Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015299.1 Kokia drynarioides strain JFW-HI SEQ_130344, whole genome shotgun sequence
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: 1333876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 300 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:398 original size:104 final size:105
Alignment explanation
Indices: 210--426 Score: 384
Period size: 104 Copynumber: 2.1 Consensus size: 105
200 TCCTCCACTT
* *
210 AACTAAACATATCATTTTGGTAAATAATAATTTGGAGATATCATTTTGGTTATTAATTTATTTTT
1 AACT-AACATATCATTTTGGTAAATAATAATTTGGAGATACCATTTTAGTTATTAATTTATTTTT
275 TTGTATTATTTAAGTAAAAAATCCTAAGATAATATATTAG-
65 TTGTATTATTTAAGTAAAAAATCCTAAGATAATATATTAGC
315 AACTAACATATCATTTTGGTAAATAATAATTTGGAGATACCATTTTAGTTATTAATTTA-TTTTT
1 AACTAACATATCATTTTGGTAAATAATAATTTGGAGATACCATTTTAGTTATTAATTTATTTTTT
379 TGTATTATTTAAGTAAAAAATCCTAAGATAATATATTAGC
66 TGTATTATTTAAGTAAAAAATCCTAAGATAATATATTAGC
*
419 AAATAACA
1 AACTAACA
427 CTTATGTTAT
Statistics
Matches: 108, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
103 44 0.41
104 60 0.56
105 4 0.04
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (105 bp):
AACTAACATATCATTTTGGTAAATAATAATTTGGAGATACCATTTTAGTTATTAATTTATTTTTT
TGTATTATTTAAGTAAAAAATCCTAAGATAATATATTAGC
Found at i:19653 original size:24 final size:23
Alignment explanation
Indices: 19626--19679 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
19616 CATTGTAAAT
19626 TTTTCTGTTAATTT-TTGTCTTTTA
1 TTTTCTGTTAATTTGTT-T-TTTTA
19650 TTTTACT-TTAATTTGTTTTTTTA
1 TTTT-CTGTTAATTTGTTTTTTTA
*
19673 GTTTCTG
1 TTTTCTG
19680 CAGGAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 2 0.08
23 8 0.31
24 12 0.46
25 4 0.15
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTTCTGTTAATTTGTTTTTTTA
Found at i:21486 original size:18 final size:17
Alignment explanation
Indices: 21463--21496 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21453 TGAGGGTGTT
*
21463 GAAGAAGAAGAGAAAAGG
1 GAAGAAAAAGA-AAAAGG
21481 GAAGAAAAAGAAAAAG
1 GAAGAAAAAGAAAAAG
21497 AAGAAGTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAGAAAAAGAAAAAGG
Found at i:21925 original size:17 final size:17
Alignment explanation
Indices: 21903--21950 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
21893 TTTTATCTAG
21903 TTGTCATTACATTTTAA
1 TTGTCATTACATTTTAA
* * *
21920 TTGTCACTGCATTTTAC
1 TTGTCATTACATTTTAA
* *
21937 TTGTTATCACATTT
1 TTGTCATTACATTT
21951 GCATTATAGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (17 bp):
TTGTCATTACATTTTAA
Found at i:28905 original size:9 final size:9
Alignment explanation
Indices: 28883--28924 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
28873 TTAACACTTT
*
28883 ATTTTTTTG
1 ATTTTTTTA
28892 A-TTTTTTA
1 ATTTTTTTA
*
28900 ATTTTTGTA
1 ATTTTTTTA
28909 ATATTTTTTA
1 AT-TTTTTTA
28919 ATTTTT
1 ATTTTT
28925 AGATACATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:38291 original size:22 final size:22
Alignment explanation
Indices: 38266--38331 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
38256 TTTTTATATA
* *
38266 ATATTTTTATTTTTTAAAATTT
1 ATATTTATATATTTTAAAATTT
*
38288 ATATTTATATATTTTAGAATTT
1 ATATTTATATATTTTAAAATTT
** *
38310 -TATAAAAATATTTTTAAAATTT
1 ATATTTATATA-TTTTAAAATTT
38332 TGAATTATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATTTATATATTTTAAAATTT
Found at i:42060 original size:29 final size:30
Alignment explanation
Indices: 42009--42065 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
41999 ATAAGGACTT
* *
42009 GATCAAATTAGTCCCTTTTACTATTAAATG
1 GATCAAATTAGTCCCATGTACTATTAAATG
*
42039 GATCAATTTAGT-CCATGTACTATTAAA
1 GATCAAATTAGTCCCATGTACTATTAAA
42066 AAGAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (30 bp):
GATCAAATTAGTCCCATGTACTATTAAATG
Found at i:42149 original size:23 final size:22
Alignment explanation
Indices: 42097--42150 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
42087 TGGAATAATG
* *
42097 TTAACATTTATTGTTTAAAAAA
1 TTAATATTTACTGTTTAAAAAA
* *
42119 ATATTATTTACTGTTTAACAAAA
1 TTAATATTTACTGTTTAA-AAAA
42142 TTAATATTT
1 TTAATATTT
42151 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAATATTTACTGTTTAAAAAA
Found at i:42419 original size:66 final size:66
Alignment explanation
Indices: 42342--42471 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
42332 TAATCCCATT
* *
42342 TACTTTAACCTATAAAGAAGCTAATGGCTAATATAATAGGGCATAATAACAAATTTAGTCCTTAT
1 TACTTTAACCTATAAAGAAGCTAATGGCTAAAATAATAGGGCATAATAACAAATTTAGTACTTAT
42407 G
66 G
*
42408 TACTTTAACCTATAAAGAAGCTAATGTCTAAAATAATAGGGCATAATAACAAATTTAGTACTTA
1 TACTTTAACCTATAAAGAAGCTAATGGCTAAAATAATAGGGCATAATAACAAATTTAGTACTTA
42472 ATATTTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (66 bp):
TACTTTAACCTATAAAGAAGCTAATGGCTAAAATAATAGGGCATAATAACAAATTTAGTACTTAT
G
Found at i:42718 original size:19 final size:20
Alignment explanation
Indices: 42686--42724 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
42676 GATATTTTTA
*
42686 TTTTTATTTCTTAAAATATT
1 TTTTTAATTCTTAAAATATT
*
42706 TTTTTAATT-TTAAATTATT
1 TTTTTAATTCTTAAAATATT
42725 GGTTGACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATTCTTAAAATATT
Found at i:47535 original size:25 final size:23
Alignment explanation
Indices: 47507--47586 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
47497 TTATATATCA
47507 TTATATTAAATTATTTCAATATTAT
1 TTATATTAAA-T-TTTCAATATTAT
*
47532 TTATATTTAATTTTCAATATT-T
1 TTATATTAAATTTTCAATATTAT
* *
47554 TATATCATT-GATTTTACAA-ATAAT
1 T-TAT-ATTAAATTTT-CAATATTAT
47578 TTATATTAA
1 TTATATTAA
47587 TTACATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
22 5 0.11
23 23 0.50
24 9 0.20
25 9 0.20
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (23 bp):
TTATATTAAATTTTCAATATTAT
Found at i:48719 original size:23 final size:23
Alignment explanation
Indices: 48688--48734 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
48678 CTACCGATAC
*
48688 AAGTGCATAGAAGTATCAGTAGA
1 AAGTACATAGAAGTATCAGTAGA
48711 AAGTACATAGAAGTATCAGTAGA
1 AAGTACATAGAAGTATCAGTAGA
48734 A
1 A
48735 CCAAGTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (23 bp):
AAGTACATAGAAGTATCAGTAGA
Found at i:54715 original size:16 final size:16
Alignment explanation
Indices: 54666--54715 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
54656 CATTTTTATA
*
54666 TTTATTTTATGTAATT
1 TTTATTTTATATAATT
* * *
54682 TATATATTATACAATT
1 TTTATTTTATATAATT
54698 TTTATTTTATAT-ATT
1 TTTATTTTATATAATT
54713 TTT
1 TTT
54716 GAATTTTTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTTTATATAATT
Found at i:56626 original size:18 final size:18
Alignment explanation
Indices: 56603--56651 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
56593 CAATATGATT
56603 TAAACTCGAATTAAAACC
1 TAAACTCGAATTAAAACC
*
56621 TAAACTTGAATTAAAACC
1 TAAACTCGAATTAAAACC
*
56639 CAAACTCGTAATT
1 TAAACTCG-AATT
56652 TCCTATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (18 bp):
TAAACTCGAATTAAAACC
Found at i:76395 original size:89 final size:89
Alignment explanation
Indices: 76283--76452 Score: 313
Period size: 89 Copynumber: 1.9 Consensus size: 89
76273 AACTTGGCCA
*
76283 ACAATTGTGGTGGACGTACGCGACTTTCTAAGAAGTTGTACCAGCAGAGACGAATACTGGCTAGG
1 ACAATTGTGGTGGACGTACGCGACTTTCTAAGAAGTTGTACAAGCAGAGACGAATACTGGCTAGG
76348 AGACATTGAAATACTGGCTAGGAG
66 AGACATTGAAATACTGGCTAGGAG
* *
76372 ACAATTGTGGTGGACGTATGCGACTTTCTAAGAAGTTGTGCAAGCAGAGACGAATACTGGCTAGG
1 ACAATTGTGGTGGACGTACGCGACTTTCTAAGAAGTTGTACAAGCAGAGACGAATACTGGCTAGG
76437 AGACATTGAAATACTG
66 AGACATTGAAATACTG
76453 ATGAATTGAA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (89 bp):
ACAATTGTGGTGGACGTACGCGACTTTCTAAGAAGTTGTACAAGCAGAGACGAATACTGGCTAGG
AGACATTGAAATACTGGCTAGGAG
Found at i:94433 original size:69 final size:69
Alignment explanation
Indices: 94322--94470 Score: 235
Period size: 69 Copynumber: 2.2 Consensus size: 69
94312 ACAACCGAAA
* *
94322 TCTCCGAGTGTTCCAACTTATCTATCGAATTCTGTGGGTAGACAGGTTNATACTGGTGTTGTTTT
1 TCTCCGAGTGTTCCAACTTATCTATCGAATTCTGTGGGTAGACAGGTTGATACTAGTGTTGTTTT
94387 AGCC
66 AGCC
** * * *
94391 TCTCCGAGTGTTTTATCTTGTCTATCGTATTCTGTGGGTAGACAGGTTGATACTAGTGTTGTTTT
1 TCTCCGAGTGTTCCAACTTATCTATCGAATTCTGTGGGTAGACAGGTTGATACTAGTGTTGTTTT
94456 AGCC
66 AGCC
94460 TCTCCGAGTGT
1 TCTCCGAGTGT
94471 GGATACATAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.40
Consensus pattern (69 bp):
TCTCCGAGTGTTCCAACTTATCTATCGAATTCTGTGGGTAGACAGGTTGATACTAGTGTTGTTTT
AGCC
Found at i:97335 original size:17 final size:18
Alignment explanation
Indices: 97313--97346 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
97303 AATTATATAG
97313 TAAATTTAAGT-AAAAAT
1 TAAATTTAAGTGAAAAAT
*
97330 TAAATTTTAGTGAAAAA
1 TAAATTTAAGTGAAAAA
97347 ATTTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (18 bp):
TAAATTTAAGTGAAAAAT
Found at i:101688 original size:41 final size:44
Alignment explanation
Indices: 101643--101741 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
101633 AGGGTCCTAG
*
101643 TGTCACTTT-AT-TCA-TCTATCACTATTCGTTTTTTAAAATCA
1 TGTCACTTTAATCTCACTCTATCACTATTCGTATTTTAAAATCA
* * *
101684 TGTCATTTTAATCTTACTCTATCACTGTTCGTATTTTAAAATCA
1 TGTCACTTTAATCTCACTCTATCACTATTCGTATTTTAAAATCA
* *
101728 TGTAATTTTAATCT
1 TGTCACTTTAATCT
101742 TACTTTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 8 0.16
42 2 0.04
43 2 0.04
44 38 0.76
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (44 bp):
TGTCACTTTAATCTCACTCTATCACTATTCGTATTTTAAAATCA
