Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold253
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: 843195
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 44520 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:503 original size:42 final size:43
Alignment explanation
Indices: 366--524 Score: 234
Period size: 43 Copynumber: 3.7 Consensus size: 43
356 TAAGAATAAA
* *
366 CGCCGCTAAAAGAGCAT-TGTCTTTAGCGGCATTTCTTTT-TAAAG
1 CGCCGCT-AAAGAACATGT-TCTTTAGCGGCGTTTCTTTTCT-AAG
*
410 CGCCGCTAAAGAACATTTTCTTTAGCGGCGTTTCTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTTCTAAG
453 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT-TTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTTCTAAG
*
495 CGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG
525 CTTTTATTTG
Statistics
Matches: 109, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
42 38 0.35
43 62 0.57
44 9 0.08
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTCTTTTCTAAG
Found at i:521 original size:85 final size:87
Alignment explanation
Indices: 366--524 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 87
356 TAAGAATAAA
* **
366 CGCCGCTAAAAGAGCATTGTCTTTAGCGGCATTTCTTTTTAAAGCGCCGCTAAAGAACATTTTCT
1 CGCCGCTAAAAGAACATTGTCTTTAGCGGCATTTCTTTTTAAAGCGCCGCTAAAGAACATGGTCT
431 TTAGCGGCGTTTCTTTTCTAAG
66 TTAGCGGCGTTTCTTTTCTAAG
*
453 CGCCGCT-AAAGAACA-TGTTCTTTAGCGGCGTTT-TTTTCT-AAGCGCCGCTAAAGAACATGGT
1 CGCCGCTAAAAGAACATTG-TCTTTAGCGGCATTTCTTTT-TAAAGCGCCGCTAAAGAACATGGT
514 CTTTAGCGGCG
64 CTTTAGCGGCG
525 CTTTTATTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
85 37 0.56
86 22 0.33
87 7 0.11
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (87 bp):
CGCCGCTAAAAGAACATTGTCTTTAGCGGCATTTCTTTTTAAAGCGCCGCTAAAGAACATGGTCT
TTAGCGGCGTTTCTTTTCTAAG
Found at i:2523 original size:16 final size:16
Alignment explanation
Indices: 2500--2556 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
2490 ATTGGAAGAA
2500 AGGCGTAATGGAATAG
1 AGGCGTAATGGAATAG
* *
2516 AGGTGTAATGTAATAG
1 AGGCGTAATGGAATAG
2532 AGGCGTAATGGAATAG
1 AGGCGTAATGGAATAG
*
2548 AGGCATAAT
1 AGGCGTAAT
2557 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.33, T:0.23
Consensus pattern (16 bp):
AGGCGTAATGGAATAG
Found at i:2844 original size:22 final size:21
Alignment explanation
Indices: 2819--2870 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
2809 TAGATATTCT
*
2819 TAATATTAA-ATTACTAAAATCA
1 TAATATTAATACTA-TAAAAT-A
2841 TAATATATAATACTATAAAATA
1 TAATAT-TAATACTATAAAATA
2863 TAAT-TTAA
1 TAATATTAA
2871 CATAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATTAATACTATAAAATA
Found at i:18406 original size:21 final size:21
Alignment explanation
Indices: 18377--18436 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
18367 ATTTAGCCAT
*
18377 TTTTATTTTTATTTTAA-TAA
1 TTTTGTTTTTATTTTAATTAA
*
18397 TTTTGTTTTTA-ATTAATTTAA
1 TTTTGTTTTTATTTTAA-TTAA
*
18418 TTTTGTTTTTAATTTAATT
1 TTTTGTTTTTATTTTAATT
18437 TTTACATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 4 0.12
20 10 0.29
21 16 0.47
22 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTGTTTTTATTTTAATTAA
Found at i:18409 original size:12 final size:12
Alignment explanation
Indices: 18375--18453 Score: 56
Period size: 12 Copynumber: 6.5 Consensus size: 12
18365 CAATTTAGCC
*
18375 ATTTTTATTTTT
1 ATTTTTAATTTT
18387 ATTTTAATAATTTT
1 ATTTT--TAATTTT
*
18401 GTTTTTAA--TT
1 ATTTTTAATTTT
*
18411 A-ATTTAATTTT
1 ATTTTTAATTTT
* *
18422 GTTTTTAATTTA
1 ATTTTTAATTTT
18434 ATTTTTACATTTT
1 ATTTTTA-ATTTT
18447 AATTTTT
1 -ATTTTT
18454 CTTTTGTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
9 5 0.10
10 2 0.04
11 2 0.04
12 22 0.43
13 4 0.08
14 16 0.31
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.70
Consensus pattern (12 bp):
ATTTTTAATTTT
Found at i:20724 original size:21 final size:21
Alignment explanation
Indices: 20691--20731 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20681 AATTACTGAT
* *
20691 AAAAGTTCTATATCTCTATAG
1 AAAAGTTCGATATATCTATAG
*
20712 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
20732 TAATCAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:32678 original size:42 final size:42
Alignment explanation
Indices: 32627--32715 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
32617 AAGACTTGTG
32627 AAGTATGTAATTTAAATTATAGAATTAGTGTGGCTTGTACAT
1 AAGTATGTAATTTAAATTATAGAATTAGTGTGGCTTGTACAT
32669 AAGTATGTAATTTAAATTATAGAATTAGTGTGGCTTGTACAT
1 AAGTATGTAATTTAAATTATAGAATTAGTGTGGCTTGTACAT
32711 AAGTA
1 AAGTA
32716 ATGGAAGTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.39
Consensus pattern (42 bp):
AAGTATGTAATTTAAATTATAGAATTAGTGTGGCTTGTACAT
Found at i:36758 original size:17 final size:17
Alignment explanation
Indices: 36738--36770 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36728 CTTCTCTTTC
*
36738 TTTTATTTTCTTTTTTT
1 TTTTAATTTCTTTTTTT
36755 TTTTAATTTCTTTTTT
1 TTTTAATTTCTTTTTT
36771 CATGTACTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTAATTTCTTTTTTT
Found at i:38509 original size:23 final size:23
Alignment explanation
Indices: 38483--38536 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
38473 GAATCGAGTT
38483 ATTCGAGTCAACTCGAATAAGTA
1 ATTCGAGTCAACTCGAATAAGTA
38506 ATTCGAGTCAACTCGAATAAGTA
1 ATTCGAGTCAACTCGAATAAGTA
38529 ATTCGAGT
1 ATTCGAGT
38537 TTTGAGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (23 bp):
ATTCGAGTCAACTCGAATAAGTA
Found at i:39119 original size:2 final size:2
Alignment explanation
Indices: 39112--39147 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39102 AGTTTATAAG
39112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39148 GCTAGTAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46450 original size:3 final size:3
Alignment explanation
Indices: 46444--46492 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
46434 GGAGCCAGAA
46444 GAT GAT GAT -AT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
46491 GA
1 GA
46493 AGCTGGAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:48483 original size:5 final size:5
Alignment explanation
Indices: 48473--48506 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
48463 TAAATGAGGA
48473 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
48507 AGATTTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:52803 original size:26 final size:27
Alignment explanation
Indices: 52745--52805 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
52735 TGGACTACTT
52745 CGTGTTTATTGTCCCGGCAAACTAACC
1 CGTGTTTATTGTCCCGGCAAACTAACC
* * * * *
52772 CATGTTTGTTGTCTCGG-AGACTACCC
1 CGTGTTTATTGTCCCGGCAAACTAACC
52798 CGTGTTTA
1 CGTGTTTA
52806 CGGTCCTGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
CGTGTTTATTGTCCCGGCAAACTAACC
Found at i:56937 original size:21 final size:21
Alignment explanation
Indices: 56911--56963 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
56901 CATTGTTTCT
* *
56911 AATCTCATCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
56932 AATCTCACCGCTATAGTAACT
1 AATCTCACCGCTACAGTAACC
56953 AATCTCACCGC
1 AATCTCACCGC
56964 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:79847 original size:87 final size:87
Alignment explanation
Indices: 79701--79874 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
79691 TGTTGCAGTT
*
79701 TCTGCTAATCCAATGATGCACTTGAAGTTTAAGTATGTTGAGTTGGATTTATATTTTGTTAGAGA
1 TCTGCTAATCCAATGATGCACTTGAAGTTTAAGTATGTTGAATTGGATTTATATTTTGTTAGAGA
79766 AAAGGTTGCTGCTGGGAAGCTG
66 AAAGGTTGCTGCTGGGAAGCTG
79788 TCTGCTAATCCAATGATGCACTTGAAGTTTAAGTATGTTGAATTGGACTTT-TATTTTGTTAGAG
1 TCTGCTAATCCAATGATGCACTTGAAGTTTAAGTATGTTGAATTGGA-TTTATATTTTGTTAGAG
79852 AAAAGGTTGCTGCTGGGAAGCTG
65 AAAAGGTTGCTGCTGGGAAGCTG
79875 AGTGTGGGAT
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
87 82 0.96
88 3 0.04
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (87 bp):
TCTGCTAATCCAATGATGCACTTGAAGTTTAAGTATGTTGAATTGGATTTATATTTTGTTAGAGA
AAAGGTTGCTGCTGGGAAGCTG
Found at i:82254 original size:19 final size:20
Alignment explanation
Indices: 82232--82303 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 20
82222 AATTATGTTA
82232 TTTTTGAATATTTTATATATT
1 TTTTTGAATATTTTATATA-T
* *
82253 TTTTTGAAT-TATGAT-TA-
1 TTTTTGAATATTTTATATAT
*
82270 TTTTTGAATATTTT-TATAG
1 TTTTTGAATATTTTATATAT
*
82289 TTTTTAAATTATTTT
1 TTTTTGAA-TATTTT
82304 TTGGTTAGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 10 0.24
18 4 0.10
19 9 0.21
20 10 0.24
21 9 0.21
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTTGAATATTTTATATAT
Found at i:82265 original size:37 final size:37
Alignment explanation
Indices: 82222--82293 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
82212 ATCCACATGT
*
82222 AATTATG-TTATTTTTGAATATTTTATATATTTTTTTG
