AAAAAGAAAAAAAG
1 GAAAAGAAAAAAAG
25241218 GAAAAAAGAAAAAAA-
1 G--AAAAGAAAAAAAG
25241233 GAAAAGAAAAAAGAG
1 GAAAAGAAAAAA-AG
25241248 GAAAAGGAAAAA
1 GAAAA-GAAAAA
25241260 TGAGAGGTCG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
13 11 0.18
14 14 0.23
15 18 0.30
16 18 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAGAAAAAAAG
Found at i:25241252 original size:8 final size:8
Alignment explanation
Indices: 25241167--25241253 Score: 55
Period size: 7 Copynumber: 11.6 Consensus size: 8
25241157 ATAAAATAAA
25241167 AAAAGAAAG
1 AAAAG-AAG
25241176 AAAA-AA-
1 AAAAGAAG
*
25241182 AAAAAAAG
1 AAAAGAAG
25241190 -AAAGAA-
1 AAAAGAAG
*
25241196 AAAAAAAG
1 AAAAGAAG
25241204 AAAAAGAA-
1 -AAAAGAAG
*
25241212 AAAA-AGG
1 AAAAGAAG
25241219 AAAA-AAG
1 AAAAGAAG
*
25241226 AAAAAAAG
1 AAAAGAAG
25241234 AAAAGAA-
1 AAAAGAAG
*
25241241 AAAAGAGG
1 AAAAGAAG
25241249 AAAAG
1 AAAAG
25241254 GAAAAATGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
6 5 0.08
7 34 0.54
8 14 0.22
9 10 0.16
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:25241252 original size:29 final size:28
Alignment explanation
Indices: 25241167--25241259 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 28
25241157 ATAAAATAAA
* *
25241167 AAAAGAAAGAAAAAAAAAAAAAGAAAGAA-
1 AAAA-AAAGAAAAGAAAAAAAGGAAA-AAG
25241196 AAAAAAAGAAAAAGAAAAAAAGGAAAAAAG
1 AAAAAAAG-AAAAGAAAAAAAGG-AAAAAG
*
25241226 AAAAAAAGAAAAGAAAAAAGAGGAAAAGG
1 AAAAAAAGAAAAGAAAAAA-AGGAAAAAG
25241255 AAAAA
1 AAAAA
25241260 TGAGAGGTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
28 4 0.07
29 39 0.68
30 14 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (28 bp):
AAAAAAAGAAAAGAAAAAAAGGAAAAAG
Found at i:25241259 original size:1 final size:1
Alignment explanation
Indices: 25241150--25241244 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
25241140 AGATTCGATG
* * * * * * * *
25241150 AAAAAAAATAAAATAAAAAAAGAAAGAAAAAAAAAAAAAGAAAGAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *
25241215 AAGGAAAAAAGAAAAAAAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25241245 GAGGAAAAGG
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (1 bp):
A
Found at i:25241259 original size:16 final size:15
Alignment explanation
Indices: 25241175--25241259 Score: 90
Period size: 16 Copynumber: 5.8 Consensus size: 15
25241165 AAAAAAGAAA
*
25241175 GAAAAA-AAAAAAAA
1 GAAAAAGAAAAAAAG
25241189 GAAAGAA-AAAAAAA-
1 GAAA-AAGAAAAAAAG
25241203 GAAAAAGAAAAAAAG
1 GAAAAAGAAAAAAAG
25241218 GAAAAAAGAAAAAAA-
1 G-AAAAAGAAAAAAAG
25241233 G-AAAAGAAAAAAGAG
1 GAAAAAGAAAAAA-AG
*
25241248 GAAAAGGAAAAA
1 GAAAAAGAAAAA
25241260 TGAGAGGTCG
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
13 13 0.21
14 16 0.25
15 12 0.19
16 22 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAAAAAG
Found at i:25242263 original size:50 final size:50
Alignment explanation
Indices: 25242209--25242724 Score: 244
Period size: 50 Copynumber: 10.4 Consensus size: 50
25242199 AGGCCGCGAT
* * * *
25242209 GGCGAATCCGATACATTAAAAGATGTGATGAGAAAGGTTGAGGTCACAAC
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * * * *
25242259 GGCGAACCCGGTACCA-T-GAAGATTTGAAGGG-AAGGATTGAGGTCGCGAC
1 GGCGAACCCGGTA-CATTAAAAGATGTGATGGGAAAGG-TTGAGGCCACAAC
*** ** * * * * *
25242308 GATAAATTCGGTACCTCAAAAGATTTAAAGGGAAAGGTTGAGGCCACAAC
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * * *
25242358 GACGAACCCGGTACCTTAAAAGATGTGACGGGAAAGGTTAAGGCCTCAAC
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * * *
25242408 GGCGAACCCGGTACCTCAAAAGATGTGATGGGAAAGATTAAGGCCGCAAC
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * ** *
25242458 GGCGAATCCGGTACCA-T-GAA-ATGTGATGAGAAAGGTTGAGGCCGTAAT
1 GGCGAACCCGGTA-CATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * * * * *
25242506 GGCGAACCCAGTACCA-T-GAAGATTTTAAGGGAAAAGTTGAAGGTGCA-AA-
1 GGCGAACCCGGTA-CATTAAAAGATGTGATGGGAAAGGTTG-AGG-CCACAAC
* ** ** * * ** * *
25242555 GGCCAACCTAGTACCGTAGAAGATATGAAAGGAAAGGTTGAGGCCGCAAT
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * * * *
25242605 GGCGAACCCGGTACAAT-GAAGATTTTAAGGGAAAGGTTGAGGCCGCAAC
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* * * * ** * * * **
25242654 GGTGAACCTGATACCTTAGTAGATATGAAGGGAAAGGTTGAGCCCGTAAC
1 GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
* *
25242704 GGCGAACCCGATACCTTAAAA
1 GGCGAACCCGGTACATTAAAA
25242725 AATGGAAAAG
Statistics
Matches: 367, Mismatches: 85, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
48 48 0.13
49 101 0.28
50 210 0.57
51 8 0.02
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.18
Consensus pattern (50 bp):
GGCGAACCCGGTACATTAAAAGATGTGATGGGAAAGGTTGAGGCCACAAC
Found at i:25242442 original size:100 final size:99
Alignment explanation
Indices: 25242174--25242724 Score: 350
Period size: 99 Copynumber: 5.6 Consensus size: 99
25242164 TTGAGAAAAA
* * * * * * * * * *
25242174 CATGAAGATTTGAAGGGAATGATTGAGGCCGCGATGGCGAATCCGATACATTAAAAGATGTGATG
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCTCAACGGCGAACCCGGTACCTCAAAAGATGTGATG
* *
25242239 AGAAAGGTTGAGGTCACAACGGCGAACCCGGTAC
66 GGAAAGGTTGAGGCCACAACGGCGAACCCGGTAC
* * * * *** ** * * *
25242273 CATGAAGATTTGAAGGG-AAGGATTGAGGTCGCGACGATAAATTCGGTACCTCAAAAGATTTAAA
1 CATGAAGATGTGAAGGGAAAGG-TTGAGGCCTCAACGGCGAACCCGGTACCTCAAAAGATGTGAT
*
25242337 GGGAAAGGTTGAGGCCACAACGACGAACCCGGTAC
65 GGGAAAGGTTGAGGCCACAACGGCGAACCCGGTAC
* * * *
25242372 CTTAAAAGATGTGACGGGAAAGGTTAAGGCCTCAACGGCGAACCCGGTACCTCAAAAGATGTGAT
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGCCTCAACGGCGAACCCGGTACCTCAAAAGATGTGAT
* * * *
25242437 GGGAAAGATTAAGGCCGCAACGGCGAATCCGGTAC
65 GGGAAAGGTTGAGGCCACAACGGCGAACCCGGTAC
* * * * * * *
25242472 CATGAA-ATGTGATGAGAAAGGTTGAGGCCGT-AATGGCGAACCCAGTA-C-CATGAAGATTTTA
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCC-TCAACGGCGAACCCGGTACCTCA-AAAGATGTGA
* * * * **
25242533 AGGGAAAAGTTGAAGGTGCA-AA-GGCCAACCTAGTAC
64 TGGGAAAGGTTG-AGG-CCACAACGGCGAACCCGGTAC
* * * * * * *
25242569 CGTAGAAGATATGAAAGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTA---CAATGAAGATTTT
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGCCTCAACGGCGAACCCGGTACCTCAA--AAGATGTG
* * * * *
25242631 AAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGATAC
63 ATGGGAAAGGTTGAGGCCACAACGGCGAACCCGGTAC
* * * * * *
25242668 CTTAGTAGATATGAAGGGAAAGGTTGAGCCCGT-AACGGCGAACCCGATACCTTAAAA
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGCC-TCAACGGCGAACCCGGTACCTCAAAA
25242725 AATGGAAAAG
Statistics
Matches: 353, Mismatches: 81, Indels: 35
0.75 0.17 0.07
Matches are distributed among these distances:
96 2 0.01
97 29 0.08
98 51 0.14
99 190 0.54
100 75 0.21
101 4 0.01
102 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.18
Consensus pattern (99 bp):
CATGAAGATGTGAAGGGAAAGGTTGAGGCCTCAACGGCGAACCCGGTACCTCAAAAGATGTGATG
GGAAAGGTTGAGGCCACAACGGCGAACCCGGTAC
Found at i:25242713 original size:99 final size:99
Alignment explanation
Indices: 25242327--25242713 Score: 358
Period size: 99 Copynumber: 3.9 Consensus size: 99
25242317 GGTACCTCAA
* * * * * * * *
25242327 AAGATTTAAAGGGAAAGGTTGAGGCCACAACGACGAACCCGGTACCTTAAAAGATGTGACGGGAA
1 AAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGATACCTTAGAAGATATGAAGGGAA
*
25242392 AGGTTAAGGCC-TCAACGGCGAACCCGGTACCTCAA--
66 AGGTTGAGGCCGT-AACGGCGAACCCGGTA---CAATG
* * * * * * * * * *
25242427 AAGATGTGATGGGAAAGATTAAGGCCGCAACGGCGAATCC-GGTACCAT-GAA-ATGTGATGAGA
1 AAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGCGAA-CCTGATACCTTAGAAGATATGAAGGGA
* * *
25242489 AAGGTTGAGGCCGTAATGGCGAACCCAGTACCATG
65 AAGGTTGAGGCCGTAACGGCGAACCCGGTACAATG
* * * * * *
25242524 AAGATTTTAAGGGAAAAGTTGAAGG-TGCAAAGGCCAACCT-AGTACCGTAGAAGATATGAAAGG
1 AAGATTTTAAGGGAAAGGTTG-AGGCCGCAACGGCGAACCTGA-TACCTTAGAAGATATGAAGGG
* *
25242587 AAAGGTTGAGGCCGCAATGGCGAACCCGGTACAATG
64 AAAGGTTGAGGCCGTAACGGCGAACCCGGTACAATG
* *
25242623 AAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGATACCTTAGTAGATATGAAGGGAA
1 AAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGATACCTTAGAAGATATGAAGGGAA
*
25242688 AGGTTGAGCCCGTAACGGCGAACCCG
66 AGGTTGAGGCCGTAACGGCGAACCCG
25242714 ATACCTTAAA
Statistics
Matches: 232, Mismatches: 44, Indels: 23
0.78 0.15 0.08
Matches are distributed among these distances:
95 2 0.01
96 2 0.01
97 29 0.12
98 43 0.19
99 116 0.50
100 38 0.16
101 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.17
Consensus pattern (99 bp):
AAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGATACCTTAGAAGATATGAAGGGAA
AGGTTGAGGCCGTAACGGCGAACCCGGTACAATG
Found at i:25242934 original size:41 final size:40
Alignment explanation
Indices: 25242873--25242970 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 40
25242863 TTACATCATC
* *
25242873 ATTCAGTCTTTTACCATTAATCAAGAAGGGCAGATTGAAG
1 ATTCAGTCTTTTACCCTTAATCAAGAAGGGCAGAATGAAG
25242913 ATTCCAGTCTTTTACCCTTAATCAAGAAGGGCAGAATGAAG
1 ATT-CAGTCTTTTACCCTTAATCAAGAAGGGCAGAATGAAG
*
25242954 ATTCTGATCTTTTACCC
1 ATTCAG-TCTTTTACCC
25242971 CGAGCTTGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 5 0.09
41 48 0.91
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (40 bp):
ATTCAGTCTTTTACCCTTAATCAAGAAGGGCAGAATGAAG
Found at i:25243047 original size:78 final size:78
Alignment explanation
Indices: 25242999--25243360 Score: 361
Period size: 78 Copynumber: 4.6 Consensus size: 78
25242989 CTATCATTTG
* * * * * *
25242999 ATCTTTTACCCCAAGCTTGGGACAGATTGCAACCATCCGATCTCTTACCTCAAGCCTAGGGCAAA
1 ATCTCTTACCCCAAGCTTGGGACAGATTGCAACCATCCGATCTCTTACCTCGAGCTTGGGGTAGA
25243064 TCACCATCAGCCA
66 TCACCATCAGCCA
* ** * * ** * * * *
25243077 ATCTCTTACCCCGAGGCTAAGG-CAAATTGCAGCCATTGGATCTTTTACCTCGAGCCTGAGGCAG
1 ATCTCTTACCCC-AAGCTTGGGACAGATTGCAACCATCCGATCTCTTACCTCGAGCTTGGGGTAG
* *
25243141 ATCACCACCAAGTCA
65 ATCACCATC-AGCCA
* * * * *
25243156 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGCCATCCGATCTCTTATCTCGAGCTTGGGGTAGA
1 ATCTCTTACCCCAAGCTTGGGACAGATTGCAACCATCCGATCTCTTACCTCGAGCTTGGGGTAGA
*
25243221 TCACCATCAACCA
66 TCACCATCAGCCA
* * *
25243234 ATCTCTTACCCCAAGCTTGAGG-CAGATTGTAACCATTCGATCT-TTGACCCCGAGCTTGGGGTA
1 ATCTCTTACCCCAAGCTTG-GGACAGATTGCAACCATCCGATCTCTT-ACCTCGAGCTTGGGGTA
25243297 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * * * *
25243312 ATCTCTTACCCCGAGCCTGCGACAGATTGCAACCGTCCAATATCTTACC
1 ATCTCTTACCCCAAGCTTGGGACAGATTGCAACCATCCGATCTCTTACC
25243361 AAAAAAAAAA
Statistics
Matches: 230, Mismatches: 47, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
77 3 0.01
78 159 0.69
79 68 0.30
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (78 bp):
ATCTCTTACCCCAAGCTTGGGACAGATTGCAACCATCCGATCTCTTACCTCGAGCTTGGGGTAGA
TCACCATCAGCCA
Found at i:25243210 original size:39 final size:38
Alignment explanation
Indices: 25243021--25243210 Score: 118
Period size: 39 Copynumber: 4.8 Consensus size: 38
25243011 AAGCTTGGGA
* *
25243021 CAGATTGCAACCATCCGATCTCTTACCTCAAGCCTAGGG
1 CAGATTGC-ACCATCCGATCTCTTACCTCGAGCCTAAGG
* * * *
25243060 CA-AAT-CACCATCAGCCAATCTCTTACCCCGAGGCTAAGG
1 CAGATTGCACCAT---CCGATCTCTTACCTCGAGCCTAAGG
* ** * *
25243099 CAAATTGCAGCCATTGGATCTTTTACCTCGAGCCTGAGG
1 CAGATTGCA-CCATCCGATCTCTTACCTCGAGCCTAAGG
** * *
25243138 CAGATCACCACCAAGT-CAATCTCTTACCCCGAGCCT-AGG
1 CAGAT-TGCACC-A-TCCGATCTCTTACCTCGAGCCTAAGG
*
25243177 ACAGATTGCAGCCATCCGATCTCTTATCTCGAGC
1 -CAGATTGCA-CCATCCGATCTCTTACCTCGAGC
25243211 TTGGGGTAGA
Statistics
Matches: 113, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
36 5 0.04
37 1 0.01
38 3 0.03
39 69 0.61
40 28 0.25
41 3 0.03
42 4 0.04
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (38 bp):
CAGATTGCACCATCCGATCTCTTACCTCGAGCCTAAGG
Found at i:25243300 original size:157 final size:155
Alignment explanation
Indices: 25242954--25243360 Score: 456
Period size: 157 Copynumber: 2.6 Consensus size: 155
25242944 CAGAATGAAG
* * * * ** * * *
25242954 ATTCTGATCTTTTACCCCGAGCTTGGGGTAAATTACTATCATTTGATCTTTTACCCCAAGCTTGG
1 ATTC-GATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCT-G
*
25243019 GACAGATTGCAACCATCCGATCTCTTACCTCAAGCCTAGGGCAAATCACCATCAGCCAATCTCTT
64 GACAGATTGCAACCATCCGATCTCTTACCTCAAGCCTAGGGCAAATCACCATCAACCAATCTCTT
* *
25243084 ACCCCGAGGCTAAGGCAAATTGCAGCC
129 ACCCCGAAGCTAAGGCAAATTGCAACC
* * * * * *
25243111 ATTGGATCTTTTACCTCGAGCCTGAGGCAGATCACCACCAAGTCAATCTCTTACCCCGAGCCTAG
1 ATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACCATC-AGTCAATCTCTTACCCCGAGCCT-G
* * * * * * *
25243176 GACAGATTGCAGCCATCCGATCTCTTATCTCGAGCTTGGGGTAGATCACCATCAACCAATCTCTT
64 GACAGATTGCAACCATCCGATCTCTTACCTCAAGCCTAGGGCAAATCACCATCAACCAATCTCTT
* * *
25243241 ACCCC-AAGCTTGAGGCAGATTGTAACC
129 ACCCCGAAGC-TAAGGCAAATTGCAACC
* *
25243268 ATTCGATCTTTGACCCCGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGCG
1 ATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTG-G
* * *
25243333 ACAGATTGCAACCGTCCAATATCTTACC
65 ACAGATTGCAACCATCCGATCTCTTACC
25243361 AAAAAAAAAA
Statistics
Matches: 205, Mismatches: 42, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
155 1 0.00
156 76 0.37
157 128 0.62
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (155 bp):
ATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGA
CAGATTGCAACCATCCGATCTCTTACCTCAAGCCTAGGGCAAATCACCATCAACCAATCTCTTAC