Found at i:101707 original size:44 final size:44
Alignment explanation
Indices: 101657--101745 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
101647 ACTTTATTCA
* *
101657 TCTATCACTATTCGTTTTTTAAAATCATGTCATTTTAATCTTAC
1 TCTATCACTATTCGTATTTTAAAATCATGTAATTTTAATCTTAC
*
101701 TCTATCACTGTTCGTATTTTAAAATCATGTAATTTTAATCTTAC
1 TCTATCACTATTCGTATTTTAAAATCATGTAATTTTAATCTTAC
101745 T
1 T
101746 TTATTTAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (44 bp):
TCTATCACTATTCGTATTTTAAAATCATGTAATTTTAATCTTAC
Found at i:101936 original size:21 final size:21
Alignment explanation
Indices: 101911--101965 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
101901 AATAGTGTAG
101911 ACTTCTACCGATACAAGTGAC-T
1 ACTTCTACCGATACAAGT--CTT
*
101933 -CTTCTACCGAAACAAGTCTT
1 ACTTCTACCGATACAAGTCTT
101953 ACTTCTACCGATA
1 ACTTCTACCGATA
101966 TTAAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 27 0.93
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTCTT
Found at i:103229 original size:27 final size:27
Alignment explanation
Indices: 103191--103244 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
103181 CAAACTTCCA
*
103191 AAACTTTCCTAAACTATCAAGAATAAG
1 AAACGTTCCTAAACTATCAAGAATAAG
103218 AAACGTTCCTAAACTATCAAGAATAAG
1 AAACGTTCCTAAACTATCAAGAATAAG
103245 CTCATTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (27 bp):
AAACGTTCCTAAACTATCAAGAATAAG
Found at i:108672 original size:46 final size:46
Alignment explanation
Indices: 108622--108716 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
108612 AAAAAATTAA
* * **
108622 AAATTATAAAAAAA-TATTAAATTTTGTAAAATTTACTTA-AAATTTT
1 AAATTATAAAAAAATTAATAAA-ATTGTAAAAAATA-TTAGAAATTTT
108668 AAATTATAAAAAAATTAATAAAATTGTAAAAAATATTAGAAATTTT
1 AAATTATAAAAAAATTAATAAAATTGTAAAAAATATTAGAAATTTT
108714 AAA
1 AAA
108717 AAGAATATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 3 0.07
46 34 0.79
47 6 0.14
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (46 bp):
AAATTATAAAAAAATTAATAAAATTGTAAAAAATATTAGAAATTTT
Found at i:108718 original size:20 final size:19
Alignment explanation
Indices: 108668--108738 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
108658 TTAAAATTTT
* *
108668 AAATTATAAAAAAATTAATA
1 AAATTTTAAAAAAA-TATTA
*
108688 AAATTGT-AAAAAATATTA
1 AAATTTTAAAAAAATATTA
*
108706 GAAATTTTAAAAAGAATATGA
1 -AAATTTTAAAAA-AATATTA
108727 AAATTATTAAAA
1 AAATT-TTAAAA
108739 TTTCTCAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.09
19 12 0.28
20 15 0.35
21 12 0.28
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
AAATTTTAAAAAAATATTA
Found at i:108723 original size:21 final size:20
Alignment explanation
Indices: 108695--108738 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
108685 ATAAAATTGT
*
108695 AAAAAATATTAGAAATT-TTA
1 AAAAAATATGA-AAATTATTA
108715 AAAAGAATATGAAAATTATTA
1 AAAA-AATATGAAAATTATTA
108736 AAA
1 AAA
108739 TTTCTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAAAATATGAAAATTATTA
Found at i:109814 original size:16 final size:16
Alignment explanation
Indices: 109789--109820 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
109779 TTTGATTTTT
*
109789 TTAATTTTTAAATTTA
1 TTAATATTTAAATTTA
109805 TTAATATTTAAATTTA
1 TTAATATTTAAATTTA
109821 ACTTAAATAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATATTTAAATTTA
Found at i:110373 original size:24 final size:23
Alignment explanation
Indices: 110346--110393 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
110336 GACTGTATTT
110346 ATTTTA-TAAATATATATTTCTTAA
1 ATTTTAGTAAATA-ATATTT-TTAA
110370 ATTTTAGTAAATAATATTTTTAA
1 ATTTTAGTAAATAATATTTTTAA
110393 A
1 A
110394 GATCATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.22
24 12 0.52
25 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTAGTAAATAATATTTTTAA
Found at i:110701 original size:55 final size:57
Alignment explanation
Indices: 110640--110746 Score: 155
Period size: 55 Copynumber: 1.9 Consensus size: 57
110630 CATTTAGTAC
* * *
110640 TTGAATTTGATATTTTTTT-AATTTGGTATCTAAG-TTTTTTTATTCAATTTGATAT
1 TTGAATTTGACATTTTTTTAAATTTAGTACCTAAGCTTTTTTTATTCAATTTGATAT
*
110695 TTGAATTTGACATTTTTTTAAATTTAGTACCTAAGCCTTTTTTTGTTCAATT
1 TTGAATTTGACATTTTTTTAAATTTAGTACCTAAG-CTTTTTTTATTCAATT
110747 CGGTACATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
55 18 0.40
56 13 0.29
58 14 0.31
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (57 bp):
TTGAATTTGACATTTTTTTAAATTTAGTACCTAAGCTTTTTTTATTCAATTTGATAT
Found at i:112217 original size:10 final size:10
Alignment explanation
Indices: 112180--112214 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
112170 AACAATTGTA
112180 TTAAAATACT
1 TTAAAATACT
112190 TTAAAATACT
1 TTAAAATACT
*
112200 TTAAATTACT
1 TTAAAATACT
112210 TTAAA
1 TTAAA
112215 TTAAAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAAAATACT
Found at i:121932 original size:12 final size:12
Alignment explanation
Indices: 121914--121991 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
121904 TCGAAGCAAT
121914 AAAAATAACAAC
1 AAAAATAACAAC
* *
121926 CAAAATAGCAAC
1 AAAAATAACAAC
*
121938 AAAAATAACAGC
1 AAAAATAACAAC
121950 ---AA-AACAAC
1 AAAAATAACAAC
*
121958 ATTAAA-AACAAC
1 A-AAAATAACAAC
121970 AAAAATAACAAC
1 AAAAATAACAAC
*
121982 AAAAACAACA
1 AAAAATAACA
121992 CGAAAACAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 5 0.09
9 2 0.04
11 3 0.06
12 43 0.81
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.08
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:121941 original size:24 final size:23
Alignment explanation
Indices: 121908--122009 Score: 73
Period size: 23 Copynumber: 4.5 Consensus size: 23
121898 ATAACATCGA
*
121908 AGCAATAAAAATAACAACCAAAAT
1 AGCAACAAAAATAAC-ACCAAAAT
* *
121932 AGCAACAAAAATAACAGCAAAAC
1 AGCAACAAAAATAACACCAAAAT
* ** *
121955 AACATTAAAAACAACA--AAAAT
1 AGCAACAAAAATAACACCAAAAT
* * * *
121976 AACAACAAAAACAACACGAAAAC
1 AGCAACAAAAATAACACCAAAAT
*
121999 AGCAACCAAAA
1 AGCAACAAAAA
122010 CAGTAAAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
21 18 0.29
23 31 0.49
24 14 0.22
ACGTcount: A:0.68, C:0.21, G:0.05, T:0.07
Consensus pattern (23 bp):
AGCAACAAAAATAACACCAAAAT
Found at i:121943 original size:44 final size:43
Alignment explanation
Indices: 121894--121996 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
121884 AAAACGCATA
* * * *
121894 AAAAATAACATCGAAGCAATA-AAAATAACAACCAAAATAGCAAC
1 AAAAATAACA-CGAAACAACATAAAA-AACAACAAAAATAACAAC
* *
121938 AAAAATAACAGCAAAACAACATTAAAAACAACAAAAATAACAAC
1 AAAAATAACA-CGAAACAACATAAAAAACAACAAAAATAACAAC
*
121982 AAAAACAACACGAAA
1 AAAAATAACACGAAA
121997 ACAGCAACCA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 4 0.08
44 42 0.86
45 3 0.06
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (43 bp):
AAAAATAACACGAAACAACATAAAAAACAACAAAAATAACAAC
Found at i:121956 original size:32 final size:32
Alignment explanation
Indices: 121920--122009 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 32
121910 CAATAAAAAT
*
121920 AACAACCAAAATAGCAACAAAAATAACAGC-AA
1 AACAACCAAAA-AGCAACAAAAATAACAACAAA
*
121952 AACAA-CATTAAAAACAACAAAAATAACAACAAA
1 AACAACCA--AAAAGCAACAAAAATAACAACAAA
*
121985 AACAACACGAAAACAGCAACCAAAA
1 AACAAC-C-AAAA-AGCAACAAAAA
122010 CAGTAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
31 2 0.04
32 21 0.45
33 10 0.21
34 3 0.06
35 10 0.21
36 1 0.02
ACGTcount: A:0.68, C:0.22, G:0.04, T:0.06
Consensus pattern (32 bp):
AACAACCAAAAAGCAACAAAAATAACAACAAA
Found at i:122010 original size:44 final size:44
Alignment explanation
Indices: 121920--122011 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
121910 CAATAAAAAT
* * * **
121920 AACAACCAAAATAGCAACAAAAATAACAGCAAAACAACATTAAA
1 AACAACAAAAATAACAACAAAAACAACAGCAAAACAACAACAAA
* *
121964 AACAACAAAAATAACAACAAAAACAACA-CGAAAACAGCAACCAA
1 AACAACAAAAATAACAACAAAAACAACAGC-AAAACAACAACAAA
122008 AACA
1 AACA
122012 GTAAAAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.67, C:0.23, G:0.04, T:0.05
Consensus pattern (44 bp):
AACAACAAAAATAACAACAAAAACAACAGCAAAACAACAACAAA
Found at i:129512 original size:20 final size:21
Alignment explanation
Indices: 129473--129512 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
129463 TTTCTTCAAA
* *
129473 AACGCTGTTTTTTTTCTATTT
1 AACGCCGTTTTATTTCTATTT
129494 AACGCCGTTTTATTT-TATT
1 AACGCCGTTTTATTTCTATT
129513 CCGAGTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (21 bp):
AACGCCGTTTTATTTCTATTT
Found at i:140334 original size:20 final size:20
Alignment explanation
Indices: 140305--140344 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
140295 TACCAAAATA
*
140305 TCTAATGATTTATCAATATT
1 TCTAAGGATTTATCAATATT
140325 TCTAAGGATTTATCAATATT
1 TCTAAGGATTTATCAATATT
140345 GGCTTTACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (20 bp):
TCTAAGGATTTATCAATATT
Found at i:140627 original size:3 final size:3
Alignment explanation
Indices: 140621--140647 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
140611 TTATTATTAC
140621 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
140648 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:140664 original size:7 final size:7
Alignment explanation
Indices: 140646--140683 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
140636 CATCATCATC
140646 ATTATT-
1 ATTATTA
140652 ATTATTA
1 ATTATTA
140659 ATTATTA
1 ATTATTA
140666 ATTATTA
1 ATTATTA
140673 ATTATT-
1 ATTATTA
140679 ATTAT
1 ATTAT
140684 AAGACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTATTA
Found at i:144322 original size:25 final size:25
Alignment explanation
Indices: 144289--144339 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
144279 GTGTAGGCAG
144289 AAAAAATTCAGTCATCATAAATCAC
1 AAAAAATTCAGTCATCATAAATCAC
144314 AAAAAATTCAGTCATCATAAATCAC
1 AAAAAATTCAGTCATCATAAATCAC
144339 A
1 A
144340 TCTCATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAAAATTCAGTCATCATAAATCAC
Found at i:147526 original size:16 final size:16
Alignment explanation
Indices: 147505--147536 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
147495 ACCAAATAAA
*
147505 ATTTTCATTGAAAATT
1 ATTTTCATCGAAAATT
147521 ATTTTCATCGAAAATT
1 ATTTTCATCGAAAATT
147537 CTAGCATAAA
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:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTTTCATCGAAAATT
Found at i:149300 original size:21 final size:19
Alignment explanation
Indices: 149268--149306 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
149258 TGGATGTCAT
149268 TAGTTTAATTAAAGCATAAG
1 TAGTTTAATTAAA-CATAAG
*
149288 TAGTGTTAGTTAAACATAA
1 TAGT-TTAATTAAACATAA
149307 TTAATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (19 bp):
TAGTTTAATTAAACATAAG
Found at i:150318 original size:19 final size:19
Alignment explanation
Indices: 150262--150318 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
150252 CGCTTATGCA
*
150262 CCAAGATACACTTCGTGTG
1 CCAAGATGCACTTCGTGTG
* ** ** *
150281 TCGGGATGCGTTTCATGTG
1 CCAAGATGCACTTCGTGTG
150300 CCAAGATGCACTTCGTGTG
1 CCAAGATGCACTTCGTGTG
150319 GTAGGATGCA
Statistics
Matches: 25, Mismatches: 13, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (19 bp):
CCAAGATGCACTTCGTGTG
Found at i:152338 original size:6 final size:6
Alignment explanation
Indices: 152316--152413 Score: 69
Period size: 6 Copynumber: 16.5 Consensus size: 6
152306 GTTTAAGTTG
* * *
152316 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
* * * **
152365 TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A ATCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
152411 ATT
1 ATT
152414 GATATTAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 53 0.77
7 2 0.03
8 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:152352 original size:17 final size:17
Alignment explanation
Indices: 152316--152424 Score: 105
Period size: 17 Copynumber: 6.2 Consensus size: 17
152306 GTTTAAGTTG
*
152316 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
152334 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
152351 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
*
152371 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTATC-TTAA
*
152388 ATTTAAATTTAATC-AAA
1 ATTTAAATTT-ATCTTAA
* *
152405 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
152422 ATT
1 ATT
152425 AAAACCCAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.03
17 49 0.63
18 11 0.14
19 2 0.03
20 14 0.18
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:152375 original size:37 final size:35
Alignment explanation
Indices: 152316--152398 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 35
152306 GTTTAAGTTG
*
152316 ATTTAAATTTATTTTTAAATTTAAATTT-ATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAATTTGCT-TTAA
152351 ATTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAA
1 ATTTAAATTTA--TTTTTAAATTTAAATTTGCTTTAA
152388 ATTTAAATTTA
1 ATTTAAATTTA
152399 ATCAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 11 0.25
37 32 0.73
38 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAATTTGCTTTAA
Found at i:152428 original size:23 final size:23
Alignment explanation
Indices: 152383--152428 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
152373 TTAAATTTGC
* *
152383 TTTAAATTTAAATTTAATCAAAA
1 TTTAAATTGAAATTAAATCAAAA
* *
152406 TTTAAATTGATATTAAATTAAAA
1 TTTAAATTGAAATTAAATCAAAA
152429 CCCAAAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAATTGAAATTAAATCAAAA
Found at i:154280 original size:29 final size:29
Alignment explanation
Indices: 154238--154316 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
154228 AAACTGTCTA
*
154238 AAAATTACATTTTTACCCCT-AAACTTTCC
1 AAAATTACAATTTTACCCCTGAAACTTT-C
*
154267 AAAATT-CTAATTTTGA-CCTTGAAACTTTC
1 AAAATTAC-AATTTT-ACCCCTGAAACTTTC
*
154296 AAAATTACCATTTTACCCCTG
1 AAAATTACAATTTTACCCCTG
154317 GACATCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 2 0.05
29 30 0.73
30 9 0.22
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTACAATTTTACCCCTGAAACTTTC
Found at i:154339 original size:58 final size:58
Alignment explanation
Indices: 154267--154490 Score: 233
Period size: 58 Copynumber: 3.8 Consensus size: 58
154257 TAAACTTTCC
* * * **
154267 AAAATTCTAATTTTGACCTTGAAACTTTCAAAATTACCATTTTACCCCTGGACATCCA
1 AAAATTCCATTTTTGACCTCGAAACTTTCAAAATTACCATTTTACCCCTGGATGTCCA
* * *
154325 AAAACTCCATTTTTGA-CTCCAAAGCTTTCAAAAATTACCATTTTACCCTTGGATGTCCA
1 AAAATTCCATTTTTGACCTCGAAA-CTTTC-AAAATTACCATTTTACCCCTGGATGTCCA
* * *
154384 AAAATTCCATTTTTTACCCCGAAACTTTCAAAATTACCATTTTA-CCCTCGGATGT-CT
1 AAAATTCCATTTTTGACCTCGAAACTTTCAAAATTACCATTTTACCCCT-GGATGTCCA
* * *
154441 AAAATTCCATTTTTAACCAT--AAATTTTACCAAAATTACCATTTTGCCCCT
1 AAAATTCCATTTTTGACC-TCGAAACTTT--CAAAATTACCATTTTACCCCT
154491 CGAGAGCCCA
Statistics
Matches: 140, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
56 6 0.04
57 26 0.19
58 54 0.39
59 49 0.35
60 5 0.04
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCGAAACTTTCAAAATTACCATTTTACCCCTGGATGTCCA
Found at i:154367 original size:59 final size:58
Alignment explanation
Indices: 154277--154430 Score: 211
Period size: 59 Copynumber: 2.6 Consensus size: 58
154267 AAAATTCTAA
**
154277 TTTTGACCTTGAAACTTTCAAAATTACCATTTTACCCCTGGACATCCAAAAACTCCAT
1 TTTTGACCCCGAAACTTTCAAAATTACCATTTTACCCCTGGACATCCAAAAACTCCAT
* * ** *
154335 TTTTGACTCC-AAAGCTTTCAAAAATTACCATTTTACCCTTGGATGTCCAAAAATTCCAT
1 TTTTGACCCCGAAA-CTTTC-AAAATTACCATTTTACCCCTGGACATCCAAAAACTCCAT
*
154394 TTTTTACCCCGAAACTTTCAAAATTACCATTTTACCC
1 TTTTGACCCCGAAACTTTCAAAATTACCATTTTACCC
154431 TCGGATGTCT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 3 0.04
58 30 0.36
59 48 0.57
60 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (58 bp):
TTTTGACCCCGAAACTTTCAAAATTACCATTTTACCCCTGGACATCCAAAAACTCCAT
Found at i:154416 original size:30 final size:29
Alignment explanation
Indices: 154228--154455 Score: 100
Period size: 30 Copynumber: 7.8 Consensus size: 29
154218 GAAGGTCCCT
* * *
154228 AAACTGTCTAAAAATTACATTTTTACCCCT
1 AAACTTTC-AAAAATTCCATTTTTACCCCG
* * * **
154258 AAACTTTCCAAAATTCTAATTTTGACCTTG
1 AAACTTTCAAAAATTC-CATTTTTACCCCG
154288 AAACTTTC-AAAATTACCA-TTTTACCCCTG
1 AAACTTTCAAAAATT-CCATTTTTACCCC-G
* * * * *
154317 -GACATCCAAAAACTCCATTTTTGACTCC-
1 AAACTTTCAAAAATTCCATTTTT-ACCCCG
*
154345 AAAGCTTTCAAAAATTACCA-TTTTACCCTTG
1 AAA-CTTTCAAAAATT-CCATTTTTACCC-CG
* *
154376 -GA-TGTCCAAAAATTCCATTTTTTACCCCG
1 AAACT-TTCAAAAATTCCA-TTTTTACCCCG
154405 AAACTTTC-AAAATTACCA-TTTTACCCTCG
1 AAACTTTCAAAAATT-CCATTTTTACCC-CG
* * *
154434 -GA-TGTCTAAAATTCCATTTTTA
1 AAACTTTCAAAAATTCCATTTTTA
154456 ACCATAAATT
Statistics
Matches: 148, Mismatches: 30, Indels: 42
0.67 0.14 0.19
Matches are distributed among these distances:
27 6 0.04
28 37 0.25
29 45 0.30
30 56 0.38
31 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (29 bp):
AAACTTTCAAAAATTCCATTTTTACCCCG
Found at i:154455 original size:28 final size:27
Alignment explanation
Indices: 154355--154453 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 27
154345 AAAGCTTTCA
*
154355 AAAATTACCATTTTACCCTTGGATGTCC
1 AAAATTACCATTTTACCCTCGGATGT-C
* *
154383 AAAAATT-CCATTTTTTACCC-CGAAACTTTC
1 -AAAATTACCA--TTTTACCCTCG-GA-TGTC
154413 AAAATTACCATTTTACCCTCGGATGTC
1 AAAATTACCATTTTACCCTCGGATGTC
154440 TAAAATT-CCATTTT
1 -AAAATTACCATTTT
154454 TAACCATAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
27 10 0.17
28 18 0.31
29 15 0.26
30 13 0.22
31 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (27 bp):
AAAATTACCATTTTACCCTCGGATGTC
Found at i:154502 original size:117 final size:117
Alignment explanation
Indices: 154287--154513 Score: 259
Period size: 116 Copynumber: 1.9 Consensus size: 117
154277 TTTTGACCTT
* *
154287 GAAACTTTCAAAATTACCATTTTACCCCTGGACATCCAAAAACTCCATTTTTGACTCCAAAGCTT
1 GAAACTTTCAAAATTACCATTTTACCCCTGGACATCCAAAAACTCCATTTTTGACACCAAAACTT
* *
154352 TCAAAAATTACCATTTTACCCTTGGATGTCCAAAAATT-CCATTTTTTACCCC
66 TCAAAAATTACCATTTTACCCTCGGATG-CCCAAAATTACCATTTTTTACCCC
** * * *
154404 GAAACTTTCAAAATTACCATTTTA-CCCTCGGATGT-CTAAAATTCCATTTTT-A-ACCATAAAT
1 GAAACTTTCAAAATTACCATTTTACCCCT-GGACATCCAAAAACTCCATTTTTGACACCA-AAAC
* *
154465 TTTACCAAAATTACCATTTTGCCCCTCGAGA-GCCCAAAATTACCATTTT
64 TTT-CAAAAATTACCATTTT-ACCCTCG-GATGCCCAAAATTACCATTTT
154514 GCCCCCGGTT
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
114 3 0.03
115 6 0.06
116 41 0.44
117 41 0.44
118 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (117 bp):
GAAACTTTCAAAATTACCATTTTACCCCTGGACATCCAAAAACTCCATTTTTGACACCAAAACTT
TCAAAAATTACCATTTTACCCTCGGATGCCCAAAATTACCATTTTTTACCCC
Found at i:166253 original size:50 final size:49
Alignment explanation
Indices: 166184--166295 Score: 145
Period size: 50 Copynumber: 2.3 Consensus size: 49
166174 GGGAAAGATT
** * *
166184 AGTACCATGAAGACATGAAGGGAAAGATTTAAGCCGCAACGG-TGAATCC
1 AGTACCACAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAG-ATCC
* *
166233 AGTACCACATAAGACGTGAAGGGAAAGATCTAAGCCGCAATGGCAGATCC
