Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold187
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: 870467
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 27366 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:327093 original size:32 final size:28
Alignment explanation
Indices: 327036--327090 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
327026 TAATAAAAAT
*
327036 TATTTAAAAATTATAAGAAATTATTAAC
1 TATTTAAAAATTATAAAAAATTATTAAC
327064 TATTTAAAAATTAATTAAAAAA-TATTA
1 TATTTAAAAATT-A-TAAAAAATTATTA
327091 TTATGAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 6 0.25
30 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TATTTAAAAATTATAAAAAATTATTAAC
Found at i:327483 original size:19 final size:19
Alignment explanation
Indices: 327451--327489 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
327441 TCATTCTGGA
327451 TGTTATTTTAAATAAATTT
1 TGTTATTTTAAATAAATTT
327470 TGTTAATTTT-AATAAATTT
1 TGTT-ATTTTAAATAAATTT
327489 T
1 T
327490 ATAATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TGTTATTTTAAATAAATTT
Found at i:327503 original size:19 final size:19
Alignment explanation
Indices: 327455--327496 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
327445 TCTGGATGTT
*
327455 ATTTTAAATAAATTTTGTTA
1 ATTTT-AATAAATTTTGATA
327475 ATTTTAATAAATTTT-ATA
1 ATTTTAATAAATTTTGATA
327493 ATTT
1 ATTT
327497 CTTATAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTAATAAATTTTGATA
Found at i:330624 original size:18 final size:18
Alignment explanation
Indices: 330598--330639 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
330588 GACTAGAAAA
* * *
330598 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
330616 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
330634 AGGATA
1 AGGATA
330640 TGCACCTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:332933 original size:19 final size:20
Alignment explanation
Indices: 332891--332933 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
332881 AACTGACATG
*
332891 TTTTATGAATTTTTTTATAG
1 TTTTATGAATTTTTTTATAA
*
332911 TTTTATTAA-TTTTTTATAA
1 TTTTATGAATTTTTTTATAA
332930 TTTT
1 TTTT
332934 TATATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTATGAATTTTTTTATAA
Found at i:337982 original size:20 final size:21
Alignment explanation
Indices: 337934--337982 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
337924 AAAAATAATA
337934 AAATCTAATTAGTTATAAAATT
1 AAAT-TAATTAGTTATAAAATT
** *
337956 ATTTTAATTA-TTATTAAATT
1 AAATTAATTAGTTATAAAATT
337976 AAATTAA
1 AAATTAA
337983 AAGTCACATC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.64
21 6 0.27
22 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTAATTAGTTATAAAATT
Found at i:338388 original size:28 final size:25
Alignment explanation
Indices: 338355--338414 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
338345 ATTAAAATTG
*
338355 ATATAAACTTATAAATATTATAAAAAT
1 ATATAAACTAAT-AA-ATTATAAAAAT
*
338382 ATGATAATCTAATAAATTATAAAAAT
1 AT-ATAAACTAATAAATTATAAAAAT
338408 ATATAAA
1 ATATAAA
338415 ATTAAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.14
26 13 0.45
27 4 0.14
28 8 0.28
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATAAACTAATAAATTATAAAAAT
Found at i:338408 original size:37 final size:38
Alignment explanation
Indices: 338318--338415 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 38
338308 ATATTTTCTC
* * *
338318 ATAAAATATTAAAAATATCATAAAAATATTAAAATTGAT
1 ATAAATTA-TAAAAATATTATAAAAATATGAAAATTGAT
*
338357 ATAAACTTAT--AAATATTATAAAAATATGATAATCT-A-
1 ATAAA-TTATAAAAATATTATAAAAATATGAAAAT-TGAT
338393 ATAAATTATAAAAATA-TATAAAA
1 ATAAATTATAAAAATATTATAAAA
338416 TTAAAAAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
35 4 0.08
36 12 0.24
37 26 0.51
38 1 0.02
39 6 0.12
40 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (38 bp):
ATAAATTATAAAAATATTATAAAAATATGAAAATTGAT
Found at i:338744 original size:15 final size:16
Alignment explanation
Indices: 338724--338758 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
338714 CAGTTCAATT
*
338724 AAATAAAATAT-TAAA
1 AAATAAAAAATATAAA
338739 AAATAAAAAATATAAA
1 AAATAAAAAATATAAA
338755 AAAT
1 AAAT
338759 GTATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAAAATATAAA
Found at i:338966 original size:21 final size:22
Alignment explanation
Indices: 338936--338987 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
338926 AATACTTTTT
*
338936 TATGATTTTTATAGAA-TTTAAA
1 TATG-TTTTTATAAAATTTTAAA
*
338958 TTTGTTTTTATAAAATTTTAAA
1 TATGTTTTTATAAAATTTTAAA
338980 TATGTTTT
1 TATGTTTT
338988 GGTAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (22 bp):
TATGTTTTTATAAAATTTTAAA
Found at i:338977 original size:22 final size:22
Alignment explanation
Indices: 338941--339011 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
338931 TTTTTTATGA
*
338941 TTTTTATAGAA-TTTAAATTTG
1 TTTTTATAAAATTTTAAATTTG
*
338962 TTTTTATAAAATTTTAAATATG
1 TTTTTATAAAATTTTAAATTTG
** *
338984 TTTTGGT--AATTTTATATTT-
1 TTTTTATAAAATTTTAAATTTG
339003 TTTTTATAA
1 TTTTTATAA
339012 TTTATTAGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.13
20 10 0.26
21 10 0.26
22 14 0.36
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTTATAAAATTTTAAATTTG
Found at i:339047 original size:20 final size:20
Alignment explanation
Indices: 339022--339086 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
339012 TTTATTAGAG
*
339022 TTTTATTAATATTTAATAAT
1 TTTTATTAATTTTTAATAAT
* *
339042 TTTTA-TATATTTTTGATAAC
1 TTTTATTA-ATTTTTAATAAT
* *
339062 TTTT-CTGATTTTTAATAAT
1 TTTTATTAATTTTTAATAAT
339081 TTTTAT
1 TTTTAT
339087 GGGAAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATTAATTTTTAATAAT
Found at i:339082 original size:10 final size:10
Alignment explanation
Indices: 339022--339085 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
339012 TTTATTAGAG
*
339022 TTTTATTAAT
1 TTTTAATAAT
*
339032 ATTTAATAAT
1 TTTTAATAAT
339042 TTTT-ATATAT
1 TTTTAATA-AT
* *
339052 TTTTGATAAC
1 TTTTAATAAT
* *
339062 TTTT-CTGAT
1 TTTTAATAAT
339071 TTTTAATAAT
1 TTTTAATAAT
339081 TTTTA
1 TTTTA
339086 TGGGAAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
9 9 0.21
10 30 0.71
11 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:341947 original size:11 final size:11
Alignment explanation
Indices: 341933--341977 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
341923 AAAAAATCAT
341933 AAAAATTATAA
1 AAAAATTATAA
341944 AAAAATTATTAA
1 AAAAATTA-TAA
341956 AAAAGA-TATAA
1 AAAA-ATTATAA
*
341967 AAAATTTATAA
1 AAAAATTATAA
341978 TTTATAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 20 0.67
12 9 0.30
13 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:342725 original size:23 final size:23
Alignment explanation
Indices: 342699--342752 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
342689 TGATTGTTAA
* * *
342699 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTAATTAGTAATAAT
342722 ATTTAGAATTAATTAGTAATAAT
1 ATTTAGAATTAATTAGTAATAAT
342745 ATTTAGAA
1 ATTTAGAA
342753 AAAATCTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (23 bp):
ATTTAGAATTAATTAGTAATAAT
Found at i:344963 original size:43 final size:43
Alignment explanation
Indices: 344899--345192 Score: 398
Period size: 43 Copynumber: 6.8 Consensus size: 43
344889 TTTTCTTTAC
* * *
344899 AACGACGCTATAAACCATGGTCTTTAGCGGCGCTTACCCATCA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* *
344942 AACGCCGCTATAGACCTTGGTCTTTAGCGGCGCTTACCAAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
344985 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * *
345028 AATGCCGCTATAGACCATGGTCTTTCGCGGCACTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* *
345071 AACGCCGCTATAGACCATGGTCTTTAGCTGCGCTTA-CCATGAAA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCA--ACA
345115 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCCTT-CACC-ACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCG-CTTAC-CCAACA
* * *
345158 AACGCCGCTAAAG-CTTATGGTTTTTAGCGGCGCTT
1 AACGCCGCTATAGAC-CATGGTCTTTAGCGGCGCTT
