Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 28 of 204
Found at i:10283080 original size:23 final size:23
Alignment explanation
Indices: 10283049--10283121 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
10283039 AATGTTATTG
*
10283049 ATCAATGGTAGCTACGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
10283072 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
10283095 TTCAATGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
10283118 ATCA
1 ATCA
10283122 GTGTGGCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
ATCAATGGTAGCTTCGGCTACAT
Found at i:10283613 original size:16 final size:16
Alignment explanation
Indices: 10283592--10283633 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
10283582 CGTTTGGTTC
10283592 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
*
10283608 GCTGTAATGGAATAGA
1 GCTGTAATAGAATAGA
*
10283624 ACTGTAATAG
1 GCTGTAATAG
10283634 TAATTCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:10283677 original size:45 final size:43
Alignment explanation
Indices: 10283613--10283705 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 43
10283603 ATAGAGCTGT
10283613 AATGGAATAGAACTGTAATAGTAATTCAATTG-TTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC--TTGATTTGGTTGAATGG
10283658 AATGGAATAGAACTGTAATAGTATTCTTGTATTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCTTG-ATTTGGTTGAATGG
10283702 AATG
1 AATG
10283706 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
42 3 0.07
44 21 0.46
45 22 0.48
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (43 bp):
AATGGAATAGAACTGTAATAGTATTCTTGATTTGGTTGAATGG
Found at i:10283927 original size:55 final size:54
Alignment explanation
Indices: 10283818--10283934 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 54
10283808 GATTATTAAT
* *
10283818 ATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAAAATTTTAACATAATTATTATT-AATATAATTTA
* * *
10283874 ATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAATTTA
1 ATAAAAATAAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AATTTA
*
10283929 CTAAAA
1 ATAAAA
10283935 TCATAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
54 4 0.08
55 29 0.55
56 20 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (54 bp):
ATAAAAATAAATAATTTAATAAAATTTTAACATAATTATTATTAATATAATTTA
Found at i:10285265 original size:38 final size:38
Alignment explanation
Indices: 10285202--10285278 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
10285192 GGTTGAGGAA
* *
10285202 AGGGAAAAAAAGGCAATTACTTTACCAAAATGGATCCC
1 AGGGAAAAAAAGGCAACTACGTTACCAAAATGGATCCC
10285240 AGGG-AAAAAAGAGCAACTACGTTACCAAAATGGATCCC
1 AGGGAAAAAAAG-GCAACTACGTTACCAAAATGGATCCC
10285278 A
1 A
10285279 ATACAAGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 7 0.19
38 29 0.81
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (38 bp):
AGGGAAAAAAAGGCAACTACGTTACCAAAATGGATCCC
Found at i:10288047 original size:49 final size:49
Alignment explanation
Indices: 10287992--10288131 Score: 226
Period size: 49 Copynumber: 2.9 Consensus size: 49
10287982 CAATAAGTGA
* * *
10287992 TATGTGATTCCGTGTAAGACCAGAGTTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGATATATGT
* *
10288041 TATGTGATTACGTGTAAGACTATAGCTGGGCTATGGCATCGATATATGT
1 TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGATATATGT
*
10288090 TATGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCGA
1 TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGA
10288132 GAAAATATGT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 83 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (49 bp):
TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGATATATGT
Found at i:10290116 original size:50 final size:50
Alignment explanation
Indices: 10290001--10290249 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
10289991 GATAATAACA
* ** * *
10290001 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
10290052 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
10290102 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
10290152 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
* * *
10290207 ATGCCAATGTCATGTCCCAGACATGGTCTTATATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
10290250 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
50 94 0.56
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 37 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:10290187 original size:100 final size:104
Alignment explanation
Indices: 10290000--10290249 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 104
10289990 TGATAATAAC
** * *
10290000 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
10290065 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
10290102 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
10290166 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* * * *
10290207 ATGCCAATGTCATGTCCCAGACATGGTCTTATATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
10290250 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 50 0.38
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 38 0.29
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:10290365 original size:13 final size:13
Alignment explanation
Indices: 10290344--10290375 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
10290334 GCTTGGATCA
*
10290344 TCATCAAATAAAT
1 TCATAAAATAAAT
10290357 TCATAAAATAAAT
1 TCATAAAATAAAT
10290370 TCATAA
1 TCATAA
10290376 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:10294512 original size:41 final size:41
Alignment explanation
Indices: 10294450--10294569 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
10294440 TCAGATTTAT
* * * *
10294450 TGCCAGTGAAATAATTCAGACTTTAGGTCTAGCAGGCTTGA
