Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 103 of 290
Found at i:35393217 original size:40 final size:40
Alignment explanation
Indices: 35393014--35393217 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
35393004 CGGAATTTAA
** *
35393014 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
35393054 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
35393094 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
35393133 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
35393173 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
35393213 CCGGA
1 CCGGA
35393218 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:35400472 original size:140 final size:140
Alignment explanation
Indices: 35400219--35400490 Score: 535
Period size: 140 Copynumber: 1.9 Consensus size: 140
35400209 CTATAAAATA
35400219 GAGGATCAAAGAAACGGAGTAAGCAATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACA
1 GAGGATCAAAGAAACGGAGTAAGCAATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACA
*
35400284 GCAAAAGTATAGCATTCATATAGCTAAACGAATAATTTCATATGCACAAATTTTCGATATCATAC
66 GCAAAAGTATAGCATTCATATAGCTAAACGAATAATTTCATATACACAAATTTTCGATATCATAC
35400349 TTAGCAACCC
131 TTAGCAACCC
35400359 GAGGATCAAAGAAACGGAGTAAGCAATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACA
1 GAGGATCAAAGAAACGGAGTAAGCAATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACA
35400424 GCAAAAGTATAGCATTCATATAGCTAAACGAATAATTTCATATACACAAATTTTCGATATCATAC
66 GCAAAAGTATAGCATTCATATAGCTAAACGAATAATTTCATATACACAAATTTTCGATATCATAC
35400489 TT
131 TT
35400491 GCTTCACATT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 131 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (140 bp):
GAGGATCAAAGAAACGGAGTAAGCAATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACA
GCAAAAGTATAGCATTCATATAGCTAAACGAATAATTTCATATACACAAATTTTCGATATCATAC
TTAGCAACCC
Found at i:35400763 original size:40 final size:40
Alignment explanation
Indices: 35400726--35400910 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
35400716 GCTACTCGTT
*
35400726 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
35400766 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
35400806 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
35400845 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
35400886 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35400911 CATCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:35400837 original size:79 final size:81
Alignment explanation
Indices: 35400726--35400908 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
35400716 GCTACTCGTT
* ** *
35400726 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
35400790 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
35400806 CAAATGCCTTCGGG-CTTAGCCCGAA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
35400869 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
35400886 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
35400909 GACATCATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 4 0.05
79 53 0.60
80 31 0.35
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:35402909 original size:49 final size:49
Alignment explanation
Indices: 35402844--35402941 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
35402834 ATCTATACGC
35402844 AACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGGG
1 AACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGGG
*
35402893 AACCGGACCAAGTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGGG
1 AACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGGG
35402942 CTCAACTTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.20
Consensus pattern (49 bp):
AACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGGG
Found at i:35408956 original size:29 final size:29
Alignment explanation
Indices: 35408893--35408960 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35408883 TAATCAACCA
35408893 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35408922 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35408951 CGCACACTTA
1 CGCACACTTA
35408961 CCTTTTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35409104 original size:29 final size:30
Alignment explanation
Indices: 35409065--35409143 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
35409055 CTTAATAATC
35409065 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
35409095 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
35409124 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
35409144 ATCTCATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:35416544 original size:40 final size:40
Alignment explanation
Indices: 35416500--35416761 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
35416490 GCTCCTCGTT
* *
35416500 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
35416540 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
35416580 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
35416619 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
35416658 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
35416697 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
35416738 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35416762 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:35417858 original size:13 final size:13
Alignment explanation
Indices: 35417840--35417864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35417830 GGATGAGCAT
35417840 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
35417853 TTTTTTTTCTTT
1 TTTTTTTTCTTT
35417865 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:35420060 original size:20 final size:20
Alignment explanation
Indices: 35420035--35420080 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
35420025 TGTGATTAGG
35420035 CCGTGTGGCTTGGGACACAC
1 CCGTGTGGCTTGGGACACAC
*
35420055 CCGTGTGGCTTGGGACACGC
1 CCGTGTGGCTTGGGACACAC
35420075 CCGTGT
1 CCGTGT
35420081 CCCTTGTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.30, G:0.37, T:0.22
Consensus pattern (20 bp):
CCGTGTGGCTTGGGACACAC
Found at i:35420086 original size:20 final size:20
Alignment explanation
Indices: 35420043--35420086 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
35420033 GGCCGTGTGG
**
35420043 CTTGGGACACACCCGTGTGG
1 CTTGGGACACACCCGTGTCC
*
35420063 CTTGGGACACGCCCGTGTCC
1 CTTGGGACACACCCGTGTCC
35420083 CTTG
1 CTTG
35420087 TCCGTGGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.34, G:0.32, T:0.23
Consensus pattern (20 bp):
CTTGGGACACACCCGTGTCC
Found at i:35428617 original size:42 final size:43
Alignment explanation
Indices: 35428569--35428663 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 43
35428559 TTCTGTTTTA
* * * *
35428569 CGTGTAAGACCTTGTCTGGGACA-TCGGCATCG-TATTTGATTT
1 CGTGTAAGACCCTATCTAGGACAGT-GGCATCGATATTTGATTG
*
35428611 CGTGTAAGACCCTATCTAGGACAGTGGCATCGATGTTTGATTG
1 CGTGTAAGACCCTATCTAGGACAGTGGCATCGATATTTGATTG
*
35428654 CATGTAAGAC
1 CGTGTAAGAC
35428664 TACGTTTGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 27 0.60
43 18 0.40
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCCTATCTAGGACAGTGGCATCGATATTTGATTG
Found at i:35431086 original size:19 final size:19
Alignment explanation
Indices: 35431058--35431096 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
35431048 AATTTAAAAC
35431058 AAATTAGAAAATTTTGGAAA
1 AAATTAGAAAATTTT-GAAA
35431078 AAATT-GAAAATTTTGAAA
1 AAATTAGAAAATTTTGAAA
35431096 A
1 A
35431097 CAGGGTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (19 bp):
AAATTAGAAAATTTTGAAA
Found at i:35440635 original size:30 final size:30
Alignment explanation
Indices: 35440601--35440661 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35440591 TCTTTAACTC
35440601 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
35440631 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
35440661 A
1 A
35440662 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:35452687 original size:17 final size:17
Alignment explanation
Indices: 35452665--35452707 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
35452655 TAAGAGATAA
35452665 ATTAATATTGTACATTC
1 ATTAATATTGTACATTC
35452682 ATTAATATTGTACATTC
1 ATTAATATTGTACATTC
35452699 ATTAATATT
1 ATTAATATT
35452708 TAATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTAATATTGTACATTC
Found at i:35452733 original size:26 final size:28
Alignment explanation
Indices: 35452695--35452762 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
35452685 AATATTGTAC
* *
35452695 ATTCATTAATATTTAATATATTT-TCTA
1 ATTCAATATTATTTAATATATTTCTCTA
35452722 ATTCAAT-TTATTTAATATATTTCTCTA
1 ATTCAATATTATTTAATATATTTCTCTA
35452749 ATTCAATATTATTT
1 ATTCAATATTATTT
35452763 TAGTTAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 14 0.38
27 17 0.46
28 6 0.16