345193 TTAGAAAAAC
Statistics
Matches: 225, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
42 7 0.03
43 180 0.80
44 33 0.15
45 3 0.01
46 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (43 bp):
AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
Found at i:345533 original size:21 final size:21
Alignment explanation
Indices: 345507--345555 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
345497 TTTAAGCTGT
* *
345507 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCACTGCAGCA
* *
345528 TCTGCTTCTCTCACTGCCGCA
1 TCTGCTTCCCTCACTGCAGCA
345549 TCTGCTT
1 TCTGCTT
345556 TAAGCTACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.43, G:0.16, T:0.35
Consensus pattern (21 bp):
TCTGCTTCCCTCACTGCAGCA
Found at i:345616 original size:87 final size:88
Alignment explanation
Indices: 345510--345672 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 88
345500 AAGCTGTTCT
345510 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACT-GCTGGAGTT
1 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAG-TACTAGCTGGAGTT
345574 CTTCATA-CTTTCGTTGAAATTCA
65 CTTCATATCTTTCGTTGAAATTCA
* * * * ** **
345597 GCTTCTCTTGCTGCTGCCTCTGCTTCTCTCGCTTTCGCATCTGCTTTAAGTTGTAGCTGGAGTTC
1 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTC
345662 TTCATATCTTT
66 TTCATATCTTT
345673 TTTGGACCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 2 0.03
87 60 0.91
88 4 0.06
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (88 bp):
GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTC
TTCATATCTTTCGTTGAAATTCA
Found at i:345685 original size:87 final size:87
Alignment explanation
Indices: 345510--345693 Score: 228
Period size: 87 Copynumber: 2.1 Consensus size: 87
345500 AAGCTGTTCT
*
345510 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTC
1 GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTC
*
345575 TTCATACTTTCGTTGAAATTCA
66 TTCATACTTTCGTTGAAACTCA
* * * ** **
345597 GCTTCTCTTGCTGCTGCCTCTGCTTCTCTCGCTTTCGCATCTGCTTTAAG-TTGTAGCTGGAGTT
1 GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACT-GCTGGAGTT
* * *
345661 CTTCATATCTTT-TTTGGACCTCA
65 CTTCATA-CTTTCGTTGAAACTCA
345684 GCTTCTCTCG
1 GCTTCTCTCG
345694 ATGTTGCCTC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 2 0.02
87 76 0.93
88 4 0.05
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (87 bp):
GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTC
TTCATACTTTCGTTGAAACTCA
Found at i:351613 original size:73 final size:74
Alignment explanation
Indices: 351453--351627 Score: 298
Period size: 73 Copynumber: 2.4 Consensus size: 74
351443 ATAACTATCA
* *
351453 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCGTTTT
1 TTTGCGGCGTTTTTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCATTTT
351518 GGTTAAACT
66 GGTTAAACT
351527 TTTGCGGCGTTTTTACCAGAAACGCCGCTAATACCAATAAACAGTAT-AAAAACGAAGTCATTTT
1 TTTGCGGCGTTTTTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCATTTT
351591 GGTTAAACT
66 GGTTAAACT
* * *
351600 TTTGCGGCGTTTTTGCAATAAACGCCGC
1 TTTGCGGCGTTTTTACCAGAAACGCCGC
351628 AAATTCGTGC
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 50 0.52
74 46 0.48
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (74 bp):
TTTGCGGCGTTTTTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCATTTT
GGTTAAACT
Found at i:352796 original size:41 final size:41
Alignment explanation
Indices: 352703--352796 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
352693 GCTAGCTACA
*
352703 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAT
1 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAG
** * * *
352744 ATGCGCCGCTAATGCTGCGGTTTTTAGCGGTGCTTTT-TAAG
1 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCG-TTTTCTAAG
*
352785 AAACGCTGCTAA
1 AAACGCCGCTAA
352797 AGACCTAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAG
Found at i:352812 original size:41 final size:40
Alignment explanation
Indices: 352767--353082 Score: 386
Period size: 41 Copynumber: 7.8 Consensus size: 40
352757 GCTGCGGTTT
* * * *
352767 TTAGCGGTGCTTTTTAAGAAACGCTGCTAAAGACCTAAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCT-AGCA
* * *
352808 TTAGCGGCGCTTCGTAAAAAACGCCGTTAAAGACTGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGAC-CTAGCA
*
352849 TTAGTGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACC-TAGCA
352890 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACC-TAGCA
352931 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACC-TAGCA
352972 TTAGCGGCGCTTTGT-AAAAACGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCT-AGCA
* * * * *
353012 TTAGCGGTGCATAT-TAGAAAACGCCGCGAAAGACCGCAGCA
1 TTAGCGGCGC-TTTGTAAAAAACGCCGCTAAAGACC-TAGCA
* * *
353053 TTAGCGACGATTATGT-AAAAGCGCCGCTAA
1 TTAGCGGCGCTT-TGTAAAAAACGCCGCTAA
353083 GGGCCCCAAA
Statistics
Matches: 243, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
39 1 0.00
40 34 0.14
41 206 0.85
42 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAGCA
Found at i:353276 original size:41 final size:41
Alignment explanation
Indices: 353190--353276 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
353180 ATATATCGCC
*
353190 GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAGCGCC
1 GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAGCGCA
* * * *
353231 GCTAATGCTCG-ATTTTTTGTGGCGTTTTTTGTCCAAA-CGCA
1 GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGT--AAAGCGCA
353272 GCTAA
1 GCTAA
353277 AAGCCTGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 17 0.44
41 19 0.49
42 3 0.08
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (41 bp):
GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAGCGCA
Found at i:354372 original size:51 final size:51
Alignment explanation
Indices: 354312--354410 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
354302 TAAATTCGGT
* *
354312 GATAATGCTCATTTTCTTGTAGTGTTGATGATTGGAAAATTACTTATAGAA
1 GATAATGCTCATTTTCTTATAGTGTTGATGAATGGAAAATTACTTATAGAA
* *
354363 GATAATGCTCATTTTCTTATAGTGTTGATTAATGGAAATTTACTTATA
1 GATAATGCTCATTTTCTTATAGTGTTGATGAATGGAAAATTACTTATA
354411 TAGGTGAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.43
Consensus pattern (51 bp):
GATAATGCTCATTTTCTTATAGTGTTGATGAATGGAAAATTACTTATAGAA
Found at i:354600 original size:17 final size:18
Alignment explanation
Indices: 354567--354600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
354557 ATAAATTTTT
*
354567 AATTTTTTAATAGTTAAA
1 AATTTTTAAATAGTTAAA
354585 AATTTTTAAATA-TTAA
1 AATTTTTAAATAGTTAA
354601 TATAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTTTAAATAGTTAAA
Found at i:358128 original size:22 final size:20
Alignment explanation
Indices: 358081--358128 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
358071 ACATGGACTA
*
358081 AAAAATTGATGACATGAATT
1 AAAAATTGATAACATGAATT
* *
358101 GAAAATTGCTAACATGGAAGTT
1 AAAAATTGATAACAT-GAA-TT
358123 AAAAAT
1 AAAAAT
358129 CTTTTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.55
21 3 0.14
22 7 0.32
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (20 bp):
AAAAATTGATAACATGAATT
Found at i:360372 original size:17 final size:16
Alignment explanation
Indices: 360346--360377 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
360336 AATCCCCTTC
360346 TTATTATATATAAATA
1 TTATTATATATAAATA
360362 TTATCTATATATAAAT
1 TTAT-TATATATAAAT
360378 GTACCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTATATATAAATA
Found at i:361952 original size:17 final size:17
Alignment explanation
Indices: 361930--361962 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
361920 TTAATTAATT
361930 AATT-AATTAATTTTCTC
1 AATTAAATT-ATTTTCTC
361947 AATTAAATTATTTTCT
1 AATTAAATTATTTTCT
361963 TAACCCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTAAATTATTTTCTC
Found at i:364484 original size:6 final size:6
Alignment explanation
Indices: 364473--364542 Score: 88
Period size: 6 Copynumber: 11.3 Consensus size: 6
364463 GGTTTTCTCC
*
364473 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAGATG AAAAATA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAA-ATG -AAAATG
