Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 131 of 318
Found at i:40555593 original size:39 final size:40
Alignment explanation
Indices: 40555544--40555635 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
40555534 TTTTTCATTT
* *
40555544 AAACGCCGCTAAAGAAT-GAGTATTAGCAGCAC-TTTTTAA
1 AAACGTCGCTAAA-AATCAAGTATTAGCAGCACTTTTTTAA
* *
40555583 AAACGTCGCTAAAAATCAAGTATTAGCGGCGCTTTTTTTAA
1 AAACGTCGCTAAAAATCAAGTATTAGCAGCAC-TTTTTTAA
*
40555624 AAACGTTGCTAA
1 AAACGTCGCTAA
40555636 TGCTTGATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 3 0.07
39 24 0.53
41 18 0.40
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (40 bp):
AAACGTCGCTAAAAATCAAGTATTAGCAGCACTTTTTTAA
Found at i:40555767 original size:40 final size:40
Alignment explanation
Indices: 40555681--40555868 Score: 172
Period size: 40 Copynumber: 4.7 Consensus size: 40
40555671 CCTTTAGTGG
* ** *
40555681 CTTTAGCGGCGCTTTTTAAAAAACGCCGCTATATG-TACAC
1 CTTTAGCAGCGCTTTTTAAAAAACGCCGCTA-ATGCTTGAT
* *
40555721 CATTAGCAGCGCTTTTCAAAAAACGCCGCTAATGCTTGAT
1 CTTTAGCAGCGCTTTTTAAAAAACGCCGCTAATGCTTGAT
* * *
40555761 CTTTAGC-GACG-TTTTTTAAAAA-GCTCGCTAAAGATTGAGT
1 CTTTAGCAG-CGCTTTTTAAAAAACGC-CGCTAATGCTTGA-T
* * * *
40555801 -ATTAGCGGCGCTTTTTAAGAAACGCCGCTAATGCTCGAT
1 CTTTAGCAGCGCTTTTTAAAAAACGCCGCTAATGCTTGAT
40555840 CTTTAGCAGCG-TTTTTCAAAAAACGCCGC
1 CTTTAGCAGCGCTTTTT-AAAAAACGCCGC
40555869 AAAAGAATTT
Statistics
Matches: 119, Mismatches: 20, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
38 2 0.02
39 37 0.31
40 78 0.66
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
CTTTAGCAGCGCTTTTTAAAAAACGCCGCTAATGCTTGAT
Found at i:40556234 original size:7 final size:7
Alignment explanation
Indices: 40556167--40556286 Score: 64
Period size: 7 Copynumber: 17.0 Consensus size: 7
40556157 GTTTAAGGGT
40556167 GGTTTAAG
1 GGTTT-AG
*
40556175 GG-TTGG
1 GGTTTAG
*
40556181 GGTTTAA
1 GGTTTAG
40556188 GGTTTA-
1 GGTTTAG
40556194 GGTGTTAG
1 GGT-TTAG
*
40556202 GGGTTAG
1 GGTTTAG
* *
40556209 GGGTAAG
1 GGTTTAG
* *
40556216 GGTTCAT
1 GGTTTAG
*
40556223 AGTTTAG
1 GGTTTAG
*
40556230 GGTTTAT
1 GGTTTAG
*
40556237 GTTTTAG
1 GGTTTAG
* *
40556244 GATTTAT
1 GGTTTAG
40556251 GGTTTAG
1 GGTTTAG
40556258 GGTTTAG
1 GGTTTAG
* *
40556265 TGATTAAG
1 -GGTTTAG
*
40556273 AGTTTAG
1 GGTTTAG
40556280 GGTTTAG
1 GGTTTAG
40556287 ATTAATTAGT
Statistics
Matches: 83, Mismatches: 25, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
6 6 0.07
7 68 0.82
8 9 0.11
ACGTcount: A:0.20, C:0.01, G:0.38, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:40556403 original size:14 final size:14
Alignment explanation
Indices: 40556393--40556425 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40556383 ATAGTTTGGA
40556393 GTTTATGGTTTAGG
1 GTTTATGGTTTAGG
*
40556407 GTATATGGTTTAGG
1 GTTTATGGTTTAGG
40556421 GTTTA
1 GTTTA
40556426 AAATGTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
GTTTATGGTTTAGG
Found at i:40556464 original size:14 final size:15
Alignment explanation
Indices: 40556445--40556477 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40556435 AGTTACTATT
*
40556445 TTAT-GGTTTATGGA
1 TTATGGGTTTAGGGA
40556459 TTATGGGTTTAGGGA
1 TTATGGGTTTAGGGA
40556474 TTAT
1 TTAT
40556478 CATTTATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (15 bp):
TTATGGGTTTAGGGA
Found at i:40558972 original size:79 final size:80
Alignment explanation
Indices: 40558869--40559053 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 80
40558859 GCTACTCGTT
* * *
40558869 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAA-GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40558932 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* ** *
40558949 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCTGG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
40559013 ATATGGTCACTTAGCA
65 ATATAGTAACTTAGCA
40559029 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
40559054 CATCATTTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:40558986 original size:39 final size:40
Alignment explanation
Indices: 40558869--40559053 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
40558859 GCTACTCGTT
* *
40558869 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
40558909 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
40558949 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
40558988 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40559029 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40559054 CATCATTTAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 74 0.61
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40562129 original size:14 final size:14
Alignment explanation
Indices: 40562095--40562136 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
40562085 TCGTGTCAAC
40562095 TAATTATTTT-TTT
1 TAATTATTTTGTTT
40562108 TAATTATTTTGTTT
1 TAATTATTTTGTTT
40562122 TCAA-TATTTTGTTT
1 T-AATTATTTTGTTT
40562136 T
1 T
40562137 TATTTGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (14 bp):
TAATTATTTTGTTT
Found at i:40562545 original size:43 final size:42
Alignment explanation
Indices: 40562496--40562726 Score: 148
Period size: 43 Copynumber: 5.4 Consensus size: 42
40562486 AAGATTATAT
*
40562496 TCTTTAGCAGCGTTTGTGAGAAAAGAGTCGCTAAAGGTCATGG
1 TCTTTAGCGGCGTTT-TGAGAAAAGAGTCGCTAAAGGTCATGG
* * * *
40562539 TCTTTAGCGGCATTTTCA-AAAAAAGTGCCGCTAAATGTCATGG
1 TCTTTAGCGGCGTTTTGAGAAAAGAGT--CGCTAAAGGTCATGG
* * * * * * *
40562582 TTTTTAGCGGCGTTTTGGGGAAAAGTGCCGTTAAATGTTATGG
1 TCTTTAGCGGCGTTTT-GAGAAAAGAGTCGCTAAAGGTCATGG
* *
40562625 TTTTTAGTGGCG-TTTGAAGAAAA-AG-CGCTGTTAAAGGTCATGG
1 TCTTTAGCGGCGTTTTG-AGAAAAGAGTCGC---TAAAGGTCATGG
* * * * * * *
40562668 TCTTTAACGGTG-TTTGAGGAAAAAGCGCCGTTAAATGTTATGG
1 TCTTTAGCGGCGTTTTGA-G-AAAAGAGTCGCTAAAGGTCATGG
40562711 TCTTTAGCGGCGTTTT
1 TCTTTAGCGGCGTTTT
40562727 TTTTAAATAA
Statistics
Matches: 145, Mismatches: 30, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.01
41 9 0.06
42 11 0.08
43 108 0.74
44 7 0.05
45 6 0.04
46 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (42 bp):
TCTTTAGCGGCGTTTTGAGAAAAGAGTCGCTAAAGGTCATGG
Found at i:40562625 original size:86 final size:86
Alignment explanation
Indices: 40562535--40562726 Score: 226
Period size: 86 Copynumber: 2.2 Consensus size: 86
40562525 GCTAAAGGTC
* * * *
40562535 ATGGTCTTTAGCGGCATTTTCAA-AAAAAGTGCCGCTAAATGTCATGGTTTTTAGCGGCGTTTTG
1 ATGGTCTTTAGCGGC-TTTTCAAGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCG-TTTG
* *
40562599 -GGGAAAAGTGCCGTTAAATGTT
64 AGGAAAAAGCGCCGTTAAATGTT
* * * * * * *
40562621 ATGGTTTTTAGTGGCGTTTGAAGAAAAAGCGCTGTTAAAGGTCATGGTCTTTAACGGTGTTTGAG
1 ATGGTCTTTAGCGGCTTTTCAAGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCGTTTGAG
40562686 GAAAAAGCGCCGTTAAATGTT
66 GAAAAAGCGCCGTTAAATGTT
40562707 ATGGTCTTTAGCGGCGTTTT
1 ATGGTCTTTAGCGGC-TTTT
40562727 TTTTAAATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
85 9 0.10
86 75 0.86
87 3 0.03
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.34
Consensus pattern (86 bp):
ATGGTCTTTAGCGGCTTTTCAAGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCGTTTGAG
GAAAAAGCGCCGTTAAATGTT
Found at i:40564422 original size:12 final size:12
Alignment explanation
Indices: 40564405--40564437 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40564395 TTCTCTGTAA
40564405 AATAGTAAAAAT
1 AATAGTAAAAAT
40564417 AATAGTAAAAAT
1 AATAGTAAAAAT
40564429 AATAGTAAA
1 AATAGTAAA
40564438 GGGGAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:40565365 original size:10 final size:10
Alignment explanation
Indices: 40565346--40565405 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
40565336 TGAAATTCTA
40565346 AAAGATAAAT
1 AAAGATAAAT
40565356 ACAA-ATAAAT
1 A-AAGATAAAT
* *
40565366 AAATATAATT
1 AAAGATAAAT
40565376 AAAGATAAAT
1 AAAGATAAAT
40565386 AAAGATAAAT
1 AAAGATAAAT
40565396 GAAA-ATAAAT
1 -AAAGATAAAT
40565406 CTTAAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.05
10 37 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40565380 original size:30 final size:30
Alignment explanation
Indices: 40565346--40565403 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
40565336 TGAAATTCTA
40565346 AAAGATAAATACAA-ATAAAT-AAATATAATT
1 AAAGATAAATA-AAGATAAATGAAA-ATAATT
40565376 AAAGATAAATAAAGATAAATGAAAATAA
1 AAAGATAAATAAAGATAAATGAAAATAA
40565404 ATCTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.08
30 21 0.81
31 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (30 bp):
AAAGATAAATAAAGATAAATGAAAATAATT
Found at i:40567465 original size:53 final size:53
Alignment explanation
Indices: 40567378--40567487 Score: 202
Period size: 53 Copynumber: 2.1 Consensus size: 53
40567368 CTTGGTCTAG
40567378 TATAATAGAGTTCATCATTTATGACCATACAATGCTTCATACAGTGCCATGTT