1 AGTACCACA-AAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCC
166283 AGTACCACAAAGA
1 AGTACCACAAAGA
166296 TACAAAAGGG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 11 0.20
50 43 0.78
51 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.14
Consensus pattern (49 bp):
AGTACCACAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCC
Found at i:166305 original size:50 final size:51
Alignment explanation
Indices: 166201--166326 Score: 143
Period size: 50 Copynumber: 2.5 Consensus size: 51
166191 TGAAGACATG
* * **
166201 AAGGGAAAGATTTAAGCCGCAACGG-TGAATCCAGTACCACATAAGACGTG
1 AAGGGAAAGATTTAAGCCGCAATGGCAGAATCCAGTACCACATAAGACGAA
*
166251 AAGGGAAAGATCTAAGCCGCAATGGCAG-ATCCAGTACCACA-AAGATAC-AA
1 AAGGGAAAGATTTAAGCCGCAATGGCAGAATCCAGTACCACATAAG--ACGAA
* *
166301 AAGGGAAAGGTTTAAGTCGCAATGGC
1 AAGGGAAAGATTTAAGCCGCAATGGC
166327 GAACCCGGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
49 3 0.05
50 59 0.91
51 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (51 bp):
AAGGGAAAGATTTAAGCCGCAATGGCAGAATCCAGTACCACATAAGACGAA
Found at i:166939 original size:207 final size:201
Alignment explanation
Indices: 166539--166944 Score: 492
Period size: 207 Copynumber: 2.0 Consensus size: 201
166529 TAAGACACTG
* * *
166539 AGAAGTGGACCAAATTCGCCTTCCTGGTAAGATACAGAGAAGCGAATAGAAACAAGTGAGGCGAT
1 AGAAGTGGACCAAATTCGCCTTCCTGATAAGATACAGAGAAGCGAATAGAAACAAGCGAGACGAT
* * * * *
166604 CATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAAGGCTCAGGGTGAGCAAATCTTCGAAC
66 CATCTTCCTAATGAGAAACAGAGAAGAAGACCAAATCAACGCTCAGGGTGAGCAAATCTTCGAAC
* * * *
166669 TCCGACTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAC
131 CCCGACTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAC
166734 ATACGA
196 ATACGA
* * * * * *
166740 AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATACGGT
1 AGAAGTGGACCAAATTCGCCTTCCTGATAAGATACAGAGAAGCGAATAGAAACAAGCGAGACGAT
* * *
166805 CATCTTCCTGATGAGAAACTGAGAAGAAAGACCAAATCAGACCCACGCTC-GATGTGAGCAAATC
66 CATCTTCCTAATGAGAAACAGAGAAG-AAGACCAAATC--A---ACGCTCAG-GGTGAGCAAATC
* * * *
166869 TTCGAACCCC-AGCTTCCTAATGAGATACTAAGAATCGGGTCGAAGTAATAAAATGGTTAGCTTC
124 TTCGAACCCCGA-CTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTC
*
166933 CTGATGAGATAC
188 CTGATGACATAC
166945 AAACAAGCGA
Statistics
Matches: 171, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
201 79 0.46
202 8 0.05
204 1 0.01
206 2 0.01
207 81 0.47
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21
Consensus pattern (201 bp):
AGAAGTGGACCAAATTCGCCTTCCTGATAAGATACAGAGAAGCGAATAGAAACAAGCGAGACGAT
CATCTTCCTAATGAGAAACAGAGAAGAAGACCAAATCAACGCTCAGGGTGAGCAAATCTTCGAAC
CCCGACTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAC
ATACGA
Found at i:167395 original size:6 final size:6
Alignment explanation
Indices: 167373--167470 Score: 69
Period size: 6 Copynumber: 16.5 Consensus size: 6
167363 GTTAAAGTTG
* * *
167373 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
* * * **
167422 TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A ATCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
167468 ATT
1 ATT
167471 GATATTAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 53 0.77
7 2 0.03
8 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:167409 original size:17 final size:17
Alignment explanation
Indices: 167373--167481 Score: 105
Period size: 17 Copynumber: 6.2 Consensus size: 17
167363 GTTAAAGTTG
*
167373 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
167391 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
167408 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
*
167428 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTATC-TTAA
*
167445 ATTTAAATTTAATC-AAA
1 ATTTAAATTT-ATCTTAA
* *
167462 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
167479 ATT
1 ATT
167482 AAAAACCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.03
17 49 0.63
18 11 0.14
19 2 0.03
20 14 0.18
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:167432 original size:37 final size:35
Alignment explanation
Indices: 167373--167455 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 35
167363 GTTAAAGTTG
*
167373 ATTTAAATTTATTTTTAAATTTAAATTT-ATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAATTTGCT-TTAA
167408 ATTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAA
1 ATTTAAATTTA--TTTTTAAATTTAAATTTGCTTTAA
167445 ATTTAAATTTA
1 ATTTAAATTTA
167456 ATCAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 11 0.25
37 32 0.73
38 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAATTTGCTTTAA
Found at i:167485 original size:23 final size:23
Alignment explanation
Indices: 167440--167485 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
167430 TTAAATTTGC
* *
167440 TTTAAATTTAAATTTAATCAAAA
1 TTTAAATTGAAATTAAATCAAAA
* *
167463 TTTAAATTGATATTAAATTAAAA
1 TTTAAATTGAAATTAAATCAAAA
167486 ACCCAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAATTGAAATTAAATCAAAA
Found at i:168232 original size:15 final size:15
Alignment explanation
Indices: 168214--168253 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
168204 TATTAATAGC
168214 AATAATAACTATT-TT
1 AATAATAA-TATTATT
168229 AATAATAATATTATT
1 AATAATAATATTATT
*
168244 ATTAATAATA
1 AATAATAATA
168254 ATGATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAATATTATT
Found at i:168237 original size:18 final size:18
Alignment explanation
Indices: 168214--168255 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
168204 TATTAATAGC
168214 AATAATAACTATT-TTAAT
1 AATAAT-ACTATTATTAAT
*
168232 AATAATATTATTATTAAT
1 AATAATACTATTATTAAT
168250 AATAAT
1 AATAAT
168256 GATAATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAATACTATTATTAAT
Found at i:168477 original size:62 final size:61
Alignment explanation
Indices: 168402--168524 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 61
168392 TTGTCCGTAC
* *
168402 CCTGTCAAACGTGGATTTGCGAAGAAACAAAGAACCGGGTTTTTAAAATCTTAAAGCAGGA
1 CCTGTCAAACGTGGATCTGCGAAGAAACAAAGAACCGAGTTTTTAAAATCTTAAAGCAGGA
168463 NCCTGTCAAACGTGGATCTGCGAAGAAACAAAGAACCGAGTTTTTAAAATCTTAAAGCAGGA
1 -CCTGTCAAACGTGGATCTGCGAAGAAACAAAGAACCGAGTTTTTAAAATCTTAAAGCAGGA
168525 ATTAACAGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (61 bp):
CCTGTCAAACGTGGATCTGCGAAGAAACAAAGAACCGAGTTTTTAAAATCTTAAAGCAGGA
Found at i:169430 original size:30 final size:29
Alignment explanation
Indices: 169394--169464 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
169384 CTTTGAACTG
* *
169394 TCCAAAAATTATATTTTTACCTCTAAACAT
1 TCCAAAAATTA-ATTTTGACCTCGAAACAT
*
169424 TCC-AAAATTCCAATTTTGACCTCGAAACTT
1 TCCAAAAATT--AATTTTGACCTCGAAACAT
*
169454 TCAAAAAATTA
1 TCCAAAAATTA
169465 CCATTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
29 7 0.21
30 20 0.59
31 7 0.21
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTAATTTTGACCTCGAAACAT
Found at i:169471 original size:31 final size:29
Alignment explanation
Indices: 169408--169480 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
169398 AAAATTATAT
* *
169408 TTTTACCTCTAAACATTCCAAAATT-CCAA
1 TTTTACCTCGAAACATTCAAAAATTACC-A
*
169437 TTTTGACCTCGAAACTTTCAAAAAATTACCA
1 TTTT-ACCTCGAAACATTC-AAAAATTACCA
169468 TTTTACCCTCGAA
1 TTTTA-CCTCGAA
169481 TGTCCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 4 0.11
30 13 0.35
31 18 0.49
32 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTACCTCGAAACATTCAAAAATTACCA
Found at i:169547 original size:29 final size:28
Alignment explanation
Indices: 169512--169598 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 28
169502 ACCCTAAAGC
169512 TTTCAAAAACTACCATTTTACCCCCGAA
1 TTTCAAAAACTACCATTTTACCCCCGAA
***
169540 TTTCCAAAAACTA-CATTTTTAACCCAAAAA
1 TTT-CAAAAACTACCA-TTTT-ACCCCCGAA
*
169570 CTTTC-AAAATTACCATTTTACCCCCGAA
1 -TTTCAAAAACTACCATTTTACCCCCGAA
169598 T
1 T
169599 GTCTGAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.02
28 11 0.23
29 23 0.49
30 9 0.19
31 3 0.06
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (28 bp):
TTTCAAAAACTACCATTTTACCCCCGAA
Found at i:169616 original size:58 final size:59
Alignment explanation
Indices: 169448--169703 Score: 238
Period size: 58 Copynumber: 4.4 Consensus size: 59
169438 TTTGACCTCG
* *
169448 AAACTTTCAAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTT-TATTTTTGACCCTA
1 AAACTTTC-AAAAATTACCATTTTACCCCCGAATGTCCAAAAACTTCTATTTTTAACCC-A
* * * *
169508 AAGCTTTCAAAAACTACCATTTTACCCCCGAATTTCCAAAAACTAC-ATTTTTAACCCAA
1 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTTCTATTTTTAACCC-A
** * * *
169567 AAACTTTC-AAAATTACCATTTTACCCCCGAATGTCTGAAAA-TTCTATTTTTNATCCT
1 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTTCTATTTTTAACCCA
* ** * * * ** *
169624 GATTTTTCTAAAATTACCGTTTTACCCCCGGATGT-TTAAAA-TTCCATTTTTAACCC-
1 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTTCTATTTTTAACCCA
*
169680 AAATTTTCCAAAAATTACCATTTT
1 AAACTTT-CAAAAATTACCATTTT
169704 GTCCCCGGGT
Statistics
Matches: 163, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
56 5 0.03
57 38 0.23
58 62 0.38
59 51 0.31
60 7 0.04
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.36
Consensus pattern (59 bp):
AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTTCTATTTTTAACCCA
Found at i:172391 original size:86 final size:86
Alignment explanation
Indices: 172289--172465 Score: 354
Period size: 86 Copynumber: 2.1 Consensus size: 86
172279 CTTTAACATG
172289 ATACATACCAAAACATCAAAATAAGCTTAAAAACTAAGCTATTACACTAGGTACATACCAACTTG