*
364523 AAAATG -ACATG AAAAATG AA
1 AAAATG AAAATG -AAAATG AA
364543 TATACGCTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.07
6 40 0.71
7 9 0.16
8 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:364742 original size:22 final size:24
Alignment explanation
Indices: 364699--364742 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
364689 GTTGAGAAAA
*
364699 TTATTTTATTGGAAATATGAAAGT
1 TTATTTTATGGGAAATATGAAAGT
364723 TTATTTT-TGGGAAATA-GAAA
1 TTATTTTATGGGAAATATGAAA
364743 AAAAATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (24 bp):
TTATTTTATGGGAAATATGAAAGT
Found at i:365993 original size:24 final size:24
Alignment explanation
Indices: 365948--365993 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
365938 AAATATGCTT
* *
365948 TAGGATGAATTTTGTAATCTTTTC
1 TAGGATGAATTTTGGAAACTTTTC
365972 TAGGATGGAA-TTTGGAAACTTT
1 TAGGAT-GAATTTTGGAAACTTT
365994 GGCTGGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (24 bp):
TAGGATGAATTTTGGAAACTTTTC
Found at i:385225 original size:14 final size:14
Alignment explanation
Indices: 385206--385232 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
385196 ATTTATTAAA
385206 AAAATTACAAATAT
1 AAAATTACAAATAT
385220 AAAATTACAAATA
1 AAAATTACAAATA
385233 CACTACACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTACAAATAT
Found at i:386587 original size:63 final size:57
Alignment explanation
Indices: 386462--386574 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
386452 AAAAATGGTG
* *
386462 AAATGGAGAAATAGGAAACATTTGGAAATGATTAAGGTTTTCTCCAAAATGAAAATAA
1 AAATGGAGAAATA-GAAACATTTGGAAATGAATAAGATTTTCTCCAAAATGAAAATAA
*
386520 AAATGGAGAAAT-GAAATCATTTGGAAATGAATATGATTTTCTCCAAAATGAAAAT
1 AAATGGAGAAATAGAAA-CATTTGGAAATGAATAAGATTTTCTCCAAAATGAAAAT
386575 GACATGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 4 0.08
57 35 0.69
58 12 0.24
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAATAGAAACATTTGGAAATGAATAAGATTTTCTCCAAAATGAAAATAA
Found at i:394796 original size:23 final size:23
Alignment explanation
Indices: 394710--394789 Score: 135
Period size: 23 Copynumber: 3.5 Consensus size: 23
394700 TTTATACATT
394710 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
394733 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
*
394756 AAGCACATTAACT-TTTAAGCATA
1 AATCACATTAA-TATTTAAGCATA
394779 AATCACATTAA
1 AATCACATTAA
394790 CTTTTAACAC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
23 53 0.98
24 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:398155 original size:20 final size:20
Alignment explanation
Indices: 398132--398170 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
398122 AGTTAGTGAT
398132 AAACACATAACTTAACTAAA
1 AAACACATAACTTAACTAAA
*
398152 AAACACATAACTTAGCTAA
1 AAACACATAACTTAACTAA
398171 TCCATCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (20 bp):
AAACACATAACTTAACTAAA
Found at i:399944 original size:16 final size:17
Alignment explanation
Indices: 399915--399947 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
399905 ATAGACCTTG
399915 AAACTATAGAATTGTGA
1 AAACTATAGAATTGTGA
399932 AAACTATAG-ATTGTGA
1 AAACTATAGAATTGTGA
399948 GACTATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (17 bp):
AAACTATAGAATTGTGA
Found at i:406296 original size:51 final size:51
Alignment explanation
Indices: 406164--406458 Score: 307
Period size: 51 Copynumber: 5.8 Consensus size: 51
406154 ACTTTTATCA
* ** *
406164 TTCGATACACGTAGTAGCCTTCACATAGTACTAAACACATGATC-AAG-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * *
406213 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * *
406265 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGC-TT
* *
406315 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACATGTGACCAAAGCTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * * *
406367 CTC-AGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TT
1 TTCGA-TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCA-AAGCTT
* *
406417 TATCGATACACGTAGTAGCCTTCACACAATACTACACATGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACATGTG
406459 TTCATCGATA
Statistics
Matches: 206, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
49 4 0.02
50 43 0.21
51 149 0.72
52 8 0.04
53 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
Found at i:406347 original size:102 final size:102
Alignment explanation
Indices: 406164--406454 Score: 404
Period size: 102 Copynumber: 2.9 Consensus size: 102
406154 ACTTTTATCA
* * * * ** * *** *
406164 TTCGATACACGTAGTAGCCTTCACATAGTACTAAACACATGATCAAGTTTTA-CGGTTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
406228 TAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
406265 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
406330 TAGCCTTCACACAGTACTACACATGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
* * * * *
406367 CTCAGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
406432 TAGCCTTCACACAATACTACACA
66 TAGCCTTCACACAGTACTACACA
406455 TGTGTTCATC
Statistics
Matches: 170, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 42 0.25
102 128 0.75
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (102 bp):
TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
Found at i:406433 original size:153 final size:151
Alignment explanation
Indices: 406165--406458 Score: 358
Period size: 153 Copynumber: 1.9 Consensus size: 151
406155 CTTTTATCAT
* * * * * *
406165 TCGATACACGTAGTAGCCTTCACATAGTACTAAACACATGATCAAGTTTTACGGTTCACGTAGTA
1 TCGATACACGTAGTAGCCTTCACACAGTACTAAACACATGACCAAGTTCTACAGTACACATAGTA
* ** *
406230 GCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAATA
406295 CTACACATGTGACCATCATTTA
130 CTACACATGTGACCATCATTTA
* * ** *
406317 TCGATTCACGTAGTAGCCTTCACACAGTACTACACATGTGACCAAAGCTTCT-CAGTACACATTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTAAACACATGACC-AAG-TTCTACAGTACACATAG
* * * *
406381 TAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCACACA
64 TAGCCTTCACATAGTACTACACACGTGACCA-AACTTT-TCGATACACATAGTAGCCTTCACACA
406445 ATACTACACATGTG
127 ATACTACACATGTG
406459 TTCATCGATA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
152 40 0.34
153 75 0.63
154 4 0.03
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (151 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTAAACACATGACCAAGTTCTACAGTACACATAGTA
GCCTTCACATAGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTCACACAATAC
TACACATGTGACCATCATTTA
Found at i:409424 original size:41 final size:40
Alignment explanation
Indices: 409285--409416 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 40
409275 AAAAATTATG
*
409285 AATTGCACATACGTGACCTTATTTGTACTTCGGTACCCCTA
1 AATTGCACATACGTGCCCTTATTTGTACTTCGGTA-CCCTA
* * * *
409326 AATTGCACAAACGTGCCCTTGTCTATACTTCGGTACCCTTA
1 AATTGCACATACGTGCCCTTATTTGTACTTCGGTACCC-TA
* * * * *
409367 AATTGCAAATATGTGCCCCTATTTGTACTTCGGTACGACTG
1 AATTGCACATACGTGCCCTTATTTGTACTTCGGTAC-CCTA
409408 AATTGCACA
1 AATTGCACA
409417 CATGTGCCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 70 0.95
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (40 bp):
AATTGCACATACGTGCCCTTATTTGTACTTCGGTACCCTA
Found at i:409725 original size:16 final size:16
Alignment explanation
Indices: 409704--409739 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
409694 TATAATGGTG
409704 TTTGATGTAGGTGTGT
1 TTTGATGTAGGTGTGT
409720 TTTGATGTAGGTGTGT
1 TTTGATGTAGGTGTGT
409736 TTTG
1 TTTG
409740 GTATCTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.53
Consensus pattern (16 bp):
TTTGATGTAGGTGTGT
Found at i:416557 original size:41 final size:40
Alignment explanation
Indices: 416504--416622 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 40
416494 TTCACATGTA
416504 TGCCCCTATTTGTACTTCGGTACCCCTAAATTGCACATATG
1 TGCCCCT-TTTGTACTTCGGTACCCCTAAATTGCACATATG
** * *
416545 TGCCCCTGTTTGTACTTTAGTACTCCTGAATTGCACATATG
1 TGCCCCT-TTTGTACTTCGGTACCCCTAAATTGCACATATG
*
416586 TGCCCCTTCTTGTACTTCGATACCCCTAAATTGCACA
1 TGCCCCTT-TTGTACTTCGGTACCCCTAAATTGCACA
416623 CACCCCTGCC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 1 0.01