1 TATAATAGAGTTCATCATTTATGACCATACAATGCTTCATACAGTGCCATGTT
* *
40567431 TATAGTAGAGTTCATCATTTATGACCATATAATGCTTCATACAGTGCCATGTT
1 TATAATAGAGTTCATCATTTATGACCATACAATGCTTCATACAGTGCCATGTT
40567484 TATA
1 TATA
40567488 CTCGATTGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (53 bp):
TATAATAGAGTTCATCATTTATGACCATACAATGCTTCATACAGTGCCATGTT
Found at i:40575825 original size:20 final size:19
Alignment explanation
Indices: 40575800--40575847 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
40575790 TCATGTTGAA
40575800 TAAATTGA-AGAATTAGAGGT
1 TAAATTGATAGAATTA-A-GT
40575820 TAAATTGATAGAATTAAGT
1 TAAATTGATAGAATTAAGT
40575839 TAGAATTGA
1 TA-AATTGA
40575848 GAAAAGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (19 bp):
TAAATTGATAGAATTAAGT
Found at i:40576285 original size:5 final size:5
Alignment explanation
Indices: 40576277--40576324 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
40576267 GTATTATGGT
* * *
40576277 ATTGA ATTGA ATTAA ATTAA ATTGA ATTGA GTTGA ATTGA ATTGA ATT
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATT
40576325 ATGAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (5 bp):
ATTGA
Found at i:40576731 original size:22 final size:23
Alignment explanation
Indices: 40576680--40576731 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
40576670 GGTAATTAAA
40576680 TGAAATGACATTATGATTGATAT
1 TGAAATGACATTATGATTGATAT
* *
40576703 TG-GATGATATTAT-ATGTGAT-T
1 TGAAATGACATTATGAT-TGATAT
40576724 TGAAATGA
1 TGAAATGA
40576732 GAAAGTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.21
22 17 0.71
23 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (23 bp):
TGAAATGACATTATGATTGATAT
Found at i:40582872 original size:15 final size:15
Alignment explanation
Indices: 40582854--40582884 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40582844 AATAAAATTG
*
40582854 AAATGAAAATAAAAA
1 AAATAAAAATAAAAA
40582869 AAATAAAAATAAAAA
1 AAATAAAAATAAAAA
40582884 A
1 A
40582885 GATAGGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATAAAAATAAAAA
Found at i:40587008 original size:79 final size:81
Alignment explanation
Indices: 40586871--40587052 Score: 230
Period size: 79 Copynumber: 2.3 Consensus size: 81
40586861 CGAATGATGT
* *
40586871 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
*
40586935 GTGCGAGTTACTA-ATT
66 GTGCGAGTTACTATA-A
* * * **
40586951 TCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCC-GAAGGCATT
40587013 TGTGCGAGTTACTATAA
65 TGTGCGAGTTACTATAA
*
40587030 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
40587053 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 28 0.32
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTATAA
Found at i:40587068 original size:40 final size:40
Alignment explanation
Indices: 40586871--40587054 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
40586861 CGAATGATGT
* * *
40586871 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
40586911 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
* *
40586951 TCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
40586989 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40587030 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40587055 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
39 34 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:40587076 original size:79 final size:79
Alignment explanation
Indices: 40586871--40587077 Score: 228
Period size: 79 Copynumber: 2.6 Consensus size: 79
40586861 CGAATGATGT
* *
40586871 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCATT
*
40586934 TGTGCGAGTTACTAATT
63 TGTGCGAGTTACTAATA
* * *
40586951 TCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAG-TCCTGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGATCC-GAAGGCATT
40587013 TGTGCGAGTTACT-ATAA
63 TGTGCGAGTTACTAAT-A
* **
40587030 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAA
40587078 ATTTCGAAGG
Statistics
Matches: 107, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
78 5 0.05
79 60 0.56
80 42 0.39
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTTGT
GCGAGTTACTAATA
Found at i:40592483 original size:16 final size:15
Alignment explanation
Indices: 40592456--40592496 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
40592446 ATCTTAAAAC
40592456 TTTATTTTTATTTGA
1 TTTATTTTTATTTGA
*
40592471 TTTATTATTTATTTTA
1 TTTATT-TTTATTTGA
40592487 TTTTATTTTT
1 -TTTATTTTT
40592497 TTAAAAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTATTTTTATTTGA
Found at i:40594049 original size:13 final size:13
Alignment explanation
Indices: 40594027--40594057 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40594017 TTTGGGATTG
*
40594027 TTTTTGTTTTGGA
1 TTTTTATTTTGGA
40594040 TTTTTATTTTGGA
1 TTTTTATTTTGGA
40594053 TTTTT
1 TTTTT
40594058 GACATTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.16, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTGGA
Found at i:40599761 original size:19 final size:19
Alignment explanation
Indices: 40599734--40599831 Score: 137
Period size: 19 Copynumber: 5.2 Consensus size: 19
40599724 AATCTTTAAG
* *
40599734 GATACGCAATCTTAGTTAT
1 GATATGCAATCTTAGATAT
*
40599753 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
40599772 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40599789 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40599808 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
40599829 GAT
1 GAT
40599832 CTTGTAATCT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 16 0.23
19 46 0.65
21 9 0.13
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40599780 original size:36 final size:37
Alignment explanation
Indices: 40599734--40599831 Score: 135
Period size: 36 Copynumber: 2.6 Consensus size: 37
40599724 AATCTTTAAG
* *
40599734 GATACGCAATCTTAGTTATGATATGCAATCTTAGATGT
1 GATA-GCAATCTTAGATATGATATGCAATCTTAGATAT
40599772 GATA-CAATCTTAGATATGATATGCAATCTTAGATAT
1 GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
40599808 GATATGCAATCTTGAAGATATGAT
1 GATA-GCAATCTT--AGATATGAT
40599832 CTTGTAATCT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
36 34 0.63
38 11 0.20
40 9 0.17
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (37 bp):
GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:40608003 original size:78 final size:77
Alignment explanation
Indices: 40607906--40608434 Score: 686
Period size: 78 Copynumber: 6.8 Consensus size: 77
40607896 CGAAGAAACA
* * *
40607906 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAAAATTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGAGAGCAGATCGAAGACATAGC-AGATTGACCTTCATTGAA
40607971 GCAGATCCAAGAT
65 GCAGATCCAAGAT
* * *
40607984 GATTTGGCATCTCCATATTCGACGGAGAGTAGATCGAAGACATAGCAGATTTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGAGAGCAGATCGAAGACATAGCAGA-TTGACCTTCATTGAA
40608049 GCAGATCCAAGAT
65 GCAGATCCAAGAT
* * *
40608062 GATTTGGCATCTCTATATTAGACGTG-GAGCAAATAGAAGACACAGCAGATCTGACCTTCATTGA
1 GATTTGGCATCTCTATATTAGACG-GAGAGCAGATCGAAGACATAGCAGAT-TGACCTTCATTGA
40608126 AGCAGATCCAAGAT
64 AGCAGATCCAAGAT
* * * * * *
40608140 GATTTGGCATCTCCATATTCGATGGAGAGCAAATTGAAGACATAGCAGATCTGACCTTTATTGAA
1 GATTTGGCATCTCTATATTAGACGGAGAGCAGATCGAAGACATAGCAGAT-TGACCTTCATTGAA
*
40608205 GCATATCCAAGAT
65 GCAGATCCAAGAT
* * * * * *
40608218 TATTTGGCATCTCTATATTAGACGG-GTAGCAGATCAAAGACACAGTAGATCTAACCTTCATTGT
1 GATTTGGCATCTCTATATTAGACGGAG-AGCAGATCGAAGACATAGCAGAT-TGACCTTCATTGA
40608282 AGCAGATCCAAGAT
64 AGCAGATCCAAGAT
* * *
40608296 GATTTGGCATCTTTGTATTAGAC-GAGGAGCAGATCGAAGACATAACAGATTGGACCTTCATTGA
1 GATTTGGCATCTCTATATTAGACGGA-GAGCAGATCGAAGACATAGCAGATT-GACCTTCATTGA
*
40608360 AGCAGATCCAATAT
64 AGCAGATCCAAGAT
* * *
40608374 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAAATTTGACCTTCAT
1 GATTTGGCATCTCTATATTAGACGGAGAGCAGATCGAAGACATAGCAGA-TTGACCTTCAT
40608435 GTGTTTACAT
Statistics
Matches: 399, Mismatches: 42, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
77 7 0.02
78 387 0.97
79 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (77 bp):
GATTTGGCATCTCTATATTAGACGGAGAGCAGATCGAAGACATAGCAGATTGACCTTCATTGAAG
CAGATCCAAGAT
Found at i:40608568 original size:44 final size:45
Alignment explanation
Indices: 40608374--40608641 Score: 247
Period size: 45 Copynumber: 5.9 Consensus size: 45
40608364 GATCCAATAT
*
40608374 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATAACA
* * * * * ** * * *
40608421 AATTTGACCT-TCATGTGTTTACATC--AAAGCAGATCCAAGATGATA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGATAACA
* * * * *
40608466 GATTTGGCATCTTTATGTTAGACGGGGAGCAAATCGGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* *
40608511 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* *
40608555 GATTTGGCGTCTCTGTATTAGATGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* * * *