1 AATTATGATTATTTTTGAATATTTT-TATAGTTTTTTG
82259 AATTATGATTATTTTTGAATATTTTTATAGTTTTT
1 AATTATGATTATTTTTGAATATTTTTATAGTTTTT
82294 AAATTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (37 bp):
AATTATGATTATTTTTGAATATTTTTATAGTTTTTTG
Found at i:82273 original size:17 final size:17
Alignment explanation
Indices: 82222--82278 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
82212 ATCCACATGT
82222 AATTATG-TTATTTTTG
1 AATTATGATTATTTTTG
* *
82238 AATATTTTATATATTTTTTTG
1 AAT-TATGAT-TA--TTTTTG
82259 AATTATGATTATTTTTG
1 AATTATGATTATTTTTG
82276 AAT
1 AAT
82279 ATTTTTATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 1 0.03
19 4 0.12
20 4 0.12
21 9 0.28
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
AATTATGATTATTTTTG
Found at i:82802 original size:12 final size:13
Alignment explanation
Indices: 82776--82800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82766 TTTCTAATTT
82776 TTATTTTTAAAAA
1 TTATTTTTAAAAA
82789 TTATTTTTAAAA
1 TTATTTTTAAAA
82801 TTTTCAACCA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTTTAAAAA
Found at i:83322 original size:2 final size:2
Alignment explanation
Indices: 83315--83350 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
83305 TTGTTTTATC
83315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83351 TCCTATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85372 original size:38 final size:39
Alignment explanation
Indices: 85317--85390 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 39
85307 GTCTGAACTA
* * *
85317 AAAACATGTATTAAAGATGT-CTAAACTAGGACATATAT
1 AAAACATATATTAAAGATATCCTAAAATAGGACATATAT
*
85355 AAAACATATAGTT-AAGATATCCTAAAATATGACATA
1 AAAACATATA-TTAAAGATATCCTAAAATAGGACATA
85391 ATTAAAAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
38 15 0.50
39 15 0.50
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (39 bp):
AAAACATATATTAAAGATATCCTAAAATAGGACATATAT
Found at i:85425 original size:39 final size:39
Alignment explanation
Indices: 85382--85473 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 39
85372 TATCCTAAAA
* * *
85382 TATGACATAATTAAAAACCCCTATTAA-AGATGTTTAGAT
1 TATGACATAATTAAAAACCCATATTAATA-ATGTTCAAAT
*
85421 TATGACATAATT-AAAACTCATATTAATAATGTTCAAAT
1 TATGACATAATTAAAAACCCATATTAATAATGTTCAAAT
85459 TATGACATAATTAAA
1 TATGACATAATTAAA
85474 GACTTAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 32 0.68
39 15 0.32
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (39 bp):
TATGACATAATTAAAAACCCATATTAATAATGTTCAAAT
Found at i:88894 original size:32 final size:32
Alignment explanation
Indices: 88851--88922 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
88841 TATACTCGAG
88851 ATCTTCCTCCTTTTCGGCGAGTGCTTCGAGTTC
1 ATCTT-CTCCTTTTCGGCGAGTGCTTCGAGTTC
88884 ATCTTCTCCTTTTCGGCGAGTGCTTCGAGTTC
1 ATCTTCTCCTTTTCGGCGAGTGCTTCGAGTTC
88916 ATCTTCT
1 ATCTTCT
88923 TTCTCTTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.10, C:0.29, G:0.19, T:0.42
Consensus pattern (32 bp):
ATCTTCTCCTTTTCGGCGAGTGCTTCGAGTTC
Found at i:91656 original size:39 final size:37
Alignment explanation
Indices: 91585--91733 Score: 140
Period size: 38 Copynumber: 3.9 Consensus size: 37
91575 TAAAGACTTG
* *
91585 TATTAAAGATG-TCTAAACTAGGACATATTTAAAACATA
1 TATTAAAGATGTTC-AAACTATGACATAATTAAAAC-TA
* * *
91623 TATTTAAGATGTCCTAAGCTATGACATAATTAAAAACCCT-
1 TATTAAAGATGTTC-AAACTATGACATAATT-AAAA--CTA
* *
91663 TATTAAAGATGTTCAGAGTATGACATAATTAAAACTCA
1 TATTAAAGATGTTCAAACTATGACATAATTAAAACT-A
* *
91701 TATTAATGATGTTCAAATTATGACATAATTAAA
1 TATTAAAGATGTTCAAACTATGACATAATTAAA
91734 GACTTAAACT
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
36 2 0.02
38 44 0.48
39 28 0.30
40 16 0.17
41 1 0.01
42 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (37 bp):
TATTAAAGATGTTCAAACTATGACATAATTAAAACTA
Found at i:97483 original size:22 final size:23
Alignment explanation
Indices: 97458--97507 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
97448 AATTAAGAAC
97458 TTAATTTTTGTATTTTT-AAATT
1 TTAATTTTTGTATTTTTCAAATT
* *
97480 TTAATTTTTTTATTTTTCATATT
1 TTAATTTTTGTATTTTTCAAATT
97503 TTAAT
1 TTAAT
97508 ATATTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TTAATTTTTGTATTTTTCAAATT
Found at i:99032 original size:16 final size:16
Alignment explanation
Indices: 99000--99030 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
98990 ACTATTAGTA
99000 ATTTTTTTAAATATTT
1 ATTTTTTTAAATATTT
99016 ATTTTTTT-AATATTT
1 ATTTTTTTAAATATTT
99031 TACCATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTTAAATATTT
Found at i:102479 original size:6 final size:6
Alignment explanation
Indices: 102445--102498 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
102435 TGCTATACCC
* **
102445 TTATT- TTATT- TTATT- TTATTTA TTGTTA TTATTA TTAACA TTATTA
1 TTATTA TTATTA TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA
102491 TTATTA TT
1 TTATTA TT
102499 TCATTCACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 13 0.32
6 26 0.63
7 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (6 bp):
TTATTA
Found at i:102496 original size:9 final size:9
Alignment explanation
Indices: 102445--102498 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
102435 TGCTATACCC
102445 TTATT-TTA
1 TTATTATTA
102453 TT-TTATT-
1 TTATTATTA
*
102460 TTATTTATTG
1 TTA-TTATTA
102470 TTATTATTA
1 TTATTATTA
**
102479 TTAACATTA
1 TTATTATTA
102488 TTATTATTA
1 TTATTATTA
102497 TT
1 TT
102499 TCATTCACAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 4 0.11
8 4 0.11
9 26 0.70
10 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
TTATTATTA
Found at i:102552 original size:24 final size:22
Alignment explanation
Indices: 102507--102552 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
102497 TTTCATTCAC
* *
102507 ACATACACATATTTTATGTATA
1 ACATACACATATTTAATATATA
102529 ACATACATGCATATTTAATATATA
1 ACATACA--CATATTTAATATATA
102553 TTTTAAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (22 bp):
ACATACACATATTTAATATATA
Found at i:112903 original size:100 final size:100
Alignment explanation
Indices: 112725--112954 Score: 329
Period size: 100 Copynumber: 2.3 Consensus size: 100
112715 AGTCTTATCC
* ** * *
112725 CCCTGATATTGCAATTAAAAAGATTGAAGCTACAACGGCGGATCTTACTTCCTTAGCAGTACAGC
1 CCCTAATATTGCAATTAAAAAGATTGAAGAAACAACGGCGGATCTTACTTCCTGAGCAGTACAGA
112790 GGAACAGATTGAAGCTACGACGGCGGATCTGGTTT
66 GGAACAGATTGAAGCTACGACGGCGGATCTGGTTT
* *
112825 CCCTAATATTGCAATTAAAAAGATTGAAGAAACAACGGCGGATCTTACTTCCCTGA-CAGTGCGG
1 CCCTAATATTGCAATTAAAAAGATTGAAGAAACAACGGCGGATCTTACTT-CCTGAGCAGTACAG
112889 AGGAACAGATTGAAGCTACGACGGCGGATCTGGTTT
65 AGGAACAGATTGAAGCTACGACGGCGGATCTGGTTT
* * * *
112925 CCCCAACATTGCAGTTGAACAA-ATTGAAGA
1 CCCTAATATTGCAATT-AAAAAGATTGAAGA
112955 TTACAGATCT
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 109 0.93
101 8 0.07
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (100 bp):
CCCTAATATTGCAATTAAAAAGATTGAAGAAACAACGGCGGATCTTACTTCCTGAGCAGTACAGA
GGAACAGATTGAAGCTACGACGGCGGATCTGGTTT
Found at i:112945 original size:50 final size:50
Alignment explanation
Indices: 112745--112953 Score: 175
Period size: 50 Copynumber: 4.2 Consensus size: 50
112735 GCAATTAAAA
* *** * * * * **
112745 AGATTGAAGCTACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTGCAGTTGAAC
* * * *
112795 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTGCAGTTGAAC
** * *** * * * **
112845 AGATTGAAGAAACAACGGCGGATCTTACTTCCCTGACAGTGCGGAGGAAC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTGCAGTTGAAC
*
112895 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATTGCAGTTGAAC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTGCAGTTGAAC
*
112945 AAATTGAAG
1 AGATTGAAG
112954 ATTACAGATC
Statistics
Matches: 117, Mismatches: 42, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
50 117 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (50 bp):
AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTGCAGTTGAAC
Found at i:113385 original size:45 final size:44
Alignment explanation
Indices: 113299--113394 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
113289 CAGTGGAATC
** *
113299 GATCGAAAAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTA
1 GATCGAAAAAAGCAGATCTTATCTTCACATACTGGCGTGAAGTA
* * * *
113343 GATCGGAAAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTA
1 GATCGAAAAAAGCAGATCTTATCTTCACATACTGG-CGTGAAGTA
113388 GATCGAA
1 GATCGAA
113395 GATACAAGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 29 0.67
45 14 0.33
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (44 bp):
GATCGAAAAAAGCAGATCTTATCTTCACATACTGGCGTGAAGTA
Found at i:113429 original size:221 final size:221
Alignment explanation
Indices: 112949--113437 Score: 607
Period size: 221 Copynumber: 2.2 Consensus size: 221