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTCAATATTATTTAATATATTTCTCTA
Found at i:35452931 original size:12 final size:12
Alignment explanation
Indices: 35452914--35452938 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35452904 TCTCGAAACA
35452914 TTATTATTTTAT
1 TTATTATTTTAT
35452926 TTATTATTTTAT
1 TTATTATTTTAT
35452938 T
1 T
35452939 GATGCAGTAA
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:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:35455706 original size:22 final size:22
Alignment explanation
Indices: 35455681--35455738 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
35455671 CAATATCCAA
* *
35455681 ACAATGACAACAAAACAACAGC
1 ACAATGGCAACAAAACAACAAC
35455703 ACAATGGCAACAAAACAACAAC
1 ACAATGGCAACAAAACAACAAC
*
35455725 AAAATGGCAACAAA
1 ACAATGGCAACAAA
35455739 CAATAGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.60, C:0.24, G:0.10, T:0.05
Consensus pattern (22 bp):
ACAATGGCAACAAAACAACAAC
Found at i:35456626 original size:34 final size:34
Alignment explanation
Indices: 35456583--35456653 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
35456573 CAAAGAAAGA
35456583 GAAATTTCCTCAGTTTCTTGTTCTAGTACAATTG
1 GAAATTTCCTCAGTTTCTTGTTCTAGTACAATTG
35456617 GAAATTTCCTCAGTTTCTTGTTCTAGTACAATTG
1 GAAATTTCCTCAGTTTCTTGTTCTAGTACAATTG
35456651 GAA
1 GAA
35456654 GCCTAATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (34 bp):
GAAATTTCCTCAGTTTCTTGTTCTAGTACAATTG
Found at i:35458298 original size:11 final size:12
Alignment explanation
Indices: 35458267--35458297 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35458257 ATTTATTCTT
35458267 GAGAAAAATAAA
1 GAGAAAAATAAA
35458279 GAGAAAAATAAA
1 GAGAAAAATAAA
35458291 GAGAAAA
1 GAGAAAA
35458298 TCTTCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
GAGAAAAATAAA
Found at i:35460865 original size:24 final size:24
Alignment explanation
Indices: 35460828--35460886 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
35460818 GCAATTTATT
*
35460828 ATTTTTTAAAAATTTAAAAATATA
1 ATTTTTTTAAAATTTAAAAATATA
* * * *
35460852 ATTTTTTTATAATTTTATAATTTA
1 ATTTTTTTAAAATTTAAAAATATA
*
35460876 ATATTTTTAAA
1 ATTTTTTTAAA
35460887 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTTTTAAAATTTAAAAATATA
Found at i:35463779 original size:35 final size:35
Alignment explanation
Indices: 35463740--35463810 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
35463730 TATGAATGAG
35463740 AAAAATATTAAATATCTATATATTACAAATGTAAA
1 AAAAATATTAAATATCTATATATTACAAATGTAAA
*
35463775 AAAAATATTGAATATCTATATATTACAAATGTAAA
1 AAAAATATTAAATATCTATATATTACAAATGTAAA
35463810 A
1 A
35463811 TGTGGAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (35 bp):
AAAAATATTAAATATCTATATATTACAAATGTAAA
Found at i:35464425 original size:31 final size:31
Alignment explanation
Indices: 35464390--35464454 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
35464380 GTCAATTAGG
*
35464390 ATAAAAGTTGAACATCATGTAGCTCATGTTC
1 ATAAAAGTTGAACATCATGCAGCTCATGTTC
35464421 ATAAAAGTTGAACATCATGCAGCTCATGTTC
1 ATAAAAGTTGAACATCATGCAGCTCATGTTC
35464452 ATA
1 ATA
35464455 CACAGAATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (31 bp):
ATAAAAGTTGAACATCATGCAGCTCATGTTC
Found at i:35470307 original size:40 final size:40
Alignment explanation
Indices: 35470252--35470403 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
35470242 ATAACCACAA
* * * *
35470252 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
35470292 GCACAAATGCCTTCGGGTCTTAGCTCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
35470332 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
35470372 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
35470404 CATTCAAATG
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:35475492 original size:23 final size:24
Alignment explanation
Indices: 35475466--35475511 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
35475456 CTTCGCTGTC
*
35475466 TCAA-ATTCAAGTCTTTTGTGACA
1 TCAAGATTCAAGACTTTTGTGACA
*
35475489 TCAAGTATTTAAGACTTTTGTGA
1 TCAAG-ATTCAAGACTTTTGTGA
35475512 TCGGTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
25 15 0.79
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
TCAAGATTCAAGACTTTTGTGACA
Found at i:35477547 original size:33 final size:33
Alignment explanation
Indices: 35477510--35477575 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
35477500 TCTCGAGTTC
35477510 CCTACACTGGCTGCAGAAGTATTCTGAGATTTA
1 CCTACACTGGCTGCAGAAGTATTCTGAGATTTA
35477543 CCTACACTGGCTGCAGAAGTATTCTGAGATTTA
1 CCTACACTGGCTGCAGAAGTATTCTGAGATTTA
35477576 GGACCCACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (33 bp):
CCTACACTGGCTGCAGAAGTATTCTGAGATTTA
Found at i:35479735 original size:19 final size:20
Alignment explanation
Indices: 35479711--35479748 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
35479701 GGTACCACCA
35479711 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
35479730 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
35479749 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:35483761 original size:27 final size:27
Alignment explanation
Indices: 35483731--35483908 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35483721 ATATTGAGTC
* * * *
35483731 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35483758 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35483785 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35483813 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
35483840 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35483867 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35483894 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35483909 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:35483870 original size:82 final size:81
Alignment explanation
Indices: 35483752--35483907 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35483742 TGCTATATAA
* *
35483752 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
35483817 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
35483834 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
35483898 CACTTAGTGC
65 CACTTAGTGC
35483908 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:35491824 original size:27 final size:27
Alignment explanation
Indices: 35491794--35491971 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35491784 ATATTGAGTC
* * * *
35491794 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35491821 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35491848 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35491876 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
35491903 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35491930 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35491957 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35491972 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:35491933 original size:82 final size:81
Alignment explanation
Indices: 35491815--35491970 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35491805 TGCTATATAA
* *
35491815 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
35491880 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
35491897 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
35491961 CACTTAGTGC
65 CACTTAGTGC
35491971 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:35501213 original size:18 final size:20
Alignment explanation
Indices: 35501190--35501232 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35501180 GTGGGTGGGG
35501190 CCGTGTGG-TT-GCACACGC
1 CCGTGTGGTTTAGCACACGC
*
35501208 CCGTGTGGTTTAGGACACGC
1 CCGTGTGGTTTAGCACACGC
35501228 CCGTG
1 CCGTG
35501233 CCATCAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 2 0.09
20 12 0.55
ACGTcount: A:0.12, C:0.30, G:0.35, T:0.23
Consensus pattern (20 bp):
CCGTGTGGTTTAGCACACGC
Found at i:35510217 original size:43 final size:42
Alignment explanation
Indices: 35510103--35510259 Score: 133
Period size: 43 Copynumber: 3.6 Consensus size: 42
35510093 TACAATGCCC
* * * *
35510103 ACGTCCCAGACGTGGTCTTACATGT-AATCAAATATTGATGCC
1 ACGTCCCAGACGTGGTCTTACATATAAATCAAGTA-CGATGCA
* * *
35510145 ACTGTCTCAGACAG-AGTCTTACAT-GAAATCAAGTACGATGCTA
1 AC-GTCCCAGAC-GTGGTCTTACATATAAATCAAGTACGATGC-A
*
35510188 ACGTCCCAGACGTGGTCTTACATATAAATCTTAAG-CCGATGCCA
1 ACGTCCCAGACGTGGTCTTACATATAAATC--AAGTACGATG-CA
*
35510232 ATGTCCCAGACGTGGTCTTACACTATAA
1 ACGTCCCAGACGTGGTCTTACA-TATAA
35510260 CACATATCGG
Statistics
Matches: 94, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 24 0.26
43 32 0.34
44 28 0.30
45 9 0.10
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (42 bp):
ACGTCCCAGACGTGGTCTTACATATAAATCAAGTACGATGCA
Found at i:35511736 original size:263 final size:263
Alignment explanation