40608600 GATTTGACGTCTCTGTATTAGACGGGGAACAGATCAAAGATA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATA
40608642 GTAGATATCG
Statistics
Matches: 174, Mismatches: 40, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
43 1 0.01
44 44 0.25
45 100 0.57
46 3 0.02
47 21 0.12
48 4 0.02
49 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
Found at i:40608576 original size:89 final size:89
Alignment explanation
Indices: 40608465--40608633 Score: 248
Period size: 89 Copynumber: 1.9 Consensus size: 89
40608455 CCAAGATGAT
* * * *
40608465 AGATTTGGCATCTTTATGTTAGACGGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTATT
1 AGATTTGGCATCTCTATATTAGACGGGGAGCAAATCGAAGATAACAGATTTGACATCTCTGTATT
*
40608530 AGACGGGGAGCAGATTGAAGAAGC
66 AGACGGGGAACAGATTGAAGAAGC
* * * * *
40608554 AGATTTGGCGTCTCTGTATTAGATGGGGAGCAGATCGAAGATAACAGATTTGACGTCTCTGTATT
1 AGATTTGGCATCTCTATATTAGACGGGGAGCAAATCGAAGATAACAGATTTGACATCTCTGTATT
40608619 AGACGGGGAACAGAT
66 AGACGGGGAACAGAT
40608634 CAAAGATAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (89 bp):
AGATTTGGCATCTCTATATTAGACGGGGAGCAAATCGAAGATAACAGATTTGACATCTCTGTATT
AGACGGGGAACAGATTGAAGAAGC
Found at i:40608641 original size:134 final size:136
Alignment explanation
Indices: 40608374--40608641 Score: 292
Period size: 134 Copynumber: 2.0 Consensus size: 136
40608364 GATCCAATAT
*
40608374 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAAATTTGACCTTCATGTGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA-ATAGCAAATTTGACCTTCATGTGA
* * * * * * **
40608439 TTACATCAAAGCAGATCCAAGATGATAGATTTGGCATCTTTATGTTAGACGGGGAGCAAATCGGA
65 TTACATCAAAGCAGATCCAAGATAACAGATTTGACATCTCTATATTAGACGGGGAACAAATCAAA
40608504 GATAACA
130 GATAACA
* * * *
40608511 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAG-A-AGCAGATTTGGCGTCTC-TGT-A
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAATAGCAAATTTGACCT-TCATGTGA
* *** * * * *
40608572 TTAGATGGGGAGCAGATCGAAGATAACAGATTTGACGTCTCTGTATTAGACGGGGAACAGATCAA
65 TTACAT-CAAAGCAGATCCAAGATAACAGATTTGACATCTCTATATTAGACGGGGAACAAATCAA
40608637 AGATA
129 AGATA
40608642 GTAGATATCG
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
133 5 0.05
134 62 0.57
135 3 0.03
137 38 0.35
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (136 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAATAGCAAATTTGACCTTCATGTGAT
TACATCAAAGCAGATCCAAGATAACAGATTTGACATCTCTATATTAGACGGGGAACAAATCAAAG
ATAACA
Found at i:40609051 original size:19 final size:19
Alignment explanation
Indices: 40609004--40609063 Score: 88
Period size: 17 Copynumber: 3.2 Consensus size: 19
40608994 AATCATTAAG
40609004 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40609023 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40609040 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
40609061 GAT
1 GAT
40609064 CTTGTAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.46
19 11 0.30
21 9 0.24
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40611618 original size:8 final size:8
Alignment explanation
Indices: 40611595--40611625 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
40611585 CATCAAACTA
40611595 TTTTTCTT
1 TTTTTCTT
40611603 TCTTTTCTT
1 T-TTTTCTT
40611612 TTTTTCTT
1 TTTTTCTT
40611620 TTTTTC
1 TTTTTC
40611626 GAATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:40621606 original size:13 final size:13
Alignment explanation
Indices: 40621577--40621619 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
40621567 TTTGTGATTG
*
40621577 TTTTTGTTTTGGA
1 TTTTTTTTTTGGA
40621590 -TTTTTTTTTGGA
1 TTTTTTTTTTGGA
40621602 TTTTTTTTTTGGA
1 TTTTTTTTTTGGA
40621615 TTTTT
1 TTTTT
40621620 GACATGATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.07, C:0.00, G:0.16, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGGA
Found at i:40621801 original size:26 final size:26
Alignment explanation
Indices: 40621772--40621824 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40621762 TTAAATAAGT
40621772 ATGACAAACACGTTTTAAATAAAGCG
1 ATGACAAACACGTTTTAAATAAAGCG
40621798 ATGACAAACACGTTTTAAATAAAGCG
1 ATGACAAACACGTTTTAAATAAAGCG
40621824 A
1 A
40621825 GCTTTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (26 bp):
ATGACAAACACGTTTTAAATAAAGCG
Found at i:40624368 original size:14 final size:15
Alignment explanation
Indices: 40624333--40624370 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
40624323 TTTACATGTT
40624333 ATAAATTT-TTTATA
1 ATAAATTTATTTATA
*
40624347 ATATATTTATTTATA
1 ATAAATTTATTTATA
40624362 A-AAATTTAT
1 ATAAATTTAT
40624371 GGTCAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAATTTATTTATA
Found at i:40627554 original size:24 final size:23
Alignment explanation
Indices: 40627527--40627616 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 23
40627517 AAGTGAATGG
40627527 TATAAAACAACTTAAAATAATTAA
1 TATAAAACAACTTAAAATAA-TAA
*
40627551 TATACAAAACAATTTAAAAT-A-AA
1 TAT--AAAACAACTTAAAATAATAA
*
40627574 -ATAAAGCAACTTAAAATAAATAA
1 TATAAAACAACTTAAAAT-AATAA
* *
40627597 TATATAACAATTTAAAATAA
1 TATAAAACAACTTAAAATAA
40627617 CATATAGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 13 0.24
22 3 0.06
23 6 0.11
24 17 0.31
25 1 0.02
26 14 0.26
ACGTcount: A:0.63, C:0.08, G:0.01, T:0.28
Consensus pattern (23 bp):
TATAAAACAACTTAAAATAATAA
Found at i:40627584 original size:46 final size:44
Alignment explanation
Indices: 40627528--40627663 Score: 148
Period size: 46 Copynumber: 3.0 Consensus size: 44
40627518 AGTGAATGGT
* *
40627528 ATAAAACAACTTAAAATAATTAATATACAAAACAATTTAAAATAAA
1 ATAAAGCAACTTAAAATAAATAATAT--AAAACAATTTAAAATAAA
* *
40627574 ATAAAGCAACTTAAAATAAATAATATATAACAATTTAAAATAAC
1 ATAAAGCAACTTAAAATAAATAATATAAAACAATTTAAAATAAA
* * * *
40627618 ATATAGAAAGTCTAAAATAAATAATATGTAAAA-AAATTAAAATAAA
1 ATAAAGCAACT-TAAAATAAATAATA--TAAAACAATTTAAAATAAA
40627664 TATTATTAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
44 24 0.31
45 14 0.18
46 35 0.45
47 4 0.05
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (44 bp):
ATAAAGCAACTTAAAATAAATAATATAAAACAATTTAAAATAAA
Found at i:40627658 original size:25 final size:25
Alignment explanation
Indices: 40627630--40627686 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
40627620 ATAGAAAGTC
40627630 TAAAATAAATAATATGTAAAAAAAT-
1 TAAAATAAATAATAT-TAAAAAAATA
* *
40627655 TAAAATAAATATTATTAAAAATATA
1 TAAAATAAATAATATTAAAAAAATA
40627680 TAAAATA
1 TAAAATA
40627687 GTTTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAAATAAATAATATTAAAAAAATA
Found at i:40627789 original size:27 final size:28
Alignment explanation
Indices: 40627759--40627835 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
40627749 TAAAAATTTA
40627759 AAATA-GATAAAATAGTTTAAAATAAAT
1 AAATATGATAAAATAGTTTAAAATAAAT
40627786 AAATATG-TAAAAATA-TTTAAAATAAAT
1 AAATATGAT-AAAATAGTTTAAAATAAAT
* *
40627813 AATATATAATAAAAAAGTTTAAA
1 AA-ATATGATAAAATAGTTTAAA
40627836 GTATAGGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 20 0.47
28 16 0.37
29 7 0.16
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (28 bp):
AAATATGATAAAATAGTTTAAAATAAAT
Found at i:40627799 original size:28 final size:30
Alignment explanation
Indices: 40627767--40627835 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 30
40627757 TAAAATAGAT
*
40627767 AAAATAGTTTAAAATAAATAA-ATAT-GTA
1 AAAATAGTTTAAAATAAATAATATATAATA
40627795 AAAATA-TTTAAAATAAATAATATATAATA
1 AAAATAGTTTAAAATAAATAATATATAATA
40627824 AAAA-AGTTTAAA
1 AAAATAGTTTAAA
40627836 GTATAGGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 14 0.38
28 11 0.30
29 12 0.32
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATAGTTTAAAATAAATAATATATAATA
Found at i:40629445 original size:46 final size:46
Alignment explanation
Indices: 40629393--40629512 Score: 131
Period size: 46 Copynumber: 2.7 Consensus size: 46
40629383 GTAATTTCAA
* * *
40629393 CCTGCTCCACTACAACTTCAGAGAGATAAGGT-TTGTGTATCTT-TAT
1 CCTGCTCCACTGCAACTTCAGAGAGATAAGGTATTATG-A-CTTCGAT
* * *
40629439 CCTGCTCTACCGCAACTTCAAAGAGATAA-GTATTATGACTTCGAT
1 CCTGCTCCACTGCAACTTCAGAGAGATAAGGTATTATGACTTCGAT
*
40629484 -CTGCTCCACTGCAACTTCAGGGAGATAAG
1 CCTGCTCCACTGCAACTTCAGAGAGATAAG
40629513 ACTTCTGCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 27 0.44
45 5 0.08
46 29 0.48
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (46 bp):
CCTGCTCCACTGCAACTTCAGAGAGATAAGGTATTATGACTTCGAT
Found at i:40629509 original size:44 final size:42
Alignment explanation
Indices: 40629394--40629914 Score: 225
Period size: 44 Copynumber: 11.8 Consensus size: 42
40629384 TAATTTCAAC
* * * * *
40629394 CTGCTCCACTACAACTTCAGAGAGATAAGGTTTGTGTATCTTTAT
1 CTGCTCCACTGCAACTTCAGGGAGATAA-GATTATG-A-CTTAAT
* * ** *
40629439 CCTGCTCTACCGCAACTTCAAAGAGATAAGTATTATGACTTCGAT
1 -CTGCTCCACTGCAACTTCAGGGAGATAAG-ATTATGACTT-AAT
40629484 CTGCTCCACTGCAACTTCAGGGAGAT---A--A-GAC-T--T