1 TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCTTAA
*
10294491 TGCCGGTGAAATTATTCAGACTATACGTCTAGCAGGCTTAA
1 TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCTTAA
* *** * *
10294532 TGCCGGTGATACGTTTCGGACTATAAGTCTAGCAGGCT
1 TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCT
10294570 AAAAGTCGGT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (41 bp):
TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCTTAA
Found at i:10298392 original size:25 final size:26
Alignment explanation
Indices: 10298350--10298400 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
10298340 CTTTTTTATT
*
10298350 TAAAAAGGTAAATTAAAA-TTTGAAAA
1 TAAAAAGGTAAATAAAAAGTTT-AAAA
*
10298376 TAAAAAGG-CAATAAAAAGTTTAAAA
1 TAAAAAGGTAAATAAAAAGTTTAAAA
10298401 GAGAGAGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (26 bp):
TAAAAAGGTAAATAAAAAGTTTAAAA
Found at i:10300842 original size:18 final size:18
Alignment explanation
Indices: 10300821--10300858 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
10300811 CCTTTTATAC
10300821 CTCTTTTTTCTTT-TTTTT
1 CTCTTTTTT-TTTCTTTTT
10300839 CTCTTTTTTTTTCTTTTT
1 CTCTTTTTTTTTCTTTTT
10300857 CT
1 CT
10300859 TTTCTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
CTCTTTTTTTTTCTTTTT
Found at i:10300845 original size:10 final size:10
Alignment explanation
Indices: 10300824--10300856 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
10300814 TTTATACCTC
10300824 TTTTTTCT-T
1 TTTTTTCTCT
10300833 TTTTTTCTCT
1 TTTTTTCTCT
*
10300843 TTTTTTTTCT
1 TTTTTTCTCT
10300853 TTTT
1 TTTT
10300857 CTTTTCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:10300846 original size:12 final size:11
Alignment explanation
Indices: 10300824--10300863 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
10300814 TTTATACCTC
10300824 TTTTTTCTTTT
1 TTTTTTCTTTT
*
10300835 TTTTCTC-TTT
1 TTTTTTCTTTT
10300845 TTTTTTCTTTT
1 TTTTTTCTTTT
*
10300856 TCTTTTCT
1 TTTTTTCT
10300864 ACATTTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:10300875 original size:27 final size:23
Alignment explanation
Indices: 10300824--10300887 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 23
10300814 TTTATACCTC
10300824 TTTTTTC-TTTT-TTTTCTCTTT
1 TTTTTTCTTTTTCTTTTCTCTTT
10300845 TTTTTTCTTTTTCTTTTCTACATTT
1 TTTTTTCTTTTTCTTTTCT-C-TTT
*
10300870 CATTTTTCTTCTTTCTTT
1 -TTTTTTCTT-TTTCTTT
10300888 CCCCCGTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 7 0.19
22 4 0.11
23 6 0.17
24 1 0.03
25 3 0.08
26 8 0.22
27 7 0.19
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTCTTTTTCTTTTCTCTTT
Found at i:10301788 original size:3 final size:3
Alignment explanation
Indices: 10301780--10301819 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
10301770 TTTGATTTTC
10301780 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
10301820 CATTGCTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:10307497 original size:6 final size:6
Alignment explanation
Indices: 10307486--10307511 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10307476 ATTGAGATTC
10307486 GGTGTA GGTGTA GGTGTA GGTGTA GG
1 GGTGTA GGTGTA GGTGTA GGTGTA GG
10307512 GTTTTTCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGTGTA
Found at i:10316049 original size:68 final size:69
Alignment explanation
Indices: 10315918--10316056 Score: 217
Period size: 68 Copynumber: 2.0 Consensus size: 69
10315908 GACTTGCAAA
* * *
10315918 ATTGTGAAAAACTAGATAGGCAAAATAAGTACAAGCAATAATGCAAATTAGGTTTCCCAAGATAT
1 ATTGTGAAAAACTAGATAGGAAAAATAAGTAAAAGCAATAATACAAATTAGGTTTCCCAAGATAT
10315983 AGAC
66 AGAC
* **
10315987 ATTGTGAAAAACTAGATAGGAAAAAT-AGTAAAAGCAATGATACAAATTAGGTTTCCTGAGATAT
1 ATTGTGAAAAACTAGATAGGAAAAATAAGTAAAAGCAATAATACAAATTAGGTTTCCCAAGATAT
10316051 AGAC
66 AGAC
10316055 AT
1 AT
10316057 GAAGAAAGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
68 39 0.61
69 25 0.39
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (69 bp):
ATTGTGAAAAACTAGATAGGAAAAATAAGTAAAAGCAATAATACAAATTAGGTTTCCCAAGATAT
AGAC
Found at i:10318226 original size:15 final size:15
Alignment explanation
Indices: 10318206--10318234 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10318196 TGGAACCAAA
10318206 TAATCATAAATTATG
1 TAATCATAAATTATG
10318221 TAATCATAAATTAT
1 TAATCATAAATTAT
10318235 CTAAAATTCA
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:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
TAATCATAAATTATG
Found at i:10321368 original size:2 final size:2
Alignment explanation
Indices: 10321361--10321394 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10321351 TTCAGGTGTT
10321361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10321395 GTCTCTCGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:10324840 original size:17 final size:18
Alignment explanation
Indices: 10324801--10324840 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
10324791 CTGCAATTTT
*
10324801 TTTTTTACTTTTTTGCTA
1 TTTTTTACTTTTTTACTA
10324819 TTTTTTA-TTTTTTCACTA
1 TTTTTTACTTTTTT-ACTA
10324837 TTTT
1 TTTT
10324841 GCTACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTTACTTTTTTACTA
Found at i:10327482 original size:41 final size:41
Alignment explanation
Indices: 10327437--10327521 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
10327427 CCGATATGTA
*
10327437 TCACCGGCATGAAGCCTGCTAGACGTAAAGTCTGAATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTATT
10327478 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTATT
10327519 TCA
1 TCA
10327522 ATCACTTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTATT
Found at i:10327931 original size:2 final size:2
Alignment explanation
Indices: 10327926--10327968 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10327916 ATTCGAACCT