CCCGAAGCTAAGGCAAATTGCAACC
Found at i:25243324 original size:39 final size:39
Alignment explanation
Indices: 25243195--25243327 Score: 124
Period size: 39 Copynumber: 3.4 Consensus size: 39
25243185 CAGCCATCCG
* *
25243195 ATCTCTTATCTCGAGCTTGGGGTAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAACCA
* * * **** * ** *
25243234 ATCTCTTACCCCAAGCTTGAGGCAGATTGTAACCATTCG
1 ATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAACCA
*
25243273 ATCT-TTGACCCCGAGCTTGGGGTAGATCACCATCAGCCA
1 ATCTCTT-ACCCCGAGCTTGGGGTAGATCACCATCAACCA
25243312 ATCTCTTACCCCGAGC
1 ATCTCTTACCCCGAGC
25243328 CTGCGACAGA
Statistics
Matches: 68, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
38 2 0.03
39 64 0.94
40 2 0.03
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAACCA
Found at i:25245360 original size:30 final size:29
Alignment explanation
Indices: 25245324--25245674 Score: 207
Period size: 30 Copynumber: 11.9 Consensus size: 29
25245314 TTTGATAGGT
*
25245324 CCTTAAACTTTACAAAAATTACATTTTAAC
1 CCTTAAACTTTTC-AAAATTACATTTTAAC
* * * *
25245354 CTTTAAACTTCTCCAAAATTATATTTTTAC
1 CCTTAAACTT-TTCAAAATTACATTTTAAC
* * *
25245384 CCCTAAAC-TTCCTAAAATTACATTTTGAC
1 CCTTAAACTTTTC-AAAATTACATTTTAAC
25245413 CCTTAAACTTTTCAAAATTACATTTTAAC
1 CCTTAAACTTTTCAAAATTACATTTTAAC
* *
25245442 CCCTAAACTTTTTCAAAATCACATTTTAAC
1 CCTTAAAC-TTTTCAAAATTACATTTTAAC
* * * * *
25245472 CCCTGAACTTTTCCAAAATCATATTTTCAC
1 CCTTAAACTTTT-CAAAATTACATTTTAAC
* * * * *
25245502 CCCTAAACTTCTCAAAAATCATATTTTGAC
1 CCTTAAACTTTTC-AAAATTACATTTTAAC
* * * * *
25245532 CAC-CAAACCTTCTCGAAATCACATTTTGA-
1 C-CTTAAA-CTTTTCAAAATTACATTTTAAC
* * *
25245561 CCTTAAA-TTTCTCCAAAATCACATTTTGAT
1 CCTTAAACTTT-T-CAAAATTACATTTTAAC
*
25245591 CC-TAAACTTTCCTC-AAATTACATTTTTAC
1 CCTTAAACTTT--TCAAAATTACATTTTAAC
* **
25245620 CCCTAAACTTTTCCAAAATTATGTTTTAA-
1 CCTTAAACTTTT-CAAAATTACATTTTAAC
*
25245649 CCTCT-AACTCTTCAAAACTT-CATTTT
1 CCT-TAAACTTTTCAAAA-TTACATTTT
25245675 CGACCCCGTT
Statistics
Matches: 267, Mismatches: 35, Indels: 40
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.01
28 15 0.06
29 97 0.36
30 142 0.53
31 11 0.04
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
CCTTAAACTTTTCAAAATTACATTTTAAC
Found at i:25245420 original size:59 final size:58
Alignment explanation
Indices: 25245338--25245638 Score: 257
Period size: 59 Copynumber: 5.1 Consensus size: 58
25245328 AAACTTTACA
* * * *
25245338 AAAATTACATTTTAACCTTTAAACTTCTCCAAAATTATATTTTTACCCCTAAACTTC-CT
1 AAAATCACATTTTGACC-CTAAACTT-TCCAAAATTACATTTTTACCCCTAAACTTCTCT
* * * *
25245397 AAAATTACATTTTGACCCTTAAACTTTTCAAAATTACATTTTAACCCCTAAACTT-TTT
1 AAAATCACATTTTGACCC-TAAACTTTCCAAAATTACATTTTTACCCCTAAACTTCTCT
* * * * * *
25245455 CAAAATCACATTTTAACCCCTGAACTTTTCCAAAATCATATTTTCACCCCTAAACTTCTCA
1 -AAAATCACATTTTGA-CCCTAAAC-TTTCCAAAATTACATTTTTACCCCTAAACTTCTCT
* * * * * * * * *
25245516 AAAATCATATTTTGACCACCAAACCTTCTCGAAATCACATTTTGA-CCTTAAATTTCTCC
1 AAAATCACATTTTGACC-CTAAACTTTC-CAAAATTACATTTTTACCCCTAAACTTCTCT
* * * *
25245575 AAAATCACATTTTGATCCTAAACTTTCCTCAAATTACATTTTTACCCCTAAACTTTTCC
1 AAAATCACATTTTGACCCTAAACTTTCC-AAAATTACATTTTTACCCCTAAACTTCTCT
25245634 AAAAT
1 AAAAT
25245639 TATGTTTTAA
Statistics
Matches: 196, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
57 1 0.01
58 47 0.24
59 87 0.44
60 60 0.31
61 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (58 bp):
AAAATCACATTTTGACCCTAAACTTTCCAAAATTACATTTTTACCCCTAAACTTCTCT
Found at i:25245647 original size:29 final size:30
Alignment explanation
Indices: 25245327--25245638 Score: 255
Period size: 30 Copynumber: 10.5 Consensus size: 30
25245317 GATAGGTCCT
* * * * **
25245327 TAAACTTTACAAAAATTACATTTTAACCTT
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* * * *
25245357 TAAACTTCTCCAAAATTATATTTTTACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* *
25245387 TAAAC--TTCCTAAAATTACATTTTGACCCT
1 TAAACTTTTCC-AAAATCACATTTTGACCCC
* *
25245416 TAAACTTTT-CAAAATTACATTTTAACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* *
25245445 TAAACTTTTTCAAAATCACATTTTAACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* * *
25245475 TGAACTTTTCCAAAATCATATTTTCACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* * *
25245505 TAAACTTCTCAAAAATCATATTTTGACCACC
1 TAAACTTTTCCAAAATCACATTTTGACC-CC
* * *
25245536 -AAAC-CTTCTCGAAATCACATTTTGA-CCT
1 TAAACTTTTC-CAAAATCACATTTTGACCCC
*
25245564 TAAA-TTTCTCCAAAATCACATTTTGA-TCC
1 TAAACTTT-TCCAAAATCACATTTTGACCCC
* * *
25245593 TAAAC-TTTCCTCAAATTACATTTTTACCCC
1 TAAACTTTTCC-AAAATCACATTTTGACCCC
25245623 TAAACTTTTCCAAAAT
1 TAAACTTTTCCAAAAT
25245639 TATGTTTTAA
Statistics
Matches: 232, Mismatches: 37, Indels: 26
0.79 0.13 0.09
Matches are distributed among these distances:
28 7 0.03
29 88 0.38
30 128 0.55
31 9 0.04
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
TAAACTTTTCCAAAATCACATTTTGACCCC
Found at i:25258013 original size:24 final size:26
Alignment explanation
Indices: 25257970--25258023 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
25257960 ATTTATAAAA
25257970 TTTTAAAAATATTAAAATTTCTAT-T
1 TTTTAAAAATATTAAAATTTCTATAT
** *
25257995 TTTTAAAAAT-TTAGTATTTTTATAT
1 TTTTAAAAATATTAAAATTTCTATAT
25258020 TTTT
1 TTTT
25258024 TAATTTCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTAAAAATATTAAAATTTCTATAT
Found at i:25258029 original size:16 final size:16
Alignment explanation
Indices: 25258010--25258081 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
25258000 AAAATTTAGT
25258010 ATTTTTATATTTTTTA
1 ATTTTTATATTTTTTA
* *
25258026 A-TTTCATATTTATTTT
1 ATTTTTATATTT-TTTA
*
25258042 ATTTTTA-ATAATTTTA
1 ATTTTTATAT-TTTTTA
* *
25258058 ATATTTTATACTTTTTC
1 AT-TTTTATATTTTTTA
25258075 ATTTTTA
1 ATTTTTA
25258082 AAGATTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
15 9 0.21
16 17 0.40
17 16 0.37
18 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATATTTTTTA
Found at i:25258035 original size:23 final size:23
Alignment explanation
Indices: 25258009--25258078 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
25257999 AAAAATTTAG
25258009 TATTTTTATATTTTTTAATTTCA
1 TATTTTTATATTTTTTAATTTCA
* *
25258032 TATTTATTTTATTTTTAATAATTTTA
1 TATTT-TTATATTTTT--TAATTTCA
* *
25258058 -ATATTTTATACTTTTTCATTT
1 TAT-TTTTATATTTTTTAATTT
25258079 TTAAAGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
23 10 0.26
24 9 0.24
25 10 0.26
26 9 0.24
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTATATTTTTTAATTTCA
Found at i:25258053 original size:26 final size:25
Alignment explanation