Indices: 35511269--35511796 Score: 921
Period size: 263 Copynumber: 2.0 Consensus size: 263
35511259 AGACAAATCA
35511269 ATTAAGCACTTTAACAAGCAGCAGACAACTTTTACATTTTACGCGATTAGGTCCTTTTATCAAAT
1 ATTAAGCACTTTAACAAGCAGCAGACAACTTTTACATTTTACGCGATTAGGTCCTTTTATCAAAT
35511334 TGAGCACACAAACGATTAAATTTTCATACGAAACTTTCAAACATACTAATTCACATATCATAAGC
66 TGAGCACACAAACGATTAAATTTTCATACGAAACTTTCAAACATACTAATTCACATATCATAAGC
* * * * * *
35511399 ATGGAAAATAATATTAAAATATTTTTTGACTTAGATTTTTTATCTTGAAACCACTATTTCAACTA
131 ACGAAAAATAATATTAAAATATTTTTTGACTCAGATTTGTGATCCTGAAACCACTATTTCAACTA
* * *
35511464 GGGTCTAAACCGGACTGTTATGGTACTAGAGCCAGAACGCTCTTTCAAATGGTGAGCATAGGATG
196 GGGTCTAAACCGGACTATTATAGTACTAGAGCCAGAACGCTCTTTCAAATGGTGAACATAGGATG
35511529 GCC
261 GCC
*
35511532 ATTAAGCACTTTAACAAGCAGCAGACAACTTTTACATTTTACGCTATTAGGTCCTTTTATCAAAT
1 ATTAAGCACTTTAACAAGCAGCAGACAACTTTTACATTTTACGCGATTAGGTCCTTTTATCAAAT
* * *
35511597 TGAGCACGCAAACGATTAAATTTTCATACGAAACTTTCAAACATGCTAATTCACATTTCATAAGC
66 TGAGCACACAAACGATTAAATTTTCATACGAAACTTTCAAACATACTAATTCACATATCATAAGC
*
35511662 ACGAAAAATAATATTAAAATATTTTTTGACTCAGATTTGTGGTCCTGAAACCACTATTTCAACTA
131 ACGAAAAATAATATTAAAATATTTTTTGACTCAGATTTGTGATCCTGAAACCACTATTTCAACTA
*
35511727 GGGTCTAAACCGGACTATTATAGTACTAGAGCCAGAACGCTCTTTCAGATGGTGAACATAGGATG
196 GGGTCTAAACCGGACTATTATAGTACTAGAGCCAGAACGCTCTTTCAAATGGTGAACATAGGATG
35511792 GCC
261 GCC
35511795 AT
1 AT
35511797 GAAAACAGGT
Statistics
Matches: 250, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
263 250 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (263 bp):
ATTAAGCACTTTAACAAGCAGCAGACAACTTTTACATTTTACGCGATTAGGTCCTTTTATCAAAT
TGAGCACACAAACGATTAAATTTTCATACGAAACTTTCAAACATACTAATTCACATATCATAAGC
ACGAAAAATAATATTAAAATATTTTTTGACTCAGATTTGTGATCCTGAAACCACTATTTCAACTA
GGGTCTAAACCGGACTATTATAGTACTAGAGCCAGAACGCTCTTTCAAATGGTGAACATAGGATG
GCC
Found at i:35515768 original size:26 final size:26
Alignment explanation
Indices: 35515732--35515785 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
35515722 AAAAACTTAA
* *
35515732 AAACATTAAAACGCACCATTTTACTT
1 AAACATAAAAACACACCATTTTACTT
* *
35515758 AAACATAAAAACACACCGTTTTATTT
1 AAACATAAAAACACACCATTTTACTT
35515784 AA
1 AA
35515786 TACCAAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (26 bp):
AAACATAAAAACACACCATTTTACTT
Found at i:35519578 original size:44 final size:44
Alignment explanation
Indices: 35519529--35519619 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
35519519 GTAGATCAAA
* * * *
35519529 TAATATTAAAATAGCCTACACTAATCAGGGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAATGAGAAAC
* *
35519573 TAATATTAAAATAACTTATACTAATCAGAGTTTAAATGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAATGAGAAAC
35519617 TAA
1 TAA
35519620 AAACAAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAATGAGAAAC
Found at i:35520499 original size:27 final size:27
Alignment explanation
Indices: 35520469--35520547 Score: 108
Period size: 26 Copynumber: 3.0 Consensus size: 27
35520459 TTTTGTGTAG
35520469 ATTAAGATAATTAGGAGTTTAAATTAT
1 ATTAAGATAATTAGGAGTTTAAATTAT
* *
35520496 ATTATGATAATTA-GAGTTTTAATT-T
1 ATTAAGATAATTAGGAGTTTAAATTAT
*
35520521 AGTTAAGATAATTAGGATTTTAAATTA
1 A-TTAAGATAATTAGGAGTTTAAATTA
35520548 ATAGGTTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 21 0.48
27 21 0.48
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (27 bp):
ATTAAGATAATTAGGAGTTTAAATTAT
Found at i:35521578 original size:103 final size:103
Alignment explanation
Indices: 35521295--35521788 Score: 655
Period size: 103 Copynumber: 4.7 Consensus size: 103
35521285 GTGATACATG
* * ** *
35521295 AAGATCACAACTTCTAAACAGCTTGTGACCTATGTTCACAGCTGATATTATAAAGGTTAGGTGAT
1 AAGATCACAACTTCTAAACAGC-TCTAACCTACATTCACAGCTGATATTATAAAGGTTAGTTGAT
* * * *
35521360 TTGAGATCGCAGCCTAAGTTTATTTGAGTTAGCTGATTT
65 TTAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
* * * * **
35521399 AAGATCGCAACTCCTAAACAACTTGCTAACCTACGTTCGTAGCTGATATTATAAAGGTTAGTTGA
1 AAGATCACAACTTCTAAACAGC-T-CTAACCTACATTCACAGCTGATATTATAAAGGTTAGTTGA
*
35521464 TTTAATATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
64 TTTAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
*
35521504 AAGATCACAACTTCTAAACAGCTCTAACCTACATTCACAACTGATATTATAAAGGTTAGTTGATT
1 AAGATCACAACTTCTAAACAGCTCTAACCTACATTCACAGCTGATATTATAAAGGTTAGTTGATT
*
35521569 TAATATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
66 TAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
*
35521607 AAGATCACAACTTCTAAACAGCTCTAACCTACATTCACAACTGATATTATAAAGGTTAGTTGATT
1 AAGATCACAACTTCTAAACAGCTCTAACCTACATTCACAGCTGATATTATAAAGGTTAGTTGATT
* * *
35521672 TAAGATCGCAACCTAAGCTTATTTGAGTTAGCTGATTT
66 TAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
* * * * * ** * * *
35521710 AAGATCACAACTCCTAAACAACTGGTTGACCTATATTTGCAGCTAATATTATACATGTTAGTTGA
1 AAGATCACAACTTCTAAACAGCT--CTAACCTACATTCACAGCTGATATTATAAAGGTTAGTTGA
35521775 TTTAAGATTGCAAC
64 TTTAAGATTGCAAC
35521789 TGCTAAACAA
Statistics
Matches: 350, Mismatches: 37, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
103 196 0.56
104 22 0.06
105 132 0.38
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (103 bp):
AAGATCACAACTTCTAAACAGCTCTAACCTACATTCACAGCTGATATTATAAAGGTTAGTTGATT
TAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTT
Found at i:35521761 original size:208 final size:208
Alignment explanation
Indices: 35521295--35521788 Score: 686
Period size: 208 Copynumber: 2.4 Consensus size: 208
35521285 GTGATACATG
* *
35521295 AAGATCACAACTTCTAAACAGCTTGTGACCTATGTTCACAGCTGATATTATAAAGGTTAGGTGAT
1 AAGATCACAACTTCTAAACAGC-TGTGACCTATATTCACAGCTGATATTATAAAGGTTAGTTGAT
* * * * *
35521360 TTGAGATCGCAGCCTAAGTTTATTTGAGTTAGCTGATTTAAGATCGCAACTCCTAAACAACTTGC
65 TTAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTTAAGATCACAACTCCTAAACAACTTGC
* ** * * * *
35521425 TAACCTACGTTCGTAGCTGATATTATAAAGGTTAGTTGATTTAATATTGCAACCTAAGTTTATTT
130 TAACCTACATTCACAACTGATATTATAAAGGTTAGTTGATTTAAGATCGCAACCTAAGCTTATTT
35521490 AAGTTAGCTGATTT
195 AAGTTAGCTGATTT
* * * *
35521504 AAGATCACAACTTCTAAACAGCTCTAACCTACATTCACAACTGATATTATAAAGGTTAGTTGATT
1 AAGATCACAACTTCTAAACAGCTGTGACCTATATTCACAGCTGATATTATAAAGGTTAGTTGATT
* * *
35521569 TAATATTGCAACCTAAGTTTATTTAAGTTAGCTGATTTAAGATCACAACTTCTAAACAGC-T-CT
66 TAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTTAAGATCACAACTCCTAAACAACTTGCT
*
35521632 AACCTACATTCACAACTGATATTATAAAGGTTAGTTGATTTAAGATCGCAACCTAAGCTTATTTG
131 AACCTACATTCACAACTGATATTATAAAGGTTAGTTGATTTAAGATCGCAACCTAAGCTTATTTA
35521697 AGTTAGCTGATTT
196 AGTTAGCTGATTT
* * ** * * *
35521710 AAGATCACAACTCCTAAACAACTGGTTGACCTATATTTGCAGCTAATATTATACATGTTAGTTGA
1 AAGATCACAACTTCTAAACAGCT-G-TGACCTATATTCACAGCTGATATTATAAAGGTTAGTTGA
35521775 TTTAAGATTGCAAC
64 TTTAAGATTGCAAC
35521789 TGCTAAACAA
Statistics
Matches: 249, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
206 93 0.37
207 1 0.00
208 133 0.53
209 22 0.09
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (208 bp):
AAGATCACAACTTCTAAACAGCTGTGACCTATATTCACAGCTGATATTATAAAGGTTAGTTGATT
TAAGATTGCAACCTAAGTTTATTTAAGTTAGCTGATTTAAGATCACAACTCCTAAACAACTTGCT
AACCTACATTCACAACTGATATTATAAAGGTTAGTTGATTTAAGATCGCAACCTAAGCTTATTTA
AGTTAGCTGATTT
Found at i:35521827 original size:68 final size:68
Alignment explanation
Indices: 35521698--35521847 Score: 165
Period size: 68 Copynumber: 2.2 Consensus size: 68
35521688 GCTTATTTGA
*** **
35521698 GTTAGCTGATTTAAGATCACAACTCCTAAACAACTGGTTGACCTATATTTGCAGCTAATATTATA
1 GTTAGCTGATTTAAGATCACAACTCCTAAACAACTCACTGACCTATATTCACAGCTAATATTATA
35521763 CAT
66 CAT
* ** * * * *
35521766 GTTAGTTGATTTAAGATTGCAACTGCTAAACAACTCACTGACCTATGTTCACAGTTGATATTATA
1 GTTAGCTGATTTAAGATCACAACTCCTAAACAACTCACTGACCTATATTCACAGCTAATATTATA
* *
35521831 AAG
66 CAT
*
35521834 GTTAGCTAATTTAA
1 GTTAGCTGATTTAA
35521848 AATTAAAACA
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (68 bp):
GTTAGCTGATTTAAGATCACAACTCCTAAACAACTCACTGACCTATATTCACAGCTAATATTATA
CAT
Found at i:35540764 original size:36 final size:36
Alignment explanation
Indices: 35540671--35540767 Score: 158
Period size: 36 Copynumber: 2.7 Consensus size: 36
35540661 ATTCTGATAC
* *
35540671 TCTGATTCGCATGTTAAGCATACCATTATTTCTTAT
1 TCTGATTTGCATGTTAAGCATGCCATTATTTCTTAT
35540707 TCTGATTTGCATGTTAAGCATGCCATTATTTCTTAT
1 TCTGATTTGCATGTTAAGCATGCCATTATTTCTTAT
* *
35540743 TCTTATTTGCATATTAAGCATGCCA
1 TCTGATTTGCATGTTAAGCATGCCA
35540768 CTGTGATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (36 bp):
TCTGATTTGCATGTTAAGCATGCCATTATTTCTTAT
Found at i:35542368 original size:15 final size:17
Alignment explanation
Indices: 35542350--35542381 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
35542340 TAGCATAATT
35542350 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
35542365 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