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTATGACTTAAT
* * * *
40629517 CTGCTCCACTACAACTTCAAGGAGATAAGACT-TGCTACTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTATG--ACTT-AAT
** * * ** *
40629561 CTGCTCCACTATAACTTCAGGGAGATAAGGTTTGTGTTTTTTTAT
1 CTGCTCCACTGCAACTTCAGGGAGATAA-GATTATG--ACTTAAT
** * ** *
40629606 CCTGCTTTACTGCAACTTCAGAGAGATAAGGATTATGGTTTTGAT
1 -CTGCTCCACTGCAACTTCAGGGAGATAA-GATTAT-GACTTAAT
* * *
40629651 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTGGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATGACTT-AAT
* * *
40629695 CTACTCCACTACAACTTCAGGAAGATAAGATTCACCATGATTTGTAGCTTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-T-----T-A--TG-A-C-TTAAT
* * * *
40629749 CTGTTCCACTGCAACTTCAGGGAAATAAGATTCACTGTCTTTAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATT-A-TGAC-TTAAT
* * * *
40629794 CTGCTCCGCTGCAACTTCAGGGAAATAAGATTCACTGTCTTTAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATT-A-TGAC-TTAAT
** * *
40629839 CTGCTCCGTTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATGACTT-AAT
*
40629883 CTACTCCACTGCAACTTCAGGGAGATAAGATT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATT
40629915 CGCCATGATG
Statistics
Matches: 377, Mismatches: 65, Indels: 69
0.74 0.13 0.14
Matches are distributed among these distances:
33 25 0.07
36 2 0.01
37 3 0.01
38 2 0.01
40 3 0.01
41 1 0.00
43 9 0.02
44 139 0.37
45 90 0.24
46 63 0.17
47 3 0.01
48 2 0.01
49 1 0.00
52 2 0.01
53 1 0.00
54 29 0.08
55 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (42 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTATGACTTAAT
Found at i:40629521 original size:33 final size:33
Alignment explanation
Indices: 40629483--40629549 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
40629473 ATGACTTCGA
* *
40629483 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTACAACTTCAAGGAGATAAGACT
40629516 TCTGCTCCACTACAACTTCAAGGAGATAAGACT
1 TCTGCTCCACTACAACTTCAAGGAGATAAGACT
40629549 T
1 T
40629550 GCTACTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (33 bp):
TCTGCTCCACTACAACTTCAAGGAGATAAGACT
Found at i:40629664 original size:167 final size:168
Alignment explanation
Indices: 40629361--40629683 Score: 495
Period size: 167 Copynumber: 1.9 Consensus size: 168
40629351 ACTCCGCTGG
* * *
40629361 AACTTCAAGGAGGTAAGAATTGGTAATTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
1 AACTTCAAGGAGATAAGAATTGCTAACTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
*
40629426 TGTGTATCTTTATCCTGCTCTACCGCAACTTCAAAGAGATAAGTATTATGACTTCGATCTGCTCC
66 TGTGTATCTTTATCCTGCTCTACCGCAACTTCAAAGAGATAAGGATTATGACTTCGATCTGCTCC
40629491 ACTGCAACTTCAGGGAGATAAGACTTCTGCTCCACTAC
131 ACTGCAACTTCAGGGAGATAAGACTTCTGCTCCACTAC
* * *
40629529 AACTTCAAGGAGATAAGACTTGCT-ACTTCAACCTGCTCCACTATAACTTCAGGGAGATAAGGTT
1 AACTTCAAGGAGATAAGAATTGCTAACTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
* * * * * ** *
40629593 TGTGTTTTTTTATCCTGCTTTACTGCAACTTCAGAGAGATAAGGATTATGGTTTTGATCTGCTCC
66 TGTGTATCTTTATCCTGCTCTACCGCAACTTCAAAGAGATAAGGATTATGACTTCGATCTGCTCC
*
40629658 ACTGCAACTTTAGGGAGATAAGACTT
131 ACTGCAACTTCAGGGAGATAAGACTT
40629684 GTGGCTTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
167 118 0.85
168 21 0.15
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (168 bp):
AACTTCAAGGAGATAAGAATTGCTAACTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
TGTGTATCTTTATCCTGCTCTACCGCAACTTCAAAGAGATAAGGATTATGACTTCGATCTGCTCC
ACTGCAACTTCAGGGAGATAAGACTTCTGCTCCACTAC
Found at i:40629808 original size:45 final size:45
Alignment explanation
Indices: 40629742--40629915 Score: 224
Period size: 45 Copynumber: 3.9 Consensus size: 45
40629732 TGATTTGTAG
*
40629742 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCACTGT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTGT
* *
40629787 CTTTAGTCTGCTCCGCTGCAACTTCAGGGAAATAAGATTCACTGT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTGT
* ** * ** *
40629832 CTTTAGTCTGCTCCGTTGCAACTTCAGGGAGATAAGATT-TGTGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTGT
* * *
40629876 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC
40629916 GCCATGATGA
Statistics
Matches: 115, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 36 0.31
45 79 0.69
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTGT
Found at i:40630368 original size:46 final size:46
Alignment explanation
Indices: 40630312--40630411 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
40630302 ATTTGTGGTT
* *
40630312 TCTTCTATCCACCCCATTGCAACTCAAT-GGTATAGGATGTGTATCA
1 TCTTCAATCCACCCCACTGCAACT-AATGGGTATAGGATGTGTATCA
* * * *
40630358 TCTTCAATCCATCCCACTGCAACTTATGGGTATAGGATTTGTATCT
1 TCTTCAATCCACCCCACTGCAACTAATGGGTATAGGATGTGTATCA
40630404 TCTTCAAT
1 TCTTCAAT
40630412 TCATACCACT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.04
46 45 0.96
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (46 bp):
TCTTCAATCCACCCCACTGCAACTAATGGGTATAGGATGTGTATCA
Found at i:40630435 original size:46 final size:46
Alignment explanation
Indices: 40630329--40630440 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
40630319 TCCACCCCAT
** *
40630329 TGCAACTCAATGGTATAGGATGTGTATCATCTTCAATCCATCCCAC
1 TGCAACTCAGGGGTATAGGATGTGTATCATCTTCAATCCATACCAC
* * * * *
40630375 TGCAACTTATGGGTATAGGATTTGTATCTTCTTCAATTCATACCAC
1 TGCAACTCAGGGGTATAGGATGTGTATCATCTTCAATCCATACCAC
* * *
40630421 TGTAGCTCAGGGGTACAGGA
1 TGCAACTCAGGGGTATAGGA
40630441 CATATGACTT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (46 bp):
TGCAACTCAGGGGTATAGGATGTGTATCATCTTCAATCCATACCAC
Found at i:40630825 original size:39 final size:39
Alignment explanation
Indices: 40630771--40630849 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
40630761 TGAAAGTTTT
40630771 ATTAGTCCATTAATCATTATTTCAATGCAAAATCTTGAA
1 ATTAGTCCATTAATCATTATTTCAATGCAAAATCTTGAA
40630810 ATTAGTCCATTAATCATTATTTCAATGCAAAATCTTGAA
1 ATTAGTCCATTAATCATTATTTCAATGCAAAATCTTGAA
40630849 A
1 A
40630850 AAGATCATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (39 bp):
ATTAGTCCATTAATCATTATTTCAATGCAAAATCTTGAA
Found at i:40630959 original size:53 final size:53
Alignment explanation
Indices: 40630894--40631050 Score: 269
Period size: 53 Copynumber: 3.0 Consensus size: 53
40630884 AAGAGCATAG
* *
40630894 CTTGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAGGAAATTAA
1 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
40630947 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
1 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
* * *
40631000 CTCGAAATGAGTAAGTTAATCAAAGATAGCAAATGTAATAAAAAGGAAATT
1 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATT
40631051 GGTTGGGAGC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 99 1.00
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.24
Consensus pattern (53 bp):
CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
Found at i:40630988 original size:27 final size:26
Alignment explanation
Indices: 40630898--40631040 Score: 73
Period size: 26 Copynumber: 5.4 Consensus size: 26
40630888 GCATAGCTTG
*
40630898 AAATGAATAAATTAATCAAAGATAGC
1 AAATGAATAAGTTAATCAAAGATAGC
** * *
40630924 AAATGCAATAAG--AAGGAAA-TTAAC
1 AAATG-AATAAGTTAATCAAAGATAGC
40630948 TTGAAATGAATAAGTTAATCAAAGATAGC
1 ---AAATGAATAAGTTAATCAAAGATAGC
** * *
40630977 AAATGTAATAAG--AAGGAAA-TTAACTC
1 AAATG-AATAAGTTAATCAAAGAT-A-GC
*
40631003 GAAATGAGTAAGTTAATCAAAGATAGC
1 -AAATGAATAAGTTAATCAAAGATAGC
40631030 AAATGTAATAA
1 AAATG-AATAA
40631041 AAAGGAAATT
Statistics
Matches: 83, Mismatches: 19, Indels: 29
0.63 0.15 0.22
Matches are distributed among these distances:
24 4 0.05
25 11 0.13
26 27 0.33
27 26 0.31
28 11 0.13
29 4 0.05
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (26 bp):
AAATGAATAAGTTAATCAAAGATAGC
Found at i:40634556 original size:13 final size:13
Alignment explanation
Indices: 40634521--40634582 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
40634511 AATATATTAA
40634521 AACCCAACTACCC
1 AACCCAACTACCC
40634534 AACTACCCAACTACCC
1 -A--ACCCAACTACCC
*
40634550 AACCCAATTACCC
1 AACCCAACTACCC
* * *
40634563 AACCTAATTTCCC
1 AACCCAACTACCC
40634576 AACCCAA
1 AACCCAA
40634583 TAATTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
13 28 0.67
14 1 0.02
15 1 0.02
16 12 0.29
ACGTcount: A:0.39, C:0.47, G:0.00, T:0.15
Consensus pattern (13 bp):
AACCCAACTACCC
Found at i:40634564 original size:8 final size:8
Alignment explanation
Indices: 40634522--40634552 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
40634512 ATATATTAAA
40634522 ACCCAACT
1 ACCCAACT
40634530 ACCCAACT
1 ACCCAACT
40634538 ACCCAACT
1 ACCCAACT
40634546 ACCCAAC
1 ACCCAAC
40634553 CCAATTACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.52, G:0.00, T:0.10
Consensus pattern (8 bp):
ACCCAACT
Found at i:40640986 original size:17 final size:17