Indices: 25257986--25258073 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 25
25257976 AAATATTAAA
* *
25257986 ATTTCTAT-TTTTTAAAAATTTAGT
1 ATTTTTATATTTTTAATAATTTAGT
25258010 ATTTTTATATTTTT--TAATTTCA-T
1 ATTTTTATATTTTTAATAATTT-AGT
* *
25258033 ATTTATTTTATTTTTAATAATTTTAAT
1 ATTT-TTATATTTTTAATAA-TTTAGT
25258060 A-TTTTATACTTTTT
1 ATTTTTATA-TTTTT
25258074 CATTTTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
23 10 0.19
24 17 0.33
25 9 0.17
26 11 0.21
27 5 0.10
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (25 bp):
ATTTTTATATTTTTAATAATTTAGT
Found at i:25259843 original size:13 final size:13
Alignment explanation
Indices: 25259825--25259849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25259815 TTAATTATTA
25259825 TTTACAATATTTT
1 TTTACAATATTTT
25259838 TTTACAATATTT
1 TTTACAATATTT
25259850 ATTATTTTTT
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:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTACAATATTTT
Found at i:25271747 original size:19 final size:20
Alignment explanation
Indices: 25271707--25271748 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
25271697 ACTTCGATTG
*
25271707 AATCTAAAGATATCTACAAA
1 AATCTAAAGATATCTAAAAA
25271727 AATCTAAA-ATAT-TAAACAA
1 AATCTAAAGATATCTAAA-AA
25271746 AAT
1 AAT
25271749 AATCTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 9 0.45
20 8 0.40
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (20 bp):
AATCTAAAGATATCTAAAAA
Found at i:25272733 original size:21 final size:20
Alignment explanation
Indices: 25272706--25272750 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
25272696 AAACACTTTC
25272706 AAAATTTTTTATTTTCTAAAA
1 AAAATTTTTTATTTT-TAAAA
*
25272727 ATAA--TTTTATTTTTAAAA
1 AAAATTTTTTATTTTTAAAA
25272745 AAAATT
1 AAAATT
25272751 GATTTCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
18 8 0.40
19 9 0.45
21 3 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTTTTTATTTTTAAAA
Found at i:25272743 original size:18 final size:19
Alignment explanation
Indices: 25272712--25272750 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
25272702 TTTCAAAATT
*
25272712 TTTTATTTTCTAAAAATAA
1 TTTTATTTTCTAAAAAAAA
25272731 TTTTATTTT-TAAAAAAAA
1 TTTTATTTTCTAAAAAAAA
25272749 TT
1 TT
25272751 GATTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTATTTTCTAAAAAAAA
Found at i:25274655 original size:10 final size:10
Alignment explanation
Indices: 25274640--25274664 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25274630 TTGTTTTAAA
25274640 TTTATAATAT
1 TTTATAATAT
25274650 TTTATAATAT
1 TTTATAATAT
25274660 TTTAT
1 TTTAT
25274665 TTTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:25285561 original size:17 final size:16
Alignment explanation
Indices: 25285530--25285577 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
25285520 TAATCCAAAA
*
25285530 AAATTA-TTATTTTTT
1 AAATTATTTATATTTT
25285545 AAATTAATTTATATTTT
1 AAATT-ATTTATATTTT
* *
25285562 TAATTATTTTTATTTT
1 AAATTATTTATATTTT
25285578 GTCCGCCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 5 0.18
16 11 0.39
17 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AAATTATTTATATTTT
Found at i:25285563 original size:18 final size:16
Alignment explanation
Indices: 25285531--25285577 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
25285521 AATCCAAAAA
25285531 AATTA-TTAT-TTTTT
1 AATTATTTATATTTTT
25285545 AAATTAATTTATATTTTT
1 -AATT-ATTTATATTTTT
*
25285563 AATTATTTTTATTTT
1 AATTATTTATATTTT
25285578 GTCCGCCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.14
16 11 0.39
17 8 0.29
18 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTATTTATATTTTT
Found at i:25291466 original size:12 final size:12
Alignment explanation
Indices: 25291444--25291494 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
25291434 AAAAAATAGC
*
25291444 AAAACAACAACA
1 AAAATAACAACA
*
25291456 AAAATAGCAACA
1 AAAATAACAACA
*
25291468 AAAGTAACAACA
1 AAAATAACAACA
* *
25291480 AAAACAACATCA
1 AAAATAACAACA
25291492 AAA
1 AAA
25291495 CAGTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.71, C:0.20, G:0.04, T:0.06
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:25291493 original size:24 final size:24
Alignment explanation
Indices: 25291449--25291494 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25291439 ATAGCAAAAC
* *
25291449 AACAACAAAAATAGCAACAAAAGT
1 AACAACAAAAACAACAACAAAAGT
*
25291473 AACAACAAAAACAACATCAAAA
1 AACAACAAAAACAACAACAAAA
25291495 CAGTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (24 bp):
AACAACAAAAACAACAACAAAAGT
Found at i:25291600 original size:24 final size:24
Alignment explanation
Indices: 25291551--25291600 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
25291541 GAAAACAGTA
* * *
25291551 AAAATAGCAACCAAAATAGTAAAT
1 AAAACAGCAACCAAAACAATAAAT
25291575 AAAACAGC-ACCAAAACAATAATAT
1 AAAACAGCAACCAAAACAATAA-AT
25291599 AA
1 AA
25291601 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.64, C:0.16, G:0.06, T:0.14
Consensus pattern (24 bp):
AAAACAGCAACCAAAACAATAAAT
Found at i:25294063 original size:21 final size:21
Alignment explanation
Indices: 25294039--25294078 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25294029 ATAGATGTGT
25294039 CAGACACGCCCAG-ATACGTAC
1 CAGACACG-CCAGAATACGTAC
*
25294060 CAGATACGCCAGAATACGT
1 CAGACACGCCAGAATACGT
25294079 TAAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.12
Consensus pattern (21 bp):
CAGACACGCCAGAATACGTAC
Found at i:25295135 original size:73 final size:73
Alignment explanation
Indices: 25295016--25295172 Score: 269
Period size: 73 Copynumber: 2.2 Consensus size: 73
25295006 TTTTTTTCAG
* *
25295016 CATGTTAATAATTGTGATGTAAAATACAAATGTGATGTCGCTTCTACATCACCCTCTACCACTCA
1 CATGTTAATAATTGTGATGTAAAATACAAAGGTGATGTCGCTTCTACATCACCCTCCACCACTCA
25295081 TAACAAAC
66 TAACAAAC
*
25295089 CATGTTAATAATTGTGGTGTAAAATACAAAGGTGATGTCGCTTCTACATCACCCTCCACCACTCA
1 CATGTTAATAATTGTGATGTAAAATACAAAGGTGATGTCGCTTCTACATCACCCTCCACCACTCA
*
25295154 TAACATAC
66 TAACAAAC
*
25295162 CATTTTAATAA
1 CATGTTAATAA
25295173 ATAATGTGGG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (73 bp):
CATGTTAATAATTGTGATGTAAAATACAAAGGTGATGTCGCTTCTACATCACCCTCCACCACTCA
TAACAAAC
Found at i:25296845 original size:3 final size:3
Alignment explanation
Indices: 25296834--25296865 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
25296824 CTCCTCCTCC
25296834 TCT TCCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT T
25296866 TTTCATCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:25296897 original size:19 final size:19
Alignment explanation