112939 TTGAACAAAT
112949 TGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTTACCT
1 TGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTTACCT
** * * **
113014 CCCTGAGGTTGTAGTGGAGTATATTGAAGCCAGTAATTCTATCTCCCCATACTGATGGTGGAATA
66 CCCTGAGGTTCCAGTAGAGTATATTGAAGCCAGTAATTCAATCTCCCCATACTGACAGTGGAATA
* * * *
113079 AATCGAAGAAAGCAGATCTTGTCTTCATGTATCAGCGTGAAGTAGATCAAATACAACATATTTTA
131 AATCGAAAAAAGCAGATCTTATCTTCATGTATCAGCGTGAAGTAGATCAAATACAACAGATCTTA
113144 TCCTCCCATACTGGCGGCAAGTAGAG
196 TCCTCCCATACTGGCGGCAAGTAGAG
* * *
113170 TGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTAGATTTTACCT
1 TGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTTACCT
** *
113235 CCCTGAGGTTCCAGTAGAGTATATTGAAGCCAGTAATTCAAT-TCCCC-TGGTCGGCAGTGGAAT
66 CCCTGAGGTTCCAGTAGAGTATATTGAAGCCAGTAATTCAATCTCCCCATACT-GACAGTGGAAT
** ** *
113298 CGATCGAAAAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGGAAA-A-AGCAGATC
130 AAATCGAAAAAAGCAGATCTTATCTTCATGTATCAGCGTGAAGTAGATC--AAATACAACAGATC
* * * *
113361 TTGTCTTCCCATACTGGTGGTGAAGTAGA-
193 TTATCCTCCCATACTGGCGG-CAAGTAGAG
** *
113390 TCGAAGA-TACA-AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CAAA
1 T-GAAGATTACAGA-TCTTATCTCCCT-AAGCAGTAGTGGAGTAGATCAAA
113438 AGTAACCAAT
Statistics
Matches: 232, Mismatches: 29, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
219 3 0.01
220 99 0.43
221 127 0.55
222 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (221 bp):
TGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGCAGATTTTACCT
CCCTGAGGTTCCAGTAGAGTATATTGAAGCCAGTAATTCAATCTCCCCATACTGACAGTGGAATA
AATCGAAAAAAGCAGATCTTATCTTCATGTATCAGCGTGAAGTAGATCAAATACAACAGATCTTA
TCCTCCCATACTGGCGGCAAGTAGAG
Found at i:114982 original size:6 final size:6
Alignment explanation
Indices: 114948--115001 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
114938 TGCTATACCC
* **
114948 TTATT- TTATT- TTATT- TTATTTA TTGTTA TTATTA TTAACA TTATTA
1 TTATTA TTATTA TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA
114994 TTATTA TT
1 TTATTA TT
115002 TCATTCACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 13 0.32
6 26 0.63
7 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (6 bp):
TTATTA
Found at i:114999 original size:9 final size:9
Alignment explanation
Indices: 114948--115001 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
114938 TGCTATACCC
114948 TTATT-TTA
1 TTATTATTA
114956 TT-TTATT-
1 TTATTATTA
*
114963 TTATTTATTG
1 TTA-TTATTA
114973 TTATTATTA
1 TTATTATTA
**
114982 TTAACATTA
1 TTATTATTA
114991 TTATTATTA
1 TTATTATTA
115000 TT
1 TT
115002 TCATTCACAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 4 0.11
8 4 0.11
9 26 0.70
10 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
TTATTATTA
Found at i:115055 original size:24 final size:22
Alignment explanation
Indices: 115010--115055 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
115000 TTTCATTCAC
* *
115010 ACATACACATATTTTATGTATA
1 ACATACACATATTTAATATATA
115032 ACATACATGCATATTTAATATATA
1 ACATACA--CATATTTAATATATA
115056 TTTTAAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (22 bp):
ACATACACATATTTAATATATA
Found at i:129515 original size:12 final size:12
Alignment explanation
Indices: 129493--129522 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
129483 CGGGTTTCTC
129493 AAAACTAAAAATG
1 AAAA-TAAAAATG
129506 AAAATAAAAATG
1 AAAATAAAAATG
129518 AAAAT
1 AAAAT
129523 GAAGATGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:135503 original size:50 final size:50
Alignment explanation
Indices: 135417--135515 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
135407 CCTTTAATTT
*** ** *
135417 TTTCCATATGAAGCTATAACCCACCAGTTATGGTCTTATACGATATGGTC
1 TTTCCATATGAAGCTATAACCCACCAACGACAGTCTTACACGATATGGTC
135467 TTTCCATATGAAG-TCATAACCCACCAACGACAGTCTTACACGATATGGT
1 TTTCCATATGAAGCT-ATAACCCACCAACGACAGTCTTACACGATATGGT
135516 GCCATGGACT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 41 0.98
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (50 bp):
TTTCCATATGAAGCTATAACCCACCAACGACAGTCTTACACGATATGGTC
Found at i:138342 original size:30 final size:31
Alignment explanation
Indices: 138308--138367 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
138298 AACTACACTC
138308 AGCTCAAATCAGCTCA-TTTCAGCTCGTTTG
1 AGCTCAAATCAGCTCATTTTCAGCTCGTTTG
* * *
138338 AGCTCAATTTAGCTTATTTTCAGCTCGTTT
1 AGCTCAAATCAGCTCATTTTCAGCTCGTTT
138368 CTTTTATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (31 bp):
AGCTCAAATCAGCTCATTTTCAGCTCGTTTG
Found at i:139164 original size:33 final size:34
Alignment explanation
Indices: 139127--139193 Score: 109
Period size: 35 Copynumber: 2.0 Consensus size: 34
139117 ACATTTCTGA
139127 TTATTA-AAAACTTGATTGTGAGATTTCCTCCTT
1 TTATTACAAAACTTGATTGTGAGATTTCCTCCTT
*
139160 TTATTATCAAAACTTGATTGTGAGGTTTCCTCCT
1 TTATTA-CAAAACTTGATTGTGAGATTTCCTCCT
139194 ATCCTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 6 0.19
35 25 0.81
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (34 bp):
TTATTACAAAACTTGATTGTGAGATTTCCTCCTT
Found at i:144033 original size:13 final size:13
Alignment explanation
Indices: 144015--144044 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
144005 TGAATGAAAA
*
144015 TTGCATTGCGGTT
1 TTGCATTGCAGTT
144028 TTGCATTGCAGTT
1 TTGCATTGCAGTT
144041 TTGC
1 TTGC
144045 TTTTCAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.47
Consensus pattern (13 bp):
TTGCATTGCAGTT
Found at i:145464 original size:42 final size:42
Alignment explanation
Indices: 145401--145480 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
145391 CTAATTGGGA
145401 AAATAATTCCCTTACTCTAATAAACTACTAAAACATAAGGGG
1 AAATAATTCCCTTACTCTAATAAACTACTAAAACATAAGGGG
* * * *
145443 AAATAATTTCCTTATTTTAATAAACTACTAAAAGATAA
1 AAATAATTCCCTTACTCTAATAAACTACTAAAACATAA
145481 AATAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.31
Consensus pattern (42 bp):
AAATAATTCCCTTACTCTAATAAACTACTAAAACATAAGGGG
Found at i:145489 original size:42 final size:42
Alignment explanation
Indices: 145399--145493 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
145389 TCCTAATTGG
**
145399 GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAGG
1 GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAAA
* * * * *
145441 GGAAATAATTTCCTTATTTTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAAA
*
145483 TAAAAT-ATTCC
1 GAAAATAATTCC
145494 TAGAATAAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (42 bp):
GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAAA
Found at i:148504 original size:15 final size:15
Alignment explanation
Indices: 148484--148520 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
148474 TGTCGTCACG
148484 AGAGTAAATTCCACC
1 AGAGTAAATTCCACC
*
148499 AGAGTAAATTTCACC
1 AGAGTAAATTCCACC
148514 AGA-TAAA
1 AGAGTAAA
148521 GCACTGCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (15 bp):
AGAGTAAATTCCACC
Found at i:150169 original size:42 final size:42
Alignment explanation
Indices: 150106--150200 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
150096 TCCTAGTTGG
* * *
150106 GAAAATAATTCCCTTACTCTAATAAACTATTAAAATATAAGA
1 GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAAA
*
150148 GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
1 GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAAA
*
150190 TAAAAT-ATTCC
1 GAAAATAATTCC
150201 TAGAATAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 5 0.10
42 43 0.90
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.31
Consensus pattern (42 bp):
GAAAATAATTCCCTTACTCTAATAAACTACTAAAACATAAAA
Found at i:156619 original size:30 final size:31
Alignment explanation
Indices: 156580--156639 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
156570 GGAGGTGAGA
*
156580 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
156611 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
156640 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:156868 original size:9 final size:9
Alignment explanation
Indices: 156851--156887 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
156841 TATAGTTTGA
*
156851 TATTTGAAT
1 TATTCGAAT
156860 TATTCGAAT
1 TATTCGAAT
*
156869 TATTCGAGT
1 TATTCGAAT
156878 TATTCGAAT
1 TATTCGAAT
156887 T
1 T
156888 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:157770 original size:30 final size:31
Alignment explanation
Indices: 157723--157783 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
157713 TTAGTCATTG
157723 AATTATTCGAAAATTTTTATTTAAGTCACTA
1 AATTATTCGAAAATTTTTATTTAAGTCACTA
* *
157754 AATTATTC-AAAGTTTTTATTTAAGTTACTA
1 AATTATTCGAAAATTTTTATTTAAGTCACTA
157784 TGTTGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.48
Consensus pattern (31 bp):
AATTATTCGAAAATTTTTATTTAAGTCACTA