Alignment explanation
Indices: 40640966--40641063 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
40640956 ATTTCAAGAC
40640966 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
40640983 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
40641002 CTTATGTAATGTTTTTTA
1 -TTATGTAATGTTTTTAA
* ***
40641020 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
40641039 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
40641057 TTATGTA
1 TTATGTA
40641064 GTGATTTAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 12
0.66 0.21 0.14
Matches are distributed among these distances:
17 25 0.44
18 7 0.12
19 7 0.12
20 18 0.32
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:40641002 original size:37 final size:37
Alignment explanation
Indices: 40640961--40641069 Score: 209
Period size: 37 Copynumber: 2.9 Consensus size: 37
40640951 TGTTAATTTC
40640961 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
*
40640998 AAGACTTATGTAATGTTTTTTATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
40641035 AAGACTTATGTAATGTTTTTAATTATGTAGTGATT
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATT
40641070 TAATTCAGTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:40641008 original size:20 final size:20
Alignment explanation
Indices: 40640983--40641046 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
40640973 ATGTTTTTAA
40640983 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
* ****
40641003 TTATGTAATG-TT-TTTTA-
1 TTATGTAGTGATTCAAAGAC
40641020 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
40641040 TTATGTA
1 TTATGTA
40641047 ATGTTTTTAA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
17 9 0.29
18 3 0.10
19 3 0.10
20 16 0.52
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.45
Consensus pattern (20 bp):
TTATGTAGTGATTCAAAGAC
Found at i:40641083 original size:9 final size:9
Alignment explanation
Indices: 40641069--40641119 Score: 75
Period size: 9 Copynumber: 5.7 Consensus size: 9
40641059 ATGTAGTGAT
*
40641069 TTAATTCAG
1 TTAATTCGG
40641078 TTAATTCGG
1 TTAATTCGG
**
40641087 TTAATTCAA
1 TTAATTCGG
40641096 TTAATTCGG
1 TTAATTCGG
40641105 TTAATTCGG
1 TTAATTCGG
40641114 TTAATT
1 TTAATT
40641120 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (9 bp):
TTAATTCGG
Found at i:40641092 original size:18 final size:18
Alignment explanation
Indices: 40641069--40641119 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
40641059 ATGTAGTGAT
40641069 TTAATTCAGTTAATTCGG
1 TTAATTCAGTTAATTCGG
*
40641087 TTAATTCAATTAATTCGG
1 TTAATTCAGTTAATTCGG
*
40641105 TTAATTCGGTTAATT
1 TTAATTCAGTTAATT
40641120 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (18 bp):
TTAATTCAGTTAATTCGG
Found at i:40642796 original size:25 final size:26
Alignment explanation
Indices: 40642759--40642811 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
40642749 TCAAACATGC
40642759 ATTTAGGTCAATTTAACC-CTAGGGGT
1 ATTTAGGTCAATTT-ACCACTAGGGGT
*
40642785 ATTTCGGT-AATTTACCTACTAGGGGT
1 ATTTAGGTCAATTTACC-ACTAGGGGT
40642811 A
1 A
40642812 AAATTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 5 0.21
26 16 0.67
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (26 bp):
ATTTAGGTCAATTTACCACTAGGGGT
Found at i:40644333 original size:26 final size:26
Alignment explanation
Indices: 40644297--40644352 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40644287 TGAAATTCCA
40644297 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40644323 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40644349 ATCA
1 ATCA
40644353 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40649842 original size:25 final size:26
Alignment explanation
Indices: 40649805--40649857 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
40649795 TCAAACATGC
40649805 ATTTAGGTCAATTTAATCT-TAGGGGT
1 ATTTAGGTCAATTT-ATCTATAGGGGT
*
40649831 ATTTCGGT-AATTTATCTACTAGGGGT
1 ATTTAGGTCAATTTATCTA-TAGGGGT
40649857 A
1 A
40649858 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.17
25 5 0.21
26 15 0.62
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (26 bp):
ATTTAGGTCAATTTATCTATAGGGGT
Found at i:40651379 original size:26 final size:26
Alignment explanation
Indices: 40651343--40651398 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40651333 TGAAATTCCA
40651343 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40651369 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40651395 ATCA
1 ATCA
40651399 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40652006 original size:19 final size:20
Alignment explanation
Indices: 40651982--40652026 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
40651972 TTGTGACATT
*
40651982 CAATGCATATG-ATGAAATG
1 CAATGCAGATGCATGAAATG
40652001 CAATGCAGATGCATGAAATG
1 CAATGCAGATGCATGAAATG
40652021 -AATGCA
1 CAATGCA
40652027 AAAAGAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (20 bp):
CAATGCAGATGCATGAAATG
Found at i:40654002 original size:24 final size:23
Alignment explanation
Indices: 40653975--40654064 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 23
40653965 ATGTGAATGG
40653975 TATAAAACAACTTAAAATAATTAA
1 TATAAAACAACTTAAAATAA-TAA
*
40653999 TATACAAAACAATTTAAAAT-A-AA
1 TAT--AAAACAACTTAAAATAATAA
*
40654022 -ATAAAGCAACTTAAAATAAATAA
1 TATAAAACAACTTAAAAT-AATAA
* *
40654045 TATATAACAATTTAAAATAA
1 TATAAAACAACTTAAAATAA
40654065 CATATAGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 13 0.24
22 3 0.06
23 6 0.11
24 17 0.31
25 1 0.02
26 14 0.26
ACGTcount: A:0.63, C:0.08, G:0.01, T:0.28
Consensus pattern (23 bp):
TATAAAACAACTTAAAATAATAA
Found at i:40654032 original size:46 final size:44
Alignment explanation
Indices: 40653976--40654064 Score: 133
Period size: 46 Copynumber: 2.0 Consensus size: 44
40653966 TGTGAATGGT
*
40653976 ATAAAACAACTTAAAATAATTAATATACAAAACAATTTAAAATAAA
1 ATAAAACAACTTAAAATAAATAATAT--AAAACAATTTAAAATAAA
* *
40654022 ATAAAGCAACTTAAAATAAATAATATATAACAATTTAAAATAA
1 ATAAAACAACTTAAAATAAATAATATAAAACAATTTAAAATAA
40654065 CATATAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 16 0.40
46 24 0.60
ACGTcount: A:0.64, C:0.08, G:0.01, T:0.27
Consensus pattern (44 bp):
ATAAAACAACTTAAAATAAATAATATAAAACAATTTAAAATAAA
Found at i:40654101 original size:28 final size:28
Alignment explanation
Indices: 40654070--40654126 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
40654060 AATAACATAT
* *
40654070 AGAAAGTCTAACATAAATAATATGTAAA
1 AGAAAATCTAAAATAAATAATATGTAAA
* *
40654098 AGAAAATTTAAAATAAATAATATTTAAA
1 AGAAAATCTAAAATAAATAATATGTAAA
40654126 A
1 A
40654127 ATATAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (28 bp):
AGAAAATCTAAAATAAATAATATGTAAA
Found at i:40654127 original size:24 final size:24
Alignment explanation
Indices: 40654032--40654134 Score: 61
Period size: 24 Copynumber: 4.2 Consensus size: 24
40654022 ATAAAGCAAC
* *
40654032 TTAAAATAAATAATATATAACAAT
1 TTAAAATAAATAATATTTAAAAAT
* *
40654056 TTAAAATAACAT-ATA---GAAAGT
1 TTAAAATAA-ATAATATTTAAAAAT
* * *
40654077 CTAACATAAATAATATGTAAAAGAAAAT
1 TTAAAATAAATAATAT-T--TA-AAAAT
40654105 TTAAAATAAATAATATTTAAAAAT
1 TTAAAATAAATAATATTTAAAAAT
*
40654129 ATAAAA
1 TTAAAA
40654135 CAGTTTAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
20 2 0.03
21 13 0.22
24 22 0.37
25 3 0.05
27 1 0.02
28 18 0.31
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
TTAAAATAAATAATATTTAAAAAT
Found at i:40659067 original size:48 final size:47
Alignment explanation
Indices: 40658967--40659094 Score: 154
Period size: 48 Copynumber: 2.7 Consensus size: 47
40658957 GTAAATTGCC
* * *
40658967 GATGCCATGTCCCAGACATGGTCTTACACCAGCTCTCGTCTCAATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCG-ATCAATGCG
*
40659015 GATGCCATGTCCCAGACATGGTCTTACATTAGCTCTC-AT-AATGTGGCG
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGATCAA--T-GCG
*
40659063 GATG-CATGTCCCAAACATGGTCTTACACTAGC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC
40659095 ACAGATATCA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
45 2 0.03
46 1 0.01
47 27 0.38
48 41 0.58
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGATCAATGCG
Found at i:40660747 original size:16 final size:17
Alignment explanation
Indices: 40660722--40660756 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40660712 TAGATCTTAG
*
40660722 ATTCATTTATGA-ATTC
1 ATTCACTTATGACATTC
40660738 ATTCACTTATGACATTC
1 ATTCACTTATGACATTC
40660755 AT
1 AT
40660757 AGTGTGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTCACTTATGACATTC
Found at i:40668117 original size:22 final size:22
Alignment explanation
Indices: 40668089--40668247 Score: 122
Period size: 22 Copynumber: 7.0 Consensus size: 22
40668079 TCTCTAATAT
*
40668089 TTAGCACGTCAGTGCTCTCTGA
1 TTAGCACATCAGTGCTCTCTGA
**
40668111 TTAGCACATTTGTGCTCTCTGATA
1 TTAGCACATCAGTGCTCTCTG--A