41 66 0.99
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.35
Consensus pattern (40 bp):
TGCCCCTTTTGTACTTCGGTACCCCTAAATTGCACATATG
Found at i:423838 original size:27 final size:25
Alignment explanation
Indices: 423808--423876 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
423798 CGTTCTGTCC
* *
423808 CACAGCTCGTGTGAGCAGACCTATTTT
1 CACAGCTCGTGTGAGCAAACCGA--TT
* *
423835 CACAGCTCATGTAAGCAAACCGATT
1 CACAGCTCGTGTGAGCAAACCGATT
423860 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
423877 TACATGTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 17 0.47
27 19 0.53
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCAAACCGATT
Found at i:428147 original size:433 final size:433
Alignment explanation
Indices: 427341--428206 Score: 1732
Period size: 433 Copynumber: 2.0 Consensus size: 433
427331 ATTTAATCAA
427341 AGATTTAAACATGCACATTAGCCACACCTTCCGATGATGGCTATGGAACACTATTAAGAACATGT
1 AGATTTAAACATGCACATTAGCCACACCTTCCGATGATGGCTATGGAACACTATTAAGAACATGT
427406 AGATGAAGTTCCTCTAATCCTCAAGCAGCTTCCATTGTCTTGCTTGCTAGCTGAACTGTCGCTGC
66 AGATGAAGTTCCTCTAATCCTCAAGCAGCTTCCATTGTCTTGCTTGCTAGCTGAACTGTCGCTGC
427471 ACCTTCCAGTGTCAGTGACCGCAATAACACTTTCGTGCTAAAAACATTCAAACCCAAAGACTAAA
131 ACCTTCCAGTGTCAGTGACCGCAATAACACTTTCGTGCTAAAAACATTCAAACCCAAAGACTAAA
427536 TAGTAGAAGCAAGTTTGAATAAAATAAAATTTAACACTGTGTACTTCTATACTAACATGAAATAG
196 TAGTAGAAGCAAGTTTGAATAAAATAAAATTTAACACTGTGTACTTCTATACTAACATGAAATAG
427601 AAAGTAATCACCATCATTTAGAAAAGAAAAATAAAAGAAACAACTAGAGAATACTATTCCTAGAC
261 AAAGTAATCACCATCATTTAGAAAAGAAAAATAAAAGAAACAACTAGAGAATACTATTCCTAGAC
427666 AACTTGACTTGAATCTCTCTATTCCCTCTTGTGTCGCACTCAGGGCTCCTCATCAAGAGCTAGTC
326 AACTTGACTTGAATCTCTCTATTCCCTCTTGTGTCGCACTCAGGGCTCCTCATCAAGAGCTAGTC
427731 TGCATCCCTTTCACGTCGGTTCACCCGTACGAGACTTAAGCTG
391 TGCATCCCTTTCACGTCGGTTCACCCGTACGAGACTTAAGCTG
427774 AGATTTAAACATGCACATTAGCCACACCTTCCGATGATGGCTATGGAACACTATTAAGAACATGT
1 AGATTTAAACATGCACATTAGCCACACCTTCCGATGATGGCTATGGAACACTATTAAGAACATGT
427839 AGATGAAGTTCCTCTAATCCTCAAGCAGCTTCCATTGTCTTGCTTGCTAGCTGAACTGTCGCTGC
66 AGATGAAGTTCCTCTAATCCTCAAGCAGCTTCCATTGTCTTGCTTGCTAGCTGAACTGTCGCTGC
427904 ACCTTCCAGTGTCAGTGACCGCAATAACACTTTCGTGCTAAAAACATTCAAACCCAAAGACTAAA
131 ACCTTCCAGTGTCAGTGACCGCAATAACACTTTCGTGCTAAAAACATTCAAACCCAAAGACTAAA
427969 TAGTAGAAGCAAGTTTGAATAAAATAAAATTTAACACTGTGTACTTCTATACTAACATGAAATAG
196 TAGTAGAAGCAAGTTTGAATAAAATAAAATTTAACACTGTGTACTTCTATACTAACATGAAATAG
428034 AAAGTAATCACCATCATTTAGAAAAGAAAAATAAAAGAAACAACTAGAGAATACTATTCCTAGAC
261 AAAGTAATCACCATCATTTAGAAAAGAAAAATAAAAGAAACAACTAGAGAATACTATTCCTAGAC
428099 AACTTGACTTGAATCTCTCTATTCCCTCTTGTGTCGCACTCAGGGCTCCTCATCAAGAGCTAGTC
326 AACTTGACTTGAATCTCTCTATTCCCTCTTGTGTCGCACTCAGGGCTCCTCATCAAGAGCTAGTC
428164 TGCATCCCTTTCACGTCGGTTCACCCGTACGAGACTTAAGCTG
391 TGCATCCCTTTCACGTCGGTTCACCCGTACGAGACTTAAGCTG
428207 CCATAACCAA
Statistics
Matches: 433, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
433 433 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (433 bp):
AGATTTAAACATGCACATTAGCCACACCTTCCGATGATGGCTATGGAACACTATTAAGAACATGT
AGATGAAGTTCCTCTAATCCTCAAGCAGCTTCCATTGTCTTGCTTGCTAGCTGAACTGTCGCTGC
ACCTTCCAGTGTCAGTGACCGCAATAACACTTTCGTGCTAAAAACATTCAAACCCAAAGACTAAA
TAGTAGAAGCAAGTTTGAATAAAATAAAATTTAACACTGTGTACTTCTATACTAACATGAAATAG
AAAGTAATCACCATCATTTAGAAAAGAAAAATAAAAGAAACAACTAGAGAATACTATTCCTAGAC
AACTTGACTTGAATCTCTCTATTCCCTCTTGTGTCGCACTCAGGGCTCCTCATCAAGAGCTAGTC
TGCATCCCTTTCACGTCGGTTCACCCGTACGAGACTTAAGCTG
Found at i:429396 original size:17 final size:17
Alignment explanation
Indices: 429374--429407 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
429364 CACTAACATT
429374 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
429391 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
429408 TTTACTAACA
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:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:436971 original size:31 final size:32
Alignment explanation
Indices: 436886--436982 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 32
436876 GTCAAAGTAT
* *
436886 AATTTTAGGAAAA-TTTGGGGGCC-AAATGTG
1 AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
** *
436916 AA---TAGGAAAAGTTAAAGGGTCAAAATGT-
1 AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
* *
436944 AATTTTAGGAAAAGTTGGGGGGCCAAAATATA
1 AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
436976 AATTTTA
1 AATTTTA
436983 AATTTTTTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
27 8 0.15
28 8 0.15
29 6 0.12
30 2 0.04
31 21 0.40
32 7 0.13
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (32 bp):
AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
Found at i:442527 original size:16 final size:15
Alignment explanation
Indices: 442502--442532 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
442492 AATGATCATC
442502 CTCATTTTCTTTCTT
1 CTCATTTTCTTTCTT
442517 CTCACTTTTCTTTCTT
1 CTCA-TTTTCTTTCTT
442533 ACCAAGCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
CTCATTTTCTTTCTT
Found at i:450766 original size:18 final size:18
Alignment explanation
Indices: 450743--450803 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
450733 CAAGGTCACG
450743 ATCAATAGCGTCACTATC
1 ATCAATAGCGTCACTATC
*
450761 ATCAATAGCGTCACTAGC
1 ATCAATAGCGTCACTATC
**
450779 ATCAATATTGTCACTATC
1 ATCAATAGCGTCACTATC
450797 ATCAATA
1 ATCAATA
450804 TTGATATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (18 bp):
ATCAATAGCGTCACTATC
Found at i:450804 original size:18 final size:18
Alignment explanation
Indices: 450752--450818 Score: 86
Period size: 18 Copynumber: 3.9 Consensus size: 18
450742 GATCAATAGC
**
450752 GTCACTATCATCAATAGC
1 GTCACTATCATCAATATT
*
450770 GTCACTAGCATCAATATT
1 GTCACTATCATCAATATT
450788 GTCACTATCATCAATATT
1 GTCACTATCATCAATATT
450806 G--A-TATCATCAATA
1 GTCACTATCATCAATA
450819 AGAAAAACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
15 11 0.24
16 1 0.02
18 33 0.73
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (18 bp):
GTCACTATCATCAATATT
Found at i:452248 original size:21 final size:20
Alignment explanation
Indices: 452208--452278 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
452198 GTTAATTTCA
*
452208 TTTTTAAT-ATTATT-TAAT
1 TTTTTAATAATTTTTATAAT
* *
452226 TTTTTATTTTATTTTTATAAT
1 TTTTTA-ATAATTTTTATAAT
*
452247 TTAATTAATAATTTTTATAAT
1 TT-TTTAATAATTTTTATAAT
*
452268 TTTTTTATAAT
1 TTTTTAATAAT
452279 AGCTGGTAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.14
19 1 0.02
20 12 0.29
21 20 0.48
22 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAATAATTTTTATAAT
Found at i:462643 original size:14 final size:14
Alignment explanation
Indices: 462624--462658 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
462614 TTGAGTACAT
462624 AAATATTATATACC
1 AAATATTATATACC
* *
462638 AAATATTGTCTACC
1 AAATATTATATACC
462652 AAATATT
1 AAATATT
462659 TTAGCTAATG
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:0.14, G:0.03, T:0.37
Consensus pattern (14 bp):
AAATATTATATACC
Found at i:464271 original size:43 final size:44
Alignment explanation
Indices: 464164--464281 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 44
464154 CTCGTACAAC
* * * *
464164 GCCAACGTCCCAAACGTGGTCTTACATG-TAATCACAAATCGAT
1 GCCAACGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
* * * * *
464207 GCCACCGTCCTAGATAGGGTCTTACACGAAAAT-ACAAGTCGAT
1 GCCAACGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
*
464250 GCCAACGTCCCAGGCATGGTCTTACACGAAAA
1 GCCAACGTCCCAGACATGGTCTTACACGAAAA
464282 CACTTATCAG
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 57 0.95
44 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (44 bp):
GCCAACGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
Found at i:466380 original size:18 final size:18
Alignment explanation
Indices: 466354--466390 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
466344 TCAGAAAGAC
*
466354 CACCGCTATCCTTATATA
1 CACCACTATCCTTATATA
466372 CACCACTATCCTTATATA
1 CACCACTATCCTTATATA
466390 C
1 C