Found at i:159854 original size:56 final size:50
Alignment explanation
Indices: 159734--159876 Score: 169
Period size: 50 Copynumber: 2.7 Consensus size: 50
159724 NNNNNNTCGG
* * * *
159734 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
* *
159784 TGCCAACGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATATCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATATC---GA
*
159840 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
159877 TCTCATTCCC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 39 0.50
53 4 0.05
56 35 0.45
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
Found at i:166468 original size:85 final size:86
Alignment explanation
Indices: 166361--166532 Score: 337
Period size: 85 Copynumber: 2.0 Consensus size: 86
166351 TCGAATTCAA
166361 AATATTTACAAGATGAGTAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGT
1 AATATTTACAAGATGAGTAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGT
166426 GTAGTAAGATTGAAACACCTT
66 GTAGTAAGATTGAAACACCTT
166447 AATATTTACAA-ATGAGTAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGT
1 AATATTTACAAGATGAGTAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGT
166511 GTAGTAAGATTGAAACACCTT
66 GTAGTAAGATTGAAACACCTT
166532 A
1 A
166533 TTCTAATCAA
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 75 0.87
86 11 0.13
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (86 bp):
AATATTTACAAGATGAGTAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGT
GTAGTAAGATTGAAACACCTT
Found at i:166578 original size:85 final size:85
Alignment explanation
Indices: 166378--166588 Score: 216
Period size: 85 Copynumber: 2.5 Consensus size: 85
166368 ACAAGATGAG
* * **
166378 TAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGTGTAGTAAGATTGAAACA
1 TAGATGATGTCTATATATAGGATTAAAAAACCATATTCTAATAGGAGTGTAGTAAGATTGAAACA
* * *
166443 CCTTAATATTTACAAATGAG
66 CCTTAATATTAACAAATAAA
* * **
166463 TAGATTATGTCTATTTATAGGATTGTAAAACCATATTCTAATAGGAGTGTAGTAAGATTGAAACA
1 TAGATGATGTCTATATATAGGATTAAAAAACCATATTCTAATAGGAGTGTAGTAAGATTGAAACA
166528 CCTT-AT-TCTAATCAATATAAAA
66 CCTTAATAT-TAA-CAA-AT-AAA
* * *
166550 TAGATGGA-GTTTA-ATA-AGGTTTAAAAAACCTTATTCTAA
1 TAGAT-GATGTCTATATATAGGATTAAAAAACCATATTCTAA
166589 AATAAAATAA
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
83 1 0.01
84 4 0.04
85 91 0.82
86 4 0.04
87 10 0.09
88 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (85 bp):
TAGATGATGTCTATATATAGGATTAAAAAACCATATTCTAATAGGAGTGTAGTAAGATTGAAACA
CCTTAATATTAACAAATAAA
Found at i:169226 original size:234 final size:235
Alignment explanation
Indices: 168588--169250 Score: 1096
Period size: 235 Copynumber: 2.8 Consensus size: 235
168578 CTTTTTTACT
*
168588 TTTCTCCCCAATGATTATCATAGATAAGATAAAAGAACATTGTTTCATGCAAATCCATGGAGGCA
1 TTTCTCCCCAAGGATTATCATAGATAAGATAAAAGAACATTGTTTCATGCAAATCCATGGAGGCA
* *
168653 AATTGTAAGGAACAAGCACAACAGGCCAAGTACTATATGAATGACTCATGATTTTAAAAGGATTA
66 AATTGTAAGAAACAAGCACAACAGGCCAAGTACTATATGAAGGACTCATGATTTTAAAAGGATTA
* *
168718 AGGCCATCAGATGTAGGCCCAAGCCTCACATTCTTAAGATTGCTTGCAAAACTTGGAAACTTTTA
131 AGGCCATCAGATGTAAGCCCAAGCCTCACATTCTTAGGATTGCTTGCAAAACTTGGAAACTTTTA
*
168783 TAAGTGACTGCATATAAATGCCAATATCATTCTTTAGACC
196 TAAGCGACTGCATATAAATGCCAATATCATTCTTTAGACC
* *
168823 TTTCTCCCCAAGGATTATCATAGATAAAATAAAAGAATATTGTTTCATGCAAATCCATGGAGGCA
1 TTTCTCCCCAAGGATTATCATAGATAAGATAAAAGAACATTGTTTCATGCAAATCCATGGAGGCA
168888 AATTGTAA-AGAACAAGCACAACAGGCCAAGTACTATATGAAGGACTCATGATTTTAAAAGGATT
66 AATTGTAAGA-AACAAGCACAACAGGCCAAGTACTATATGAAGGACTCATGATTTTAAAAGGATT
* * *
168952 AAGGCCATTAGATGTAAACCCAAGCCTCACACTCTTAGGATTGCTTGCAAAACTTGGAAACTTTT
130 AAGGCCATCAGATGTAAGCCCAAGCCTCACATTCTTAGGATTGCTTGCAAAACTTGGAAACTTTT
**
169017 ATAAGCGACTGCATATAAATGCCAATATTGTTCTTTAGACC
195 ATAAGCGACTGCATATAAATGCCAATATCATTCTTTAGACC
* * * *
169058 TTTCTCCCCAAGGATTATCATAGATAAGAT-AAAGAAGATTGTTTCATGCAAATTCATGAAGGGA
1 TTTCTCCCCAAGGATTATCATAGATAAGATAAAAGAACATTGTTTCATGCAAATCCATGGAGGCA
* *
169122 AATTGTAAGAAACAATCACAACAAGCCAAGTACTATATGAAGGACTCATGATTTTAAAAGGATTA
66 AATTGTAAGAAACAAGCACAACAGGCCAAGTACTATATGAAGGACTCATGATTTTAAAAGGATTA
* * * *
169187 AAGCCATCAGATGCAAGCCCAAGCCTTACATTCTTAGGATTTCTTGCAAAACTTGGAAACTTTT
131 AGGCCATCAGATGTAAGCCCAAGCCTCACATTCTTAGGATTGCTTGCAAAACTTGGAAACTTTT
169251 TATCAAATGA
Statistics
Matches: 399, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
234 148 0.37
235 251 0.63
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (235 bp):
TTTCTCCCCAAGGATTATCATAGATAAGATAAAAGAACATTGTTTCATGCAAATCCATGGAGGCA
AATTGTAAGAAACAAGCACAACAGGCCAAGTACTATATGAAGGACTCATGATTTTAAAAGGATTA
AGGCCATCAGATGTAAGCCCAAGCCTCACATTCTTAGGATTGCTTGCAAAACTTGGAAACTTTTA
TAAGCGACTGCATATAAATGCCAATATCATTCTTTAGACC
Found at i:170848 original size:30 final size:29
Alignment explanation
Indices: 170783--170849 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
170773 AGTTTAATTT
*
170783 CCAAACTTTGGGGCAAAAGCATAATTATG
1 CCAAAGTTTGGGGCAAAAGCATAATTATG
** * *
170812 TAAAAGTTTAGGGGCAAAATCATAATTTTG
1 CCAAAGTTT-GGGGCAAAAGCATAATTATG
170842 CCAAAGTT
1 CCAAAGTT
170850 AGAGTCGAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (29 bp):
CCAAAGTTTGGGGCAAAAGCATAATTATG
Found at i:173788 original size:9 final size:9
Alignment explanation
Indices: 173759--173795 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
173749 TGAGTTTTCG
173759 AATTCGAAT
1 AATTCGAAT
*
173768 AACTCGAAT
1 AATTCGAAT
173777 AATTCGAAT
1 AATTCGAAT
*
173786 AATTTGAAT
1 AATTCGAAT
173795 A
1 A
173796 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:176495 original size:93 final size:94
Alignment explanation
Indices: 176377--176563 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 94
176367 AGAGCAACTC
176377 TTCTCAAAATCTCAAAAGGTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTATGGTTCTAG
1 TTCTCAAAATCTCAAAAGGTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTATGGTTCTAG
176442 AGGATCCTGCTACAGGAAAACCAGCAATG
66 AGGATCCTGCTACAGGAAAACCAGCAATG
176471 TTCTCAAAAT-TCAAAAGGTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTATGGTTCTAG
1 TTCTCAAAATCTCAAAAGGTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTATGGTTCTAG
176535 AGGATCCTGCTACAGGAAAACCAGCAATG
66 AGGATCCTGCTACAGGAAAACCAGCAATG
176564 ACTATCTAGG
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 83 0.89
94 10 0.11
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (94 bp):
TTCTCAAAATCTCAAAAGGTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTATGGTTCTAG
AGGATCCTGCTACAGGAAAACCAGCAATG
Found at i:178054 original size:21 final size:21
Alignment explanation
Indices: 178029--178081 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
178019 AGCGGTGGCA
* *
178029 GTGAGATTAGTTACTGTAGCT
1 GTGAGATTAGATACTGTAGCG
* *
178050 GTGAGATTGGATATTGTAGCG
1 GTGAGATTAGATACTGTAGCG
178071 GTGAGATTAGA
1 GTGAGATTAGA
178082 AATAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCG
Found at i:180114 original size:114 final size:114
Alignment explanation
Indices: 179882--180561 Score: 929
Period size: 114 Copynumber: 6.0 Consensus size: 114
179872 CAGCGCCACT
** * *
179882 AAAAACCTAAGCCCAACGACGCCGTTTTCCAAGCTTTCGGGGATTTAGCAGCG-TTTGAAGAAAG
1 AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAG
* *
179946 -GCCGCTAATGCTCAGGGCTTTAGCTGCGTTTTTTAGAAAGCGCCGCAA
66 CGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
* * * *
179994 AAAAACCT-AGTCCCAACGACTCCGTTTTCTGAGCTTTCGGGGATTTGGCGGCGTTATTAATAAA
1 AAAAACCTAAG-CCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAA
* * *
180058 GCGCCGCTAATGTTCAAGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGTAA
65 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
* * * * * *
180108 AAAAACCTAAGTCCAACGACGTCGTTTTCTGAGCTTCCGAGGATTTAGCGGCTTTTTTAATAAAG
1 AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAG
* * * *
180173 CGCCGCTAATGTTCAGGGCTTTAGCGGCTTTTTTTAGAAAGCGCCTC-A
66 CGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
* * *
180221 AAAAACCTAAGCCCAACAACACCGTTTTCTGAGCTTTTGGGGATTTAGCGGCGTTTTTAAGAAAG
1 AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAG
* *
180286 CGCTGCTAATGCTCAGGGCTTTTAGCGGCATTTTTG-GAAAAGCGCCGCAA
66 CGCCGCTAATGCTCAGGGC-TTTAGCGGCGTTTTTGAG-AAAGCGCCGCAA
* * *
180336 AAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAGGAAAG
1 AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAG
* * * *
180401 CGCTGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGAAAGCGCTGCAA
66 CGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
* * * *
180450 AAAAACCTAAGCTCAACGACGCCATTTTCTGAGCTTTCGAGGATTTAGCGGCGTTTTTAATAAAG
1 AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAG
* *
180515 CGCCGCTAATGCTCAGTGCTTTAGTGGCGTTTTTGAGAAAGCGCCGC
66 CGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGC
180562 TAATGCTCAG
Statistics
Matches: 498, Mismatches: 62, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
111 2 0.00
112 45 0.09
113 83 0.17
114 287 0.58
115 81 0.16
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (114 bp):
AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAG
CGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
Found at i:180556 original size:41 final size:41
Alignment explanation
Indices: 180493--180571 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
180483 CTTTCGAGGA
*
180493 TTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGTGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGTGC
* *
180534 TTTAGTGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAG
180572 GGATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGTGC
Found at i:180849 original size:21 final size:21
Alignment explanation
Indices: 180816--180864 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
180806 TATAGATTAT
** *
180816 AGGTTTAGGGGTTATGGTTTA
1 AGGTTTAAAGGTTAGGGTTTA
* *
180837 TGGTTTAAAGGTTGGGGTTTA
1 AGGTTTAAAGGTTAGGGTTTA
180858 AGGTTTA
1 AGGTTTA
180865 TAATAGATAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (21 bp):
AGGTTTAAAGGTTAGGGTTTA
Found at i:181140 original size:19 final size:18
Alignment explanation
Indices: 181111--181164 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
181101 GGGCCAATTT
*
181111 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
181129 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
181148 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
181165 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:181218 original size:47 final size:48
Alignment explanation
Indices: 181149--181247 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
181139 AAAAATGAAA
*
181149 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
181197 TAAAAA-ACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
181244 TAAA
1 TAAA
181248 CAAAACTATG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (48 bp):
TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
Found at i:185789 original size:43 final size:43
Alignment explanation
Indices: 185742--185907 Score: 260
Period size: 43 Copynumber: 3.9 Consensus size: 43
185732 GCTTTTATCA
* *
185742 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGGTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
185785 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
* *
185828 AAGGCGCCACTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
* * * *
185871 AAAGTGCCGCTAAAGAACATGATCTTTAGTGGCGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
185908 TGCCTCATAA
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 113 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
Found at i:186036 original size:22 final size:22
Alignment explanation
Indices: 186001--186043 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
185991 TAGCAGCGCT
* * *
186001 AAAAAGCGCTGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAGCCTA
186023 AAAAAACGCCGCTAAAAGCCT
1 AAAAAACGCCGCTAAAAGCCT
186044 GTTTTGATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAGCCTA
Found at i:197500 original size:15 final size:16
Alignment explanation
Indices: 197470--197502 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
197460 CATAAGGGCT
197470 AATATGCGCCTCTCTC
1 AATATGCGCCTCTCTC
*
197486 AATATG-GCCTGTCTC
1 AATATGCGCCTCTCTC
197501 AA
1 AA
197503 ATCAGTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (16 bp):
AATATGCGCCTCTCTC
Found at i:199769 original size:76 final size:76
Alignment explanation
Indices: 199678--199831 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
199668 TGGTGTATGT
199678 AAGATTCAGAAAACAAAGTTAAGAGTTTCCAAAACCATTTTAAGGGTTCTGCATGTTCCTGGAAA
1 AAGATTCAGAAAACAAAGTTAAGAGTTTCCAAAACCATTTTAAGGGTTCTGCATGTTCCTGGAAA
199743 ACTAAGTTTAA
66 ACTAAGTTTAA
199754 AAGATTCAGAAAACAAAGTTAAGAGTTTCCAAAACCATTTTAAGGGTTCTGCATGTTCCTGGAAA
1 AAGATTCAGAAAACAAAGTTAAGAGTTTCCAAAACCATTTTAAGGGTTCTGCATGTTCCTGGAAA
199819 ACTAAGTTTAA
66 ACTAAGTTTAA
199830 AA
1 AA
199832 AGAGATTTAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (76 bp):
AAGATTCAGAAAACAAAGTTAAGAGTTTCCAAAACCATTTTAAGGGTTCTGCATGTTCCTGGAAA
ACTAAGTTTAA
Found at i:200156 original size:21 final size:21
Alignment explanation
Indices: 200130--200169 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
200120 ATGGGAAACG
*
200130 AGACTTTCTATCAGATATCGC
1 AGACTTTCTATCAAATATCGC
200151 AGACTTTCTATCAAATATC
1 AGACTTTCTATCAAATATC
200170 ACCATACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (21 bp):
AGACTTTCTATCAAATATCGC
Found at i:201874 original size:24 final size:25
Alignment explanation
Indices: 201847--201910 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
201837 ATACATGTAT
*
201847 GCTCATACGAGCT-ATAAACGGTAA
1 GCTCATACGAGCTGAAAAACGGTAA
* * * *
201871 GCTCCTCCGAGTTGAAAAATGGTAA
1 GCTCATACGAGCTGAAAAACGGTAA
*
201896 GCTCATACAAGCTGA
1 GCTCATACGAGCTGA
201911 GTATCGATAA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGAAAAACGGTAA
Found at i:206123 original size:25 final size:25
Alignment explanation
Indices: 206087--206182 Score: 106
Period size: 26 Copynumber: 3.8 Consensus size: 25
206077 AATTCAAGCA
* *
206087 AGCCA-TATCAGGAAGCTC-CAGAG
1 AGCCATTAACAGGAAGCTCACAAAG
206110 AGCCATTAATCAGGAAGCTCACAAAG
1 AGCCATTAA-CAGGAAGCTCACAAAG
* *
206136 AGCCTTTAACCGAGAAGCTCACAAAG
1 AGCCATTAACAG-GAAGCTCACAAAG
*
206162 AGCCATATAACAGGACGCTCA
1 AGCCAT-TAACAGGAAGCTCA
206183 TATGTGTTGC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.08
24 2 0.03
25 12 0.20
26 37 0.61
27 5 0.08
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.15
Consensus pattern (25 bp):
AGCCATTAACAGGAAGCTCACAAAG
Found at i:216874 original size:29 final size:29
Alignment explanation
Indices: 216832--216893 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
216822 GAGGTTTATT
*
216832 CGAGCTCTCCTCTTGCAGCCTCATTTCTG
1 CGAGCTCTCCTCTTGCAACCTCATTTCTG
* *
216861 CGAGCTTTCCTCTTGCAACCTCATTTTTG
1 CGAGCTCTCCTCTTGCAACCTCATTTCTG
216890 CGAG
1 CGAG
216894 GTCTACGCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.34, G:0.18, T:0.35
Consensus pattern (29 bp):
CGAGCTCTCCTCTTGCAACCTCATTTCTG
Found at i:220272 original size:2 final size:2
Alignment explanation
Indices: 220267--220291 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
220257 TATATATATA
220267 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
220292 TTTATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:223331 original size:9 final size:9
Alignment explanation
Indices: 223317--223353 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
223307 TGCGTTAAAC
223317 TTCTTTTCT
1 TTCTTTTCT
223326 TTC-TTTCT
1 TTCTTTTCT
*
223334 TTATTTTCT
1 TTCTTTTCT
223343 TTCTTTTCT
1 TTCTTTTCT
223352 TT
1 TT
223354 TGATTAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:223335 original size:13 final size:13
Alignment explanation
Indices: 223317--223353 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
223307 TGCGTTAAAC
223317 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
223330 TTCTTTAT-TTTCT
1 TTCTTT-TCTTTCT
223343 TTCTTTTCTTT
1 TTCTTTTCTTT
223354 TGATTAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:229939 original size:20 final size:21
Alignment explanation
Indices: 229901--229940 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
229891 AAAGAAATAA
229901 ATAAAGAAAAAGAATAAGATT
1 ATAAAGAAAAAGAATAAGATT
229922 ATAAA-AAAAAGTAA-AAGAT
1 ATAAAGAAAAAG-AATAAGAT
229941 ATATGTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
ATAAAGAAAAAGAATAAGATT
Found at i:236931 original size:69 final size:69
Alignment explanation
Indices: 236811--237034 Score: 225
Period size: 69 Copynumber: 3.2 Consensus size: 69
236801 AAATTTTACA
* * * * * * * *
236811 TACGAACCTTAGTTTTACAGTTGGGAGCTTTGCTCTTGCTAACCATGTTGGAGGTCGCGGCTGTT
1 TACGAACCTTAATTTTATAGCTAGGAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCAGCTCTT
*
236876 CGCC
66 CACC
** * * *
236880 TGTGAACCTTAATTTTATAGCTAGGAGCTTTGCTCTCACTAACTATATTGGAGGTTGCAGCTCTT
1 TACGAACCTTAATTTTATAGCTAGGAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCAGCTCTT
*
236945 CATC
66 CACC
* * * **
236949 TACAAACCTGAATTTTATAGCTAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGT-TAATGCTCT
1 TACGAACCTTAATTTTATAGCTAGGAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCA-GCTCT
* *
237013 TCGCT
65 TCACC
*
237018 TGCGAACCTTAATTTTA
1 TACGAACCTTAATTTTA
237035 CAGGTGATAT
Statistics
Matches: 124, Mismatches: 30, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
68 1 0.01
69 123 0.99
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (69 bp):