35542382 AAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:35551313 original size:40 final size:40
Alignment explanation
Indices: 35551205--35551352 Score: 203
Period size: 40 Copynumber: 3.7 Consensus size: 40
35551195 TATTCGGATG
* *
35551205 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCT-AGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACT
*
35551245 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
*
35551284 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
* *
35551324 GTAACTGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
35551353 AGCAAGTAGC
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
38 1 0.01
39 33 0.34
40 63 0.65
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
Found at i:35551336 original size:79 final size:79
Alignment explanation
Indices: 35551205--35551352 Score: 219
Period size: 79 Copynumber: 1.9 Consensus size: 79
35551195 TATTCGGATG
* *
35551205 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAG-CCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAA-TCCGGGCTAAGTCCCGAAGGCA
35551269 TTTGTGTGAGTTACT
65 TTTGTGTGAGTTACT
* *
35551284 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTGTAA-CTGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGAC--TAATCCGGGCTAAGTCCCGAAGGC
35551348 ATTTG
64 ATTTG
35551353 AGCAAGTAGC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
79 45 0.73
80 14 0.23
81 3 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATCCGGGCTAAGTCCCGAAGGCAT
TTGTGTGAGTTACT
Found at i:35551385 original size:79 final size:78
Alignment explanation
Indices: 35551205--35551385 Score: 206
Period size: 79 Copynumber: 2.3 Consensus size: 78
35551195 TATTCGGATG
*
35551205 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTGACTAA-TCCGGGCTAAGCCCGAAGGCAT
* **
35551270 TTGTGTGAGTTACT
65 TTGAGCAAGTTACT
* * *
35551284 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTGTAA-CTGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTGAC--TAATCCGGGCTAAG-CCCGAAGGC
35551348 ATTTGAGCAAG-TAGCT
63 ATTTGAGCAAGTTA-CT
* * *
35551364 ATATCC-GGCTAAATTCTGAAGG
1 ATAACCGGGCTAAGTCCTGAAGG
35551386 TACTTGGCTT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
79 60 0.69
80 24 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (78 bp):
ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTGACTAATCCGGGCTAAGCCCGAAGGCATT
TGAGCAAGTTACT
Found at i:35555155 original size:9 final size:9
Alignment explanation
Indices: 35555141--35555173 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
35555131 GTTAACAATT
35555141 TTTTTTATC
1 TTTTTTATC
35555150 TTTTTTATC
1 TTTTTTATC
35555159 TTTTTTATTC
1 TTTTTTA-TC
35555169 TTTTT
1 TTTTT
35555174 CACGAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTATC
Found at i:35555755 original size:18 final size:18
Alignment explanation
Indices: 35555734--35555777 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35555724 TTTTCTAATT
* *
35555734 TTTTTTTCAATTTAAATA
1 TTTTTTACAAATTAAATA
*
35555752 TTTTTTAGAAATTAAATA
1 TTTTTTACAAATTAAATA
35555770 TATTTTTA
1 T-TTTTTA
35555778 AATATTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTTTACAAATTAAATA
Found at i:35555956 original size:29 final size:30
Alignment explanation
Indices: 35555914--35555980 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
35555904 AATATCTCTT
* * *
35555914 ATTTTTTAATATTTATATA-TTCTTTTAGA
1 ATTTTTTAAAATTTATATACATATTTTAGA
35555943 ATTTTTTAAAATTTATATACATATTTTAGA
1 ATTTTTTAAAATTTATATACATATTTTAGA
*
35555973 ACTTTTTA
1 ATTTTTTA
35555981 TTTTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (30 bp):
ATTTTTTAAAATTTATATACATATTTTAGA
Found at i:35556101 original size:17 final size:17
Alignment explanation
Indices: 35556081--35556131 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
35556071 AAATTTAATG
*
35556081 AATTATCTATATTTTTT
1 AATTATATATATTTTTT
* *
35556098 AATTGTATATA-TATTT
1 AATTATATATATTTTTT
35556114 AA-TATATATCATTTTTT
1 AATTATATAT-ATTTTTT
35556131 A
1 A
35556132 GATATATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 14 0.52
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTATATATATTTTTT
Found at i:35558336 original size:46 final size:50
Alignment explanation
Indices: 35558272--35558414 Score: 141
Period size: 53 Copynumber: 2.8 Consensus size: 50
35558262 ACACAGCGAA
* ** *
35558272 GCCATAGCCCTGCCATGGTCTTACACGAATCACATA-ACAT-AC-C-GAT
1 GCCATAGCCCAGATATGGTCTTATACGAATCACATACACATCACACTGAT
* *
35558318 GCCATATCCTAGATATGGTCTTATACGAAATCACATTATCACATCACACTGAT
1 GCCATAGCCCAGATATGGTCTTATACG-AATCACA-TA-CACATCACACTGAT
* *
35558371 GCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATC
1 GCCATAGCCCAGATATGGTCTTATAC-GAATCACATA-CACATC
35558415 TTTTCCGTCA
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
46 21 0.27
47 7 0.09
48 2 0.03
50 4 0.05
51 2 0.03
52 10 0.13
53 32 0.41
54 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (50 bp):
GCCATAGCCCAGATATGGTCTTATACGAATCACATACACATCACACTGAT
Found at i:35558388 original size:53 final size:52
Alignment explanation
Indices: 35558315--35558414 Score: 146
Period size: 53 Copynumber: 1.9 Consensus size: 52
35558305 ATAACATACC
* * *
35558315 GATGCCATATCCTAGATATGGTCTTATACGAAATCACATTATCACATCACACT
1 GATGCCATAGCCCAGATATGGTCTTATACGAAAGCACA-TATCACATCACACT
* *
35558368 GATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATC
1 GATGCCATAGCCCAGATATGGTCTTATACGAAAGCACATATCACATC
35558415 TTTTCCGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 9 0.21
53 33 0.79
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (52 bp):
GATGCCATAGCCCAGATATGGTCTTATACGAAAGCACATATCACATCACACT
Found at i:35563045 original size:39 final size:39
Alignment explanation
Indices: 35562986--35563064 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
35562976 GCAGGTCTAT
* *
35562986 CAGATGCCTTATAATTAGATTGTCTTGGTCTACTCTTTC
1 CAGATGCCTTATAATCAGATTGTCTTGGTCTACTATTTC
35563025 CAGATGCCTTATAATCAGATTGTCTTGGTCTACTATTTC
1 CAGATGCCTTATAATCAGATTGTCTTGGTCTACTATTTC
35563064 C
1 C
35563065 CGATCTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (39 bp):
CAGATGCCTTATAATCAGATTGTCTTGGTCTACTATTTC
Found at i:35565209 original size:53 final size:52
Alignment explanation
Indices: 35565136--35565287 Score: 155
Period size: 52 Copynumber: 2.9 Consensus size: 52
35565126 ATAACATACT
* * * *
35565136 AATGCCATATCCTAGATATGGTCTTATACAGAATCACATTATCACATCACACC
1 AATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TATCACATCACACC
* * ***
35565189 GATGCCATAGCCCAGCTATGGTCTTATACGGGAACTC-GA-ATCACATTGTACC
1 AATGCCATAGCCCAGCTATGGTCTTATAC-GGAA-TCACATATCACATCACACC
* **
35565241 AATGCCATAGCCCAACTATGGTCTTATACGGAAGAACATATCACATC
1 AATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATC
35565288 TTTTCTGTCA
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
51 5 0.06
52 44 0.55
53 25 0.31
54 4 0.05
55 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (52 bp):
AATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATCACACC
Found at i:35577463 original size:43 final size:41
Alignment explanation
Indices: 35577415--35577505 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
35577405 GTAGACACAC
* * *
35577415 GGGCATGTGTCTAGGCCGTGTGTGACACACGGTCAGTCCCTAT
1 GGGCATGT-TCTACGAC-TGTGTGACACACAGTCAGTCCCTAT
*
35577458 GGGCATGTTGTACGACTGTGTGACACACAGTCAGTCCCTAT
1 GGGCATGTTCTACGACTGTGTGACACACAGTCAGTCCCTAT
35577499 GGGCATG
1 GGGCATG
35577506 GTAGTAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 31 0.70
42 5 0.11
43 8 0.18
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.25
Consensus pattern (41 bp):
GGGCATGTTCTACGACTGTGTGACACACAGTCAGTCCCTAT
Found at i:35577791 original size:19 final size:19
Alignment explanation
Indices: 35577749--35577791 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
35577739 AGGACATAGA
35577749 CGTGTCCAAAGCACACAGG
1 CGTGTCCAAAGCACACAGG
* *
35577768 TGTGTCCAAAGCACACGGG
1 CGTGTCCAAAGCACACAGG
35577787 CGTGT
1 CGTGT
35577792 GCATTGCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (19 bp):
CGTGTCCAAAGCACACAGG
Found at i:35582067 original size:50 final size:50
Alignment explanation
Indices: 35581952--35582888 Score: 1783
Period size: 50 Copynumber: 18.8 Consensus size: 50
35581942 CAAGATAAAT
* * *
35581952 ATATGTATATGTGGTAAAGCTGAATGGCTAATGTG-AA-ATATGTATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
*
35582000 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582050 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582100 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582150 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582200 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582250 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582300 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582350 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582400 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582450 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582500 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582550 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582600 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582650 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582700 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