1 ATACATACCAAAACATCAAAATAAGCTTAAAAACTAAGCTATTACACTAGGTACATACCAACTTG
172354 CTATAAAACATATCAAAAGCT
66 CTATAAAACATATCAAAAGCT
172375 ATACATACCAAAACATCAAAATAAGCTTAAAAACTAAGCTATTACACTAGGTACATACCAACTTG
1 ATACATACCAAAACATCAAAATAAGCTTAAAAACTAAGCTATTACACTAGGTACATACCAACTTG
172440 CTATAAAACATATCAAAAGCT
66 CTATAAAACATATCAAAAGCT
172461 ATACA
1 ATACA
172466 AACTTTGTTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (86 bp):
ATACATACCAAAACATCAAAATAAGCTTAAAAACTAAGCTATTACACTAGGTACATACCAACTTG
CTATAAAACATATCAAAAGCT
Found at i:188070 original size:62 final size:62
Alignment explanation
Indices: 187973--188100 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
187963 TATTTGGAGA
187973 GGCAAATGAATGTGATGTGCAGACTTTGAAATGGGTTCTCAAGGAATATGAAGAATGTTCTG
1 GGCAAATGAATGTGATGTGCAGACTTTGAAATGGGTTCTCAAGGAATATGAAGAATGTTCTG
188035 GGCAAATGAATGTGATGTGCAGACTTTGAAATGGGTTCTCAAGGAATATGAAGAATGTTCTG
1 GGCAAATGAATGTGATGTGCAGACTTTGAAATGGGTTCTCAAGGAATATGAAGAATGTTCTG
188097 GGCA
1 GGCA
188101 GAGTATTAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (62 bp):
GGCAAATGAATGTGATGTGCAGACTTTGAAATGGGTTCTCAAGGAATATGAAGAATGTTCTG
Found at i:190723 original size:63 final size:63
Alignment explanation
Indices: 190624--190751 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
190614 ATGAAATAAA
190624 ATAAAACAATACTAACAATCTTATAAATATAAGGGAAAGTGAAAACATGGGAAAAAAGGCTAT
1 ATAAAACAATACTAACAATCTTATAAATATAAGGGAAAGTGAAAACATGGGAAAAAAGGCTAT
*
190687 ATAAAACAATACTAACAATCTTATAAATATAAGGGAAAGTGAAAACATGGGAAAAAATGCTAT
1 ATAAAACAATACTAACAATCTTATAAATATAAGGGAAAGTGAAAACATGGGAAAAAAGGCTAT
190750 AT
1 AT
190752 TTGTATACCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (63 bp):
ATAAAACAATACTAACAATCTTATAAATATAAGGGAAAGTGAAAACATGGGAAAAAAGGCTAT
Found at i:196296 original size:6 final size:6
Alignment explanation
Indices: 196285--196318 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
196275 TATCCATCTT
196285 CAACTC CAACTC CAACTC CAACTC CAACTC CAAC
1 CAACTC CAACTC CAACTC CAACTC CAACTC CAAC
196319 ACAGAGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (6 bp):
CAACTC
Found at i:196371 original size:3 final size:3
Alignment explanation
Indices: 196363--196393 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
196353 CCATAACTTT
*
196363 TTG TTG TTG TTG TTG TTG TTG CTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
196394 CGAACTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:201264 original size:31 final size:30
Alignment explanation
Indices: 201226--201297 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
201216 GCCTCTAAAT
* *
201226 TTTTAAAAATTCTCATTGAGCCTTT-CAAAAA
1 TTTTAAAAATTCTAATT-AG-ATTTCCAAAAA
* *
201257 TTTTAAAAATCCTAATTAGATTTCCAAAAT
1 TTTTAAAAATTCTAATTAGATTTCCAAAAA
201287 TTTTAAAAATT
1 TTTTAAAAATT
201298 TCCATTCAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 3 0.09
30 17 0.49
31 15 0.43
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATTCTAATTAGATTTCCAAAAA
Found at i:201291 original size:30 final size:31
Alignment explanation
Indices: 201222--201296 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
201212 TTAGGCCTCT
* * *
201222 AAATTTTTAAAAATTCTCATTGAGCCTTTCA
1 AAATTTTTAAAAATCCTAATTGAGCATTTCA
*
201253 AAAATTTTAAAAATCCTAATT-AG-ATTTCCA
1 AAATTTTTAAAAATCCTAATTGAGCATTT-CA
201283 AAATTTTTAAAAAT
1 AAATTTTTAAAAAT
201297 TTCCATTCAG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 3 0.08
30 17 0.45
31 18 0.47
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (31 bp):
AAATTTTTAAAAATCCTAATTGAGCATTTCA
Found at i:206139 original size:23 final size:23
Alignment explanation
Indices: 206109--206185 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
206099 ATGCTAGCGC
206109 GCTTACTG-TTCAGCACTAT-GTGT
1 GCTTACTGTTTC-GCACT-TCGTGT
206132 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* * *
206155 GCTTATTATTTCGCACCTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
206178 GCCTACTG
1 GCTTACTG
206186 ATTTGCGCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.02
23 42 0.91
24 3 0.07
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:210265 original size:62 final size:59
Alignment explanation
Indices: 210156--210272 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
210146 ATCACTTTAA
* * *
210156 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAAGATTAAATCT
* *
210215 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTATATTTAAGATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAAGATTAA
210273 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAAGATTAAATCT
Found at i:210298 original size:20 final size:18
Alignment explanation
Indices: 210248--210299 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
210238 CTACAAGATA
210248 AATATTAAATT-ATATTT
1 AATATTAAATTAATATTT
*
210265 AAGATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
210285 AATATTAAATTAATA
1 AATATTAAATTAATA
210300 AAATACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.29
18 3 0.11
19 3 0.11
20 14 0.50
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:213663 original size:2 final size:2
Alignment explanation
Indices: 213656--213691 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
213646 TTCTTTCTTC
213656 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
213692 GATGAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:217218 original size:2 final size:2
Alignment explanation
Indices: 217213--217244 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
217203 GTATTATTTA
217213 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
217245 CGAATAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:217677 original size:12 final size:12
Alignment explanation
Indices: 217660--217696 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
217650 AAAACTATAC
217660 AAAATAATTCAA
1 AAAATAATTCAA
*
217672 AAAATAATT-AT
1 AAAATAATTCAA
217683 AAAA-AATTCAA
1 AAAATAATTCAA
217694 AAA
1 AAA
217697 CATATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 4 0.18
11 9 0.41
12 9 0.41
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATTCAA
Found at i:218614 original size:22 final size:21
Alignment explanation
Indices: 218575--218615 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
218565 TCTGTCCATA
218575 TTATTTTTTTAAATATTTATT
1 TTATTTTTTTAAATATTTATT
*
218596 TTATTTTATTTTAATATTTA
1 TTATTTT-TTTAAATATTTA
218616 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTTTTTTAAATATTTATT
Found at i:222265 original size:20 final size:20
Alignment explanation
Indices: 222229--222266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
222219 CTGACTTGAA
222229 TAAATATTTCAAATTAAAGT
1 TAAATATTTCAAATTAAAGT
*
222249 TAAAT-TTTACAATTTAAA
1 TAAATATTT-CAAATTAAA
222267 TAACTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TAAATATTTCAAATTAAAGT
Found at i:226319 original size:74 final size:74
Alignment explanation
Indices: 226224--226378 Score: 220
Period size: 74 Copynumber: 2.1 Consensus size: 74
226214 TACACTTCGT
* **
226224 ATATCGGACACGAGAAAAATCACGAATCCTATTAACATATTGTAACTAAAACCCCATGTAATTGG
1 ATATCGGACACGAGAAAAATCACGAATCCTAATAACATATTGTAACTAAAACCCCATGTAACCGG
226289 GACGTATTG
66 GACGTATTG
* * * * *
226298 ATATCGGACATGAGGACAATCATGAATCCTAATAACATATTGTAACTAAAACCTCATGTAACCGG
1 ATATCGGACACGAGAAAAATCACGAATCCTAATAACATATTGTAACTAAAACCCCATGTAACCGG
*
226363 TACGTATTG
66 GACGTATTG
*
226372 GTATCGG
1 ATATCGG
226379 GCATTCATCA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.26
Consensus pattern (74 bp):
ATATCGGACACGAGAAAAATCACGAATCCTAATAACATATTGTAACTAAAACCCCATGTAACCGG
GACGTATTG
Found at i:233006 original size:2 final size:2
Alignment explanation
Indices: 232999--233027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
232989 GGTCTATGAT
232999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
233028 TATGGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:234580 original size:36 final size:37
Alignment explanation
Indices: 234517--234586 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
234507 AATATTACTT
* *
234517 TTATTATTATTGTGTAATAATACTAATA-AATTATTA
1 TTATTATTATTATGTAATAATAATAATATAATTATTA
*
234553 TTATTATTATTATGTGAAT-TTAATAATATAATTA
1 TTATTATTATTATGT-AATAATAATAATATAATTA
234587 AAAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 21 0.72
37 8 0.28
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (37 bp):
TTATTATTATTATGTAATAATAATAATATAATTATTA
Found at i:235715 original size:13 final size:14
Alignment explanation
Indices: 235685--235719 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
235675 GTTTGCATGT
*
235685 AAAATGGTTTCCGA
1 AAAATGATTTCCGA
*
235699 AAAATGATTTCTGA
1 AAAATGATTTCCGA
235713 AAAATGA
1 AAAATGA
235720 GTTACTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:237963 original size:7 final size:7
Alignment explanation
Indices: 237951--237983 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
237941 ATAAACTGAT
237951 AAAAAGA
1 AAAAAGA
237958 AAAAAGA
1 AAAAAGA
237965 AAAAAGA
1 AAAAAGA
237972 AAAAAGA
1 AAAAAGA
237979 AAAAA
1 AAAAA
237984 AAAGTACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:241689 original size:30 final size:29
Alignment explanation
Indices: 241610--241689 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
241600 GCCTAGACGG
*
241610 GTAACCTCGATATAATGTCAGCTTGTGTGA
1 GTAACCT-GATATAATGTCAGCTTGTCTGA
* ** *
241640 GCAATATTGTTATAATGTCAGCTTGTCTGA
1 GTAA-CCTGATATAATGTCAGCTTGTCTGA
*
241670 GTAACCCTGATATATTGTCA