TACGAACCTTAATTTTATAGCTAGGAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCAGCTCTT
CACC
Found at i:237353 original size:92 final size:92
Alignment explanation
Indices: 237196--237384 Score: 369
Period size: 92 Copynumber: 2.1 Consensus size: 92
237186 TTGTATGGTC
237196 CCTCTCAGCTCGAGGTATTTTTATTGTGTTGGGAAGCGGAAAATCTGGCTTCAGTGTTTCTTAGC
1 CCTCTCAGCTCGAGGTATTTTTATTGTGTTGGGAAGCGGAAAATCTGGCTTCAGTGTTTCTTAGC
237261 ACAAGGTCAGCTAATTGAAACTACTTT
66 ACAAGGTCAGCTAATTGAAACTACTTT
*
237288 CCTCTCAGCTCGAGGTATTTTTATTGTGTTGGGAAGCTGAAAATCTGGCTTCAGTGTTTCTTAGC
1 CCTCTCAGCTCGAGGTATTTTTATTGTGTTGGGAAGCGGAAAATCTGGCTTCAGTGTTTCTTAGC
237353 ACAAGGTCAGCTAATTGAAACTACTTT
66 ACAAGGTCAGCTAATTGAAACTACTTT
237380 CCTCT
1 CCTCT
237385 AACATTGGAA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (92 bp):
CCTCTCAGCTCGAGGTATTTTTATTGTGTTGGGAAGCGGAAAATCTGGCTTCAGTGTTTCTTAGC
ACAAGGTCAGCTAATTGAAACTACTTT
Found at i:246175 original size:11 final size:10
Alignment explanation
Indices: 246134--246200 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
246124 ACTTAATCCT
246134 TTCTCTCAAA
1 TTCTCTCAAA
246144 TTCTCTCTAATA
1 TTCTCTC-AA-A
246156 TTCTCTCAAA
1 TTCTCTCAAA
246166 TTCTTCTCAAA
1 TTC-TCTCAAA
* * *
246177 TGCCTTTCTAA
1 T-TCTCTCAAA
246188 TTCCTCTCAAA
1 TT-CTCTCAAA
246199 TT
1 TT
246201 ATTTTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
10 11 0.24
11 26 0.57
12 9 0.20
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.45
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:246252 original size:30 final size:29
Alignment explanation
Indices: 246197--246253 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
246187 ATTCCTCTCA
246197 AATTATTTTTAAAAAAGCTTTAATTTTTT
1 AATTATTTTTAAAAAAGCTTTAATTTTTT
* *
246226 AATTATTTTTAAAAAAGTTTTAAATTTT
1 AATTATTTTTAAAAAAGCTTTAATTTTT
246254 ATTTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (29 bp):
AATTATTTTTAAAAAAGCTTTAATTTTTT
Found at i:247390 original size:7 final size:7
Alignment explanation
Indices: 247374--247405 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
247364 TAGTCAATTG
*
247374 GTATTCA
1 GTATTTA
247381 GTATTTA
1 GTATTTA
247388 GTATTTA
1 GTATTTA
247395 GTATTTA
1 GTATTTA
247402 GTAT
1 GTAT
247406 ATATAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (7 bp):
GTATTTA
Found at i:248727 original size:125 final size:126
Alignment explanation
Indices: 248505--248856 Score: 589
Period size: 125 Copynumber: 2.8 Consensus size: 126
248495 TCAGGCCTAA
* *
248505 CAGGAGCTACTGCAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* *
248570 ATCTTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCAACTCAAAATTAT-TTTT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCAACTCAAAATTATCTTTT
*
248630 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
**
248695 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATCTTTT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCAACTCAAAATTATCTTTT
* * * * *
248756 CAGGAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGATAAAAC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
248821 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAG
66 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAG
248857 GAACGTCTTC
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
125 114 0.54
126 99 0.46
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCAACTCAAAATTATCTTTT
Found at i:248824 original size:126 final size:125
Alignment explanation
Indices: 248505--248877 Score: 595
Period size: 126 Copynumber: 3.0 Consensus size: 125
248495 TCAGGCCTAA
*
248505 CAGGAGCTACTGCAGCAAAA-ACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAG
1 CAGGAGCTACTGTAGCAAAAGA-GCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAG
* * **
248569 CATCTTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCAACTCAAAATTATTTTT
65 CATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
* *
248630 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
248695 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATCTTTT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTAT-TTTT
* * * *
248756 CAGGAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGATAAAAC
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * *
248821 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGGAACGTCTTCTTAAAATTATT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATT
248878 AATTCAAATT
Statistics
Matches: 230, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
125 114 0.50
126 116 0.50
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (125 bp):
CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
Found at i:249155 original size:93 final size:94
Alignment explanation
Indices: 248978--249155 Score: 206
Period size: 93 Copynumber: 1.9 Consensus size: 94
248968 CCTAAACCCC
* *
248978 AAACCTTAATTTAATTAAGTTTTTACTTAAAAACTCTAAACACTAAACCCTAATCTAATTTTTAA
1 AAACCCTAATTTAATT-A-TTTTTACTTAAAAACTCTAAACACTAAACCCTAATCTAATTTTGAA
* *
249043 ACAATTTTTAATTATTTACTCAAGAAATCGT
64 ACAAATTATAATTATTTACTCAAGAAATCGT
*
249074 AAACCCTAATTTAATT-TTTTTTCTTTAAAAAC-CATAAACA-TGAAA-CCTAATAC-AATTTTG
1 AAACCCTAATTTAATTATTTTTAC-TTAAAAACTC-TAAACACT-AAACCCTAAT-CTAATTTTG
249134 AAA-AAATTATAATTAATTTACT
62 AAACAAATTATAATT-ATTTACT
249156 TGACAAACCC
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
92 9 0.12
93 30 0.42
94 18 0.25
96 15 0.21
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (94 bp):
AAACCCTAATTTAATTATTTTTACTTAAAAACTCTAAACACTAAACCCTAATCTAATTTTGAAAC
AAATTATAATTATTTACTCAAGAAATCGT
Found at i:251028 original size:29 final size:30
Alignment explanation
Indices: 250966--251031 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
250956 ATCTCAAAAC
*
250966 TATACATGAACTAGGGTTTATGTGCAATTA
1 TATACATGAACTAGGATTTATGTGCAATTA
** *
250996 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTAGGATTTATGTGCAATTA
251025 TATACAT
1 TATACAT
251032 AAATTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (30 bp):
TATACATGAACTAGGATTTATGTGCAATTA
Found at i:258168 original size:9 final size:9
Alignment explanation
Indices: 258150--258215 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
258140 ACAATTATTA
*
258150 TTTTAGAAT
1 TTTTAAAAT
258159 TTTTAAAAT
1 TTTTAAAAT
258168 TTTTAATATAT
1 TTTTAA-A-AT
*
258179 TCTTTAGAAT
1 T-TTTAAAAT
*
258189 TTTTAATAT
1 TTTTAAAAT
* *
258198 TTTATATATT
1 TTT-TAAAAT
258208 TTTTAAAA
1 TTTTAAAA
258216 ATATAAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 26 0.59
10 10 0.23
11 4 0.09
12 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:258185 original size:30 final size:28
Alignment explanation
Indices: 258151--258212 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
258141 CAATTATTAT
258151 TTTAGAATTTTTAAAATTTTTAATATATTC
1 TTTAGAATTTTTAAAA-TTTT-ATATATTC
* *
258181 TTTAGAATTTTTAATATTTTATATATTT
1 TTTAGAATTTTTAAAATTTTATATATTC
258209 TTTA
1 TTTA
258213 AAAATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
29 4 0.13
30 15 0.50
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTAGAATTTTTAAAATTTTATATATTC
Found at i:258250 original size:19 final size:19
Alignment explanation
Indices: 258217--258271 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
258207 TTTTTAAAAA
*
258217 TATAAA-ATTTAGAATTTT
1 TATAAATATTTTGAATTTT
258235 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
258253 TAAAAACTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
258272 CTTTTTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.44
19 16 0.50
20 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:260951 original size:91 final size:91
Alignment explanation
Indices: 260791--260964 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 91
260781 AGTTGTGGAT
* * ** * *
260791 GAACCACCAAATGTTGCAGGTTAATACGTTGCTAGATGATTGTGAGTACACAACATAATTGCAGA
1 GAACAACCAAAAGTTGCAGGTTAATACGCCGCCAGATGATTGTGAATACACAACATAATTGCAGA
260856 TAAAAGCTACCAGATAATGGGTGGGC
66 TAAAAGCTACCAGATAATGGGTGGGC
* * * **
260882 GAACAACCAAAAGTTGTAGGTTAATACGCCGCCAGATGGTTGTGAATACACAACTTAATTTTAGA
1 GAACAACCAAAAGTTGCAGGTTAATACGCCGCCAGATGATTGTGAATACACAACATAATTGCAGA
*
260947 TAAAAGCTGCCAGATAAT
66 TAAAAGCTACCAGATAAT
260965 ATGTGGATGA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (91 bp):
GAACAACCAAAAGTTGCAGGTTAATACGCCGCCAGATGATTGTGAATACACAACATAATTGCAGA
TAAAAGCTACCAGATAATGGGTGGGC
Found at i:263442 original size:17 final size:17
Alignment explanation
Indices: 263416--263449 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
263406 AAAACATCAT
263416 AGTTTCTAAATAACTAAA
1 AGTTTCTAAATAA-TAAA
263434 AGTTT-TAAATAATAAA
1 AGTTTCTAAATAATAAA
263450 TCTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
AGTTTCTAAATAATAAA
Found at i:273112 original size:51 final size:51