* * *
40668135 TTTAGCACGTCAGAGCTCTATGA
1 -TTAGCACATCAGTGCTCTCTGA
** * *
40668158 TTAGCACATTTGTGATCTCTAATA
1 TTAGCACATCAGTGCTCTCT--GA
*
40668182 TTTAGCACGTCAGTGCTCTCTGA
1 -TTAGCACATCAGTGCTCTCTGA
**
40668205 TTAGCACATTTGTGCTCTCTG-
1 TTAGCACATCAGTGCTCTCTGA
*
40668226 TATAGCACTTCAGTGCTCTCTG
1 T-TAGCACATCAGTGCTCTCTG
40668248 TTCATTAGTG
Statistics
Matches: 104, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
21 1 0.01
22 67 0.64
23 2 0.02
24 2 0.02
25 32 0.31
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (22 bp):
TTAGCACATCAGTGCTCTCTGA
Found at i:40668145 original size:47 final size:47
Alignment explanation
Indices: 40668076--40668247 Score: 269
Period size: 47 Copynumber: 3.7 Consensus size: 47
40668066 GACTTCAGCA
40668076 TGCTCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
1 TGCTCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* * *
40668123 TGCTCTCTGATATTTAGCACGTCAGAGCTCTATGATTAGCACATTTG
1 TGCTCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
*
40668170 TGATCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
1 TGCTCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* *
40668217 TGCTCTCT-GTA--TAGCACTTCAGTGCTCTCTG
1 TGCTCTCTAATATTTAGCACGTCAGTGCTCTCTG
40668248 TTCATTAGTG
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 19 0.17
46 2 0.02
47 94 0.82
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (47 bp):
TGCTCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
Found at i:40670798 original size:13 final size:13
Alignment explanation
Indices: 40670780--40670806 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40670770 AGCAGGGGAG
40670780 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
40670793 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
40670806 G
1 G
40670807 GGAGAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAGAAA
Found at i:40675815 original size:3 final size:3
Alignment explanation
Indices: 40675802--40675831 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
40675792 GTAAAATATA
40675802 ATT ACTT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT
40675832 GTTGTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:40690943 original size:16 final size:16
Alignment explanation
Indices: 40690922--40690953 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40690912 GTCCCCTGAT
40690922 GCTTCTTTTGAAACCA
1 GCTTCTTTTGAAACCA
40690938 GCTTCTTTTGAAACCA
1 GCTTCTTTTGAAACCA
40690954 AGTCAGTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
GCTTCTTTTGAAACCA
Found at i:40694029 original size:17 final size:17
Alignment explanation
Indices: 40694004--40694048 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
40693994 ATGACCCAGA
*
40694004 TCGAAATTGACATGAAC
1 TCGAAATTGACACGAAC
*
40694021 TCTAAATTGACACGAAC
1 TCGAAATTGACACGAAC
40694038 TCGAAATTGAC
1 TCGAAATTGAC
40694049 TTAAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (17 bp):
TCGAAATTGACACGAAC
Found at i:40695369 original size:21 final size:21
Alignment explanation
Indices: 40695327--40695369 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40695317 TAAGTTGTAC
* *
40695327 AAGACAAATTTAGATAAGTAT
1 AAGACAAATTTAGAAAAATAT
40695348 AAGACAAATTTA-AAACAATAT
1 AAGACAAATTTAGAAA-AATAT
40695369 A
1 A
40695370 GATAAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (21 bp):
AAGACAAATTTAGAAAAATAT
Found at i:40695481 original size:26 final size:26
Alignment explanation
Indices: 40695428--40695490 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
40695418 AAAAGAAATC
* * *
40695428 TAAAGTAAATAATATATATGAAATTT
1 TAAAGTAAATAACATATATAAAAGTT
40695454 TAAAGTAAATAACATATA-AAACAGTT
1 TAAAGTAAATAACATATATAAA-AGTT
*
40695480 TAAATTAAATA
1 TAAAGTAAATA
40695491 TTATACGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (26 bp):
TAAAGTAAATAACATATATAAAAGTT
Found at i:40700225 original size:26 final size:26
Alignment explanation
Indices: 40700189--40700296 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
40700179 CATGAAATTC
40700189 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
40700215 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
40700241 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
40700267 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
40700293 TTAT
1 TTAT
40700297 TAATTTGTAT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:40704511 original size:26 final size:26
Alignment explanation
Indices: 40704465--40704517 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
40704455 TCAAACATGC
*
40704465 ATTTAGGTCAATTTAACCCTATGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* *
40704491 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAAC-CCTAGGGGT
40704517 A
1 A
40704518 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:40706043 original size:26 final size:26
Alignment explanation
Indices: 40706002--40706083 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
40705992 CATGAAATTC
* * *
40706002 TTATCATGAAATATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
40706028 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
40706054 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
40706080 TTAT
1 TTAT
40706084 TAATTTGTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:40711802 original size:21 final size:23
Alignment explanation
Indices: 40711766--40711813 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
40711756 TTTATTTCAA
*
40711766 AAATATTTTTATAAAAATATAT-
1 AAATATTTTCATAAAAATATATC
40711788 AAATA-TTTCATAAAAATATATC
1 AAATATTTTCATAAAAATATATC
40711810 AAAT
1 AAAT
40711814 TTAAAAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATTTTCATAAAAATATATC
Found at i:40711916 original size:98 final size:98
Alignment explanation
Indices: 40711802--40712009 Score: 357
Period size: 98 Copynumber: 2.1 Consensus size: 98
40711792 ATTTCATAAA
*
40711802 AATATATCAAATTTAAAAAGCAAAAAAATATATAAAAAGTTAAAAATT-TGAAATTCACAG-ATA
1 AATATAT-ATATTTAAAAAGCAAAAAAATATATAAAAAGTT-AAAATTGTGAAATTCAC-GTATA
40711865 CCCTTAAATATAATTAAAGAGAATGATAGGATTTAT
63 CCCTTAAATATAATTAAAGAGAATGATAGGATTTAT
*
40711901 AATATATATATTTAAAAAGCAAAAATATATATAAAAAGTTAAAATTGTGAAATTCACGTATACCC
1 AATATATATATTTAAAAAGCAAAAAAATATATAAAAAGTTAAAATTGTGAAATTCACGTATACCC
40711966 TTAAATATAATTAAAGAGAATGATAGGATTTAT
66 TTAAATATAATTAAAGAGAATGATAGGATTTAT
40711999 AATATATATAT
1 AATATATATAT
40712010 ATATATATCA
Statistics
Matches: 105, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
97 7 0.07
98 91 0.87
99 7 0.07
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (98 bp):
AATATATATATTTAAAAAGCAAAAAAATATATAAAAAGTTAAAATTGTGAAATTCACGTATACCC
TTAAATATAATTAAAGAGAATGATAGGATTTAT
Found at i:40716451 original size:17 final size:18
Alignment explanation
Indices: 40716425--40716465 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
40716415 TTTATTGTTT
40716425 AGTAACAATCAGTCA-TC
1 AGTAACAATCAGTCATTC
* *
40716442 AGTAATAATCAGTTATTC
1 AGTAACAATCAGTCATTC
40716460 AGTAAC
1 AGTAAC
40716466 GGTCGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (18 bp):
AGTAACAATCAGTCATTC
Found at i:40716463 original size:18 final size:18
Alignment explanation
Indices: 40716425--40716518 Score: 68
Period size: 18 Copynumber: 5.3 Consensus size: 18
40716415 TTTATTGTTT
* *
40716425 AGTAACAATCAGTCA-TC
1 AGTAATAATCAGTTATTC
40716442 AGTAATAATCAGTTATTC
1 AGTAATAATCAGTTATTC
***
40716460 AGTAACGGTC-GTTTATTC
1 AGTAATAATCAG-TTATTC
* *
40716478 AAT-ATCAATCAATTATTC
1 AGTAAT-AATCAGTTATTC
* *
40716496 AGTAGTAGTCAGTTATTC
1 AGTAATAATCAGTTATTC
40716514 AGTAA
1 AGTAA
40716519 CAGTTATTGA
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
17 15 0.26
18 41 0.72
19 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (18 bp):
AGTAATAATCAGTTATTC
Found at i:40717508 original size:16 final size:16
Alignment explanation
Indices: 40717474--40717517 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
40717464 TTCTGTTTCG
*
40717474 TTTCATTCTATTCTCTT
1 TTTCTTTCT-TTCTCTT
*
40717491 TTTCTTTCTTTCTTTT
1 TTTCTTTCTTTCTCTT
*
40717507 TTTATTTCTTT
1 TTTCTTTCTTT
40717518 TACTTTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCTTTCTTTCTCTT
Found at i:40730892 original size:27 final size:27
Alignment explanation
Indices: 40730856--40730910 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40730846 GATTATAATA
40730856 ATATTAATAAACTAAATAAATTGAAAT
1 ATATTAATAAACTAAATAAATTGAAAT
40730883 ATATTAATAAACTAAATAAATTGAAAT
1 ATATTAATAAACTAAATAAATTGAAAT
40730910 A
1 A
40730911 AACTTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (27 bp):
ATATTAATAAACTAAATAAATTGAAAT
Found at i:40730911 original size:10 final size:9
Alignment explanation
Indices: 40730847--40730919 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
40730837 TGGAAGGAAG
40730847 ATTATAATAA
1 ATTA-AATAA