1 GTAA-CCTGATATAATGTCA
241690 ACTTCTATGA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (29 bp):
GTAACCTGATATAATGTCAGCTTGTCTGA
Found at i:242045 original size:30 final size:30
Alignment explanation
Indices: 242011--242071 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
242001 TTTAGTTTCC
242011 AGTTGAACTTATTAAGCATTTTGAAAGCTT
1 AGTTGAACTTATTAAGCATTTTGAAAGCTT
*
242041 AGTTGAACTTATTAAGCATTTTGAATGCTT
1 AGTTGAACTTATTAAGCATTTTGAAAGCTT
242071 A
1 A
242072 CTTTGGTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (30 bp):
AGTTGAACTTATTAAGCATTTTGAAAGCTT
Found at i:245474 original size:28 final size:28
Alignment explanation
Indices: 245442--245548 Score: 85
Period size: 28 Copynumber: 3.8 Consensus size: 28
245432 CATTCCACAT
245442 AAGATAGTCCTTGGCGAACTTTACAGAA
1 AAGATAGTCCTTGGCGAACTTTACAGAA
* * *
245470 TAGATAATCCTTAGC-AGACTTTACAGAA
1 AAGATAGTCCTTGGCGA-ACTTTACAGAA
* * *
245498 CAA-ATAGTCATTGGCTG-ACATTACACATA
1 -AAGATAGTCCTTGGC-GAACTTTACAGA-A
* *
245527 AAGATAGCCCTTGGCGGACTTT
1 AAGATAGTCCTTGGCGAACTTT
245549 TTTCTTCCAA
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (28 bp):
AAGATAGTCCTTGGCGAACTTTACAGAA
Found at i:247049 original size:29 final size:29
Alignment explanation
Indices: 246979--247073 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 29
246969 GTTAATAATT
* * * *
246979 TATAAGAATTGGATAAAATCAAAATTTTATG
1 TATAA-AATTGCACAAAATC-AAAGTTCATG
247010 TATAAAATTGCACAAAATCAAAGTTCATG
1 TATAAAATTGCACAAAATCAAAGTTCATG
* * *
247039 TATACAATTGCACATTAAACCATAGTTCATG
1 TATAAAATTGCACA--AAATCAAAGTTCATG
247070 TATA
1 TATA
247074 GTTTTGGCCA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.38
30 12 0.22
31 22 0.40
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (29 bp):
TATAAAATTGCACAAAATCAAAGTTCATG
Found at i:256873 original size:21 final size:21
Alignment explanation
Indices: 256847--256896 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
256837 CGTTACAGTG
256847 CTGACGTGACTTTTAACGACA
1 CTGACGTGACTTTTAACGACA
256868 CTGACGTGACTTTTAACGACA
1 CTGACGTGACTTTTAACGACA
256889 CTGACGTG
1 CTGACGTG
256897 GTGCTTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (21 bp):
CTGACGTGACTTTTAACGACA
Found at i:257094 original size:10 final size:9
Alignment explanation
Indices: 257090--257136 Score: 76
Period size: 9 Copynumber: 5.0 Consensus size: 9
257080 ATAAAAAGAA
257090 TTAAATAAAAT
1 TTAAA-AAA-T
257101 TTAAAAAAT
1 TTAAAAAAT
257110 TTAAAAAAT
1 TTAAAAAAT
257119 TTAAAAAAT
1 TTAAAAAAT
257128 TTAAAAAAT
1 TTAAAAAAT
257137 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 28 0.78
10 3 0.08
11 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:257110 original size:9 final size:9
Alignment explanation
Indices: 257096--257136 Score: 82
Period size: 9 Copynumber: 4.6 Consensus size: 9
257086 AGAATTAAAT
257096 AAAATTTAA
1 AAAATTTAA
257105 AAAATTTAA
1 AAAATTTAA
257114 AAAATTTAA
1 AAAATTTAA
257123 AAAATTTAA
1 AAAATTTAA
257132 AAAAT
1 AAAAT
257137 AAAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:259048 original size:29 final size:30
Alignment explanation
Indices: 258984--259049 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
258974 CTTTGACCTT
* * *
258984 ATTTGATTCTTTTTAAAAATACATGGATTA
1 ATTTGATTCTATTTAAAAATACAAGGACTA
* * *
259014 AATTGATTC-ATTTAATAATAGAAGGACTA
1 ATTTGATTCTATTTAAAAATACAAGGACTA
259043 ATTTGAT
1 ATTTGAT
259050 AAATTCCCTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (30 bp):
ATTTGATTCTATTTAAAAATACAAGGACTA
Found at i:263172 original size:11 final size:11
Alignment explanation
Indices: 263158--263199 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
263148 AGGGTTTAAT
263158 AAATAATATTA
1 AAATAATATTA
263169 AAATAATATTTTA
1 AAATAATA--TTA
263182 AAATTAAT-TTA
1 AAA-TAATATTA
263193 AAATAAT
1 AAATAAT
263200 TCTATTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.14
11 14 0.50
13 6 0.21
14 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATAATATTA
Found at i:263193 original size:24 final size:26
Alignment explanation
Indices: 263152--263199 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
263142 TAAATAAGGG
263152 TTTAATAAATAATATTAAAATAATAT
1 TTTAATAAATAATATTAAAATAATAT
*
263178 TTTAA-AATTAAT-TTAAAATAAT
1 TTTAATAAATAATATTAAAATAAT
263200 TCTATTCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTAATAAATAATATTAAAATAATAT
Found at i:263880 original size:8 final size:8
Alignment explanation
Indices: 263867--263891 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
263857 TGTTGTCAAA
263867 TAATTATT
1 TAATTATT
263875 TAATTATT
1 TAATTATT
263883 TAATTATT
1 TAATTATT
263891 T
1 T
263892 TTATATATTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTATT
Found at i:264249 original size:18 final size:18
Alignment explanation
Indices: 264226--264261 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
264216 TGCCTGATGG
*
264226 TTCTTCTCCATCATCATC
1 TTCTTCTCCACCATCATC
264244 TTCTTCTCCACCATCATC
1 TTCTTCTCCACCATCATC
264262 ATCATCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.42, G:0.00, T:0.42
Consensus pattern (18 bp):
TTCTTCTCCACCATCATC
Found at i:265281 original size:2 final size:2
Alignment explanation
Indices: 265276--265300 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
265266 ATAAGCTTAT
265276 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
265301 GTCATGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:265367 original size:4 final size:4
Alignment explanation
Indices: 265358--265392 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
265348 AGATTAGATA
*
265358 TATG TATG TATG TATG TATCG TATG TATA TATG TA
1 TATG TATG TATG TATG TAT-G TATG TATG TATG TA
265393 AATATACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:272774 original size:40 final size:39
Alignment explanation
Indices: 272703--272818 Score: 101
Period size: 40 Copynumber: 2.9 Consensus size: 39
272693 CCAATAACAC
* * *
272703 ACCAGTTTGTAGACAAGCCACTAATAA-TGCAGATAAATT
1 ACCAGTATGTGGACAAGCCACCAA-AATTGCAGATAAATT
* * * *
272742 ACCAAAGT-TGTGGATAAGCCACCAGAATTGCAGACAAGTT
1 ACC--AGTATGTGGACAAGCCACCAAAATTGCAGATAAATT
* *
272782 GCCAGTAATGTGGACAAGCCACCAAAATTGTAGATAA
1 ACCAGT-ATGTGGACAAGCCACCAAAATTGCAGATAA
272819 GTTGCTAGCA
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
38 3 0.05
39 5 0.08
40 50 0.82
41 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.22
Consensus pattern (39 bp):
ACCAGTATGTGGACAAGCCACCAAAATTGCAGATAAATT
Found at i:278983 original size:20 final size:20
Alignment explanation
Indices: 278958--279001 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
278948 GTTAGGCTAC
*
278958 AATGCTGCTAC-GTAATGGGG
1 AATGCT-CTACAGTAATAGGG
278978 AATGCTCTACAGGTAATAGGG
1 AATGCTCTACA-GTAATAGGG
278999 AAT
1 AAT
279002 AGTCAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 11 0.52
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (20 bp):
AATGCTCTACAGTAATAGGG
Found at i:281068 original size:30 final size:30
Alignment explanation
Indices: 281034--281334 Score: 103
Period size: 30 Copynumber: 10.2 Consensus size: 30
281024 AACTGTCTAG
* *
281034 AAATTATATTTTAAACCTTAAAC-TTCTATA
1 AAATTATATTTTAAACCTCAAACTTTCCA-A
*
281064 AAATTATATTTTAACCCTCAAACTTTCCAA
1 AAATTATATTTTAAACCTCAAACTTTCCAA
* *
281094 AAATTACATTTT--ACCACCAAACTTTCC-A
1 AAATTATATTTTAAACC-TCAAACTTTCCAA
* * * *
281122 AAATTCCAT-TTTTTACCCT-GAACTTTCTAA
1 AAATT--ATATTTTAAACCTCAAACTTTCCAA
* * ** *
281152 AAATTACATTTT-TACCAAAAAACTTT-CGA
1 AAATTATATTTTAAACC-TCAAACTTTCCAA
* **
281181 AAATTCA-ATTTT-AACCTCGATTTTTCCAA
1 AAATT-ATATTTTAAACCTCAAACTTTCCAA
* * *
281210 AAATTACCATTTT-ACCCCCAAAC-TTCACAA
1 AAATTA-TATTTTAAACCTCAAACTTTC-CAA
* * *
281240 AAATCCAT-TTTT-AACCCCAAAATTTCCAA
1 AAAT-TATATTTTAAACCTCAAACTTTCCAA
** * *
281269 AAATTATCATTTTAGCCCT-GAAC-TTCTAA
1 AAATTAT-ATTTTAAACCTCAAACTTTCCAA
* * ** **
281298 AAATTCTATTTTTAACCTTGATTTTTCCAA
1 AAATTATATTTTAAACCTCAAACTTTCCAA
281328 AAATTAT
1 AAATTAT
281335 CGTTTTACCC
Statistics
Matches: 200, Mismatches: 49, Indels: 44
0.68 0.17 0.15
Matches are distributed among these distances:
28 26 0.13
29 81 0.41
30 84 0.42
31 9 0.05
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (30 bp):
AAATTATATTTTAAACCTCAAACTTTCCAA
Found at i:281147 original size:58 final size:58
Alignment explanation
Indices: 281072--281464 Score: 289
Period size: 59 Copynumber: 6.7 Consensus size: 58
281062 TAAAATTATA
*
281072 TTTTAACCCTCAAACTTTCCAAAAATTA-CATTTTACCACCAAACTTTCCAAAATTCCAT
1 TTTTAACCCT-GAACTTTCCAAAAATTACCATTTTACC-CCAAACTTTCCAAAATTCCAT
* * ** * *
281131 TTTTTACCCTGAACTTTCTAAAAATTA-CATTTTTACCAAAAAACTTTCGAAAATT-CAA
1 TTTTAACCCTGAACTTTCCAAAAATTACCA-TTTTACC-CCAAACTTTCCAAAATTCCAT
** *
281189 TTTTAA-CCTCGATTTTTCCAAAAATTACCATTTTACCCCCAAAC-TTCACAAAAATCCAT
1 TTTTAACCCT-GAACTTTCCAAAAATTACCATTTTA-CCCCAAACTTTC-CAAAATTCCAT
** * * ** * *
281248 TTTTAACCCCAAAATTTCCAAAAATTATCATTTTAGCCCTGAAC-TTCTAAAAATTCTAT
1 TTTTAACCCTGAACTTTCCAAAAATTACCATTTTA-CCCCAAACTTTC-CAAAATTCCAT
* ** * * * * *
281307 TTTTAACCTTGATTTTTCCAAAAATTATCGTTTTACCCTAAACTTCCCAAAATTCCAA
1 TTTTAACCCTGAACTTTCCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCAT
** ** * * *
281365 TTTTAA-CCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTGGA-TGTCTAAAATTTCAT
1 TTTTAACCCT-GA---ACTTTCCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCAT
* *
281426 TTTTAACCCCGAACTTTCCCAAAATTACCATTTTACCCC
1 TTTTAACCCTGAACTTTCCAAAAATTACCATTTTACCCC
281465 CGCGTACCCA