35582750 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
*
35582800 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATGAG
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
* *
35582848 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATAT
35582889 GTAGGAGATG
Statistics
Matches: 879, Mismatches: 6, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
48 77 0.09
49 6 0.01
50 796 0.91
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (50 bp):
ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
Found at i:35583145 original size:37 final size:37
Alignment explanation
Indices: 35583037--35583145 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
35583027 GGAAATATAT
* *
35583037 TCCGGGTAAGACCCGATGACTACATGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
35583074 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
35583111 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
35583146 CATCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:35584805 original size:13 final size:13
Alignment explanation
Indices: 35584787--35584812 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35584777 AAGCAATCGT
35584787 ACACGGGCGTGTC
1 ACACGGGCGTGTC
35584800 ACACGGGCGTGTC
1 ACACGGGCGTGTC
35584813 CCTACCGTGC
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:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:35591226 original size:29 final size:30
Alignment explanation
Indices: 35591193--35591252 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35591183 TCCTTAATTC
35591193 AAACTTTTG-AAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
35591222 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
35591252 A
1 A
35591253 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:35592794 original size:61 final size:63
Alignment explanation
Indices: 35592661--35592794 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 63
35592651 ACTAGGCCTA
*
35592661 AGCCCTATT-CAGAAATCAGAGTTAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCAT
1 AGCCCTATTACAGAAATCAGAGTTAACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCAT
* * * * *
35592723 AGCCC-CTTACAG-TATCAGAG-TATACTGGGCC-TAGCCCATATCAGTCTCAATCTGGGCCGT
1 AGCCCTATTACAGAAATCAGAGTTA-ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCAT
35592783 AGCCCTATTACA
1 AGCCCTATTACA
35592795 AGTTGAGATA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
60 32 0.52
61 22 0.35
62 8 0.13
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (63 bp):
AGCCCTATTACAGAAATCAGAGTTAACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCAT
Found at i:35592820 original size:60 final size:60
Alignment explanation
Indices: 35592675--35592823 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
35592665 CTATTCAGAA
* *
35592675 ATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGT
1 ATCAGAGTAT-ACTGGGCCTT-GCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGT
* * * *
35592736 ATCAGAGTATACTGGGCCTAGCCCATATCAGTCTCAATCTGGGCCGTAGCCCTATTACAAGT
1 ATCAGAGTATACTGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTAC-AGT
* **
35592798 -TGAGA-TATGTTGGGCCTTGCCCATAT
1 ATCAGAGTATACTGGGCCTTGCCCATAT
35592824 TAACACAGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
60 46 0.61
61 25 0.33
62 4 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (60 bp):
ATCAGAGTATACTGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGT
Found at i:35592859 original size:19 final size:20
Alignment explanation
Indices: 35592816--35592861 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
35592806 GTTGGGCCTT
35592816 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
35592836 GCCCAT-TTCAACACAGTT-G
1 GCCCATATT-AACACAGTTGG
35592855 GCCCATA
1 GCCCATA
35592862 ACAAAACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:35592870 original size:19 final size:20
Alignment explanation
Indices: 35592828--35592871 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
35592818 CCATATTAAC
** *
35592828 ACAGTTGGGCCCATTTCAAC
1 ACAGTTGGGCCCATAACAAA
35592848 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
35592867 ACAGT
1 ACAGT
35592872 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:35596101 original size:18 final size:18
Alignment explanation
Indices: 35596080--35596117 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35596070 ATATTCATAG
35596080 TTCTCACTACAGTCATGC
1 TTCTCACTACAGTCATGC
35596098 TTCTCACTACAGTCATGC
1 TTCTCACTACAGTCATGC
35596116 TT
1 TT
35596118 ATACGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.37
Consensus pattern (18 bp):
TTCTCACTACAGTCATGC
Found at i:35598775 original size:12 final size:13
Alignment explanation
Indices: 35598750--35598783 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
35598740 TGTTCTTAAA
35598750 AAAATAATAAAAT
1 AAAATAATAAAAT
35598763 AAAATAA-AAAAT
1 AAAATAATAAAAT
*
35598775 AAAAAAATA
1 AAAATAATA
35598784 CATGTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:35601028 original size:20 final size:19
Alignment explanation
Indices: 35601003--35601046 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
35600993 GACTAAATTG
35601003 GAAACTTAGAAAATATTTCA
1 GAAACTTAGAAAAT-TTTCA
*
35601023 GAAACTTATAAAATTTTCA
1 GAAACTTAGAAAATTTTCA
35601042 -AAACT
1 GAAACT
35601047 GCAGGGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (19 bp):
GAAACTTAGAAAATTTTCA
Found at i:35603152 original size:25 final size:25
Alignment explanation
Indices: 35603113--35603172 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
35603103 CCATATAATA
* *
35603113 GGAAGCTCATGTGAGCTATGTAACG
1 GGAAGCTCATCTGAGCTATATAACG
* *
35603138 GGAAGCTTATCTGAGCTTTATAACG
1 GGAAGCTCATCTGAGCTATATAACG
*
35603163 GAAAGCTCAT
1 GGAAGCTCAT
35603173 AAGAGTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (25 bp):
GGAAGCTCATCTGAGCTATATAACG
Found at i:35603265 original size:25 final size:25
Alignment explanation
Indices: 35603200--35603265 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
35603190 AGCTCATCCA
* *
35603200 AGCCAATAA-TGGGTAGCTCCGAAG
1 AGCCATTAATTGGGAAGCTCCGAAG
* * *
35603224 AGCCATTAATCGAGAAGCTCCGAAT
1 AGCCATTAATTGGGAAGCTCCGAAG
*
35603249 AGCCATTTATTGGGAAG
1 AGCCATTAATTGGGAAG
35603266 TTCAAGTGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 8 0.24
25 25 0.76
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (25 bp):
AGCCATTAATTGGGAAGCTCCGAAG
Found at i:35603523 original size:54 final size:54
Alignment explanation
Indices: 35603441--35603545 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 54
35603431 ACCAATTCGA
35603441 GAACCCTGCATCCATCAAATCTCATTTATCCAAACAG-GACTTATTATTTATCGG
1 GAACCCTGCATCCATCAAATCTCATTTATCCAAA-AGAGACTTATTATTTATCGG
* * *
35603495 GAACCCTGTATCCATCGAATCTCATTTATCCAAATGAGACTTATTATTTAT
1 GAACCCTGCATCCATCAAATCTCATTTATCCAAAAGAGACTTATTATTTAT
35603546 TAGGTACTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 1 0.02
54 46 0.98
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (54 bp):
GAACCCTGCATCCATCAAATCTCATTTATCCAAAAGAGACTTATTATTTATCGG
Found at i:35610914 original size:25 final size:24
Alignment explanation
Indices: 35610886--35610993 Score: 72
Period size: 25 Copynumber: 4.3 Consensus size: 24
35610876 ATTTGGTAAT
*
35610886 GCTCATATGAGCACATAAACGGGAA
1 GCTCATATAAGC-CATAAACGGGAA
* * *
35610911 GCTCTCTCTCAAGCCATATACGGGAA
1 GCTC-ATAT-AAGCCATAAACGGGAA
* *
35610937 GCTCATGTAAGCCATGTAACGGGAA
1 GCTCATATAAGCCAT-AAACGGGAA
* * ** *
35610962 GCTTATCTGGGCTATATAACGGGAA
1 GCTCATATAAGCCATA-AACGGGAA
35610987 GCTCATA
1 GCTCATA
35610994 AGAGACAAAT
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
24 7 0.11
25 36 0.57
26 17 0.27
27 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (24 bp):
GCTCATATAAGCCATAAACGGGAA
Found at i:35611141 original size:26 final size:26
Alignment explanation
Indices: 35611069--35611174 Score: 94
Period size: 26 Copynumber: 4.2 Consensus size: 26
35611059 AGCTTTGGAT
* * **
35611069 AGCCGTTAATCGAGAAGCTCA-AGCG
1 AGCCATTAATCGGGAAGCTCACAAAG
* *
35611094 AGCCA-T-ATCGGAAATCTC-CAAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
*
35611117 AGCCATTAATCGGGAAGCTCACAAAA
1 AGCCATTAATCGGGAAGCTCACAAAG
* * *
35611143 AGCCTTTAATCAGGAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
35611169 AGCCAT
1 AGCCAT
35611175 ATATTGGGAC
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