466391 TTAAGTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (18 bp):
CACCACTATCCTTATATA
Found at i:470991 original size:42 final size:42
Alignment explanation
Indices: 470925--471014 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
470915 ACGGCCTAGC
* * * * *
470925 ACACAGCCTGGCACACGGGCGTGTGTGGCAACGCAAAGAGTT
1 ACACGGCCTGACACACGGACGTGTGGGGCAACCCAAAGAGTT
* * **
470967 ACACGGCCTGACACATGGACGTGTGGGGCATCCCAGTGAGTT
1 ACACGGCCTGACACACGGACGTGTGGGGCAACCCAAAGAGTT
471009 ACACGG
1 ACACGG
471015 GTGAGGACAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.16
Consensus pattern (42 bp):
ACACGGCCTGACACACGGACGTGTGGGGCAACCCAAAGAGTT
Found at i:471622 original size:25 final size:25
Alignment explanation
Indices: 471574--471622 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
471564 TACTCCACAA
* * *
471574 AGGCTTTCTATTCAGAATAAGCCAT
1 AGGCTTTCCACTCAGAACAAGCCAT
*
471599 AGGCTTTCCACTCAGAACATGCCA
1 AGGCTTTCCACTCAGAACAAGCCA
471623 CAAAGGCGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (25 bp):
AGGCTTTCCACTCAGAACAAGCCAT
Found at i:475288 original size:1 final size:1
Alignment explanation
Indices: 475282--475311 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
475272 AAATCTCTTC
*
475282 TTTTTTTTTTTTTCTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
475312 GGGGGTTANN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:475298 original size:14 final size:14
Alignment explanation
Indices: 475279--475308 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
475269 AGAAAATCTC
475279 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
475293 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
475307 TT
1 TT
475309 TTTGGGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:475311 original size:17 final size:17
Alignment explanation
Indices: 475277--475310 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
475267 AAAGAAAATC
475277 TCTTCTTTTTTTTTTTT
1 TCTTCTTTTTTTTTTTT
475294 TCTT-TTTTTTTTTTTT
1 TCTTCTTTTTTTTTTTT
475310 T
1 T
475311 TGGGGGTTAN
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TCTTCTTTTTTTTTTTT
Found at i:475440 original size:1 final size:1
Alignment explanation
Indices: 475434--475465 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
475424 GAAGAAAATC
*
475434 TTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
475466 GTTGAGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:477237 original size:21 final size:21
Alignment explanation
Indices: 477196--477248 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
477186 TTTGGTTGAA
*
477196 AAATTATTTAATTGAGAAATT
1 AAATTAATTAATTGAGAAATT
* * **
477217 AATTTAGTTAATTGATTAATT
1 AAATTAATTAATTGAGAAATT
477238 AAATTAATTAA
1 AAATTAATTAA
477249 ATAAAATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (21 bp):
AAATTAATTAATTGAGAAATT
Found at i:477854 original size:22 final size:22
Alignment explanation
Indices: 477804--477854 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
477794 TCCTTTTCAT
* *
477804 AATCT-AAGCTTAATTCCTATC
1 AATCTCAAGCCTAATTCCAATC
*
477825 AATTTCAAGCCTAATT-CAATC
1 AATCTCAAGCCTAATTCCAATC
477846 AAATCTCAA
1 -AATCTCAA
477855 TCAGGGAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (22 bp):
AATCTCAAGCCTAATTCCAATC
Found at i:486807 original size:29 final size:30
Alignment explanation
Indices: 486750--486828 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
486740 TAATTTTTAG
486750 GGGTTCT-AAAAAATAA-TTTGTACAAGAT
1 GGGTTCTGAAAAAATAATTTTGTACAAGAT
***
486778 GGGTTCTGAAAAAATAATTTTGT-GGGGAT
1 GGGTTCTGAAAAAATAATTTTGTACAAGAT
* *
486807 GGGCTCTGAAAAAGTAATTTTG
1 GGGTTCTGAAAAAATAATTTTG
486829 ACGATATGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 7 0.16
29 32 0.73
30 5 0.11
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33
Consensus pattern (30 bp):
GGGTTCTGAAAAAATAATTTTGTACAAGAT
Found at i:486837 original size:29 final size:29
Alignment explanation
Indices: 486757--486838 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
486747 TAGGGGTTCT
* *
486757 AAAAAATAA-TTTGTACAAGATGGGTTCTG
1 AAAAAATAATTTTG-ACGAGATGGGCTCTG
** *
486786 AAAAAATAATTTTGTGGGGATGGGCTCTG
1 AAAAAATAATTTTGACGAGATGGGCTCTG
* *
486815 AAAAAGTAATTTTGACGATATGGG
1 AAAAAATAATTTTGACGAGATGGG
486839 TTGAGTTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
29 38 0.90
30 4 0.10
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (29 bp):
AAAAAATAATTTTGACGAGATGGGCTCTG
Found at i:487409 original size:16 final size:13
Alignment explanation
Indices: 487374--487398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487364 TAATGTTTTG
487374 ATTTTTCGTGTTA
1 ATTTTTCGTGTTA
487387 ATTTTTCGTGTT
1 ATTTTTCGTGTT
487399 TCAAATTTTT
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:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
ATTTTTCGTGTTA
Found at i:490892 original size:25 final size:24
Alignment explanation
Indices: 490847--490898 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
490837 GTCATTAGAG
490847 TTATCGATTTCAGCTCTTATGAGC
1 TTATCGATTTCAGCTCTTATGAGC
*
490871 TTATCGATCTTTAGCT-TGTATGAGC
1 TTATCGAT-TTCAGCTCT-TATGAGC
490896 TTA
1 TTA
490899 CCCTTATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (24 bp):
TTATCGATTTCAGCTCTTATGAGC
Found at i:490942 original size:24 final size:24
Alignment explanation
Indices: 490881--490942 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
490871 TTATCGATCT
*
490881 TTAGCTTGTATGAGCTTACCCTTA
1 TTAGCTCGTATGAGCTTACCCTTA
* * *
490905 TTCAGCTCGGATGAGGTTACCGTT-
1 TT-AGCTCGTATGAGCTTACCCTTA
490929 TATAGCTCGTATGA
1 T-TAGCTCGTATGA
490943 ACATACATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (24 bp):
TTAGCTCGTATGAGCTTACCCTTA
Found at i:497221 original size:25 final size:25
Alignment explanation
Indices: 497167--497256 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
497157 AGTTATCGAT
* ** *
497167 TTCAGCTCTTATGAGCTTATTGATA
1 TTCAGCTCGTATGAGCTTACCGTTA
*
497192 CTCAGCTCGTATGAGCTTACCGTTA
1 TTCAGCTCGTATGAGCTTACCGTTA
* * *
497217 TTCAGCTTGGAAGAGCTTACCGTT-
1 TTCAGCTCGTATGAGCTTACCGTTA
497241 TAT-AGCTCGTATGAGC
1 T-TCAGCTCGTATGAGC
497257 ATACATGTAC
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 11 0.21
25 41 0.79
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (25 bp):
TTCAGCTCGTATGAGCTTACCGTTA
Found at i:497605 original size:42 final size:42
Alignment explanation
Indices: 497546--497634 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
497536 TACTTTCGTC
*
497546 CACACGGGCAGAGACACGGGCATGTGTCTCAGCCGTGTATGA
1 CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
497588 CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
1 CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
497630 CACAC
1 CACAC
497635 AGCTAGGTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (42 bp):
CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
Found at i:498667 original size:11 final size:11
Alignment explanation
Indices: 498643--498734 Score: 52
Period size: 11 Copynumber: 8.3 Consensus size: 11
498633 AATGCTTATC
498643 TTAACATTAA-A
1 TTAA-ATTAATA
498654 TTAAATTAATA
1 TTAAATTAATA
498665 TTAAATTAATA
1 TTAAATTAATA
*
498676 --AAA-TACTA
1 TTAAATTAATA
*
498684 TCAAGA-TAAGTA
1 TTAA-ATTAA-TA
498696 TTAAATTAA-A
1 TTAAATTAATA
498706 TCTAATATTAAACTA
1 T-TAA-ATT-AA-TA
*
498721 TTAAAATAATA
1 TTAAATTAATA
498732 TTA
1 TTA
498735 TTTTTAGAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
8 4 0.06
9 3 0.05
10 9 0.14
11 28 0.42
12 13 0.20
13 4 0.06
14 3 0.05
15 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.38
Consensus pattern (11 bp):
TTAAATTAATA
Found at i:498667 original size:16 final size:16
Alignment explanation
Indices: 498643--498673 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
498633 AATGCTTATC
498643 TTAACATTAAATTAAA
1 TTAACATTAAATTAAA
*
498659 TTAATATTAAATTAA
1 TTAACATTAAATTAA
498674 TAAAATACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAACATTAAATTAAA
Found at i:501011 original size:27 final size:26
Alignment explanation
Indices: 500973--501026 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 26