10327926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10327968 T
1 T
10327969 CTTATACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10338289 original size:9 final size:9
Alignment explanation
Indices: 10338275--10338351 Score: 75
Period size: 9 Copynumber: 8.4 Consensus size: 9
10338265 TTTGGTTAAA
10338275 AATTACCCG
1 AATTACCCG
*
10338284 AATTACCCA
1 AATTACCCG
**
10338293 AATTAATCG
1 AATTACCCG
*
10338302 AATTAACCG
1 AATTACCCG
*
10338311 AATTAACCG
1 AATTACCCG
10338320 AATTA-CCG
1 AATTACCCG
*
10338328 AAAAATACCCG
1 --AATTACCCG
10338339 AATTACCCG
1 AATTACCCG
10338348 AATT
1 AATT
10338352 TTTTTATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
8 3 0.05
9 48 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:10338447 original size:6 final size:6
Alignment explanation
Indices: 10338436--10338464 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
10338426 TTGGGTTGTC
10338436 TTTTAG TTTTAG TTTTAG TTTTAG TTTTA
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTA
10338465 TTGGATTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTTTAG
Found at i:10338521 original size:13 final size:13
Alignment explanation
Indices: 10338503--10338532 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
10338493 TTTTAGTTTT
10338503 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
10338516 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
10338529 ATTG
1 ATTG
10338533 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:10343543 original size:22 final size:22
Alignment explanation
Indices: 10343515--10343595 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
10343505 TTGGTCTACA
10343515 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
10343537 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
* * * **
10343559 AACTAAACCCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
10343581 TACTAAGCTCTCATG
1 TACTAAGCTCTCATG
10343596 GCTAGGTAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:10345898 original size:31 final size:31
Alignment explanation
Indices: 10345858--10345921 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
10345848 AAAAAAAACC
*
10345858 CAATGACTTAAATAAAAACTTTCGAATAGTT
1 CAATAACTTAAATAAAAACTTTCGAATAGTT
* *
10345889 CAATAACTTAAGTGAAAACTTTCGAATAGTT
1 CAATAACTTAAATAAAAACTTTCGAATAGTT
10345920 CA
1 CA
10345922 GTGGCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTTCGAATAGTT
Found at i:10346818 original size:6 final size:7
Alignment explanation
Indices: 10346803--10346835 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
10346793 TTTGTCTCTT
10346803 AAAACAA
1 AAAACAA
10346810 AAAACAA
1 AAAACAA
10346817 AAAACAA
1 AAAACAA
*
10346824 AAAACAG
1 AAAACAA
10346831 AAAAC
1 AAAAC
10346836 GCAATCTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:10353480 original size:16 final size:16
Alignment explanation
Indices: 10353452--10353493 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
10353442 TTAAAACTTC
10353452 AAAA-AAAAA-AAAAA
1 AAAAGAAAAAGAAAAA
* *
10353466 AAAAGAAGAAGAAAAG
1 AAAAGAAAAAGAAAAA
10353482 AAAAGAAAAAGA
1 AAAAGAAAAAGA
10353494 GGCTAGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 4 0.17
15 4 0.17
16 15 0.65
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAA
Found at i:10358871 original size:39 final size:40
Alignment explanation
Indices: 10358822--10358900 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 40
10358812 TTAAGTTGCA
10358822 TTTATCTTAGTATTATTTAGGTGAAAATATTTATTTTAAT
1 TTTATCTTAGTATTATTTAGGTGAAAATATTTATTTTAAT
*
10358862 TTTAT-TTAGTATTATTTAGGTGAAATTATTTATTTTAAT
1 TTTATCTTAGTATTATTTAGGTGAAAATATTTATTTTAAT
10358901 ATTTTTGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 33 0.87
40 5 0.13
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (40 bp):
TTTATCTTAGTATTATTTAGGTGAAAATATTTATTTTAAT
Found at i:10367346 original size:46 final size:47
Alignment explanation
Indices: 10367266--10367361 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 47
10367256 TTTGCCAAGG
10367266 AGTACGTATGGTACTGGATAACTAGGAATAGGAAAGCTGCTTTCTAC
1 AGTACGTATGGTACTGGATAACTAGGAATAGGAAAGCTGCTTTCTAC
*
10367313 AGTACGTATGGTACTGG-TAACTAGGAATAGGAAAGCTGCTTTGTAC
1 AGTACGTATGGTACTGGATAACTAGGAATAGGAAAGCTGCTTTCTAC
10367359 AGT
1 AGT
10367362 TATTCTTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 31 0.65
47 17 0.35
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (47 bp):
AGTACGTATGGTACTGGATAACTAGGAATAGGAAAGCTGCTTTCTAC
Found at i:10367737 original size:12 final size:12
Alignment explanation
Indices: 10367717--10367747 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10367707 ATTGAGTGCA
10367717 TGCATGTGTATG
1 TGCATGTGTATG
*
10367729 TGTATGTGTATG
1 TGCATGTGTATG
10367741 TGCATGT
1 TGCATGT
10367748 ATACAGCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.32, T:0.45
Consensus pattern (12 bp):
TGCATGTGTATG
Found at i:10377508 original size:22 final size:21
Alignment explanation
Indices: 10377483--10377535 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
10377473 ATGTAGAATT
10377483 TTTAATTAAATAAAAAAATAAA
1 TTTAATTAAAT-AAAAAATAAA
*
10377505 TTTAATATTAAATAAAAATTAAA
1 TTT-A-ATTAAATAAAAAATAAA
*
10377528 TTAAATTA
1 TTTAATTA
10377536 TCATTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 12 0.44
24 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAATTAAATAAAAAATAAA
Found at i:10377519 original size:16 final size:16
Alignment explanation
Indices: 10377486--10377533 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
10377476 TAGAATTTTT
* *
10377486 AATTAAATAAAAAAATA
1 AATTAAATTAAATAA-A
10377503 AATTTAATATTAAATAAA
1 AA-TTAA-ATTAAATAAA
10377521 AATTAAATTAAAT
1 AATTAAATTAAAT