23 16 0.25
24 2 0.03
25 14 0.22
26 31 0.49
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (26 bp):
AGCCATTAATCGGGAAGCTCACAAAG
Found at i:35618058 original size:65 final size:65
Alignment explanation
Indices: 35617984--35618111 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
35617974 ACTCAACATA
*
35617984 TTCACTATGACCGAA-TGGTTTATTTTCATTTTTGAGATTCAAAACAGTCCAAAAACATAAACTT
1 TTCACTATGACC-AATTGATTTATTTTCATTTTTGAGATTCAAAACAGTCCAAAAACATAAACTT
35618048 G
65 G
* * *
35618049 TTCACTATGACCAATTGATTTATTTTCATTTTTGGGCTTCAAAACAGTCCAATAACATAAACT
1 TTCACTATGACCAATTGATTTATTTTCATTTTTGAGATTCAAAACAGTCCAAAAACATAAACT
35618112 CATTCTTCCG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 2 0.03
65 56 0.97
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (65 bp):
TTCACTATGACCAATTGATTTATTTTCATTTTTGAGATTCAAAACAGTCCAAAAACATAAACTTG
Found at i:35623748 original size:24 final size:24
Alignment explanation
Indices: 35623721--35623766 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
35623711 GGTTAAGAGG
35623721 CATTACCAAACTTATACACTAAGC
1 CATTACCAAACTTATACACTAAGC
35623745 CATTACCAAACTTATACACTAA
1 CATTACCAAACTTATACACTAA
35623767 CATATATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (24 bp):
CATTACCAAACTTATACACTAAGC
Found at i:35623959 original size:20 final size:20
Alignment explanation
Indices: 35623931--35623977 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35623921 AGGGGCACAC
35623931 GCCCATGTGCCCTGGGACAT
1 GCCCATGTGCCCTGGGACAT
* *
35623951 GCCCGTGTGGCCTGGGACAT
1 GCCCATGTGCCCTGGGACAT
*
35623971 GGCCATG
1 GCCCATG
35623978 GGGCCAGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.36, T:0.19
Consensus pattern (20 bp):
GCCCATGTGCCCTGGGACAT
Found at i:35625809 original size:8 final size:8
Alignment explanation
Indices: 35625796--35625831 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
35625786 TTATAACACA
35625796 TATATTAT
1 TATATTAT
35625804 TATATTAT
1 TATATTAT
*
35625812 TAAATTAT
1 TATATTAT
35625820 TATAATTAT
1 TAT-ATTAT
35625829 TAT
1 TAT
35625832 TTCTTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATTAT
Found at i:35631997 original size:27 final size:28
Alignment explanation
Indices: 35631967--35632035 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
35631957 AAATCTGACC
*
35631967 CACAGCTTGTGTGAAC-AATCCAAATAT
1 CACAGCTTGTGTGAACAAATACAAATAT
*
35631994 CACAGCTTGTGTGATCAAATACAAATAT
1 CACAGCTTGTGTGAACAAATACAAATAT
35632022 CACAGCTTGTGTGA
1 CACAGCTTGTGTGA
35632036 GAAAACTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 15 0.38
28 24 0.62
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
CACAGCTTGTGTGAACAAATACAAATAT
Found at i:35633046 original size:7 final size:7
Alignment explanation
Indices: 35633034--35633156 Score: 158
Period size: 7 Copynumber: 17.7 Consensus size: 7
35633024 TTAATCACTC
35633034 TTTCTCT
1 TTTCTCT
*
35633041 TTTCTCC
1 TTTCTCT
35633048 TTTCTCT
1 TTTCTCT
35633055 TTTCTCT
1 TTTCTCT
35633062 TTTCTC-
1 TTTCTCT
35633068 TTTCTCT
1 TTTCTCT
35633075 TTTCTCT
1 TTTCTCT
35633082 TTTCTCT
1 TTTCTCT
35633089 TTTCTCT
1 TTTCTCT
*
35633096 TTTATCT
1 TTTCTCT
*
35633103 TTTATCT
1 TTTCTCT
*
35633110 TTTATCT
1 TTTCTCT
*
35633117 TTTATCT
1 TTTCTCT
*
35633124 TTTATCT
1 TTTCTCT
*
35633131 TTTATCT
1 TTTCTCT
*
35633138 TTTATCT
1 TTTCTCT
*
35633145 TTTATCT
1 TTTCTCT
35633152 TTTCT
1 TTTCT
35633157 TTTCATCTTA
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
6 6 0.05
7 105 0.95
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTCTCT
Found at i:35633060 original size:21 final size:21
Alignment explanation
Indices: 35633034--35633170 Score: 136
Period size: 21 Copynumber: 6.6 Consensus size: 21
35633024 TTAATCACTC
*
35633034 TTTCTCTTTTCTCCTTTCTCT
1 TTTCTCTTTTATCCTTTCTCT
*
35633055 TTTCTCTTTTCT-CTTTCTCT
1 TTTCTCTTTTATCCTTTCTCT
* *
35633075 TTTCTCTTTTCTCTTTTCTCT
1 TTTCTCTTTTATCCTTTCTCT
* * *
35633096 TTTATCTTTTATCTTTTATCT
1 TTTCTCTTTTATCCTTTCTCT
* * *
35633117 TTTATCTTTTATCTTTTATCT
1 TTTCTCTTTTATCCTTTCTCT
*
35633138 TTTATCTTTTAT-CTTT-TCT
1 TTTCTCTTTTATCCTTTCTCT
35633157 TTTCATCTTATTAT
1 TTTC-TCTT-TTAT
35633171 TTTAAAATAA
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.06
20 27 0.25
21 74 0.69
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTCTTTTATCCTTTCTCT
Found at i:35633549 original size:7 final size:7
Alignment explanation
Indices: 35633537--35633561 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35633527 GTTGAAAGTG
35633537 ATTTCTA
1 ATTTCTA
35633544 ATTTCTA
1 ATTTCTA
35633551 ATTTCTA
1 ATTTCTA
35633558 ATTT
1 ATTT
35633562 GGTTACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTCTA
Found at i:35633866 original size:52 final size:52
Alignment explanation
Indices: 35633809--35633910 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
35633799 ATCCTTACTG
* * * *
35633809 TTTGATATGTTGATTGTTGATTCTACGTGATTTTTTCTAATTCTCGTGGCTA
1 TTTGATATGTTGATTGTTGATACTACGTCATTTGTTCTAATTCTAGTGGCTA
*
35633861 TTTGATATGTTGATTGTTGATACTATGTCATTTGTTCTAATTCTAGTGGC
1 TTTGATATGTTGATTGTTGATACTACGTCATTTGTTCTAATTCTAGTGGC
35633911 ATGTGACATC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.19, C:0.11, G:0.20, T:0.51
Consensus pattern (52 bp):
TTTGATATGTTGATTGTTGATACTACGTCATTTGTTCTAATTCTAGTGGCTA
Found at i:35638777 original size:49 final size:49
Alignment explanation
Indices: 35638721--35638843 Score: 169
Period size: 49 Copynumber: 2.5 Consensus size: 49
35638711 GTCAATGATG
*
35638721 TGTCCCAGATAGGTCTTACACTGACTTTCATATATCGAAG-CT-GATGCCA
1 TGTCCCAGATAGGTCTTACACTGACTCTCATATATC--AGTCTCGATGCCA
* * *
35638770 TGTCCCAGATAGGTCTTACACTGGCTCTCATTTATCAGTGTCGATGCCA
1 TGTCCCAGATAGGTCTTACACTGACTCTCATATATCAGTCTCGATGCCA
*
35638819 TGTCCCAGACAGGTCTTACACTGAC
1 TGTCCCAGATAGGTCTTACACTGAC
35638844 ACCTAACATG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
47 2 0.03
48 1 0.02
49 63 0.95
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (49 bp):
TGTCCCAGATAGGTCTTACACTGACTCTCATATATCAGTCTCGATGCCA
Found at i:35638927 original size:48 final size:46
Alignment explanation
Indices: 35638861--35639023 Score: 157
Period size: 46 Copynumber: 3.5 Consensus size: 46
35638851 ATGCTGACAC
* * * * *
35638861 CATGTCCCAAACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-CATCTCAAGGCCGATG
* * *
35638909 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCGATG
* * * * *** *
35638955 CACGTCCCAGACATGTCTTACACTGGCACTCATGTTGTGGTCG-TG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCGATG
35639000 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
35639024 CACTCACATA
Statistics
Matches: 97, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 25 0.26
46 45 0.46
47 2 0.02
48 25 0.26
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCGATG
Found at i:35647110 original size:20 final size:21
Alignment explanation
Indices: 35647085--35647124 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35647075 CCCTTGAAAC
*
35647085 AGGGC-ACACGCTCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
35647105 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
35647125 TCAATATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.28, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:35650663 original size:26 final size:26
Alignment explanation
Indices: 35650627--35650679 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
35650617 TGGTTTTGAC
35650627 ATTTTAAACTGAATAAACTGATTAAG
1 ATTTTAAACTGAATAAACTGATTAAG
* *
35650653 ATTTTAAACTGGATAAATTGATTAAG
1 ATTTTAAACTGAATAAACTGATTAAG
35650679 A
1 A
35650680 CAATAAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (26 bp):
ATTTTAAACTGAATAAACTGATTAAG
Found at i:35650780 original size:9 final size:9
Alignment explanation
Indices: 35650768--35650796 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
35650758 CTTAAAGCCC
35650768 AAACCCATT
1 AAACCCATT
35650777 AAACCCATT
1 AAACCCATT
35650786 AAACCCATT
1 AAACCCATT
35650795 AA
1 AA
35650797 TATTTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACCCATT
Found at i:35655192 original size:24 final size:24
Alignment explanation
Indices: 35655165--35655214 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
35655155 AGCAGTTCTT
35655165 TTAGAATGCTAAGTTCAATCAAGA
1 TTAGAATGCTAAGTTCAATCAAGA
35655189 TTAGAATGCTAAGTTCAATCAAGA
1 TTAGAATGCTAAGTTCAATCAAGA
35655213 TT
1 TT
35655215 TTTTATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (24 bp):
TTAGAATGCTAAGTTCAATCAAGA
Found at i:35667878 original size:21 final size:21
Alignment explanation
Indices: 35667846--35667885 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
35667836 GCAATTTTTT
*
35667846 ATTTTTTTTTAA-GTTTAGGG
1 ATTTTTTATTAAGGTTTAGGG
35667866 ATTTTTATATTAAGGTTTAG
1 ATTTTT-TATTAAGGTTTAG
35667886 TATTTAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