Statistics
Matches: 266, Mismatches: 54, Indels: 29
0.76 0.15 0.08
Matches are distributed among these distances:
57 8 0.03
58 99 0.37
59 112 0.42
60 2 0.01
61 42 0.16
62 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
TTTTAACCCTGAACTTTCCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCAT
Found at i:281463 original size:29 final size:29
Alignment explanation
Indices: 281084--281464 Score: 146
Period size: 29 Copynumber: 13.0 Consensus size: 29
281074 TTAACCCTCA
*
281084 AACTTTCCAAAAATTA-CATTTTACCACCA
1 AACTTTCCAAAAATTACCATTTTACC-CCG
*
281113 AACTTTCC-AAAATT-CCATTTTTTACCCTG
1 AACTTTCCAAAAATTACCA--TTTTACCCCG
* ***
281142 AACTTTCTAAAAATTA-CATTTTTACCAAAA
1 AACTTTCCAAAAATTACCA-TTTTACC-CCG
* * *
281172 AACTTT-CGAAAATT-CAATTTTAACCTCG
1 AACTTTCCAAAAATTACCATTTT-ACCCCG
** *
281200 ATTTTTCCAAAAATTACCATTTTACCCCCA
1 AACTTTCCAAAAATTACCATTTTA-CCCCG
*
281230 AAC-TTCACAAAAA-T-CCATTTTTAACCCCA
1 AACTTTC-CAAAAATTACCA-TTTT-ACCCCG
* * *
281259 AAATTTCCAAAAATTATCATTTTAGCCCTG
1 AACTTTCCAAAAATTACCATTTTA-CCCCG
* * **
281289 AAC-TTCTAAAAATT-CTATTTTTAACCTTG
1 AACTTTCCAAAAATTACCA-TTTT-ACCCCG
** * * **
281318 ATTTTTCCAAAAATTATCGTTTTACCCTA
1 AACTTTCCAAAAATTACCATTTTACCCCG
* *
281347 AAC-TTCCCAAAATT-CCAATTTTAACCTCG
1 AACTTTCCAAAAATTACC-ATTTT-ACCCCG
**
281376 ATTTTTTTTCCAAAAATTACCATTTTACCCCTG
1 A---ACTTTCCAAAAATTACCATTTTACCCC-G
* * * *
281409 GA-TGT-CTAAAATT-TCATTTTTAACCCCG
1 AACTTTCCAAAAATTACCA-TTTT-ACCCCG
*
281437 AACTTTCCCAAAATTACCATTTTACCCC
1 AACTTTCCAAAAATTACCATTTTACCCC
281465 CGCGTACCCA
Statistics
Matches: 259, Mismatches: 58, Indels: 70
0.67 0.15 0.18
Matches are distributed among these distances:
27 3 0.01
28 47 0.18
29 106 0.41
30 77 0.30
31 4 0.02
32 4 0.02
33 16 0.06
34 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTTCCAAAAATTACCATTTTACCCCG
Found at i:281477 original size:119 final size:120
Alignment explanation
Indices: 281054--281463 Score: 290
Period size: 117 Copynumber: 3.5 Consensus size: 120
281044 TTAAACCTTA
* * *
281054 AACTTCTATAAAATTATA-TTTTAACCCTCAAACTTTCCAAAAATTA-CATTTTACCACCAAACT
1 AACTTCTA-AAAATTCTATTTTTAACCC-CGAACTTTCCAAAAATTACCATTTTACC-CTAAACT
** * * ** * ****
281117 TTCCAAAATTCCATTTTTTACC-CTGA---ACTTTCTAAAAATTA-CATTTTTACCAAAA
63 ACCCAAAATTCCAATTTTAACCTC-GATTTTTTTTCCAAAAATTACCA-TTTTACCCCTG
* * * ** * *
281172 AACTT-TCGAAAATTC-AATTTTAACCTCGATTTTTCCAAAAATTACCATTTTACCCCCAAACTT
1 AACTTCT-AAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTA-CCCTAAACTA
* * * * *** * *
281235 CACAAAAATCCATTTTTAACC-CCA--AAATTTCCAAAAATTATCATTTTAGCCCTG
64 CCCAAAATTCCAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTG
** ** * * *
281289 AACTTCTAAAAATTCTATTTTTAACCTTGATTTTTCCAAAAATTATCGTTTTACCCTAAACTTCC
1 AACTTCTAAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTAAACTACC
281354 CAAAATTCCAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTG
66 CAAAATTCCAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTG
* * *
281409 GA-TGTCTAAAATTTC-ATTTTTAACCCCGAACTTTCCCAAAATTACCATTTTACCC
1 AACT-TCTAAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCC
281464 CCGCGTACCC
Statistics
Matches: 238, Mismatches: 42, Indels: 23
0.79 0.14 0.08
Matches are distributed among these distances:
116 17 0.07
117 106 0.45
118 45 0.19
119 34 0.14
120 36 0.15
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (120 bp):
AACTTCTAAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTAAACTACC
CAAAATTCCAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTG
Found at i:281487 original size:119 final size:120
Alignment explanation
Indices: 281180--281463 Score: 274
Period size: 120 Copynumber: 2.4 Consensus size: 120
281170 AAAACTTTCG
* * ** * * * *
281180 AAAATTC-AATTTTAACCTCGATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCACAAAAAT
1 AAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTA-CCCTAAACTACCCAAAAGT
* * *** * *
281244 CCATTTTTAACC-CCA--AAATTTCCAAAAATTATCATTTTAGCCCTGAACTTCTA
65 CCAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTGAACTTCTA
** ** * * * *
281297 AAAATTCTATTTTTAACCTTGATTTTTCCAAAAATTATCGTTTTACCCTAAACTTCCCAAAATTC
1 AAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTAAACTACCCAAAAGTC
*
281362 CAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTGGA-TGTCTA
66 CAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTGAACT-TCTA
* *
281417 AAATTTC-ATTTTTAACCCCGAACTTTCCCAAAATTACCATTTTACCC
1 AAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCC
281464 CCGCGTACCC
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
117 34 0.24
118 35 0.25
119 34 0.24
120 36 0.26
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (120 bp):
AAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTAAACTACCCAAAAGTC
CAATTTTAACCTCGATTTTTTTTCCAAAAATTACCATTTTACCCCTGAACTTCTA
Found at i:292808 original size:49 final size:49
Alignment explanation
Indices: 292640--293102 Score: 297
Period size: 49 Copynumber: 9.4 Consensus size: 49
292630 CCAGTACCGC
* * * * *
292640 AAGGGAAAGGTTTAAGTCACAATGGTGAACCTAATACCTCAGAAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAATACCTCA-AAGACATG
** * * * *
292690 AAGGGAAAGATTTAAGCCATAACGGCGGATCC-AATACCACATAGA-ATA
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAATACCTCAAAGACATG
* * * * *
292738 AAGGGAAAGGTTTAAGTCGTAACGGTGAACCTTATACCTCAAAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAATACCTCAAAGACATG
* * * * **
292787 AAGGGAAAGATCTAAGCCGTAACGGCGGATCC-AATACCGCAAAGACACA
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAATACCTCAAAGACATG
* * * ** *
292836 AAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAATACCTCAAAGACATG
* * * * * * **
292885 AAGGGAAATATCTAAGCCGTAACGACGGATCC-AATACCACAAAGACACA
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAATACCTCAAAGACATG
* * * * ** * *
292934 AAAGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTTAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAATACCTCAAAGACATG
* * * * * **
292983 AAGGGAAAGATCTAAGCTGCAACGGCGGATCC-AGTACCGCAAAGACAAA
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAATACCTCAAAGACATG
* * * * ** * *
293032 AAGGGAAAGGTTTAAGTCACAACGGCGAGCCTTGTACCTTAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAATACCTCAAAGACATG
* *
293081 AAGGGAAAGATCTAAGCTGCAA
1 AAGGGAAAGATTTAAGCCGCAA
293103 TGGCAGATCC
Statistics
Matches: 307, Mismatches: 97, Indels: 19
0.73 0.23 0.04
Matches are distributed among these distances:
47 4 0.01
48 46 0.15
49 212 0.69
50 41 0.13
51 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAATACCTCAAAGACATG
Found at i:292839 original size:98 final size:98
Alignment explanation
Indices: 292640--293168 Score: 727
Period size: 98 Copynumber: 5.4 Consensus size: 98
292630 CCAGTACCGC
* * ** *
292640 AAGGGAAAGGTTTAAGTCACAATGGTGAACCTAATACCTCAGAAGACATGAAGGGAAAGATTTAA
1 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAG-AGACATGAAGGGAAAGATCTAA
* * * *
292705 GCCATAACGGCGGATCCAATACCACATAGA-ATA
65 GCCGTAACGGCGGATCCAATACCGCAAAGACACA
** * * *
292738 AAGGGAAAGGTTTAAGTCGTAACGGTGAACCTTATACCTCAAAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAGACATGAAGGGAAAGATCTAAG
292803 CCGTAACGGCGGATCCAATACCGCAAAGACACA
66 CCGTAACGGCGGATCCAATACCGCAAAGACACA
* * *
292836 AAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAGACATGAAGGGAAATATCTAAG
1 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAGACATGAAGGGAAAGATCTAAG
* *
292901 CCGTAACGACGGATCCAATACCACAAAGACACA
66 CCGTAACGGCGGATCCAATACCGCAAAGACACA
* *
292934 AAAGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTTAGAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAGACATGAAGGGAAAGATCTAAG
* * * *
292999 CTGCAACGGCGGATCCAGTACCGCAAAGACAAA
66 CCGTAACGGCGGATCCAATACCGCAAAGACACA
* *
293032 AAGGGAAAGGTTTAAGTCACAACGGCGAGCCTTGTACCTTAGAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAGACATGAAGGGAAAGATCTAAG
* * * * * * *
293097 CTGCAATGGCAGATCCAGTACTGCAAAGAAACA
66 CCGTAACGGCGGATCCAATACCGCAAAGACACA
*
293130 AAGGGAAAGGTTTAAGTCACAATGGCGAACCTTGTACCT
1 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCT
293169 TAGAAGCATA
Statistics
Matches: 392, Mismatches: 38, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
97 48 0.12
98 344 0.88
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (98 bp):
AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAGACATGAAGGGAAAGATCTAAG
CCGTAACGGCGGATCCAATACCGCAAAGACACA
Found at i:293134 original size:49 final size:47
Alignment explanation
Indices: 292787--293138 Score: 133
Period size: 49 Copynumber: 7.2 Consensus size: 47
292777 CAAAGACATG
* * * *
292787 AAGGGAAAGATCTAAGCCGTAACGGCGGATCCAATACCGCAAAGACACA
1 AAGGGAAAGATCTAAGCTGCAACGGC-GATCCAGTA-CGCAAAGAAACA
* * * * * ** *
292836 AAGGGAAAGGTTTAAG-TCGCAACGACGAACCTTGTAC-CTCAGAGACA
1 AAGGGAAAGATCTAAGCT-GCAACGGCGATCC-AGTACGCAAAGAAACA
* * * * * * *
292883 TGAAGGGAAATATCTAAGCCGTAACGACGGATCCAATACCACAAAGACACA
1 --AAGGGAAAGATCTAAGCTGCAACGGC-GATCCAGTA-CGCAAAGAAACA
* * * * * * ** *
292934 AAAGGAAAGGTTTAAG-TCACAACGGCGAACCTTGTAC-CTTAGAGACA
1 AAGGGAAAGATCTAAGCT-GCAACGGCGATCC-AGTACGCAAAGAAACA
292981 TGAAGGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCGCAAAGACAA-A
1 --AAGGGAAAGATCTAAGCTGCAACGGC-GATCCAGTA-CGCAAAGA-AACA
* * * * * ** *
293032 AAGGGAAAGGTTTAAG-TCACAACGGCGAGCCTTGTAC-CTTAGAGACA
1 AAGGGAAAGATCTAAGCT-GCAACGGCGATCC-AGTACGCAAAGAAACA
*
293079 TGAAGGGAAAGATCTAAGCTGCAATGGCAGATCCAGTACTGCAAAGAAACA
1 --AAGGGAAAGATCTAAGCTGCAACGGC-GATCCAGTAC-GCAAAGAAACA