500963 CCTGAAATAA
500973 ATATAAATCCT-CCATAACACACCAAT
1 ATATAAATCCTCCCA-AACACACCAAT
500999 ATATAATATCCTCCCAAACACACCAAT
1 ATATAA-ATCCTCCCAAACACACCAAT
501026 A
1 A
501027 AGGCATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.23
27 17 0.65
28 3 0.12
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (26 bp):
ATATAAATCCTCCCAAACACACCAAT
Found at i:506633 original size:55 final size:55
Alignment explanation
Indices: 506560--506668 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
506550 CTACTTTAAG
506560 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATTA
1 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATTA
*
506615 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAGTAGATTATTTTAAAGATT
1 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATT
506669 TCATATAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (55 bp):
ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATTA
Found at i:508985 original size:32 final size:32
Alignment explanation
Indices: 508944--509007 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
508934 AAATTAACTA
508944 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
1 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
508976 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
1 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
509008 CACGATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (32 bp):
AGTAATAAAAATAAAAAGTAAAAACTCCAATG
Found at i:510515 original size:27 final size:27
Alignment explanation
Indices: 510485--510537 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
510475 AAAATAATTA
*
510485 AAATCCAA-TATTTTAATAATTTAAGTT
1 AAATCCAATTATTTT-ATAATTAAAGTT
**
510512 AAATTTAATTATTTTATAATTAAAGT
1 AAATCCAATTATTTTATAATTAAAGT
510538 ATTAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
AAATCCAATTATTTTATAATTAAAGTT
Found at i:510934 original size:32 final size:32
Alignment explanation
Indices: 510894--510957 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
510884 AAAAAAAAGA
510894 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
1 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
510926 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
1 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
510958 GTGTTTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (32 bp):
TTAACCAATTTTGGAAGAAAAACTTTGATTTG
Found at i:511860 original size:11 final size:11
Alignment explanation
Indices: 511844--511870 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
511834 GAGATTGTCA
511844 CACAATTAAAG
1 CACAATTAAAG
511855 CACAATTAAAG
1 CACAATTAAAG
511866 CACAA
1 CACAA
511871 ATTTGGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (11 bp):
CACAATTAAAG
Found at i:513263 original size:11 final size:11
Alignment explanation
Indices: 513247--513273 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
513237 GAGATTGTCA
513247 CACAATTAAAG
1 CACAATTAAAG
513258 CACAATTAAAG
1 CACAATTAAAG
513269 CACAA
1 CACAA
513274 ATTTGGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (11 bp):
CACAATTAAAG
Found at i:523992 original size:9 final size:9
Alignment explanation
Indices: 523965--524001 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
523955 TGAGTTTTTG
523965 AATTCGAAT
1 AATTCGAAT
* *
523974 AACTCAAAT
1 AATTCGAAT
523983 AATTCGAAT
1 AATTCGAAT
523992 AATTCGAAT
1 AATTCGAAT
524001 A
1 A
524002 TCAAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:525301 original size:39 final size:39
Alignment explanation
Indices: 525202--525301 Score: 137
Period size: 39 Copynumber: 2.6 Consensus size: 39
525192 CATATTCACT
* * * *
525202 TTTAAGAATATATCACATTACACATATAATCACATGACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
525241 TTTAAACATATATCATAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
525280 TTTAAGCATATATTACAATACT
1 TTTAAGCATATATCACAATACT
525302 AAAAAACATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:526402 original size:14 final size:14
Alignment explanation
Indices: 526383--526409 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
526373 GAACCTTATT
526383 ATCATGTTAAAATC
1 ATCATGTTAAAATC
526397 ATCATGTTAAAAT
1 ATCATGTTAAAAT
526410 AAGTTGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (14 bp):
ATCATGTTAAAATC
Found at i:531699 original size:31 final size:30
Alignment explanation
Indices: 531639--531733 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
531629 CTTTTTCTAG
* * *
531639 TTGA-TCAGCTCGATCTTGGCTTATTGAGC
1 TTGATTCAGCTCAATCTTAGCTCATTGAGC
* *
531668 TTGATTCAGCTCACAT-TTCAGTTCCTTGAGC
1 TTGATTCAGCTCA-ATCTT-AGCTCATTGAGC
**
531699 TCAATTCAGCTCAATCTTAGCTCATTGAGC
1 TTGATTCAGCTCAATCTTAGCTCATTGAGC
531729 TTGAT
1 TTGAT
531734 GCTATTTTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
29 4 0.08
30 24 0.47
31 23 0.45
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (30 bp):
TTGATTCAGCTCAATCTTAGCTCATTGAGC
Found at i:531729 original size:30 final size:30
Alignment explanation
Indices: 531643--531729 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
531633 TTCTAGTTGA
* * * **
531643 TCAGCTCGATCTTGGCTTATTGAGCTTGAT
1 TCAGCTCAATCTTAGCTCATTGAGCTCAAT
* *
531673 TCAGCTCACAT-TTCAGTTCCTTGAGCTCAAT
1 TCAGCTCA-ATCTT-AGCTCATTGAGCTCAAT
531704 TCAGCTCAATCTTAGCTCATTGAGCT
1 TCAGCTCAATCTTAGCTCATTGAGCT
531730 TGATGCTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
30 22 0.49
31 23 0.51
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (30 bp):
TCAGCTCAATCTTAGCTCATTGAGCTCAAT
Found at i:534060 original size:29 final size:29
Alignment explanation
Indices: 534001--534156 Score: 154
Period size: 29 Copynumber: 5.4 Consensus size: 29
533991 TACCCGTCCT
* * *
534001 TTTTCATATTCGATGGTCGA-AACCATTCA
1 TTTTCATAATCGATGGTC-ATCACCATCCA
534030 TTTTCATTAATCGATGGTCATCA-CATCCA
1 TTTTCA-TAATCGATGGTCATCACCATCCA
* * *
534059 TTTTCATAGTTGATGGTCATCACCATCCC
1 TTTTCATAATCGATGGTCATCACCATCCA
* * * *
534088 TTTTCATATTCGATAGTCGTCACCATCCT
1 TTTTCATAATCGATGGTCATCACCATCCA
* * * *
534117 TTTTCATATTTGATGGTCGTCACCATCCC
1 TTTTCATAATCGATGGTCATCACCATCCA
534146 TTTTCATAATC
1 TTTTCATAATC
534157 AACAGCGGAA
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
28 14 0.13
29 82 0.76
30 12 0.11
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTTCATAATCGATGGTCATCACCATCCA
Found at i:534092 original size:58 final size:58
Alignment explanation
Indices: 534030--534156 Score: 184
Period size: 58 Copynumber: 2.2 Consensus size: 58
534020 AAACCATTCA
*
534030 TTTTCATTAATCGATGGTCATCA-CATCCATTTTCATAGTTGATGGTCATCACCATCCC
1 TTTTCA-TAATCGATAGTCATCACCATCCATTTTCATAGTTGATGGTCATCACCATCCC
* * * * *
534088 TTTTCATATTCGATAGTCGTCACCATCCTTTTTCATATTTGATGGTCGTCACCATCCC
1 TTTTCATAATCGATAGTCATCACCATCCATTTTCATAGTTGATGGTCATCACCATCCC
534146 TTTTCATAATC
1 TTTTCATAATC
534157 AACAGCGGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 13 0.21
58 48 0.79
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTTCATAATCGATAGTCATCACCATCCATTTTCATAGTTGATGGTCATCACCATCCC
Found at i:534173 original size:29 final size:29
Alignment explanation
Indices: 534141--534211 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
534131 GGTCGTCACC
*
534141 ATCCCTTTTCATAATCAACAGCGGAAGTT
1 ATCCCTTTTCATAATCAACAGCGGAAGCT
* * *
534170 ATCCCTTTTCATAATTAATAGTGGAAGCT
1 ATCCCTTTTCATAATCAACAGCGGAAGCT
*
534199 ATCTCTTTTCATA
1 ATCCCTTTTCATA
534212 TTTGATGGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATAATCAACAGCGGAAGCT
Found at i:538164 original size:21 final size:21
Alignment explanation
Indices: 538138--538179 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
538128 ATCATCATTT
538138 CTTTGATGTCAATCTCCAAAG
1 CTTTGATGTCAATCTCCAAAG
538159 CTTTGATGTCAATCTCCAAAG
1 CTTTGATGTCAATCTCCAAAG
538180 ATTGGCGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (21 bp):
CTTTGATGTCAATCTCCAAAG
Found at i:540003 original size:24 final size:24
Alignment explanation
Indices: 539953--540004 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
539943 AATCAATGTC