10377534 TATCATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 7 0.26
19 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAATTAAATAAA
Found at i:10378374 original size:29 final size:28
Alignment explanation
Indices: 10378330--10378391 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
10378320 TTAAATTTAT
10378330 TTAATTTTTTAATAATATAAAGGCTAAA
1 TTAATTTTTTAATAATATAAAGGCTAAA
* *
10378358 TTAATTTATTTAATAATATAGAGGCTAAT
1 TTAATTT-TTTAATAATATAAAGGCTAAA
10378387 TTAAT
1 TTAAT
10378392 CTAGTCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (28 bp):
TTAATTTTTTAATAATATAAAGGCTAAA
Found at i:10381798 original size:12 final size:13
Alignment explanation
Indices: 10381772--10381805 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
10381762 ATGCATCCAG
10381772 ATAATTAATAAAT
1 ATAATTAATAAAT
10381785 ATAATTAA-AAAT
1 ATAATTAATAAAT
10381797 ATAATTAAT
1 ATAATTAAT
10381806 TTGACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATTAATAAAT
Found at i:10381840 original size:26 final size:27
Alignment explanation
Indices: 10381786--10381838 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
10381776 TTAATAAATA
*
10381786 TAATTAAAAATATAATTAATTTGACTT
1 TAATTAAAAATATAATTAATTAGACTT
10381813 TAATTAAAAA-ATAATT-ATTAGACTT
1 TAATTAAAAATATAATTAATTAGACTT
10381838 T
1 T
10381839 TACTGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 6 0.24
27 10 0.40
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATTAAAAATATAATTAATTAGACTT
Found at i:10381920 original size:29 final size:28
Alignment explanation
Indices: 10381888--10381948 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
10381878 AAAAGCCGTC
*
10381888 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTGTCAAAATTTACCGAAATGGGCC-A
* ** *
10381917 TTTTGTGATTATTTACCGGAATGGGCCA
1 TTTTGTCAAAATTTACCGAAATGGGCCA
10381945 TTTT
1 TTTT
10381949 CCGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (28 bp):
TTTTGTCAAAATTTACCGAAATGGGCCA
Found at i:10382409 original size:122 final size:124
Alignment explanation
Indices: 10382187--10382534 Score: 612
Period size: 122 Copynumber: 2.8 Consensus size: 124
10382177 TTATTTCGAG
10382187 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
*
10382251 GAAATCGCGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAAT-A-TTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* *
10382309 TTGATGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
10382374 AAATCGCGCCCTCGTGGACGTGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* *
10382433 TTAACGTTTTTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
10382498 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
10382535 CAAGTTTGGG
Statistics
Matches: 214, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
122 110 0.51
123 2 0.01
124 102 0.48
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:10384110 original size:25 final size:25
Alignment explanation
Indices: 10384060--10384114 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
10384050 ATTTTTAAAA
* **
10384060 TAAAATACTTTTCATAATTTGTATT
1 TAAAATACTTTTCATAATATAAATT
10384085 TAAAATACTATTTC-TAATATAAATT
1 TAAAATACT-TTTCATAATATAAATT
10384110 TAAAA
1 TAAAA
10384115 CTATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (25 bp):
TAAAATACTTTTCATAATATAAATT
Found at i:10384143 original size:18 final size:18
Alignment explanation
Indices: 10384116--10384151 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10384106 AATTTAAAAC
*
10384116 TATTTAATTAAAATATTT
1 TATTTAATTAAAAAATTT
*
10384134 TATTTTATTAAAAAATTT
1 TATTTAATTAAAAAATTT
10384152 AAGCATCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTAATTAAAAAATTT
Found at i:10386834 original size:50 final size:50
Alignment explanation
Indices: 10386719--10387011 Score: 478
Period size: 50 Copynumber: 5.8 Consensus size: 50
10386709 GATAATAACA
* ** *
10386719 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
10386770 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
10386820 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
10386870 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
10386920 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
10386970 TGCCAATGCCATGTCCCAGACAAGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
10387012 TTACCCAAAT
Statistics
Matches: 227, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
50 194 0.85
51 33 0.15
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:10387127 original size:13 final size:13
Alignment explanation
Indices: 10387106--10387136 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10387096 GCTTAGATCA
*
10387106 TCATCAAATAAAT
1 TCATAAAATAAAT
10387119 TCATAAAATAAAT
1 TCATAAAATAAAT
10387132 TCATA
1 TCATA
10387137 GTTGCTGGAA
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:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:10387383 original size:30 final size:30
Alignment explanation
Indices: 10387349--10387406 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
10387339 CCTCGACTCT
**
10387349 AACTTTTTTAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
10387379 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
10387407 AAGGCACGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:10393373 original size:25 final size:24
Alignment explanation
Indices: 10393320--10393365 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10393310 GTTTTTCATT
*
10393320 CTGTTTTTGCTTGCTTTGCTGTTAA
1 CTGTTTTTGCTTGC-TTGCTGCTAA
10393345 -TGTTTTTGCTTGC-TGCTGCTA
1 CTGTTTTTGCTTGCTTGCTGCTA
10393366 CCACTGTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.07, C:0.17, G:0.22, T:0.54
Consensus pattern (24 bp):
CTGTTTTTGCTTGCTTGCTGCTAA