40730857 TATT-AATAA
1 -ATTAAATAA
*
40730866 ACTAAATAA
1 ATTAAATAA
*
40730875 ATTGAAATAT
1 ATT-AAATAA
40730885 ATT-AATAA
1 ATTAAATAA
*
40730893 ACTAAATAA
1 ATTAAATAA
40730902 ATTGAAATAA
1 ATT-AAATAA
40730912 ACTTAAAT
1 A-TTAAAT
40730920 CTACTCCTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 8 0.16
9 19 0.37
10 19 0.37
11 5 0.10
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (9 bp):
ATTAAATAA
Found at i:40732490 original size:16 final size:16
Alignment explanation
Indices: 40732469--40732504 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
40732459 ACAAATTGAA
40732469 ATTTTATTTTT-ATTTT
1 ATTTTATTTTTCA-TTT
40732485 ATTTTATTTTTCATTT
1 ATTTTATTTTTCATTT
40732501 ATTT
1 ATTT
40732505 GAAAATCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTATTTTTCATTT
Found at i:40732687 original size:43 final size:41
Alignment explanation
Indices: 40732628--40732713 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 41
40732618 ATTAGCAATG
**
40732628 AAAATATCACAATTTTA-CTTTAAATGAATATTATTAACAATAA
1 AAAATATCACAATTTTAGAATT-AA--AATATTATTAACAATAA
40732671 AAAATATCA-AATTTTTAGAATTAAAATATTATTAACAATAA
1 AAAATATCACAA-TTTTAGAATTAAAATATTATTAACAATAA
40732712 AA
1 AA
40732714 TATTTATAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 19 0.49
42 2 0.05
43 16 0.41
44 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (41 bp):
AAAATATCACAATTTTAGAATTAAAATATTATTAACAATAA
Found at i:40735542 original size:19 final size:19
Alignment explanation
Indices: 40735518--40735575 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 19
40735508 ACTTATAAAT
40735518 TTATTTATTTAAAATTTTA
1 TTATTTATTTAAAATTTTA
*
40735537 TTATTTATTTAATATATATTA
1 TTATTTATTTAA-A-ATTTTA
40735558 TTATTTTATATTAAAATT
1 TTA-TTTAT-TTAAAATT
40735576 GTATGTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 12 0.36
20 1 0.03
21 10 0.30
22 6 0.18
23 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTATTTAAAATTTTA
Found at i:40738680 original size:22 final size:20
Alignment explanation
Indices: 40738642--40738693 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
40738632 TATTAACATT
40738642 ATATTATGTATATTTTTTAA
1 ATATTATGTATATTTTTTAA
40738662 ATATTATGTATGTATTTTTT--
1 ATATTATGTA--TATTTTTTAA
40738682 -TATTATGTATAT
1 ATATTATGTATAT
40738694 ATATTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
19 9 0.30
20 10 0.33
22 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
ATATTATGTATATTTTTTAA
Found at i:40740530 original size:28 final size:29
Alignment explanation
Indices: 40740497--40740597 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
40740487 TATAGTAAGT
* *
40740497 CCGCACACTTAGTGTTATACAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
40740525 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
40740554 CCGCACACTTAGTGCTATACAATTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
40740583 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
40740598 CAATTTCATG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
28 20 0.30
29 47 0.70
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTTGAAC
Found at i:40742249 original size:23 final size:23
Alignment explanation
Indices: 40742223--40742267 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40742213 TTACTATCAT
40742223 GTTTAATACCATATGTTA-TTATC
1 GTTTAATACCAT-TGTTACTTATC
* *
40742246 GTTTTATACTATTGTTACTTAT
1 GTTTAATACCATTGTTACTTAT
40742268 ATTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (23 bp):
GTTTAATACCATTGTTACTTATC
Found at i:40752651 original size:20 final size:22
Alignment explanation
Indices: 40752609--40752654 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
40752599 TTACACCAAA
*
40752609 CCCAAAACCTATTTACTTACCT
1 CCCAAAACCTATTTACTCACCT
*
40752631 CCCAAAA-CT-TTTACTCCCCT
1 CCCAAAACCTATTTACTCACCT
40752651 CCCA
1 CCCA
40752655 TCCCACCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.28, C:0.43, G:0.00, T:0.28
Consensus pattern (22 bp):
CCCAAAACCTATTTACTCACCT
Found at i:40758879 original size:24 final size:25
Alignment explanation
Indices: 40758843--40758914 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
40758833 AAATAAAAAT
*
40758843 TTTAACATAAATAATATATAAAAGG
1 TTTAAAATAAATAATATATAAAAGG
*
40758868 TTTAAAAT-AATAATATATGAAACGG
1 TTTAAAATAAATAATATAT-AAAAGG
* * *
40758893 TTCAGAATAAACAATATATAAA
1 TTTAAAATAAATAATATATAAA
40758915 TTTTTAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 10 0.25
25 21 0.52
26 9 0.22
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAGG
Found at i:40759242 original size:11 final size:11
Alignment explanation
Indices: 40759228--40759254 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40759218 TTTTGCTACC
40759228 ATTTTACTATT
1 ATTTTACTATT
40759239 ATTTTACTATT
1 ATTTTACTATT
40759250 ATTTT
1 ATTTT
40759255 GTTGTTATTG
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:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTACTATT
Found at i:40759326 original size:30 final size:31
Alignment explanation
Indices: 40759292--40759353 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
40759282 ATTTATTTTA
*
40759292 TTGTTAATTTTCTTATTATTTTA-AAGGAAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAAT
*
40759322 TTGTTAATTTTTTTATTATTTTAGAAGCAAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAAT
40759353 T
1 T
40759354 GCTTGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAAT
Found at i:40759686 original size:27 final size:27
Alignment explanation
Indices: 40759656--40759748 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
40759646 AAATAATTTA
40759656 AAATAATAATACAAAACAAATTAAAAT
1 AAATAATAATACAAAACAAATTAAAAT
* * * *
40759683 AAATAAT-ATGATATAACAATTTAAAAC
1 AAATAATAAT-ACAAAACAAATTAAAAT
* ** *
40759710 AAATACTATATGGAAAA-AGACTTAAAAT
1 AAATAATA-ATACAAAACA-AATTAAAAT
40759738 AAATAATAATA
1 AAATAATAATA
40759749 AAACTGTTCA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
26 2 0.04
27 29 0.58
28 17 0.34
29 2 0.04
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAATAATAATACAAAACAAATTAAAAT
Found at i:40761107 original size:25 final size:26
Alignment explanation
Indices: 40761079--40761128 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
40761069 CCAGGATAGG
40761079 TTGGGCTTAG-TTGGTTTAATTGGGA
1 TTGGGCTTAGTTTGGTTTAATTGGGA
*
40761104 TTGGGTTTAGTTTGGTTTAATTGGG
1 TTGGGCTTAGTTTGGTTTAATTGGG
40761129 TTTTGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (26 bp):
TTGGGCTTAGTTTGGTTTAATTGGGA
Found at i:40768991 original size:19 final size:19
Alignment explanation
Indices: 40768945--40768992 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
40768935 GTATATATTT
40768945 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
40768963 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
40768982 TAAGTTTTATT
1 TAAATTTTATT
40768993 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:40769073 original size:42 final size:42
Alignment explanation
Indices: 40769009--40769097 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
40768999 CTAGGAATAT
* *
40769009 TTTTATTTTATCTTTTTGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
*
40769051 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
40769093 TTTTC
1 TTTTC
40769098 CCAATTAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.53
Consensus pattern (42 bp):
TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:40770222 original size:11 final size:11
Alignment explanation
Indices: 40770189--40770241 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
40770179 CAATGACAAC
* *
40770189 AAAATAGTAGC
1 AAAATAATAGA
*
40770200 AATATAATAGA
1 AAAATAATAGA
*
40770211 AAAATGATAGA
1 AAAATAATAGA
*
40770222 AAAATAATAGC
1 AAAATAATAGA
*
40770233 AAAACAATA
1 AAAATAATA
40770242 ACAAATGGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (11 bp):
AAAATAATAGA
Found at i:40771758 original size:49 final size:49
Alignment explanation
Indices: 40771686--40771979 Score: 345
Period size: 49 Copynumber: 5.9 Consensus size: 49
40771676 TCTATTGTGA
*
40771686 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
40771735 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
** * * * * **
40771785 CAATCACGTGTGTAGTACTAAATGCAGGCTATTACGTGTATCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * **
40771835 AGGTCACGTGTGTAGTACTAAGTGCAGGCTCCTACGTGTACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
40771885 GGTCACATGTGTAATATTAAGTGCAGGGTACTACATGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
40771934 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40771980 GCTTTGGCTA
Statistics
Matches: 202, Mismatches: 41, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
49 123 0.61
50 43 0.21
51 36 0.18
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:40776427 original size:19 final size:19