Indices: 25296861--25296898 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25296851 CTTCTTCTTC
25296861 TTCTTTTTCATCTCTTTTT
1 TTCTTTTTCATCTCTTTTT
*
25296880 TTCTTATTTGATCT-TTTTT
1 TTCTT-TTTCATCTCTTTTT
25296899 AAACCCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.74
Consensus pattern (19 bp):
TTCTTTTTCATCTCTTTTT
Found at i:25297000 original size:30 final size:30
Alignment explanation
Indices: 25296927--25297003 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 30
25296917 ATATGGGTGT
*
25296927 TAAGTTAGTGATTGTTTTGTCACTTTTCGA
1 TAAGTTAGTGACTGTTTTGTCACTTTTCGA
25296957 TAACGTTAGTGACTGTTTTGTCACATTTTC-A
1 TAA-GTTAGTGACTGTTTTGTCAC-TTTTCGA
25296988 -AAGTTGAGTGACTGTT
1 TAAGTT-AGTGACTGTT
25297004 GTATTAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.07
30 15 0.35
31 20 0.47
32 5 0.12
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (30 bp):
TAAGTTAGTGACTGTTTTGTCACTTTTCGA
Found at i:25306840 original size:60 final size:61
Alignment explanation
Indices: 25306758--25307046 Score: 261
Period size: 62 Copynumber: 4.8 Consensus size: 61
25306748 AAATTTAAGA
* * * *
25306758 GTGTTGGCCATGAAATGGCCGACACCCCTTTTTTTTC-A-AAAAAATTTTCAAAATTTTTGG
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAA-ATTCAAAATTTTTGG
* *
25306818 GTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTCAAAATTTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTCAAAATTTTTGG
** * **** ** * *
25306879 GTGTTGGCCATCGCATAGCCGACACCCCC-TTTTCTC--GAAATTTTTTTTAATTTTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTCAAAATTTTTGG
* ** * * *
25306937 GTGCTGGCCA-CTGTATGGTCGACACCCCC-TTTTCTCGAGAAAAAAATTTAAAATTTTTTTTG
1 GTGTTGGCCATC-AAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTCAAAA--TTTTTGG
* *
25306999 ATGTTGGCCATCAAATGGCCGACACCCCC-TATTCTCGAGAAAAAAATT
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATT
25307047 TCAATTTTTT
Statistics
Matches: 188, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
57 1 0.01
58 45 0.24
60 48 0.26
61 40 0.21
62 53 0.28
63 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (61 bp):
GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTCAAAATTTTTGG
Found at i:25306882 original size:61 final size:60
Alignment explanation
Indices: 25306758--25307085 Score: 297
Period size: 61 Copynumber: 5.4 Consensus size: 60
25306748 AAATTTAAGA
* * * * *
25306758 GTGTTGGCCATGAAATGGCCGACACCCCTTTTTTTTC-A-AAAAAATTTTCAAAATTTTTGG
1 GTGTTGGCCATCAAATGGCCGACACCCC-CTTTTCTCGAGAAAAAA-ATTCAAAATTTTTTG
25306818 GTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTCAAAATTTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCCCT-TTTCTCGAGAAAAAAATTCAAAATTTTTTG
** * **** ** *
25306879 GTGTTGGCCATCGCATAGCCGACACCCCCTTTTCTC--GAAATTTTTTTTAATTTTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTCAAAATTTTTTG
* ** * *
25306937 GTGCTGGCCA-CTGTATGGTCGACACCCCCTTTTCTCGAGAAAAAAATTTAAAATTTTTTTTG
1 GTGTTGGCCATC-AAATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTCAAAA--TTTTTTG
* * ** *
25306999 ATGTTGGCCATCAAATGGCCGACACCCCCTATTCTCGAGAAAAAAATTTCAATTTTTTTTT
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGAGAAAAAAA-TTCAAAATTTTTTG
* * * *
25307060 GTGTAGGCTATCAAATAGCGGACACC
1 GTGTTGGCCATCAAATGGCCGACACC
25307086 AACTTCTTCT
Statistics
Matches: 218, Mismatches: 40, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.00
58 45 0.21
59 1 0.00
60 47 0.22
61 68 0.31
62 51 0.23
63 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (60 bp):
GTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTCAAAATTTTTTG
Found at i:25307096 original size:62 final size:62
Alignment explanation
Indices: 25306823--25307086 Score: 186
Period size: 62 Copynumber: 4.4 Consensus size: 62
25306813 TTTGGGTGTT
* * * * *
25306823 GGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTCAAAA--TTTTTTGGTGTT
1 GGCCATCAAATAGCCGACACCACCTA-TTCTCGAGAAAAAAATTTAAAATTTTTTTTGATGTA
** * * *** ** *
25306884 GGCCATCGCATAGCCGACACCCCCTTTTCTC--G-AAATTTTTTTTAA-TTTTTTTGGTGCT-
1 GGCCATCAAATAGCCGACACCACCTATTCTCGAGAAAAAAATTTAAAATTTTTTTTGATG-TA
** * * * * *
25306942 GGCCA-CTGTATGGTCGACACCCCCTTTTCTCGAGAAAAAAATTTAAAATTTTTTTTGATGTT
1 GGCCATC-AAATAGCCGACACCACCTATTCTCGAGAAAAAAATTTAAAATTTTTTTTGATGTA
* * * *
25307004 GGCCATCAAATGGCCGACACCCCCTATTCTCGAGAAAAAAATTTCAATTTTTTTTTG-TGTA
1 GGCCATCAAATAGCCGACACCACCTATTCTCGAGAAAAAAATTTAAAATTTTTTTTGATGTA
* *
25307065 GGCTATCAAATAGCGGACACCA
1 GGCCATCAAATAGCCGACACCA
25307087 ACTTCTTCTC
Statistics
Matches: 164, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
57 8 0.05
58 37 0.23
59 1 0.01
60 6 0.04
61 52 0.32
62 59 0.36
63 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (62 bp):
GGCCATCAAATAGCCGACACCACCTATTCTCGAGAAAAAAATTTAAAATTTTTTTTGATGTA
Found at i:25310494 original size:83 final size:83
Alignment explanation
Indices: 25310374--25310549 Score: 334
Period size: 83 Copynumber: 2.1 Consensus size: 83
25310364 TAAATATAAA
25310374 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
*
25310439 TTATCAAATCAACATATT
66 TTATCAAATCAACACATT
*
25310457 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
25310522 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
25310540 ATATGATAAA
1 ATATGATAAA
25310550 CACATTATAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 91 1.00
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (83 bp):
ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
TTATCAAATCAACACATT
Found at i:25310551 original size:16 final size:16
Alignment explanation
Indices: 25310532--25310565 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
25310522 TTATCAAATC
25310532 AACACATTATATGATA
1 AACACATTATATGATA
25310548 AACACATTATATGATA
1 AACACATTATATGATA
25310564 AA
1 AA
25310566 AATTGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (16 bp):
AACACATTATATGATA
Found at i:25310624 original size:83 final size:83
Alignment explanation
Indices: 25310548--25310996 Score: 609
Period size: 83 Copynumber: 5.4 Consensus size: 83
25310538 TTATATGATA
25310548 AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
1 AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
*
25310613 ATATTGTATTATCAAATC
66 ATATTATATTATCAAATC
* *
25310631 AACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
1 AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
25310696 ATATTATATTATCAAATC
66 ATATTATATTATCAAATC
* *
25310714 AACACATTATGT-ATTAAAAATTGTAATATAATAAAAAAAATTATTTAAAGATATAAAATTAATA
1 AACACATTATATGA-TAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATA
*
25310778 AATATTGTATTATCAAATC
65 AATATTATATTATCAAATC