Found at i:10394660 original size:35 final size:35
Alignment explanation
Indices: 10394620--10394687 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
10394610 ATACAGAGAA
*
10394620 CAAAGGAGGAAGAAACAAAGAATAATTTACTTAGG
1 CAAAGGAGGAAGAAACAAAGAACAATTTACTTAGG
10394655 CAAAGGAGGAAGAAACAAAGAACAATTTACTTA
1 CAAAGGAGGAAGAAACAAAGAACAATTTACTTA
10394688 AGCCTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.53, C:0.10, G:0.21, T:0.16
Consensus pattern (35 bp):
CAAAGGAGGAAGAAACAAAGAACAATTTACTTAGG
Found at i:10395369 original size:21 final size:21
Alignment explanation
Indices: 10395345--10395396 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
10395335 CATTGTTTCT
* *
10395345 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
10395366 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
10395387 AATCTCACCG
1 AATCTCACCG
10395397 TCACCGCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.35, G:0.10, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:10402179 original size:2 final size:2
Alignment explanation
Indices: 10402172--10402196 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10402162 AACAAATCTA
10402172 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
10402197 GGAGAAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10411587 original size:15 final size:15
Alignment explanation
Indices: 10411552--10411593 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10411542 TTAAGAATTT
*
10411552 TATTAAATTAT-ATA
1 TATTTAATTATAATA
10411566 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
10411580 TATTTAATAATAAT
1 TATTTAATTATAAT
10411594 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:10411820 original size:45 final size:43
Alignment explanation
Indices: 10411722--10411831 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
10411712 TTTTCCATTA
10411722 TGCTATTACACCTCTATTCCA-T---TTAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTAACCAAACACAAGAT
* * ***
10411761 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATT-AACCAAACACAAGA-T
10411806 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
10411832 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 19 0.33
40 1 0.02
43 2 0.03
44 11 0.19
45 25 0.43
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATTACATTAACCAAACACAAGAT
Found at i:10411831 original size:16 final size:16
Alignment explanation
Indices: 10411812--10411863 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
10411802 GATTTGCTAT
* *
10411812 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
10411828 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10411844 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10411860 TACA
1 TACA
10411864 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:10420846 original size:24 final size:24
Alignment explanation
Indices: 10420810--10420856 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
10420800 TGATTTTACA
*
10420810 AATAATTTTAAAATAAAATAAACC
1 AATAATTTAAAAATAAAATAAACC
*
10420834 AATAATTTAAAAATAAGATAAAC
1 AATAATTTAAAAATAAAATAAAC
10420857 TGTATTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAATTTAAAAATAAAATAAACC
Found at i:10421065 original size:40 final size:39
Alignment explanation
Indices: 10421002--10421127 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 39
10420992 TTGGATAATT
*
10421002 TTTTAAAAGTAATTTTTAAAATAAATTGTGATAATTTTCA
1 TTTTAAAAGTAA-TTTTAAAATAAATTGAGATAATTTTCA
* * *
10421042 TTTTAACAA-TAATTTATACAATAATTTGGGATAACTTTTGC-
1 TTTTAA-AAGTAATTT-TAAAATAAATTGAGATAA-TTTT-CA
** *
10421083 TTTTAAAAGTAATTTT-TTA-AAATTCAGATAATTTTCA
1 TTTTAAAAGTAATTTTAAAATAAATTGAGATAATTTTCA
10421120 TTTTAAAA
1 TTTTAAAA
10421128 ATAAACTGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
36 1 0.01
37 12 0.17
38 9 0.12
39 4 0.06
40 27 0.38
41 18 0.25
42 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (39 bp):
TTTTAAAAGTAATTTTAAAATAAATTGAGATAATTTTCA
Found at i:10428668 original size:15 final size:15
Alignment explanation
Indices: 10428648--10428684 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
10428638 TATAATTGTA
*
10428648 CAAATATTTGTTATT
1 CAAATATTTGATATT
10428663 CAAATA-TTGATATT
1 CAAATATTTGATATT
10428677 -AAATATTT
1 CAAATATTT
10428685 TTCACTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (15 bp):
CAAATATTTGATATT
Found at i:10431915 original size:22 final size:21
Alignment explanation
Indices: 10431877--10431941 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
10431867 AAAAATTCAG
10431877 AAAAATA-TAAAAATATTTTT
1 AAAAATATTAAAAATATTTTT
*
10431897 AAAAATCATTAAAATTA-TTTT
1 AAAAAT-ATTAAAAATATTTTT
10431918 AAAAATATTAAAAAATATTTTT
1 AAAAATATT-AAAAATATTTTT
10431940 AA
1 AA
10431942 TACTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.23
21 17 0.44
22 13 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATATTAAAAATATTTTT
Found at i:10433343 original size:6 final size:6
Alignment explanation
Indices: 10433334--10433366 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
10433324 TAAGATAAAG
10433334 AAACTT AAACTT AAACTT AAACTT AAACTT AAA
1 AAACTT AAACTT AAACTT AAACTT AAACTT AAA
10433367 AAAAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAACTT
Found at i:10445186 original size:25 final size:25
Alignment explanation
Indices: 10445158--10445208 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
10445148 CCCGTTTTCT
*
10445158 AAACGGGCCTCATTTTTTTACCCAA
1 AAACAGGCCTCATTTTTTTACCCAA
10445183 AAACAGGCCTCATTTTTTTACCCAA
1 AAACAGGCCTCATTTTTTTACCCAA
10445208 A
1 A
10445209 CCCATATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (25 bp):
AAACAGGCCTCATTTTTTTACCCAA
Found at i:10448970 original size:18 final size:19
Alignment explanation