Alignment explanation
Indices: 273026--273226 Score: 194
Period size: 51 Copynumber: 4.0 Consensus size: 51
273016 ATTAATGATA
* * * * *
273026 CCGGTTCACATAGTAGCATGCATATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* * * *
273077 CCGATACACGTAGTAGCGTGCACATAGTGCTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * * * *
273128 CCGGTACGCATAGTAGCCTGCACATCGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
** *
273178 TTGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
273227 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
49 4 0.03
50 39 0.33
51 73 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:273202 original size:101 final size:102
Alignment explanation
Indices: 273034--273218 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 102
273024 TACCGGTTCA
* * * *
273034 CATAGTAGCATGCATATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCGTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
*
273099 CATAGTGCTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * ** *
273136 CATAGTAGCCTGCACATCGTACTACACATGCGACCTATCA-T-TTTGGTACACGTAGTAGCCTAC
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTAC
273199 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
273219 CCATCACTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
101 36 0.50
102 32 0.44
103 4 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:273242 original size:101 final size:102
Alignment explanation
Indices: 273026--273218 Score: 246
Period size: 102 Copynumber: 1.9 Consensus size: 102
273016 ATTAATGATA
* * *
273026 CCGGTTCACATAGTAGCATGCATATAGTACTACACATGTGACCATCACTATCCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
* * * *
273091 AGCGTGCACATAGTGCTACACACGTGATCGAAGCTAT
66 AGCCTACACATAGTACTACACACGTGATCCAAGCTAT
* * * ** *
273128 CCGGTACGCATAGTAGCCTGCACATCGTACTACACATGCGACCTATCA-T-TTTGGTACACGTAG
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAG
273191 TAGCCTACACATAGTACTACACACGTGA
65 TAGCCTACACATAGTACTACACACGTGA
273219 CCATCACTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
101 36 0.46
102 38 0.49
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
AGCCTACACATAGTACTACACACGTGATCCAAGCTAT
Found at i:288067 original size:13 final size:14
Alignment explanation
Indices: 288045--288073 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
288035 AACTTCTCTG
288045 TTTTGTTTTGTTTT
1 TTTTGTTTTGTTTT
288059 TTTTG-TTTGTTTT
1 TTTTGTTTTGTTTT
288072 TT
1 TT
288074 CTTTGGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTGTTTTGTTTT
Found at i:288845 original size:21 final size:21
Alignment explanation
Indices: 288821--288860 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
288811 TATAATTTGG
288821 ATTTAGAAACTTTATGTTTAT
1 ATTTAGAAACTTTATGTTTAT
**
288842 ATTTCTAAACTTTATGTTT
1 ATTTAGAAACTTTATGTTT
288861 GGATTATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTTAGAAACTTTATGTTTAT
Found at i:291098 original size:17 final size:17
Alignment explanation
Indices: 291076--291109 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
291066 GTAGAACCTC
291076 CTTTTTATTGGAGTTGT
1 CTTTTTATTGGAGTTGT
291093 CTTTTTATTGGAGTTGT
1 CTTTTTATTGGAGTTGT
291110 TTGTTATCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.59
Consensus pattern (17 bp):
CTTTTTATTGGAGTTGT
Found at i:294577 original size:3 final size:3
Alignment explanation
Indices: 294571--294609 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
294561 AATAATCATT
294571 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
294610 ATCATGGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:295109 original size:7 final size:8
Alignment explanation
Indices: 295085--295109 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
295075 ATTATTTTTA
295085 TTTAATTT
1 TTTAATTT
295093 TTTAATTT
1 TTTAATTT
295101 TTTAATTT
1 TTTAATTT
295109 T
1 T
295110 AATATTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTAATTT
Found at i:295580 original size:2 final size:2
Alignment explanation
Indices: 295569--295601 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
295559 TTTTACTTTG
295569 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
295602 ATACTAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:297693 original size:37 final size:36
Alignment explanation
Indices: 297635--297705 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
297625 TTGGATAGAC
* *
297635 TAGCTTTTATGAGCATCTGGCGTGTTATCGGGTGGTT
1 TAGCTCTTATGAGCATCTGGCGTGTT-TCAGGTGGTT
*
297672 TAGCTCTTATGAGCGGT-TGGCGTGTTTCAGGTGG
1 TAGCTCTTATGAGC-ATCTGGCGTGTTTCAGGTGG
297706 AATATCTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 7 0.23
37 22 0.73
38 1 0.03
ACGTcount: A:0.13, C:0.14, G:0.35, T:0.38
Consensus pattern (36 bp):
TAGCTCTTATGAGCATCTGGCGTGTTTCAGGTGGTT
Found at i:300543 original size:27 final size:27
Alignment explanation
Indices: 300496--300560 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
300486 AAATATTCTC
300496 TAAATTAAT-AAATATTAATTTATCAA
1 TAAATTAATAAAATATTAATTTATCAA
* *
300522 TAAATTAATAAAATATTTATTTATCGA
1 TAAATTAATAAAATATTAATTTATCAA
* *
300549 TTAACTAATAAA
1 TAAATTAATAAA
300561 CTTGATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCAA
Found at i:307492 original size:34 final size:34
Alignment explanation
Indices: 307449--307517 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
307439 AATTAAAAAC
307449 TATGCATTTTTTAATTAAAAATATTATATTATGT
1 TATGCATTTTTTAATTAAAAATATTATATTATGT
307483 TATGCATTTTTTAATTAAAAATATTATATTATGT
1 TATGCATTTTTTAATTAAAAATATTATATTATGT
307517 T
1 T
307518 CTTTTTAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (34 bp):
TATGCATTTTTTAATTAAAAATATTATATTATGT
Found at i:308476 original size:16 final size:15
Alignment explanation
Indices: 308451--308484 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
308441 ACAGCATAAC
*
308451 TAAATGTATATAAATA
1 TAAATATATAT-AATA
308467 TAAATATATATAATA
1 TAAATATATATAATA
308482 TAA
1 TAA
308485 CCTGTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAATATATATAATA
Found at i:309110 original size:41 final size:40
Alignment explanation
Indices: 309065--309166 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 40
309055 TGATTCAGTA
309065 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * *
309106 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
309147 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
309167 AGCGCTAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 2 0.04
41 51 0.93
42 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:309181 original size:41 final size:41
Alignment explanation
Indices: 309065--309181 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
309055 TGATTCAGTA
* * * * *
309065 CACCGGCACTTAGCCTGCTAGACA-TATAGTCTGAAATATTT
1 CACCGGCAATAAGCCTGCTAGACACTA-AGCCTGAAGTGTTT
* * * *
309106 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
*
309147 CACCGGCAATAAGCCTGCTA-AGCGCTAAGCCTGAA
1 CACCGGCAATAAGCCTGCTAGA-CACTAAGCCTGAA
309182 AATCTCAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
Found at i:311562 original size:35 final size:35
Alignment explanation
Indices: 311516--311785 Score: 276
Period size: 35 Copynumber: 7.5 Consensus size: 35
311506 CCTTAAACGT
311516 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACAG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACAG
* * *
311551 GTCTATCCCAACCTTTTTTAAAGATTGCCTTAGACAAT
1 GTCTATCCCAACC-TTTTT-AAGGTTGTCTTAGAC-AG
* * *
311589 GTCTATCTCAACCTTTTTAGGGTTG-CTTTCGACAAG
1 GTCTATCCCAACCTTTTTAAGGTTGTC-TTAGAC-AG
* * *
311625 GTCTATCCCAACCTTTCTAAGGTTATTTTAGACAG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACAG
*
311660 GTCTATCCTAACCTTTTTTAAAGGTTG-CTTTAGACAAG
1 GTCTATCCCAACC-TTTTT-AAGGTTGTC-TTAGAC-AG
* ** *
311698 GTCTATTCCAAATTTTTTAAGGTTGTCTTAGATAG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACAG
* *
311733 GTCTATCCTAACCTTTTTAAGATT-TCTTCAGACAG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTT-AGACAG
*
311768 GTTTATCCCAACCTTTTT
1 GTCTATCCCAACCTTTTT
311786 TAAATGTCGG
Statistics
Matches: 193, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
34 4 0.02
35 70 0.36
36 59 0.31
37 36 0.19
38 24 0.12
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (35 bp):
GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACAG
Found at i:311700 original size:73 final size:70
Alignment explanation
Indices: 311516--311785 Score: 292
Period size: 73 Copynumber: 3.8 Consensus size: 70
311506 CCTTAAACGT
* * *
311516 GTCTATCCCAACCTTTTTAAGGTTG-TCTTAGACAGGTCTATCCCAACCTTTTTTAAAGATTGCC
1 GTCTATCCTAACCTTTTTAAGGTTGCT-TTAGACAGGTCTATCCCAACC-TTTTT-AAGGTTGTC
*
311580 TTAGACAAT
63 TTAGAC-AG
* * * * *
311589 GTCTAT-CTCAACCTTTTTAGGGTTGCTTTCGACAAGGTCTATCCCAACCTTTCTAAGGTTATTT