ATTTTTTATTAAGGTTTAGGG
Found at i:35668145 original size:26 final size:27
Alignment explanation
Indices: 35668103--35668156 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
35668093 TGTTGTTGAT
35668103 AAGTGCTTTTAAAAAAT-ATTATGAAA
1 AAGTGCTTTTAAAAAATGATTATGAAA
*
35668129 AAGTGCTTATT-AAAAATGATTTTGAAA
1 AAGTGCTT-TTAAAAAATGATTATGAAA
35668156 A
1 A
35668157 GCTTGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (27 bp):
AAGTGCTTTTAAAAAATGATTATGAAA
Found at i:35674165 original size:79 final size:81
Alignment explanation
Indices: 35674029--35674213 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
35674019 TTGAATGATG
*
35674029 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
35674093 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
35674108 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
35674170 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
35674188 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
35674214 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:35674227 original size:40 final size:40
Alignment explanation
Indices: 35674030--35674213 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
35674020 TGAATGATGT
* * * *
35674030 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
35674070 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
35674110 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
35674148 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
35674189 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
35674214 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:35674235 original size:79 final size:79
Alignment explanation
Indices: 35674082--35674246 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
35674072 GGACTAAGAT
* **
35674082 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
35674147 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
35674161 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
35674224 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
35674240 CCGAAGG
1 CCGAAGG
35674247 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:35677249 original size:21 final size:20
Alignment explanation
Indices: 35677202--35677243 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
35677192 GAAGTTACCA
35677202 TTGATGAATTTCGATTGTTT
1 TTGATGAATTTCGATTGTTT
35677222 TTGATGAATTTCGATTGTTT
1 TTGATGAATTTCGATTGTTT
35677242 TT
1 TT
35677244 TTATGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (20 bp):
TTGATGAATTTCGATTGTTT
Found at i:35677254 original size:23 final size:22
Alignment explanation
Indices: 35677203--35677254 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
35677193 AAGTTACCAT
35677203 TGATGAATTTCGATTGTTTTTGA
1 TGAT-AATTTCGATTGTTTTTGA
*
35677226 TG--AATTTCGATTGTTTTTTTA
1 TGATAATTTCGATTG-TTTTTGA
35677247 TGATAATT
1 TGATAATT
35677255 ATATGTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.44
21 8 0.32
23 6 0.24
ACGTcount: A:0.23, C:0.04, G:0.17, T:0.56
Consensus pattern (22 bp):
TGATAATTTCGATTGTTTTTGA
Found at i:35677963 original size:36 final size:36
Alignment explanation
Indices: 35677913--35678037 Score: 178
Period size: 36 Copynumber: 3.4 Consensus size: 36
35677903 AGATCCATTA
* * * *
35677913 GTGTGTTATCGGATGGACTGGCTCGTATGAGCATTTG
1 GTGTGTT-TCGGATGGATTAGCTCTTATGAGCATCTG
*
35677950 GTGTGTTTCGGATGGATTAACTCTTATGAGCATCTG
1 GTGTGTTTCGGATGGATTAGCTCTTATGAGCATCTG
*
35677986 GTGTGTTTCGGATGGATTAGCTTTTATGAGCATCTG
1 GTGTGTTTCGGATGGATTAGCTCTTATGAGCATCTG
*
35678022 GTGTGTTTCGGTTGGA
1 GTGTGTTTCGGATGGA
35678038 ATATCGATGT
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 73 0.91
37 7 0.09
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (36 bp):
GTGTGTTTCGGATGGATTAGCTCTTATGAGCATCTG
Found at i:35690380 original size:24 final size:23
Alignment explanation
Indices: 35690353--35690399 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
35690343 TTCCATAATA
35690353 TTTTTACAATTTTAATAAGTATAT
1 TTTTTACAATTTTAA-AAGTATAT
* *
35690377 TTTTTATAATTTTAAAATTATAT
1 TTTTTACAATTTTAAAAGTATAT
35690400 CCAAAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTACAATTTTAAAAGTATAT
Found at i:35690528 original size:15 final size:16
Alignment explanation
Indices: 35690505--35690538 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35690495 TTTAAATAAA
35690505 TTTTATAAT-TTTATT
1 TTTTATAATATTTATT
*
35690520 TTTTTTAATATTTATT
1 TTTTATAATATTTATT
35690536 TTT
1 TTT
35690539 CATTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATAATATTTATT
Found at i:35695191 original size:16 final size:15
Alignment explanation
Indices: 35695170--35695201 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
35695160 CAAAATTAAG
35695170 AAAAGAAAGAAAGAAA
1 AAAAGAAAG-AAGAAA
35695186 AAAAGAAAGAAGAAA
1 AAAAGAAAGAAGAAA
35695201 A
1 A
35695202 GAATGAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAGAAA
Found at i:35695192 original size:12 final size:12
Alignment explanation
Indices: 35695167--35695204 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
35695157 AAACAAAATT
35695167 AAGAAAAGAAAGA
1 AAGAAAA-AAAGA
35695180 AAGAAAAAAAGA
1 AAGAAAAAAAGA
*
35695192 AAGAAGAAAAGA
1 AAGAAAAAAAGA
35695204 A
1 A
35695205 TGAGAACTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:35696392 original size:23 final size:23
Alignment explanation
Indices: 35696310--35696396 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
35696300 CCTGATCAGT
*
35696310 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
35696332 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
35696352 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
35696375 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
35696397 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:35696792 original size:15 final size:15
Alignment explanation
Indices: 35696767--35696824 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
35696757 TCATATATAT
35696767 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
35696783 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
35696798 AATAATTTCAATCAA
1 TATAAATTCAATCAA
35696813 TATAAATTCAAT
1 TATAAATTCAAT
35696825 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:35697146 original size:15 final size:15
Alignment explanation
Indices: 35697126--35697154 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35697116 AACTAGACTC
35697126 ACAAATCTTCTTACG
1 ACAAATCTTCTTACG
35697141 ACAAATCTTCTTAC
1 ACAAATCTTCTTAC
35697155 AATAAAATTT
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:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (15 bp):
ACAAATCTTCTTACG
Found at i:35697614 original size:5 final size:5
Alignment explanation
Indices: 35697606--35697647 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
35697596 TCTTTAGTTT
*
35697606 ATATA ATATA ATATA ATATA ATATA ATATA ATACA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
35697648 TAAAACATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:35699795 original size:21 final size:19
Alignment explanation
Indices: 35699755--35699797 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
35699745 ACACCTAGGA
35699755 TGATTGTTTTGACATGTTT
1 TGATTGTTTTGACATGTTT
*
35699774 TGATTGTATTTGATCTTGTTT
1 TGATTGT-TTTGA-CATGTTT
35699795 TGA
1 TGA
35699798 ACTAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (19 bp):
TGATTGTTTTGACATGTTT
Found at i:35706486 original size:43 final size:43
Alignment explanation
Indices: 35706427--35706512 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
35706417 GATATACGTG
* ** *
35706427 GCATCTGAGCTCGTTGAGTGGTCTGAGTTCATTATGGATGCAA
1 GCATCCGAGCTCGTTGAGTGGTCCAAGTTCATAATGGATGCAA
*
35706470 GCATCCGAGCTTGTTGAGTGGTCCAAGTTCATAATGGATGCAA
1 GCATCCGAGCTCGTTGAGTGGTCCAAGTTCATAATGGATGCAA
35706513 TACATGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGTGGTCCAAGTTCATAATGGATGCAA
Found at i:35709506 original size:28 final size:28
Alignment explanation
Indices: 35709455--35709514 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
35709445 ACAAGGGTTT
35709455 TCACACGGCCTGACACATGCCCGTGTCTC
1 TCACACGGCCTGA-ACATGCCCGTGTCTC
35709484 TCACACGGCCATG-ACATGCCCGTGTCTC
1 TCACACGGCC-TGAACATGCCCGTGTCTC
35709512 TCA
1 TCA
35709515 TATATTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 18 0.60
29 10 0.33
30 2 0.07
ACGTcount: A:0.18, C:0.40, G:0.20, T:0.22
Consensus pattern (28 bp):
TCACACGGCCTGAACATGCCCGTGTCTC
Found at i:35710011 original size:94 final size:93
Alignment explanation
Indices: 35709751--35710018 Score: 267
Period size: 94 Copynumber: 2.8 Consensus size: 93
35709741 CGAGGCCGAC
* * * *
35709751 GCCATGTCCCAGGCATGGTCTTACACTAGCTTTCATATATCCGT-GCTGATGCAATATCACAGAC
1 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATA-AT--GTAGCTGATGC-ATGTCACAAAC