* * **
25310797 AACACATTATATGATAAAAATTATAATATAAT-AAAAATTTTATTTAAAGATATAAAATTGTTAA
1 AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
* *
25310861 ATAATATATTGTCAAATC
66 ATATTATATTATCAAATC
* ** * *
25310879 AACACATTATATGATAAAAATTGTAATATAATAATAATGTGTACTTT-AA-ATATGAAAATTTGA
1 AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTA-TTTAAAGATAT-AAAA-TTAA
* * * *
25310942 TAAATAATGTATTGTCAAATT
63 TAAATATTATATTATCAAATC
* * * *
25310963 AATACAATATTTGATATAAATTGTAATATAATAA
1 AACACATTATATGATAAAAATTGTAATATAATAA
25310997 CTATCTTTTT
Statistics
Matches: 331, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
82 79 0.24
83 196 0.59
84 56 0.17
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.37
Consensus pattern (83 bp):
AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
ATATTATATTATCAAATC
Found at i:25310681 original size:182 final size:176
Alignment explanation
Indices: 25310369--25310897 Score: 828
Period size: 182 Copynumber: 3.0 Consensus size: 176
25310359 GTTAATAAAT
25310369 ATAAAATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATA
1 ATAAAATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATA
* * *
25310434 ATGTATTATCAAATCAACATATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAG
66 TTGTATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAG
*
25310499 ATATAAAATTAATAAATATTGTATTATCAAATCAACACATTATATG
131 ATATAAAATTAATAAATATTATATTATCAAATCAACACATTATATG
25310545 ATAAACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAA
1 AT--A-A-A--ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAA
25310610 TAAATATTGTATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTAT
60 TAAATATTGTATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTAT
25310675 TTAAAGATATAAAATTAATAAATATTATATTATCAAATCAACACA-T-TATG
125 TTAAAGATATAAAATTAATAAATATTATATTATCAAATCAACACATTATATG
*
25310725 ------TAT--TAAAAATTGTAATATAATAAAAAAAATTATTTAAAGATATAAAATTAATAAATA
1 ATAAAATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATA
* *
25310782 TTGTATTATCAAATCAACACATTATATGATAAAAATTATAATATAAT-AAAAATTTTATTTAAAG
66 TTGTATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAG
** * *
25310846 ATATAAAATTGTTAAATAATATATTGTCAAATCAACACATTATATG
131 ATATAAAATTAATAAATATTATATTATCAAATCAACACATTATATG
25310892 ATAAAA
1 ATAAAA
25310898 ATTGTAATAT
Statistics
Matches: 328, Mismatches: 11, Indels: 31
0.89 0.03 0.08
Matches are distributed among these distances:
165 51 0.16
166 100 0.30
167 4 0.01
168 3 0.01
176 2 0.01
178 1 0.00
179 1 0.00
180 5 0.02
181 1 0.00
182 160 0.49
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (176 bp):
ATAAAATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATA
TTGTATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAG
ATATAAAATTAATAAATATTATATTATCAAATCAACACATTATATG
Found at i:25310996 original size:249 final size:249
Alignment explanation
Indices: 25310548--25310996 Score: 636
Period size: 248 Copynumber: 1.8 Consensus size: 249
25310538 TTATATGATA
*
25310548 AACACATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
1 AACACATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
* * *
25310613 ATATTGTATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTA
66 ATAATATATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATGTATTTA
* *
25310678 AAGATATAAAATTAATAAATATTATATTATCAAATCAACACATTATGTATTAAAAATTGTAATAT
131 AAGATATAAAATTAATAAATAATATATTATCAAATCAACACAATATGTATTAAAAATTGTAATAT
25310743 AATAAAAAAAATTATTTAAAGATATAAAATTAATAAATATTGTATTATCAAATC
196 AATAAAAAAAATTATTTAAAGATATAAAATTAATAAATATTGTATTATCAAATC
* **
25310797 AACACATTATATGATAAAAATTATAATATAAT-AAAAATTTTATTTAAAGATATAAAATTGTTAA
1 AACACATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
* * * * **
25310861 ATAATATATTGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAATAATGTGTACTTT
66 ATAATATATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATGTA-TTT
* * * * * * *
25310926 -AA-ATATGAAAATTTGATAAATAATGTATTGTCAAATTAATACAATATTTGA-TATAAATTGTA
130 AAAGATAT-AAAA-TTAATAAATAATATATTATCAAATCAACACAATATGT-ATTAAAAATTGTA
25310988 ATATAATAA
192 ATATAATAA
25310997 CTATCTTTTT
Statistics
Matches: 174, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
247 4 0.02
248 87 0.50
249 82 0.47
250 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.37
Consensus pattern (249 bp):
AACACATTATATGATAAAAATTATAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAA
ATAATATATTATCAAATCAACAAATTATATGATAAAAATTATAATATAATAAAAAAATGTATTTA
AAGATATAAAATTAATAAATAATATATTATCAAATCAACACAATATGTATTAAAAATTGTAATAT
AATAAAAAAAATTATTTAAAGATATAAAATTAATAAATATTGTATTATCAAATC
Found at i:25311730 original size:20 final size:22
Alignment explanation
Indices: 25311705--25311750 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
25311695 CATTAAATTA
25311705 AAAATAAATT-AA-TTT-TTATT
1 AAAAT-AATTCAATTTTATTATT
25311725 AAAATAATTCAATTTTATTATT
1 AAAATAATTCAATTTTATTATT
25311747 AAAA
1 AAAA
25311751 ATTAGTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 7 0.30
21 3 0.13
22 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATAATTCAATTTTATTATT
Found at i:25312285 original size:5 final size:5
Alignment explanation
Indices: 25312252--25312284 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
25312242 TTCATTTTTG
*
25312252 AATAA AAT-A AATAA AATAA AATAA AATAT AATA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATA
25312285 TTTTATGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:25319408 original size:20 final size:20
Alignment explanation
Indices: 25319383--25319420 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25319373 AATGGCAAAC
25319383 CAGCCACTCAACTTTCAATT
1 CAGCCACTCAACTTTCAATT
*
25319403 CAGCCATTCAACTTTCAA
1 CAGCCACTCAACTTTCAA
25319421 AAAATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (20 bp):
CAGCCACTCAACTTTCAATT
Found at i:25321272 original size:18 final size:18
Alignment explanation
Indices: 25321249--25321286 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
25321239 TTATTTAATA
25321249 ATAATTTTAA-AAACAATT
1 ATAATTTTAATAAA-AATT
25321267 ATAATTTTAATAAAAATT
1 ATAATTTTAATAAAAATT
25321285 AT
1 AT
25321287 TAGACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTTTAATAAAAATT
Found at i:25328072 original size:20 final size:21
Alignment explanation
Indices: 25328041--25328081 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
25328031 TCTAATTAAA
*
25328041 TAAAAAAGTTATGTTAATATT
1 TAAAAAAGTTATATTAATATT
25328062 TAAAAAA-TTATATTAATATT
1 TAAAAAAGTTATATTAATATT
25328082 ACATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAAAAAGTTATATTAATATT
Found at i:25328386 original size:31 final size:31
Alignment explanation
Indices: 25328336--25328395 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
25328326 GAGAGAGACT
*
25328336 AAAATAGAAACAATCTAAAATGTGAGTGACC
1 AAAATAGAAACAATCTAAAACGTGAGTGACC
** * *
25328367 AAAATAGAAATGATTTAAAACGTTAGTGA
1 AAAATAGAAACAATCTAAAACGTGAGTGA
25328396 TTAAATTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (31 bp):
AAAATAGAAACAATCTAAAACGTGAGTGACC
Found at i:25335026 original size:6 final size:6
Alignment explanation
Indices: 25335015--25335040 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25335005 CCCATCTCGC
25335015 CACCTT CACCTT CACCTT CACCTT CA
1 CACCTT CACCTT CACCTT CACCTT CA
25335041 TCCTCCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CACCTT
Found at i:25336133 original size:11 final size:10
Alignment explanation
Indices: 25336107--25336131 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25336097 CAATATGAAC
25336107 TTTTTAAATA
1 TTTTTAAATA
25336117 TTTTTAAATA
1 TTTTTAAATA
25336127 TTTTT
1 TTTTT
25336132 TATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:25337846 original size:17 final size:18
Alignment explanation
Indices: 25337824--25337861 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25337814 TAATTTTATT
25337824 AATATTAAATAAATAA-A
1 AATATTAAATAAATAATA
**
25337841 AATATTATTTAAATAATA
1 AATATTAAATAAATAATA
25337859 AAT
1 AAT
25337862 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATTAAATAAATAATA
Found at i:25337860 original size:28 final size:29
Alignment explanation
Indices: 25337807--25337861 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
25337797 TCATTCTGAC
* *
25337807 ATAAAAATAATTTTATTAATATTAAATAA
1 ATAAAAATAATTTTATAAATAATAAATAA
25337836 ATAAAAAT-ATTATT-TAAATAATAAAT
1 ATAAAAATAATT-TTATAAATAATAAAT
25337862 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAAAAATAATTTTATAAATAATAAATAA
Found at i:25337873 original size:18 final size:17
Alignment explanation
Indices: 25337833--25337870 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
25337823 TAATATTAAA
25337833 TAAATAAAAATATTATT
1 TAAATAAAAATATTATT
*
25337850 TAAATAATAAAT-TTTTT
1 TAAATAA-AAATATTATT
25337867 TAAA
1 TAAA
25337871 ATACTGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAAAAATATTATT
Found at i:25338341 original size:17 final size:17
Alignment explanation
Indices: 25338308--25338341 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25338298 AAAAAAATTT
* *
25338308 ATTTAAATGTTATTTAA
1 ATTTAAATATTACTTAA
25338325 ATTTAAATATTACTTAA
1 ATTTAAATATTACTTAA
25338342 TTATTGTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTAAATATTACTTAA
Found at i:25341718 original size:28 final size:28
Alignment explanation
Indices: 25341682--25341739 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
25341672 ATTATTAAAT
**
25341682 AAATTCAATTTTAAACAAAATTAATTCC
1 AAATTCAATCATAAACAAAATTAATTCC
**
25341710 AAATTCAATCATAAACTTAATTAATTCC
1 AAATTCAATCATAAACAAAATTAATTCC
25341738 AA
1 AA
25341740 TAGAAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (28 bp):
AAATTCAATCATAAACAAAATTAATTCC
Found at i:25344481 original size:27 final size:26
Alignment explanation
Indices: 25344421--25344486 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
25344411 ATAGCTTTGA
25344421 CAAAGGCACCACTAGTGCCGCCTACC
1 CAAAGGCACCACTAGTGCCGCCTACC
* * *
25344447 CAGTAGGCACCATTGGTGCCGCCTACC
1 CA-AAGGCACCACTAGTGCCGCCTACC
25344474 CTAAAGGCACCAC
1 C-AAAGGCACCAC
25344487 CTGTCAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 30 0.91
28 1 0.03
ACGTcount: A:0.26, C:0.39, G:0.21, T:0.14
Consensus pattern (26 bp):
CAAAGGCACCACTAGTGCCGCCTACC
Found at i:25344813 original size:15 final size:15
Alignment explanation
Indices: 25344775--25344819 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
25344765 ATTAATTTTA
*
25344775 TTTTTTGTATTATAT
1 TTTTTTGTATTATTT
** *
25344790 TTTAGTGTATAATTT
1 TTTTTTGTATTATTT
25344805 TTTTTTGTATTATTT
1 TTTTTTGTATTATTT
25344820 ATGTAAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (15 bp):
TTTTTTGTATTATTT
Found at i:25359405 original size:15 final size:16
Alignment explanation
Indices: 25359385--25359414 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25359375 AAAATAATCA
25359385 CCTCTTA-TTTTCTTT
1 CCTCTTACTTTTCTTT
25359400 CCTCTTACTTTTCTT
1 CCTCTTACTTTTCTT
25359415 CTCTACCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (16 bp):
CCTCTTACTTTTCTTT
Found at i:25363292 original size:18 final size:18
Alignment explanation
Indices: 25363266--25363301 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25363256 AAATAACACA
25363266 TAATAAATAATAAAAAAT
1 TAATAAATAATAAAAAAT
* *
25363284 TAATTAATAATAATAAAT
1 TAATAAATAATAAAAAAT
25363302 AAAATGTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAAATAATAAAAAAT
Found at i:25390071 original size:16 final size:17
Alignment explanation
Indices: 25390050--25390087 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
25390040 TTAGTGTATT
25390050 ATATTTTTTAAA-AAAA
1 ATATTTTTTAAATAAAA
25390066 ATA-TTTTTAAATAAAA
1 ATATTTTTTAAATAAAA
25390082 ACTATT
1 A-TATT
25390088 ACAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.42
16 8 0.42
17 2 0.11
18 1 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTTTTTAAATAAAA
Found at i:25390074 original size:15 final size:17
Alignment explanation
Indices: 25390054--25390087 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
25390044 TGTATTATAT
25390054 TTTTTAAA-AAAAA-TA
1 TTTTTAAATAAAAACTA
25390069 TTTTTAAATAAAAACTA
1 TTTTTAAATAAAAACTA
25390086 TT
1 TT
25390088 ACAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 5 0.29
17 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTTAAATAAAAACTA
Found at i:25402552 original size:2 final size:2
Alignment explanation
Indices: 25402547--25402596 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
25402537 TATATATATA
25402547 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
25402589 TG TG TG TG
1 TG TG TG TG
25402597 ATACGCTGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25406560 original size:41 final size:39
Alignment explanation
Indices: 25406461--25406568 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 39
25406451 AGGGTTTAAT
* *
25406461 ATTTAAGATTTAGGATTTAATGCTTATAATTTAAGTTTGG
1 ATTTAAGATTAAGG-TTTAATGTTTATAATTTAAGTTTGG
* * *
25406501 AGTTTGGAGTTTAGGGTTTAATGTTTATAATTTAAGTTTGGG
1 A-TTT-AAGATTAAGGTTTAATGTTTATAATTTAAGTTT-GG
*
25406543 ATTTAAGATTCAAGGTTTAATATTTA
1 ATTTAAGATT-AAGGTTTAATGTTTA