293130 AAGGGAAAG
1 AAGGGAAAG
293139 GTTTAAGTCA
Statistics
Matches: 215, Mismatches: 62, Indels: 52
0.65 0.19 0.16
Matches are distributed among these distances:
46 1 0.00
47 19 0.09
48 16 0.07
49 143 0.67
50 16 0.07
51 19 0.09
52 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.15
Consensus pattern (47 bp):
AAGGGAAAGATCTAAGCTGCAACGGCGATCCAGTACGCAAAGAAACA
Found at i:293823 original size:6 final size:6
Alignment explanation
Indices: 293812--293890 Score: 69
Period size: 6 Copynumber: 14.0 Consensus size: 6
293802 CCCACATTTC
* **
293812 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
293858 TTT-AA TTTAAG TTT-AA TTT-TT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
293891 ATTATTCTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
5 19 0.33
6 38 0.67
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:293834 original size:17 final size:17
Alignment explanation
Indices: 293812--293910 Score: 128
Period size: 17 Copynumber: 5.8 Consensus size: 17
293802 CCCACATTTC
293812 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
293829 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTAT
*
293846 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAT
* *
293863 TTTAAGTTT-AATTTTT
1 TTTAAATTTAAATTTAT
*
293879 TTTAAATTTAAAATTAT
1 TTTAAATTTAAATTTAT
*
293896 TCTAAATTTTAAATT
1 TTTAAA-TTTAAATT
293911 AAGAGAAGTC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.19
17 49 0.71
18 7 0.10
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:293864 original size:11 final size:11
Alignment explanation
Indices: 293816--293876 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
293806 CATTTCTTTA
293816 AATTTAAATTT
1 AATTTAAATTT
*
293827 ATTTTAAATTT
1 AATTTAAATTT
**
293838 AAATTT-GTTTT
1 -AATTTAAATTT
293849 AAATTTAAATTT
1 -AATTTAAATTT
*
293861 AATTTAAGTTT
1 AATTTAAATTT
293872 AATTT
1 AATTT
293877 TTTTTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 34 0.83
12 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:294683 original size:15 final size:15
Alignment explanation
Indices: 294630--294684 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
294620 AAATAAAGGC
294630 ATTAATAATTATGGTAAT
1 ATTAAT-ATTAT--TAAT
294648 ATTAAGTA-TATTAAT
1 ATTAA-TATTATTAAT
294663 -TATAATATTATTAAT
1 AT-TAATATTATTAAT
294678 ATTAATA
1 ATTAATA
294685 AATAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.09
15 19 0.58
16 1 0.03
17 3 0.09
18 6 0.18
19 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (15 bp):
ATTAATATTATTAAT
Found at i:295929 original size:58 final size:58
Alignment explanation
Indices: 295849--296370 Score: 376
Period size: 58 Copynumber: 9.0 Consensus size: 58
295839 TTTAACCCCC
* ** * * * *
295849 AAACTTCTCCAAAATTATATTTTGACCCTCGAACTTTATGAAAATTACAATTTTACCCT
1 AAACTT-TCTAAAATTCCATTTTGACCCTCGAATTTTCTAAAAATTACCATTTTACCCT
* * * *
295908 GAACTTTCTAAAATTCCATTTTTAACCCT-AAATTTTTTAAAAATTA-CATTTTACCCCT
1 AAACTTTCTAAAATTCCA-TTTTGACCCTCGAATTTTCTAAAAATTACCATTTTA-CCCT
* ** *
295966 AAACTTTCCAAAATTTAATTTTAGA-CCTCG-ATTTTCCAAAAATTACCATTTTACCCTT
1 AAACTTTCTAAAATTCCATTTT-GACCCTCGAATTTTCTAAAAATTACCATTTTACCC-T
* *
296024 GAAC-TTCTAAAAATTCCATTTTGA-CCTC-AATTTTTCCAAAAATTACCATTTTACCCT
1 AAACTTTCT-AAAATTCCATTTTGACCCTCGAA-TTTTCTAAAAATTACCATTTTACCCT
* * *
296081 CAAACTTCCCAAAATTCCATTTTTAACCC-CGAATTTTCT-AAAATTACCATTTTACCCT
1 -AAACTTTCTAAAATTCCA-TTTTGACCCTCGAATTTTCTAAAAATTACCATTTTACCCT
* * * * * * * *
296139 CGAAC-TTCTAAAAATTTCATTTTTAACCTTGAATTTTCCAAAAATTATCGTTTTACCCTT
1 -AAACTTTCT-AAAATTCCATTTTGACCCTCGAATTTTCTAAAAATTACCATTTTACCC-T
* *
296199 AAACTTTCTAAAATTCCATTTTTGA-CCT-TAATTTTTCCAAAAATTACCATTTTACCCT
1 AAACTTTCTAAAATTCCA-TTTTGACCCTCGAA-TTTTCTAAAAATTACCATTTTACCCT
* * * * *
296257 AAACTTCCCAAAATTTCATTTTAACCC-C-AATTTTTCCAAAAATTACCA-TTTACCCT
1 AAACTTTCTAAAATTCCATTTTGACCCTCGAA-TTTTCTAAAAATTACCATTTTACCCT
* * *** * * **
296313 CGAA-TGTCTAAAATTTTGTTTTTAACCC-CGAACTTTCCCAAAATTACCATTTTACCCT
1 -AAACTTTCTAAAA-TTCCATTTTGACCCTCGAATTTTCTAAAAATTACCATTTTACCCT
296371 TGGGTACCCA
Statistics
Matches: 381, Mismatches: 55, Indels: 55
0.78 0.11 0.11
Matches are distributed among these distances:
56 14 0.04
57 104 0.27
58 169 0.44
59 80 0.21
60 14 0.04
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (58 bp):
AAACTTTCTAAAATTCCATTTTGACCCTCGAATTTTCTAAAAATTACCATTTTACCCT
Found at i:295935 original size:29 final size:27
Alignment explanation
Indices: 295867--296279 Score: 170
Period size: 29 Copynumber: 14.2 Consensus size: 27
295857 CCAAAATTAT
* *
295867 ATTTTGACCCTCGAACTTTATGAAAATTACA
1 ATTTT-ACCCT-GAACTTTCT-AAAATT-CC
295898 ATTTTACCCTGAACTTTCTAAAATTCC
1 ATTTTACCCTGAACTTTCTAAAATTCC
* * * *
295925 ATTTTTAACCCTAAATTTTTTAAAAATTAC
1 A-TTTT-ACCCTGAACTTTCT-AAAATTCC
* * **
295955 ATTTTACCCCTAAACTTTCCAAAATTTA
1 ATTTTA-CCCTGAACTTTCTAAAATTCC
* * *
295983 ATTTTAGACCTCG-ATTTTCCAAAAATTACC
1 ATTTTA-CCCT-GAACTTT-CTAAAATT-CC
296013 ATTTTACCCTTGAAC-TTCTAAAAATTCC
1 ATTTTACCC-TGAACTTTCT-AAAATTCC
* * *
296041 ATTTTGA-CCTCAATTTTTCCAAAAATTACC
1 ATTTT-ACCCTGAA-CTTT-CTAAAATT-CC
* * *
296071 ATTTTACCCTCAAACTTCCCAAAATTCC
1 ATTTTACCCT-GAACTTTCTAAAATTCC
* *
296099 ATTTTTAACCCCGAATTTTCTAAAATTACC
1 A-TTTT-ACCCTGAACTTTCTAAAATT-CC
*
296129 ATTTTACCCTCGAAC-TTCTAAAAATTTC
1 ATTTTACCCT-GAACTTTCT-AAAATTCC
* * * *
296157 ATTTTTAACCTTGAATTTTCCAAAAATTATC
1 A-TTTT-ACCCTGAACTTT-CTAAAATT-CC
* *
296188 GTTTTACCCTTAAACTTTCTAAAATTCC
1 ATTTTACCC-TGAACTTTCTAAAATTCC
* * *
296216 ATTTTTGA-CCTTAATTTTTCCAAAAATTACC
1 A-TTTT-ACCCTGAA-CTTT-CTAAAATT-CC
* * * *
296247 ATTTTACCCTAAACTTCCCAAAATTTC
1 ATTTTACCCTGAACTTTCTAAAATTCC
296274 ATTTTA
1 ATTTTA
296280 ACCCCAATTT
Statistics
Matches: 294, Mismatches: 54, Indels: 72
0.70 0.13 0.17
Matches are distributed among these distances:
27 12 0.04
28 64 0.22
29 125 0.43
30 80 0.27
31 13 0.04
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTGAACTTTCTAAAATTCC
Found at i:296037 original size:116 final size:118
Alignment explanation
Indices: 295827--296372 Score: 493
Period size: 116 Copynumber: 4.7 Consensus size: 118
295817 TTAAACTGTT
* * * ***
295827 CAAAAATTA-TATTTTAACCCCCAAACTTCTCCAAAA-TTATATTTT-GACCCTCGAACTTTATG
1 CAAAAATTACCATTTT-ACCCCTAAACTT-TCCAAAATTTA-ATTTTAGA-CCTCGAATTTTCCA
* *
295889 AAAATTACAATTTTACCC-TGAACTTTCT-AAAATTCCATTTTTAACCCTAAATTTTT-
62 AAAATTACCATTTTACCCTTGAAC-TTCTAAAAATTCCA-TTTTAACCCTCAATTTTTC
*
295945 TAAAAATTA-CATTTTACCCCTAAACTTTCCAAAATTTAATTTTAGACCTCG-ATTTTCCAAAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTAATTTTAGACCTCGAATTTTCCAAAAA
*
296008 TTACCATTTTACCCTTGAACTTCTAAAAATTCCATTTTGA-CCTCAATTTTTC
66 TTACCATTTTACCCTTGAACTTCTAAAAATTCCATTTTAACCCTCAATTTTTC
* * * * *
296060 CAAAAATTACCATTTTA-CCCTCAAACTTCCCAAAATTCCATTTTTA-ACCCCGAATTTT-CTAA
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATT-TAATTTTAGACCTCGAATTTTCCAAA
* * * *
296122 AATTACCATTTTACCCTCGAACTTCTAAAAATTTCATTTTTAACCTTGAA-TTTTC
64 AATTACCATTTTACCCTTGAACTTCTAAAAATTCCA-TTTTAACCCTCAATTTTTC
* * * * ** * *
296177 CAAAAATTATCGTTTTACCCTTAAACTTTCTAAAATTCCATTTTTGACCT-TAATTTTTCCAAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTAATTTTAGACCTCGAA-TTTTCCAAAA
* ** *
296241 ATTACCATTTTACCC-TAAACTTCCCAAAATTTCATTTTAACCC-CAATTTTTC
65 ATTACCATTTTACCCTTGAACTTCTAAAAATTCCATTTTAACCCTCAATTTTTC
* * * ** * * *
296293 CAAAAATTACCA-TTTA-CCCTCGAA-TGTCTAAAATTTTGTTTTTA-ACCCCGAACTTTCCCAA
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAA-TTTAATTTTAGACCTCGAATTTTCCAAA
296354 AATTACCATTTTACCCTTG
64 AATTACCATTTTACCCTTG
296373 GGTACCCAAA
Statistics
Matches: 356, Mismatches: 52, Indels: 43
0.79 0.12 0.10
Matches are distributed among these distances:
114 47 0.13
115 59 0.17
116 124 0.35
117 87 0.24
118 39 0.11
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTAATTTTAGACCTCGAATTTTCCAAAAA
TTACCATTTTACCCTTGAACTTCTAAAAATTCCATTTTAACCCTCAATTTTTC
Found at i:296308 original size:29 final size:29
Alignment explanation
Indices: 296228--296308 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
296218 TTTTGACCTT
* *
296228 AATTTTTCCAAAAATTACCATTTTACCCT
1 AATTTTTCCAAAAATTACCATTTAACCCC
** * *
296257 AA-ACTTCCCAAAATT-TCATTTTAACCCC
1 AATTTTTCCAAAAATTACCA-TTTAACCCC
296285 AATTTTTCCAAAAATTACCATTTA
1 AATTTTTCCAAAAATTACCATTTA
296309 CCCTCGAATG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.05
28 19 0.49
29 16 0.41
30 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.38
Consensus pattern (29 bp):
AATTTTTCCAAAAATTACCATTTAACCCC
Found at i:297773 original size:15 final size:15
Alignment explanation
Indices: 297753--297781 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
297743 TAGCTATAGA
297753 AATAAAATAAATGAT
1 AATAAAATAAATGAT
297768 AATAAAATAAATGA
1 AATAAAATAAATGA
297782 AGTGAGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAATAAATGAT
Found at i:304530 original size:2 final size:2
Alignment explanation
Indices: 304511--304547 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
304501 ATACATTCTC
* *
304511 AT AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
304548 GTCTCTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:304690 original size:15 final size:15
Alignment explanation
Indices: 304670--304700 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
304660 TAAAAGTAAA
304670 ATAATAAAATATAAT
1 ATAATAAAATATAAT
304685 ATAATAAAATATAAT
1 ATAATAAAATATAAT
304700 A
1 A
304701 AATCTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAAAATATAAT
Done.