* * *
35709815 ATGGTCTTACATTGGCACCTCTATACGTGCCGAT
62 AT-GTCTTACACTAGCACCTCTATAC-TGCCAAT
* * * ** * *
35709849 GCTATGTCCCAGACATGGTCTTACACTGAC--ACATCCTGTAGCCGATGCATGTCCCAAACATGT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAATGTAGCTGATGCATGTCACAAACATGT
*
35709912 CTTACACTAGCTCTCGTCTCA-A-TGCCAAT
66 CTTACACTAGCAC-C-TCT-ATACTGCCAAT
* *
35709941 GCCATGTCCCAGCCATGGTCTTACACTGGCTTTCATAATGTAGCTGATGCATGTCTCAAACATGT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAATGTAGCTGATGCATGTCACAAACATGT
35710006 CTTACACTAGCAC
66 CTTACACTAGCAC
35710019 ACAAATAACC
Statistics
Matches: 140, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
92 45 0.32
93 13 0.09
94 51 0.36
95 2 0.01
96 3 0.02
98 26 0.19
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (93 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAATGTAGCTGATGCATGTCACAAACATGT
CTTACACTAGCACCTCTATACTGCCAAT
Found at i:35725119 original size:43 final size:43
Alignment explanation
Indices: 35725070--35725152 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
35725060 GATTACCAAG
35725070 TTACGTTCTCGAAATGGAGTTAACACTCTAAAAAAGTGACAAC
1 TTACGTTCTCGAAATGGAGTTAACACTCTAAAAAAGTGACAAC
35725113 TTACGTTCTCGAAATGGAGTTAACACTCTAAAAAAGTGAC
1 TTACGTTCTCGAAATGGAGTTAACACTCTAAAAAAGTGAC
35725153 TTGAAAGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.27
Consensus pattern (43 bp):
TTACGTTCTCGAAATGGAGTTAACACTCTAAAAAAGTGACAAC
Found at i:35731160 original size:19 final size:19
Alignment explanation
Indices: 35731132--35731169 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35731122 TTCAAAAATG
35731132 TGTAACCTTAGATATGATA
1 TGTAACCTTAGATATGATA
*
35731151 TGTAATCTTAGATATGATA
1 TGTAACCTTAGATATGATA
35731170 CGATTCTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (19 bp):
TGTAACCTTAGATATGATA
Found at i:35739568 original size:30 final size:30
Alignment explanation
Indices: 35739532--35739592 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
35739522 TATTGATGAG
*
35739532 TAAGTTGTGTTTAT-GCGTACTTTAGTACTA
1 TAAGTTGTGCTTATGGC-TACTTTAGTACTA
35739562 TAAGTTGTGCTTATGGCTACTTTAGTACTA
1 TAAGTTGTGCTTATGGCTACTTTAGTACTA
35739592 T
1 T
35739593 GAGCATGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (30 bp):
TAAGTTGTGCTTATGGCTACTTTAGTACTA
Found at i:35741360 original size:35 final size:35
Alignment explanation
Indices: 35741311--35741388 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
35741301 GGTTTAAAAC
*
35741311 TTTAACCACAAATTCAGTGAATTCTATAAGTAAATT
1 TTTAA-CACAAATTCAGTGAATTCAATAAGTAAATT
* *
35741347 TTTAACAGAAATTCAGTGAATTCAATAGGTAAATT
1 TTTAACACAAATTCAGTGAATTCAATAAGTAAATT
35741382 TTTAACA
1 TTTAACA
35741389 AACGCTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 34 0.87
36 5 0.13
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (35 bp):
TTTAACACAAATTCAGTGAATTCAATAAGTAAATT
Found at i:35741493 original size:27 final size:27
Alignment explanation
Indices: 35741463--35741514 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
35741453 TATCAAGTAA
35741463 AGAAAATGTACCAGTAATGATGTCTAG
1 AGAAAATGTACCAGTAATGATGTCTAG
35741490 AGAAAATGTACCAGTAATGATGTCT
1 AGAAAATGTACCAGTAATGATGTCT
35741515 GGTGCAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (27 bp):
AGAAAATGTACCAGTAATGATGTCTAG
Found at i:35750318 original size:25 final size:25
Alignment explanation
Indices: 35750290--35750338 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
35750280 TTTAATCCTT
* *
35750290 TTTAAATTTTTTATATATAATTTAC
1 TTTAAATATTTTAAATATAATTTAC
*
35750315 TTTAAATATTTTAAATATTATTTA
1 TTTAAATATTTTAAATATAATTTA
35750339 TTTTTACTAT
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:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTAAATATTTTAAATATAATTTAC
Found at i:35750436 original size:13 final size:14
Alignment explanation
Indices: 35750408--35750460 Score: 76
Period size: 15 Copynumber: 3.9 Consensus size: 14
35750398 TATTGTTCAT
35750408 ATTTTATTATAT--
1 ATTTTATTATATAC
35750420 ATTTTATT-TATAC
1 ATTTTATTATATAC
35750433 ATTTTATTATATATC
1 ATTTTATTATATA-C
35750448 ATTTTATTATATA
1 ATTTTATTATATA
35750461 TTATTCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.08
12 8 0.22
13 8 0.22
14 4 0.11
15 14 0.38
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTATTATATAC
Found at i:35750452 original size:15 final size:14
Alignment explanation
Indices: 35750406--35750508 Score: 82
Period size: 13 Copynumber: 7.9 Consensus size: 14
35750396 TGTATTGTTC
35750406 ATATTTTA-T-TAT
1 ATATTTTATTATAT
35750418 ATATTTTATT-TAT
1 ATATTTTATTATAT
*
35750431 ACATTTTATTATAT
1 ATATTTTATTATAT
35750445 ATCATTTTATTATAT
1 AT-ATTTTATTATAT
*
35750460 AT-TATTCATTATAT
1 ATAT-TTTATTATAT
35750474 -TATTTTA-TAT-T
1 ATATTTTATTATAT
*
35750485 ATATAATTATT-TAT
1 ATAT-TTTATTATAT
35750499 -TA-TTTATTAT
1 ATATTTTATTAT
35750509 TATGTATAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
11 6 0.08
12 15 0.20
13 24 0.32
14 16 0.21
15 14 0.19
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTTATTATAT
Found at i:35750457 original size:27 final size:26
Alignment explanation
Indices: 35750408--35750481 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
35750398 TATTGTTCAT
35750408 ATTTTA-T-TATATATTTTATTTATAC
1 ATTTTATTATATATATTTTA-TTATAC
*
35750433 ATTTTATTATATATCATTTTATTATAT
1 ATTTTATTATATAT-ATTTTATTATAC
35750460 ATTATTCATTATAT-TATTTTAT
1 ATT-TT-ATTATATATATTTTAT
35750482 ATTATATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
25 6 0.14
26 1 0.02
27 20 0.47
28 9 0.21
29 7 0.16
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTTTATTATATATATTTTATTATAC
Found at i:35750464 original size:7 final size:7
Alignment explanation
Indices: 35750412--35750508 Score: 67
Period size: 7 Copynumber: 13.9 Consensus size: 7
35750402 GTTCATATTT
35750412 TATTATA
1 TATTATA
*
35750419 TATTTTA
1 TATTATA
35750426 T-TTATA
1 TATTATA
*
35750432 CATT-T-
1 TATTATA
35750437 TATTATA
1 TATTATA
* *
35750444 TATCATTT
1 TATTA-TA
35750452 TATTATA
1 TATTATA
35750459 TATTAT-
1 TATTATA
35750465 TCATTATA
1 T-ATTATA
*
35750473 TTATTTTA
1 -TATTATA
35750481 TATTATA
1 TATTATA
*
35750488 TAATTATT
1 T-ATTATA
*
35750496 TATTATT
1 TATTATA
35750503 TATTAT
1 TATTAT
35750509 TATGTATAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
5 3 0.04
6 7 0.10
7 44 0.62
8 16 0.23
9 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (7 bp):
TATTATA
Found at i:35750476 original size:22 final size:21
Alignment explanation
Indices: 35750450--35750510 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
35750440 TATATATCAT
*
35750450 TTTATTATATATTATTCATTA
1 TTTATTATATATTATTAATTA
*
35750471 TATTATTTTATATTATATAATTA
1 T-TTATTATATATTAT-TAATTA
*
35750494 TTTATTATTTATTATTA
1 TTTATTATATATTATTA
35750511 TGTATAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 25 0.74
23 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATTATATATTATTAATTA
Found at i:35750487 original size:27 final size:24
Alignment explanation
Indices: 35750406--35750503 Score: 92
Period size: 25 Copynumber: 3.8 Consensus size: 24
35750396 TGTATTGTTC
35750406 ATATTTTATTATA-TATTTTATTT
1 ATATTTTATTATATTATTTTATTT
35750429 ATACATTTTATTATATATCATTTTATTAT
1 AT--ATTTTATTATAT-T-ATTTTATT-T
35750458 ATATTATTCATTATATTATTTTATATT
1 ATATT-TT-ATTATATTATTTTAT-TT
*
35750485 ATATAATTATT-TATTATTT
1 ATAT-TTTATTATATTATTT
35750504 ATTATTATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
23 2 0.03
25 19 0.30
26 3 0.05
27 18 0.28
28 12 0.19
29 10 0.16
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATTTTATTATATTATTTTATTT
Found at i:35750508 original size:27 final size:28
Alignment explanation
Indices: 35750410--35750508 Score: 84
Period size: 29 Copynumber: 3.6 Consensus size: 28
35750400 TTGTTCATAT
*
35750410 TTTATTATA-TATTTTATT-TATACA-T-
1 TTTATTATATTATTATATTATATA-ATTA
*
35750435 TTTATTATATATCATTTTATTATAT-ATTA
1 TTTATTATAT-T-ATTATATTATATAATTA
*
35750464 TTCATTATATTATTTTATATTATATAATTA
1 TTTATTATATTA--TTATATTATATAATTA
35750494 TTTATTAT-TTATTAT
1 TTTATTATATTATTAT
35750509 TATGTATAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
25 9 0.15
27 7 0.11
28 10 0.16
29 25 0.40
30 11 0.18
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTATTATATTATTATATTATATAATTA
Found at i:35750510 original size:10 final size:10
Alignment explanation
Indices: 35750451--35750511 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 10
35750441 ATATATCATT
*
35750451 TTATTATATA
1 TTATTATTTA
35750461 TTATTCATTATA
1 TTATT-ATT-TA
35750473 TTATT-TTATA
1 TTATTATT-TA
*
35750483 TTATATAATTA
1 TTAT-TATTTA
35750494 TTTATTATTTA
1 -TTATTATTTA
35750505 TTATTAT
1 TTATTAT
35750512 GTATAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 21 0.49
11 10 0.23
12 12 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTATTTA
Done.