25406569 ATATTTAGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
40 5 0.09
41 41 0.75
42 9 0.16
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (39 bp):
ATTTAAGATTAAGGTTTAATGTTTATAATTTAAGTTTGG
Found at i:25407658 original size:21 final size:20
Alignment explanation
Indices: 25407627--25407675 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
25407617 TTCATCAACA
25407627 ATTTTATAATTATTATTTTTAT
1 ATTTTATAATTA--ATTTTTAT
25407649 ATTTT-TAATTAATTTTTA-
1 ATTTTATAATTAATTTTTAT
*
25407667 ATTGTATAA
1 ATTTTATAA
25407676 CAAATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
21 6 0.24
22 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTATAATTAATTTTTAT
Found at i:25421767 original size:18 final size:18
Alignment explanation
Indices: 25421744--25421780 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25421734 ATAATTCATA
25421744 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
25421762 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
25421780 T
1 T
25421781 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:25422272 original size:13 final size:13
Alignment explanation
Indices: 25422254--25422280 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25422244 ATTTTTACTT
25422254 TAGCCAATTTGTA
1 TAGCCAATTTGTA
25422267 TAGCCAATTTGTA
1 TAGCCAATTTGTA
25422280 T
1 T
25422281 GGTAAATTCT
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):
TAGCCAATTTGTA
Found at i:25428069 original size:20 final size:20
Alignment explanation
Indices: 25428044--25428083 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25428034 TAATTTCATA
25428044 CTTGTTAAAAGGAAGTTAAT
1 CTTGTTAAAAGGAAGTTAAT
25428064 CTTGTTAAAAGGAAGTTAAT
1 CTTGTTAAAAGGAAGTTAAT
25428084 GCACTGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (20 bp):
CTTGTTAAAAGGAAGTTAAT
Found at i:25436248 original size:38 final size:36
Alignment explanation
Indices: 25436198--25436290 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 36
25436188 TTATTACATA
* *
25436198 TAAAAA-ATT-AAAAAATATATAATATATCAAATACACT
1 TAAAAACATTAAAAAAATAT-TAA-AAAT-AAATAAACT
*
25436235 TAAAAACATTAAAATAAATATTAAAAATAAATAAATT
1 TAAAAACATTAAAA-AAATATTAAAAATAAATAAACT
25436272 TAAAATACATTAAAAAAAT
1 TAAAA-ACATTAAAAAAAT
25436291 TTTATATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
37 22 0.45
38 15 0.31
39 6 0.12
40 6 0.12
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (36 bp):
TAAAAACATTAAAAAAATATTAAAAATAAATAAACT
Found at i:25436431 original size:12 final size:12
Alignment explanation
Indices: 25436414--25436537 Score: 80
Period size: 12 Copynumber: 10.8 Consensus size: 12
25436404 ATAACATCCA
25436414 AACAACAAAAAC
1 AACAACAAAAAC
*
25436426 AACAACAAAAAT
1 AACAACAAAAAC
**
25436438 AACAGTAAAAA-
1 AACAACAAAAAC
*
25436449 AAC-ACGAAAAC
1 AACAACAAAAAC
* *
25436460 AGCAACCAAAAC
1 AACAACAAAAAC
**
25436472 AGTAA-AAAAAC
1 AACAACAAAAAC
*
25436483 AAC-ACAAATAC
1 AACAACAAAAAC
*
25436494 AACAA-AAAAAT
1 AACAACAAAAAC
* *
25436505 AGCAACCAAAAC
1 AACAACAAAAAC
*
25436517 AATAA-AAAAAC
1 AACAACAAAAAC
*
25436528 AACACCAAAA
1 AACAACAAAA
25436538 CAATAATATA
Statistics
Matches: 83, Mismatches: 23, Indels: 12
0.70 0.19 0.10
Matches are distributed among these distances:
10 5 0.06
11 35 0.42
12 43 0.52
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.05
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:25436435 original size:11 final size:11
Alignment explanation
Indices: 25436414--25436540 Score: 60
Period size: 11 Copynumber: 11.2 Consensus size: 11
25436404 ATAACATCCA
25436414 AACAACAAAAAC
1 AACAAC-AAAAC
*
25436426 AACAACAAAAAT
1 AACAAC-AAAAC
** *
25436438 AACAGTAAAAA
1 AACAACAAAAC
25436449 AAC-ACGAAAAC
1 AACAAC-AAAAC
*
25436460 AGCAACCAAAAC
1 AACAA-CAAAAC
** *
25436472 AGTAAAAAAAC
1 AACAACAAAAC
25436483 AAC-ACAAATAC
1 AACAACAAA-AC
* *
25436494 AACAAAAAAAT
1 AACAACAAAAC
*
25436505 AGCAACCAAAAC
1 AACAA-CAAAAC
* *
25436517 AATAAAAAAAC
1 AACAACAAAAC
*
25436528 AACACCAAAAC
1 AACAACAAAAC
25436539 AA
1 AA
25436541 TAATATAATT
Statistics
Matches: 85, Mismatches: 24, Indels: 13
0.70 0.20 0.11
Matches are distributed among these distances:
10 4 0.05
11 44 0.52
12 36 0.42
13 1 0.01
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.05
Consensus pattern (11 bp):
AACAACAAAAC
Found at i:25436459 original size:34 final size:36
Alignment explanation
Indices: 25436413--25436505 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 36
25436403 AATAACATCC
25436413 AAACAACA-AAAACAACAACAAAAATAACAGTAAAA
1 AAACAACACAAAACAACAACAAAAATAACAGTAAAA
* * *
25436448 AAAC-AC-GAAAACAGCAAC--CAA-AACAGTAAAA
1 AAACAACACAAAACAACAACAAAAATAACAGTAAAA
25436479 AAACAACACAAATACAACAA-AAAAATA
1 AAACAACACAAA-ACAACAACAAAAATA
25436506 GCAACCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
31 14 0.30
32 4 0.09
33 3 0.07
34 18 0.39
35 6 0.13
36 1 0.02
ACGTcount: A:0.71, C:0.19, G:0.04, T:0.05
Consensus pattern (36 bp):
AAACAACACAAAACAACAACAAAAATAACAGTAAAA
Found at i:25436480 original size:22 final size:22
Alignment explanation
Indices: 25436455--25436543 Score: 85
Period size: 22 Copynumber: 4.0 Consensus size: 22
25436445 AAAAAACACG
*
25436455 AAAACAGCAACCAAAACAGTAA
1 AAAACAGCAACCAAAACAATAA
*
25436477 AAAA-A-CAACACAAATACAACAAA
1 AAAACAGCAAC-CAAA-ACAA-TAA
*
25436500 AAAATAGCAACCAAAACAATAAA
1 AAAACAGCAACCAAAACAAT-AA
*
25436523 AAAACAAC-ACCAAAACAATAA
1 AAAACAGCAACCAAAACAATAA
25436544 TATAATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
20 4 0.07
21 7 0.12
22 18 0.32
23 18 0.32
24 5 0.09
25 4 0.07
ACGTcount: A:0.70, C:0.21, G:0.03, T:0.06
Consensus pattern (22 bp):
AAAACAGCAACCAAAACAATAA
Found at i:25436509 original size:45 final size:45
Alignment explanation
Indices: 25436455--25436540 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
25436445 AAAAAACACG
*
25436455 AAAACAGCAACCAAAACAGTAAAAAAACAACA-CAAATACAACAAA
1 AAAACAGCAACCAAAACAATAAAAAAACAACACCAAA-ACAACAAA
*
25436500 AAAATAGCAACCAAAACAATAAAAAAACAACACCAAAACAA
1 AAAACAGCAACCAAAACAATAAAAAAACAACACCAAAACAA
25436541 TAATATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.70, C:0.22, G:0.03, T:0.05
Consensus pattern (45 bp):
AAAACAGCAACCAAAACAATAAAAAAACAACACCAAAACAACAAA
Found at i:25448217 original size:16 final size:16
Alignment explanation
Indices: 25448193--25448224 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25448183 TACTTACAAA
*
25448193 TTTATTTCTTTAACAT
1 TTTAGTTCTTTAACAT
25448209 TTTAGTTCTTTAACAT
1 TTTAGTTCTTTAACAT
25448225 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTAGTTCTTTAACAT
Done.