Alignment explanation
Indices: 40776405--40776441 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40776395 AAAATTTTTA
* *
40776405 AAAATCATTAAAATCCAAC
1 AAAATCATAAAAAACCAAC
40776424 AAAATCATAAAAAACCAA
1 AAAATCATAAAAAACCAA
40776442 AAACAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAATCATAAAAAACCAAC
Found at i:40776523 original size:40 final size:39
Alignment explanation
Indices: 40776454--40776530 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
40776444 ACAATTAATA
40776454 ACTTAGAAAATTATAAAAACTAAAAAAAAATTCATAATCT
1 ACTTAGAAAATTATAAAAAC-AAAAAAAAATTCATAATCT
* *
40776494 ACTTTGAAAATTATAAAAA-AAAGATAAAAATTTATAA
1 ACTTAGAAAATTATAAAAACAAA-A-AAAAATTCATAA
40776531 GTATGTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 3 0.09
39 1 0.03
40 29 0.88
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (39 bp):
ACTTAGAAAATTATAAAAACAAAAAAAAATTCATAATCT
Found at i:40776688 original size:11 final size:11
Alignment explanation
Indices: 40776674--40776699 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40776664 AATTTTAAGA
40776674 TTTTTTTGTAT
1 TTTTTTTGTAT
40776685 TTTTTTTGTAT
1 TTTTTTTGTAT
40776696 TTTT
1 TTTT
40776700 ATATTTTTAA
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:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTAT
Found at i:40777022 original size:13 final size:14
Alignment explanation
Indices: 40776995--40777021 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40776985 TTCGCCTATG
40776995 TATTGATGAAAAAA
1 TATTGATGAAAAAA
40777009 TATTGATGAAAAA
1 TATTGATGAAAAA
40777022 TGGGGAAGAA
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:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TATTGATGAAAAAA
Found at i:40783362 original size:61 final size:61
Alignment explanation
Indices: 40783267--40783386 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
40783257 ATATCATGTC
*
40783267 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGCAAAGTCAACCAACAT
1 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACAT
40783328 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAAC
1 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAAC
40783387 TTCATAACTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (61 bp):
CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACAT
Found at i:40791643 original size:17 final size:19
Alignment explanation
Indices: 40791601--40791645 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
40791591 CTCAAAGTAA
*
40791601 AGAAAATAAGCATAACAAT
1 AGAAAATAAGCACAACAAT
*
40791620 AGAAAATAAG-ACAACCAT
1 AGAAAATAAGCACAACAAT
40791638 -GAAAATAA
1 AGAAAATAA
40791646 AGCTTGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.13
Consensus pattern (19 bp):
AGAAAATAAGCACAACAAT
Found at i:40794499 original size:14 final size:15
Alignment explanation
Indices: 40794474--40794502 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40794464 AATATTTGTA
40794474 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
40794489 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
40794503 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:40795333 original size:28 final size:25
Alignment explanation
Indices: 40795278--40795336 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
40795268 AGATTTGTAT
* * *
40795278 TTTATTTAATATTACTATAATTATA
1 TTTATTTAATAATAATATAATTAAA
40795303 TTTATTTAATAATAATATAAAATTTAAA
1 TTTATTTAATAATAATAT--AA-TTAAA
40795331 TTTATT
1 TTTATT
40795337 ATTATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 16 0.57
27 2 0.07
28 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATTTAATAATAATATAATTAAA
Found at i:40795439 original size:17 final size:17
Alignment explanation
Indices: 40795417--40795455 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40795407 TTTTTTTATT
40795417 TTTATATATTTAAAATA
1 TTTATATATTTAAAATA
* *
40795434 TTTATATATTTTATATA
1 TTTATATATTTAAAATA
40795451 TTTAT
1 TTTAT
40795456 TTGAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATATTTAAAATA
Found at i:40795446 original size:9 final size:9
Alignment explanation
Indices: 40795360--40795453 Score: 59
Period size: 9 Copynumber: 10.3 Consensus size: 9
40795350 AAATATTAAT
40795360 TTTTATATA
1 TTTTATATA
*
40795369 TTTTA-AAA
1 TTTTATATA
*
40795377 TTTTATACA
1 TTTTATATA
*
40795386 TTATTATTTA
1 TT-TTATATA
*
40795396 TTGTCA-ATAA
1 TT-TTATAT-A
* *
40795406 TTTTTTTTA
1 TTTTATATA
40795415 TTTTTATATA
1 -TTTTATATA
* *
40795425 TTTAAAATA
1 TTTTATATA
40795434 -TTTATATA
1 TTTTATATA
40795442 TTTTATATA
1 TTTTATATA
40795451 TTT
1 TTT
40795454 ATTTGAATTT
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
8 13 0.21
9 30 0.48
10 20 0.32
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATATA
Found at i:40796558 original size:21 final size:21
Alignment explanation
Indices: 40796524--40796567 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
40796514 AAAATTCTAC
*
40796524 AATTTCTCCCTAAAACTCTCA
1 AATTTCTCACTAAAACTCTCA
* **
40796545 AATTTCTCATTAAATTTCTCA
1 AATTTCTCACTAAAACTCTCA
40796566 AA
1 AA
40796568 ACTCTTTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTCTCACTAAAACTCTCA
Found at i:40796844 original size:54 final size:54
Alignment explanation
Indices: 40796725--40796843 Score: 179
Period size: 52 Copynumber: 2.2 Consensus size: 54
40796715 GTAACGGTTT
* *
40796725 ATTTTAAATTTTGAATATTATTTAATATTTTTTTCATTTCTGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
*
40796779 ATTTTAATTTTTGAATATTATTT-A-ATTTTTTTCATTTATGTAATTTTCATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
*
40796831 ATTTGTATTTTTT
1 ATTT-TAATTTTT
40796844 TATTTTTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
52 30 0.50
53 8 0.13
54 22 0.37
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (54 bp):
ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
Found at i:40797788 original size:7 final size:7
Alignment explanation
Indices: 40797776--40797807 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40797766 AGTCGCTTCA
40797776 TATTTAG
1 TATTTAG
40797783 TATTTAG
1 TATTTAG
40797790 TATTTAG
1 TATTTAG
40797797 TATTTAG
1 TATTTAG
40797804 TATT
1 TATT
40797808 ATTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:40798888 original size:27 final size:26
Alignment explanation
Indices: 40798858--40798917 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
40798848 TATTGTTTCA
40798858 TTTAATAAAAAAAGAATTTTTTTATAT
1 TTTAATAAAAAAAGAATTTTTTTAT-T
** **
40798885 TTTAATAGTAAATTAATTTTTTTATT
1 TTTAATAAAAAAAGAATTTTTTTATT
40798911 TTATAAT
1 TT-TAAT
40798918 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTAATAAAAAAAGAATTTTTTTATT
Found at i:40798941 original size:33 final size:31
Alignment explanation
Indices: 40798877--40798941 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
40798867 AAAAGAATTT
*
40798877 TTTTATATTTTAATAGTAAATTAATTTTTTTA
1 TTTTATATTTTAATAG-AAATTAATTCTTTTA
40798909 TTTTATAATTTTAATA-AAATATAAGTTCTTTTA
1 TTTTAT-ATTTTAATAGAAAT-TAA-TTCTTTTA
40798942 AATAAGGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.14
32 9 0.31
33 16 0.55
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTATATTTTAATAGAAATTAATTCTTTTA
Found at i:40802451 original size:24 final size:24
Alignment explanation
Indices: 40802419--40802473 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
40802409 GTTGGGACAT
*
40802419 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
*
40802443 ATTAAATTCGTCAACCAGCAGCTT
1 ATTAAATTCGTCAACCAGCAGCTC
40802467 ATTAAAT
1 ATTAAAT
40802474 CTGTCCAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAGCTC
Found at i:40802567 original size:17 final size:18
Alignment explanation
Indices: 40802547--40802581 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40802537 TGTACACACA
40802547 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
40802564 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
40802582 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:40802713 original size:14 final size:14
Alignment explanation
Indices: 40802702--40802731 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40802692 GCAATTAATA
40802702 AATTTGTCTTAAGT
1 AATTTGTCTTAAGT
40802716 AATTTGTCTTAAGT
1 AATTTGTCTTAAGT
40802730 AA
1 AA
40802732 GACTAAATAA
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:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
AATTTGTCTTAAGT
Found at i:40804672 original size:25 final size:24
Alignment explanation
Indices: 40804644--40804691 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40804634 ACAATTGACC
*
40804644 AAACTAAGAT-ATGGGAAGCTTTTAA
1 AAACTAA-ATCATCGGAA-CTTTTAA
40804669 AAACTAAATCATCGGAACTTTTA
1 AAACTAAATCATCGGAACTTTTA
40804692 TCGACAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (24 bp):
AAACTAAATCATCGGAACTTTTAA
Done.