* *
539953 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
539977 AAATATATTATACTAATAAATATT
1 AAATATATTATACTAATAAATACT
540001 AAAT
1 AAAT
540005 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:544297 original size:24 final size:24
Alignment explanation
Indices: 544270--544326 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
544260 AAACCTAATT
* *
544270 CTAATCAATGTCT-AATATATTATG
1 CTAATAAATGT-TAAATATATTATA
544294 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTTAAATATATTATA
544318 CTAATAAAT
1 CTAATAAAT
544327 ACTAAATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (24 bp):
CTAATAAATGTTAAATATATTATA
Found at i:544332 original size:24 final size:24
Alignment explanation
Indices: 544283--544333 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
544273 ATCAATGTCT
* **
544283 AATATATTATGCTAATAAATGTTA
1 AATATATTATACTAATAAATACTA
544307 AATATATTATACTAATAAATACTA
1 AATATATTATACTAATAAATACTA
544331 AAT
1 AAT
544334 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (24 bp):
AATATATTATACTAATAAATACTA
Found at i:546497 original size:25 final size:25
Alignment explanation
Indices: 546463--546511 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
546453 TATACATCCC
* * *
546463 CATTTGTTATGAACCTCATTTTATG
1 CATTTATTATCAACATCATTTTATG
546488 CATTTATTATCAACATCATTTTAT
1 CATTTATTATCAACATCATTTTAT
546512 TAAAGCTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (25 bp):
CATTTATTATCAACATCATTTTATG
Found at i:547872 original size:14 final size:14
Alignment explanation
Indices: 547853--547879 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
547843 AAATGATAAC
547853 AACATAATAGTAAT
1 AACATAATAGTAAT
547867 AACATAATAGTAA
1 AACATAATAGTAA
547880 AATGGTAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (14 bp):
AACATAATAGTAAT
Found at i:551009 original size:24 final size:24
Alignment explanation
Indices: 550991--551039 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
550981 CAATGTCAAC
*
550991 TATATTATGCTAATAAATGCTAAA
1 TATATTATACTAATAAATGCTAAA
*
551015 TATATTATACTAATAAATACTAAA
1 TATATTATACTAATAAATGCTAAA
551039 T
1 T
551040 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (24 bp):
TATATTATACTAATAAATGCTAAA
Found at i:552766 original size:15 final size:14
Alignment explanation
Indices: 552746--552776 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
552736 AAAGATACAA
552746 TATTTTTAATTCTTT
1 TATTTTTAATT-TTT
552761 TATTTTTAATTTTT
1 TATTTTTAATTTTT
552775 TA
1 TA
552777 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTAATTTTT
Found at i:552776 original size:23 final size:26
Alignment explanation
Indices: 552748--552798 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
552738 AGATACAATA
552748 TTTTTAATT-CTTTTA-TT-TTTAAT
1 TTTTTAATTACTTTTATTTGTTTAAT
*
552771 TTTTTAATTATTTTTATTTGTTTAAT
1 TTTTTAATTACTTTTATTTGTTTAAT
552797 TT
1 TT
552799 CTTTTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 5 0.21
25 2 0.08
26 8 0.33
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTAATTACTTTTATTTGTTTAAT
Found at i:552783 original size:18 final size:19
Alignment explanation
Indices: 552759--552811 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
552749 TTTTAATTCT
552759 TTTATTTTTAATTTTTTAA
1 TTTATTTTTAATTTTTTAA
552778 -TTATTTTT-ATTTGTTTAA
1 TTTATTTTTAATTT-TTTAA
*
552796 TTTCTTTTTAACTTTT
1 TTTATTTTTAA-TTTT
552812 AGGTTGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 13 0.45
19 7 0.24
20 2 0.07
21 3 0.10
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTATTTTTAATTTTTTAA
Found at i:556193 original size:13 final size:13
Alignment explanation
Indices: 556121--556197 Score: 52
Period size: 12 Copynumber: 6.0 Consensus size: 13
556111 GTTTTTGGAG
556121 TTATAATTTTTAT
1 TTATAATTTTTAT
* **
556134 TAACGA-TTTT-T
1 TTATAATTTTTAT
*
556145 TTATAATATTT-T
1 TTATAATTTTTAT
* *
556157 TTAGAATTTTTGGAA
1 TTATAATTTTT--AT
556172 TTATAATTTTTAT
1 TTATAATTTTTAT
*
556185 TTATTATTTTTAT
1 TTATAATTTTTAT
556198 AAAATTTAAC
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
11 4 0.09
12 17 0.36
13 16 0.34
15 10 0.21
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (13 bp):
TTATAATTTTTAT
Found at i:568443 original size:30 final size:30
Alignment explanation
Indices: 568407--568485 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
568397 TTTCAATATT
568407 TTAAAAGTATAATGATTAAAATTAAT-CAA
1 TTAAAAGTATAATGATTAAAATTAATCCAA
* * *
568436 GTTAAAAGTACAAAGATTAAAGTTAATCCAA
1 -TTAAAAGTATAATGATTAAAATTAATCCAA
* *
568467 TTCAAA-TATAATGAATAAA
1 TTAAAAGTATAATGATTAAA
568486 TTCATAACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 10 0.24
30 28 0.68
31 3 0.07
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.30
Consensus pattern (30 bp):
TTAAAAGTATAATGATTAAAATTAATCCAA
Found at i:568604 original size:2 final size:2
Alignment explanation
Indices: 568597--568635 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
568587 AGATATAGTA
568597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
568636 CAGTNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:586851 original size:22 final size:22
Alignment explanation
Indices: 586812--586853 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
586802 CCAACAACCA
586812 AAATTTGAAAAAAGTCATTACT
1 AAATTTGAAAAAAGTCATTACT
*
586834 AAATTTTAAATAAA-TCATTA
1 AAATTTGAAA-AAAGTCATTA
586854 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATTTGAAAAAAGTCATTACT
Found at i:586969 original size:16 final size:16
Alignment explanation
Indices: 586940--586980 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
586930 TAGAATCGGC
* *
586940 ATATTAATATTATTTA
1 ATATTAAAAATATTTA
*
586956 ATCTTAAAAATATTTA
1 ATATTAAAAATATTTA
586972 ATATTAAAA
1 ATATTAAAA
586981 TAATACAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTAAAAATATTTA
Found at i:612812 original size:18 final size:19
Alignment explanation
Indices: 612780--612822 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
612770 CTCTTCCTCT
*
612780 TATTTTCTTTCTTTCTTTC
1 TATTTTCTTTCTTTCCTTC
612799 T-TTTTC-TTCTTTTCCTTC
1 TATTTTCTTTC-TTTCCTTC
612817 TATTTT
1 TATTTT
612823 ATTATTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTCTTTCTTTCCTTC
Found at i:614186 original size:22 final size:22
Alignment explanation
Indices: 614158--614203 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
614148 TTGTACTTGG
614158 TCTGTTCTGCGATCTTATCTGA
1 TCTGTTCTGCGATCTTATCTGA
* *
614180 TCTGTTCTGTGATTTTATCTGA
1 TCTGTTCTGCGATCTTATCTGA
614202 TC
1 TC
614204 CGTTGCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (22 bp):
TCTGTTCTGCGATCTTATCTGA
Found at i:615094 original size:13 final size:13
Alignment explanation
Indices: 615076--615101 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
615066 TGGCTAAAAA
615076 ATTTACTAAAGTT
1 ATTTACTAAAGTT
615089 ATTTACTAAAGTT
1 ATTTACTAAAGTT
615102 TAGCAATTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTACTAAAGTT
Found at i:627735 original size:21 final size:21
Alignment explanation
Indices: 627711--627750 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
627701 TGTATAAAAC
627711 TTTTACAAAA-AAAAAAAGACA
1 TTTT-CAAAATAAAAAAAGACA
*
627732 TTTTCAAAATAAATAAAGA
1 TTTTCAAAATAAAAAAAGA
627751 GTTTTCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (21 bp):
TTTTCAAAATAAAAAAAGACA
Found at i:631499 original size:12 final size:12
Alignment explanation
Indices: 631482--631506 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
631472 TCATTGAATA
631482 TGGCTAGAAGTC
1 TGGCTAGAAGTC
631494 TGGCTAGAAGTC
1 TGGCTAGAAGTC
631506 T
1 T
631507 CTCGACTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (12 bp):
TGGCTAGAAGTC
Found at i:632279 original size:12 final size:13
Alignment explanation
Indices: 632258--632301 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
632248 TGATTAGGTC
*
632258 AAATAAATTATTA
1 AAATAAATTATAA
632271 AAA-AAATTATAA
1 AAATAAATTATAA
632283 AAATAAATTA-AA
1 AAATAAATTATAA
*
632295 AATTAAA
1 AAATAAA
632302 AATAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTATAA
Found at i:632637 original size:28 final size:26
Alignment explanation
Indices: 632584--632640 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
632574 TTAAGAAAAA
*
632584 AAAGGAAATAAATAAAAAAGGTAAAG
1 AAAGGAAATAAATAAAAAAAGTAAAG
632610 AAAGAGAAATAAGATAAAAGAAAG-AAAG
1 AAAG-GAAATAA-ATAAAA-AAAGTAAAG
632638 AAA
1 AAA
632641 TAAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 7 0.26
28 13 0.48
29 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (26 bp):
AAAGGAAATAAATAAAAAAAGTAAAG
Found at i:632652 original size:24 final size:20
Alignment explanation
Indices: 632606--632651 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
632596 TAAAAAAGGT
*
632606 AAAGAAAGAGAAATAAGATA
1 AAAGAAAGAGAAATAAAATA
632626 AAAGAAAGAAAGAAATAAAATTA
1 AAAGAAAG--AGAAATAAAA-TA
632649 AAA
1 AAA
632652 AATTAAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAGAAAGAGAAATAAAATA
Found at i:634797 original size:17 final size:16
Alignment explanation
Indices: 634775--634808 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
634765 TGGGATGGCA
634775 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
634792 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
634808 T
1 T
634809 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:640447 original size:11 final size:11
Alignment explanation
Indices: 640431--640456 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
640421 TGGTCGAAAA
640431 ATTTTAATTTT
1 ATTTTAATTTT
640442 ATTTTAATTTT
1 ATTTTAATTTT
640453 ATTT
1 ATTT
640457 ATGTTCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:646008 original size:12 final size:13
Alignment explanation
Indices: 645983--646011 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
645973 GACGCTTTAT
645983 CTATGTCTCCCAC
1 CTATGTCTCCCAC
645996 CTATGTC-CCCAC
1 CTATGTCTCCCAC
646008 CTAT
1 CTAT
646012 CATCCTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.45, G:0.07, T:0.31
Consensus pattern (13 bp):
CTATGTCTCCCAC
Found at i:646906 original size:22 final size:22
Alignment explanation
Indices: 646878--646923 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
646868 AGATGTGGAC
646878 TGCCCTAGCTTAGTATGAATTT
1 TGCCCTAGCTTAGTATGAATTT
*
646900 TGCCCTAGTTTAGTATGAATTT
1 TGCCCTAGCTTAGTATGAATTT
646922 TG
1 TG
646924 GTTAACTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (22 bp):
TGCCCTAGCTTAGTATGAATTT
Found at i:647319 original size:20 final size:20
Alignment explanation
Indices: 647290--647448 Score: 133
Period size: 20 Copynumber: 8.0 Consensus size: 20
647280 TATGTGAATA
*
647290 TACTTCGGTACTCTTGTTTG
1 TACTTCGGTACTCCTGTTTG
*
647310 TACTTTGGTAC-CCATGTTTG
1 TACTTCGGTACTCC-TGTTTG
** * *
647330 TACTTCAATACTCTTGTATG
1 TACTTCGGTACTCCTGTTTG
* * * *
647350 TATTTAGATACTCCTGTATG
1 TACTTCGGTACTCCTGTTTG
* *
647370 TACTTCGGTATTCCTATTTG
1 TACTTCGGTACTCCTGTTTG
* * *
647390 TACTTCGATACTCTTGTATG
1 TACTTCGGTACTCCTGTTTG
*
647410 TACTTC-GTACCCCTGTTTG
1 TACTTCGGTACTCCTGTTTG
* *
647429 TACTTCGGTATTCCTATTTG
1 TACTTCGGTACTCCTGTTTG
647449 CACATTCGTG
Statistics
Matches: 107, Mismatches: 29, Indels: 6
0.75 0.20 0.04
Matches are distributed among these distances:
19 16 0.15
20 90 0.84
21 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.47
Consensus pattern (20 bp):
TACTTCGGTACTCCTGTTTG
Found at i:649884 original size:16 final size:17
Alignment explanation
Indices: 649855--649886 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
649845 ACTAGGACAA
649855 AAAGAAATAGAAAAATG
1 AAAGAAATAGAAAAATG
649872 AAAGAAA-AGAAAAAT
1 AAAGAAATAGAAAAAT
649887 AATGATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAGAAATAGAAAAATG
Found at i:650198 original size:68 final size:69
Alignment explanation
Indices: 650093--650240 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 69
650083 AAAAAAAAAA
* * * *
650093 GGGAAG-ACATACTCCTTGTTTCTTTAAACAAGGGAGAATGACCT-CTATTGTGTTTCTTAAAAA
1 GGGAAGAACATGCTCCTTATTTCTCTAAACAAGGGAGAACGACCTACTATTGTGTTTCTTAAAAA
650156 TAGT
66 TAGT
* * *
650160 GGGAAGAACATGCTCTTTATTTCTCTAAA-AAGGTGAGAACGACCTATTTTTGTGTTTCTTAAAA
1 GGGAAGAACATGCTCCTTATTTCTCTAAACAAGG-GAGAACGACCTACTATTGTGTTTCTTAAAA
*
650224 TTAGT
65 ATAGT
*
650229 AGGAAGAACATG
1 GGGAAGAACATG
650241 TTTTTATGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
67 10 0.14
68 28 0.41
69 31 0.45
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (69 bp):
GGGAAGAACATGCTCCTTATTTCTCTAAACAAGGGAGAACGACCTACTATTGTGTTTCTTAAAAA
TAGT
Found at i:651224 original size:16 final size:16
Alignment explanation
Indices: 651178--651229 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
651168 GTAAAGGTTG
*
651178 TTCTAAACAAGAGTTA
1 TTCTCAACAAGAGTTA
**
651194 TT-TCATACATTAGTTA
1 TTCTCA-ACAAGAGTTA
*
651210 TTCTCAACAAGAGTTG
1 TTCTCAACAAGAGTTA
651226 TTCT
1 TTCT
651230 TAAATTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 2 0.07
16 23 0.82
17 3 0.11
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (16 bp):
TTCTCAACAAGAGTTA
Found at i:654464 original size:28 final size:29
Alignment explanation
Indices: 654428--654607 Score: 105
Period size: 28 Copynumber: 5.8 Consensus size: 29
654418 CGAATTAACC
654428 GAAAAAATTTCGG-TCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
* ****
654456 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGGTTCGGTT-----A---ATTTTTTT
654493 GAAAAAATTTCGG-TCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
* ****
654521 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGGTTCGGTT-----A---ATTTTTTT
654558 GAAAAAATTTCGG-TCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
654586 GAAAAAATTTCGGTTCGGTTAA
1 GAAAAAATTTCGGTTCGGTTAA
654608 CGGTTAAAGA
Statistics
Matches: 113, Mismatches: 20, Indels: 37
0.66 0.12 0.22
Matches are distributed among these distances:
28 45 0.40
29 20 0.18
31 2 0.02
34 2 0.02
36 12 0.11
37 32 0.28
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (29 bp):
GAAAAAATTTCGGTTCGGTTAATTTTTTT
Found at i:654486 original size:65 final size:65
Alignment explanation
Indices: 654410--654608 Score: 398
Period size: 65 Copynumber: 3.1 Consensus size: 65
654400 CCCAATCTAA
654410 TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
1 TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
654475 TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
1 TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
654540 TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
1 TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
654605 TAAC
1 TAAC
654609 GGTTAAAGAT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 134 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (65 bp):
TAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGGTTCGGT
Found at i:654510 original size:36 final size:37
Alignment explanation
Indices: 654456--654578 Score: 131
Period size: 37 Copynumber: 3.6 Consensus size: 37
654446 TAATTTTTTT
654456 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
* ****
654493 GAAAAAATTTCGG-TCGGTT-----A---ATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
654521 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
654558 GAAAAAATTTCGG-TCGGTTAA
1 GAAAAAATTTCGGTTCGGTTAA
654579 TTTTTTTGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
28 16 0.24
29 6 0.09
31 1 0.01
34 1 0.01
36 14 0.21
37 29 0.43
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (37 bp):
GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
Found at i:655664 original size:45 final size:45
Alignment explanation
Indices: 655600--655687 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
655590 GACAATGTTG
* *
655600 TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGACATTTATATTA
1 TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGAAATATATATTA
* *
655645 TGAGAGACAAATGTTAGAAACTAATTAAAAGAGAAATATATAT
1 TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGAAATATATAT
655688 GATCGTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (45 bp):
TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGAAATATATATTA
Done.