1 GTCTATCCT-AACCTTTTTAAGGTTGCTTTAGAC-AGGTCTATCCCAACCTTTTTAAGGTTGTCT
311653 TAGACAG
64 TAGACAG
* **
311660 GTCTATCCTAACCTTTTTTAAAGGTTGCTTTAGACAAGGTCTATTCCAAATTTTTTAAGGTTGTC
1 GTCTATCCTAACC-TTTTT-AAGGTTGCTTTAGAC-AGGTCTATCCCAACCTTTTTAAGGTTGTC
*
311725 TTAGATAG
63 TTAGACAG
* * * *
311733 GTCTATCCTAACCTTTTTAAGATTTCTTCAGACAGGTTTATCCCAACCTTTTT
1 GTCTATCCTAACCTTTTTAAGGTTGCTTTAGACAGGTCTATCCCAACCTTTTT
311786 TAAATGTCGG
Statistics
Matches: 166, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
70 16 0.10
71 23 0.14
72 24 0.14
73 87 0.52
74 16 0.10
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (70 bp):
GTCTATCCTAACCTTTTTAAGGTTGCTTTAGACAGGTCTATCCCAACCTTTTTAAGGTTGTCTTA
GACAG
Found at i:311715 original size:109 final size:107
Alignment explanation
Indices: 311516--311789 Score: 345
Period size: 109 Copynumber: 2.5 Consensus size: 107
311506 CCTTAAACGT
*
311516 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACAGGTCTATCCCAACCTTTTTTAAAGATTGCCT
1 GTCTATCCCAACCTTTTTAAGGTT-TTTTAGACAGGTCTATCCCAACCTTTTTTAAAGATTGCCT
* * * *
311581 TAGACAATGTCTATCTCAACCTTTTTAGGGTTG-CTTTCGACAAG
65 TAGACAAGGTCTATCTCAAACTTTTTAAGGTTGTC-TTAGA-AAG
* * * *
311625 GTCTATCCCAACCTTTCTAAGGTTATTTTAGACAGGTCTATCCTAACCTTTTTTAAAGGTTGCTT
1 GTCTATCCCAACCTTTTTAAGGTT-TTTTAGACAGGTCTATCCCAACCTTTTTTAAAGATTGCCT
* *
311690 TAGACAAGGTCTAT-TCCAAATTTTTTAAGGTTGTCTTAGATAG
65 TAGACAAGGTCTATCT-CAAACTTTTTAAGGTTGTCTTAGAAAG
* * * *
311733 GTCTATCCTAACCTTTTTAAGATTTCTTCAGACAGGTTTATCCCAACCTTTTTTAAA
1 GTCTATCCCAACCTTTTTAAGGTTT-TTTAGACAGGTCTATCCCAACCTTTTTTAAA
311790 TGTCGGCCTT
Statistics
Matches: 144, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
107 1 0.01
108 52 0.36
109 90 0.62
110 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (107 bp):
GTCTATCCCAACCTTTTTAAGGTTTTTTAGACAGGTCTATCCCAACCTTTTTTAAAGATTGCCTT
AGACAAGGTCTATCTCAAACTTTTTAAGGTTGTCTTAGAAAG
Found at i:319443 original size:12 final size:12
Alignment explanation
Indices: 319426--319451 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
319416 GCAATCCAAG
319426 TTTGTTTTACAC
1 TTTGTTTTACAC
319438 TTTGTTTTACAC
1 TTTGTTTTACAC
319450 TT
1 TT
319452 CTCTATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTGTTTTACAC
Found at i:321128 original size:36 final size:36
Alignment explanation
Indices: 321081--321152 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
321071 AATAACTTAA
321081 CATTGAACGAACCATGTCAAGCAAGGTTTTATTCAT
1 CATTGAACGAACCATGTCAAGCAAGGTTTTATTCAT
*
321117 CATTGAACGAACCATGTCAAGTAAGGTTTTATTCAT
1 CATTGAACGAACCATGTCAAGCAAGGTTTTATTCAT
321153 TCTCTCAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (36 bp):
CATTGAACGAACCATGTCAAGCAAGGTTTTATTCAT
Found at i:323788 original size:7 final size:7
Alignment explanation
Indices: 323778--323804 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
323768 AAGAAATAAG
323778 ATAAAAT
1 ATAAAAT
323785 ATAAAAT
1 ATAAAAT
323792 ATAAAAT
1 ATAAAAT
323799 ATAAAA
1 ATAAAA
323805 AAACGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
ATAAAAT
Found at i:328032 original size:19 final size:20
Alignment explanation
Indices: 328004--328042 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
327994 ACTTAGAAAA
328004 AAAAATCCAC-GAACAAATAG
1 AAAAATCCACAGAA-AAATAG
328024 AAAAA-CCACAGAAAAATAG
1 AAAAATCCACAGAAAAATAG
328043 CGTACACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.64, C:0.18, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAAATCCACAGAAAAATAG
Found at i:335992 original size:13 final size:13
Alignment explanation
Indices: 335974--335998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335964 TATTTTAATA
335974 TTATTTTGTGTGT
1 TTATTTTGTGTGT
335987 TTATTTTGTGTG
1 TTATTTTGTGTG
335999 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:338087 original size:40 final size:40
Alignment explanation
Indices: 337990--338133 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 40
337980 GACTTTAAGT
* * *
337990 CTAGCAGGCTAAGTGTCGGTGATCTGAACCATGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
338031 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
* * *
338071 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTGTAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-C
*
338112 CTAGCAGGCTAAGTGCCAGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
338134 ATATGTTAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 39 0.41
41 55 0.59
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.24
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
Found at i:345059 original size:39 final size:41
Alignment explanation
Indices: 345016--345096 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 41
345006 GGCTCTTATA
345016 CCAATTGTTG-AAAAAAAA-TTTGTTTGAAAATGATTTTCT
1 CCAATTGTTGAAAAAAAAACTTTGTTTGAAAATGATTTTCT
345055 CCAATTGTTGAAAAAAAAAACTTTGTTTGAAAATGATTTTCT
1 CCAATTGTTG-AAAAAAAAACTTTGTTTGAAAATGATTTTCT
345097 TACATAGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 10 0.26
41 8 0.21
42 21 0.54
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (41 bp):
CCAATTGTTGAAAAAAAAACTTTGTTTGAAAATGATTTTCT
Found at i:345976 original size:12 final size:12
Alignment explanation
Indices: 345959--345997 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
345949 GGATTGCAAG
345959 TTTTCATTTCCA
1 TTTTCATTTCCA
*
345971 TTTTCATTTTCA
1 TTTTCATTTCCA
*
345983 TTTCCATTTCCA
1 TTTTCATTTCCA
345995 TTT
1 TTT
345998 CTAGAAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTCATTTCCA
Found at i:345978 original size:6 final size:6
Alignment explanation
Indices: 345963--345998 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
345953 TGCAAGTTTT
* *
345963 CATTTC CATTTT CATTTT CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
345999 TAGAAACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (6 bp):
CATTTC
Found at i:345982 original size:18 final size:18
Alignment explanation
Indices: 345959--345997 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
345949 GGATTGCAAG
*
345959 TTTTCATTTCCATTTTCA
1 TTTTCATTTCCATTTCCA
345977 TTTTCATTTCCATTTCCA
1 TTTTCATTTCCATTTCCA
345995 TTT
1 TTT
345998 CTAGAAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTCATTTCCATTTCCA
Found at i:347740 original size:26 final size:26
Alignment explanation
Indices: 347693--347759 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 26
347683 ATCCAACACC
* * * * *
347693 TCTGGCCAACTTAACCTTAAGGGTCA
1 TCTGACCAACTCAAACTCAAGGGACA
*
347719 TCTGACCAACTCAAACTCAAGGGACC
1 TCTGACCAACTCAAACTCAAGGGACA
**
347745 TCCAACCAACTCAAA
1 TCTGACCAACTCAAA
347760 TAGGAGGATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.19
Consensus pattern (26 bp):
TCTGACCAACTCAAACTCAAGGGACA
Found at i:350007 original size:21 final size:21
Alignment explanation
Indices: 349963--350007 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
349953 TTATTTGCAT
* *
349963 TAAAAATTTCCATTTAATTCA
1 TAAAAAATTCCATTTAATTAA
*
349984 TAAAAAATTCCATTTACTTAA
1 TAAAAAATTCCATTTAATTAA
350005 TAA
1 TAA
350008 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAATTCCATTTAATTAA
Found at i:351081 original size:127 final size:125
Alignment explanation
Indices: 350797--351239 Score: 611
Period size: 127 Copynumber: 3.5 Consensus size: 125
350787 GATAAAATCG
* * * * * * *
350797 AAGCAGGATGATTTATCAGAAGGATTTTTTAAGTCGCGCCCACGTGTACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
* * *
350862 AGGTCCTAGAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * *
350922 AAGCAGGATGCTTTATGAGAAGAATTTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
* * * *
350987 TGGTCCTGGAAGAAATAATTTCGAGTTGATGTTTTTGAGCAAATAGTATAAAACAACGCTGC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCTTC
* * * *
351049 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGTGCCCTCGTGGATGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAG
* * * *
351113 TAGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAGTAT-AAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
*
351173 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
351238 AG
66 AG
351240 CATGTTTGGG
Statistics
Matches: 283, Mismatches: 31, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
123 2 0.01
124 65 0.23
125 69 0.24
126 69 0.24
127 76 0.27
128 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:354387 original size:15 final size:15
Alignment explanation
Indices: 354359--354397 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
354349 ATTTTTACGG
354359 TTTAAAAA-AA-TTT
1 TTTAAAAATAATTTT
354372 TTTAAAAATTAATTTT
1 TTTAAAAA-TAATTTT
354388 TTTAAAAATA
1 TTTAAAAATA
354398 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
15 4 0.17
16 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAAAAATAATTTT
Done.