Indices: 10448923--10448973 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
10448913 TAGTTTTTGA
* *
10448923 TTTTTATATTATTTTTAAT
1 TTTTTATAATATATTTAAT
* *
10448942 TATTTAAAATATATTT-AT
1 TTTTTATAATATATTTAAT
10448960 TTTTTATAATATAT
1 TTTTTATAATATAT
10448974 AATAAATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATAATATATTTAAT
Found at i:10448977 original size:25 final size:24
Alignment explanation
Indices: 10448927--10448977 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
10448917 TTTTGATTTT
* *
10448927 TATATTATTTTTAATTATTTAAAA
1 TATATTATTTTTAATAATATAAAA
* *
10448951 TATATTTATTTTTTATAATATATAA
1 TATA-TTATTTTTAATAATATAAAA
10448976 TA
1 TA
10448978 AATATATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATTATTTTTAATAATATAAAA
Found at i:10449284 original size:3 final size:3
Alignment explanation
Indices: 10449271--10449300 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
10449261 TATTAAAAAT
*
10449271 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10449301 GAGTGCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10452752 original size:21 final size:21
Alignment explanation
Indices: 10452700--10452752 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
10452690 TTTAACTTTC
* *
10452700 TTTATATTTTTTTAGAATTTT
1 TTTATATATATTTAGAATTTT
10452721 TTT-TGGA-ATATTTAGAATTTT
1 TTTAT--ATATATTTAGAATTTT
10452742 TTTATATATAT
1 TTTATATATAT
10452753 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
TTTATATATATTTAGAATTTT
Found at i:10455276 original size:46 final size:46
Alignment explanation
Indices: 10455202--10455743 Score: 690
Period size: 46 Copynumber: 12.6 Consensus size: 46
10455192 TACGTATGAT
* * *
10455202 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
10455246 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAACTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10455292 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
10455338 CAGTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10455384 CACTTATCACTTTGTCAC-T--T--GATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
10455425 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10455471 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG-T--
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
10455508 -ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10455553 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG-T--
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
10455590 -ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10455635 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
10455671 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
10455717 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
10455744 AGTACTCAAA
Statistics
Matches: 442, Mismatches: 19, Indels: 72
0.83 0.04 0.14
Matches are distributed among these distances:
36 85 0.19
38 6 0.01
39 5 0.01
40 9 0.02
41 38 0.09
42 10 0.02
43 6 0.01
44 17 0.04
45 6 0.01
46 260 0.59
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:10455513 original size:36 final size:36
Alignment explanation
Indices: 10455472--10455706 Score: 254
Period size: 36 Copynumber: 6.0 Consensus size: 36
10455462 TAAAGCTACC
*
10455472 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGT
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
10455508 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG-T
*
10455551 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGT
1 ---ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
10455590 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG-T
* *
10455633 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 ---ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
10455672 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
10455707 CTAAAGCTAC
Statistics
Matches: 173, Mismatches: 6, Indels: 40
0.79 0.03 0.18
Matches are distributed among these distances:
36 90 0.52
38 4 0.02
39 3 0.02
40 6 0.03
42 6 0.03
43 4 0.02
44 4 0.02
46 56 0.32
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (36 bp):
ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
Found at i:10455553 original size:82 final size:82
Alignment explanation
Indices: 10455341--10455743 Score: 664
Period size: 82 Copynumber: 4.9 Consensus size: 82
10455331 AGGCTACCAG
* * *
10455341 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAACACTTATCACTTTGTCACTTGA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
* * *
10455406 TAAGTGTAGCTAAAG-CTAACAC
66 TCA--G-A--T-AAGTGTAGCAC
10455428 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
*
10455493 TCAGATAAGTGTAGTAC
66 TCAGATAAGTGTAGCAC
10455510 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
*
10455575 TCAGATAAGTGTAGTAC
66 TCAGATAAGTGTAGCAC
10455592 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
10455657 TCAGATAAGTGTAGCAC
66 TCAGATAAGTGTAGCAC
*
10455674 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCTTGA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
10455739 TCAGA
66 TCAGA
10455744 AGTACTCAAA
Statistics
Matches: 306, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
81 3 0.01
82 237 0.77
84 1 0.00
85 1 0.00
87 64 0.21
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (82 bp):
TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
TCAGATAAGTGTAGCAC
Found at i:10455644 original size:164 final size:165
Alignment explanation
Indices: 10455246--10455743 Score: 739
Period size: 164 Copynumber: 2.9 Consensus size: 165
10455236 CTAAGGCTGC
* * *
10455246 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAACTAAGGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
10455311 TGATCAGATAAGTGTAGCTAAGGCTACCAGTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT
66 TGATCAGATAA--GT-G-T-A-GC-A-C--TTATCACTTTGTCACTTGATCAGATAAGTGTAGCT
* * * *
10455376 AAAGTTAACACTTATCACTTTGTCACTTGATAAGTGTAGCTAAAGCTAA
121 AAAGCTACCACTTATCACTTTGTCTCTTGATCA--G-A-CTAAAGCTAA
10455425 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
10455490 TGATCAGATAAGTGTAGTACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
66 TGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
* *
10455555 CTTATCACTTTGTCTCTTGATCAGA-T-AAGTGTAG
131 CTTATCACTTTGTCTCTTGATCAGACTAAAG-CTAA
*
10455589 TACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
10455654 TGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
66 TGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
10455719 CTTATCACTTTATCTCTTGATCAGA
131 CTTATCACTTTGTCTCTTGATCAGA
10455744 AGTACTCAAA
Statistics
Matches: 305, Mismatches: 13, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
163 3 0.01
164 155 0.51
166 1 0.00
167 1 0.00
169 64 0.21
171 1 0.00
172 1 0.00
173 1 0.00
174 1 0.00
175 1 0.00
176 1 0.00
177 2 0.01
179 73 0.24
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (165 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
CTTATCACTTTGTCTCTTGATCAGACTAAAGCTAA
Found at i:10480275 original size:26 final size:25
Alignment explanation
Indices: 10480241--10480301 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
10480231 TTTATAAAGA
*
10480241 TTAATTTAATCTATTTTA-AATTTTAT
1 TTAA-TTAATCTATTGTAGAATTTT-T
*
10480267 TTACATTAATTTATTGTAGAATTTTT
1 TTA-ATTAATCTATTGTAGAATTTTT
10480293 TTAATTAAT
1 TTAATTAAT
10480302 TGAATTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 6 0.19
26 18 0.58
27 7 0.23
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (25 bp):
TTAATTAATCTATTGTAGAATTTTT
Found at i:10488677 original size:91 final size:91
Alignment explanation
Indices: 10488552--10488759 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
10488542 TTGATTTTAG
*
10488552 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* *
10488617 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATATTAATTATTTTAAATTATA
*
10488644 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
10488709 TGTAATATTTATTATTTTAAATTATA
66 TGTAATATTAATTATTTTAAATTATA
* * * *
10488735 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
10488760 GTTATAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 91 0.85
92 16 0.15
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATATTAATTATTTTAAATTATA
Found at i:10488679 original size:44 final size:44
Alignment explanation
Indices: 10488552--10488690 Score: 122
Period size: 47 Copynumber: 3.0 Consensus size: 44
10488542 TTGATTTTAG
*
10488552 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTA-GAAATTA
* * * ** *
10488598 TATA-TCATTATTAA-ATTATATTTAATATTAATTATTTTA-AATTGTA
1 TAAATTCA-TA-TAAGA--AAATTTATTATTAAGAATTTTAGAAAT-TA
10488644 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTA-GAAATTA
10488689 TA
1 TA
10488691 TATTATTATT
Statistics
Matches: 71, Mismatches: 13, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
44 18 0.25
45 13 0.18
46 17 0.24
47 22 0.31
48 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (44 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTAGAAATTA
Found at i:10488721 original size:27 final size:28
Alignment explanation
Indices: 10488663--10488734 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 28
10488653 ATAAGAAAAT
*
10488663 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATTATATA
* *
10488693 TTATTATTAAATTATATGTAA-TATTTA
1 TTATTATTAAATTATATGAAATTATATA
10488720 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
10488735 CAAATTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 10 0.26
28 10 0.26
29 1 0.03
30 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATTATATA
Found at i:10488726 original size:47 final size:47
Alignment explanation
Indices: 10488584--10488727 Score: 138
Period size: 47 Copynumber: 3.1 Consensus size: 47
10488574 ATTATTAAGA
*
10488584 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
* * * **
10488631 A-TTT-T-AAATTGTATA-AATTCATATAAGA--AAATTTATTATTAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATATTAATT
* * *
10488675 ATTTTATGAAATTATATATTATTATTAAATTATATGTAATATTTATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
10488722 ATTTTA
1 ATTTTA
10488728 AATTATACAA
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.32
45 8 0.11
46 8 0.11
47 28 0.38
48 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
Found at i:10488734 original size:44 final size:43
Alignment explanation
Indices: 10488592--10488734 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
10488582 GAATTTTATG
*
10488592 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATATTAATTATTTT
* ** * ** *
10488636 AAATTGTATAAATTCATATAAGAAAATT-TATTATTAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAATATTAATTATT-TT
*
10488683 AAATTATATATTATTATTAAATTATATGTAATATTTATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATATTAATTATTTT
10488727 AAATTATA
1 AAATTATA
10488735 CAAATTCATA
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 10 0.14
46 9 0.12
47 15 0.20
48 3 0.04
49 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATATTAATTATTTT
Found at i:10489007 original size:120 final size:119
Alignment explanation
Indices: 10488775--10489070 Score: 445
Period size: 120 Copynumber: 2.5 Consensus size: 119
10488765 AATTATTTTA
* *
10488775 AATTTTATTAAATCATATATTTTAATT-TAAATATATTTAATATTAATTAT-TTCAAATTTCTTT
1 AATTTTATTAAATTATATATTTTAATTAT-AATATATTTAATAATAATTATGTTCAAATTTCTTT
*
10488838 ATAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAGTAATTATTAAG
65 ACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAGTAATTATTAAG
* * *
10488893 AATTTTATTAAATTATATATTTTAATTATAACATATTTAATAATAATTATGTT-AATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATT-T-CTT
* * *
10488957 TACAGTATCATATATTATGATTTGAGTAAATTCATGTAAGAATATTAATTATTAAG
64 TACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAGTAATTATTAAG
* *
10489013 AATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAAT
10489071 ATGATTAAAT
Statistics
Matches: 161, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
118 49 0.30
119 4 0.02
120 105 0.65
121 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTCTTTA
CAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAGTAATTATTAAG
Found at i:10489052 original size:15 final size:15
Alignment explanation
Indices: 10489018--10489059 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10489008 TTAAGAATTT
*
10489018 TATTAAATTAT-ATA
1 TATTTAATTATAATA
10489032 -ATTTAATTATAATA
1 TATTTAATTATAATA
*
10489046 TATTTAATAATAAT
1 TATTTAATTATAAT
10489060 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:10489197 original size:18 final size:17
Alignment explanation
Indices: 10489169--10489203 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10489159 ATTATTAAGA
*
10489169 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
10489186 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
10489204 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:10489208 original size:155 final size:157
Alignment explanation
Indices: 10489002--10489316 Score: 535
Period size: 155 Copynumber: 2.0 Consensus size: 157
10488992 GTAAGAATAT
*
10489002 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
* *
10489067 AAATATGATTAAATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAATAACAATAAC-A
66 AAATATGATTAAATTATTTATTACTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
* *
10489131 -AATAATTTACCAAAATAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
10489157 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
*
10489222 AAATATGATTAAATTATTTATTATTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTACTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
* *
10489287 TAATCATTTACCCAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
10489314 TAA
1 TAA
10489317 GGGTATTCTA
Statistics
Matches: 149, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
155 123 0.83
156 1 0.01
157 25 0.17
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTACTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:10489453 original size:45 final size:44
Alignment explanation
Indices: 10489364--10489456 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 44
10489354 TTACACATCT
*
10489364 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
10489408 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
10489453 ATTA
1 ATTA
10489457 AACCTCTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.47
45 23 0.53
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:10489461 original size:16 final size:16
Alignment explanation
Indices: 10489437--10489506 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
10489427 TTGATTTGCT
10489437 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
10489453 ATTAAACCTCTATTCC
1 ATTACACCTCTATTCC
*
10489469 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
10489485 AATT-CACCTCTAATCC
1 -ATTACACCTCTATTCC
*
10489501 AATACA
1 ATTACA
10489507 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
15 2 0.04
16 43 0.90
17 3 0.06
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:10489888 original size:115 final size:114
Alignment explanation
Indices: 10489685--10489899 Score: 270
Period size: 115 Copynumber: 1.9 Consensus size: 114
10489675 ATTCCATTAA
* * *
10489685 TTTGTGATGCTAATTTAATTTGATATTTTAATTTTTTTAATTAAATTGGGGTCTGATTAACTTGT
1 TTTGTGATGCTAATTTAATTTAATATTTTAATTTTTTTAATTAAATTAGGATCTGATTAACTTGT
* * * ** *
10489750 AATGTCAACTTTGTCAAGGGTTTAATATTAGTATTGATATTTTCATAAG
66 AATATCAACTCTATCAAAAGTTTAATATTAATATTGATATTTTCATAAG
* * * *
10489799 TTTGTGATGCTATTTTAATTTAAT-TTTTAATTTTTTATTAATTGATTTAGTATCTGATTAACTT
1 TTTGTGATGCTAATTTAATTTAATATTTTAA-TTTTT-TTAATTAAATTAGGATCTGATTAACTT
* *
10489863 GTGATATCAACTCTATTAAAAGTTTAATATTAATATT
64 GTAATATCAACTCTATCAAAAGTTTAATATTAATATT
10489900 CATGTAGATA
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
113 6 0.07
114 27 0.32
115 51 0.61
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (114 bp):
TTTGTGATGCTAATTTAATTTAATATTTTAATTTTTTTAATTAAATTAGGATCTGATTAACTTGT
AATATCAACTCTATCAAAAGTTTAATATTAATATTGATATTTTCATAAG
Found at i:10491926 original size:14 final size:15
Alignment explanation
Indices: 10491896--10491926 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10491886 TATAATCTTT
10491896 ATAATTTTAATAAAA
1 ATAATTTTAATAAAA
10491911 ATAATTTTAA-AAAA
1 ATAATTTTAATAAAA
10491925 AT
1 AT
10491927 TAGATTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATTTTAATAAAA
Found at i:10501933 original size:24 final size:24
Alignment explanation
Indices: 10501905--10501957 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
10501895 TTAGTTAGTC
* *
10501905 AAATAAACAATGCTAATAAATGCT
1 AAATAAACAATACTAATAAATACT
* * *
10501929 AAATATACTATATTAATAAATACT
1 AAATAAACAATACTAATAAATACT
10501953 AAATA
1 AAATA
10501958 TTCTAGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATAAACAATACTAATAAATACT
Found at i:10503756 original size:3 final size:3
Alignment explanation
Indices: 10503748--10503774 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10503738 AAGAATCTCT
10503748 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
10503775 ATCATCGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:10504395 original size:25 final size:25
Alignment explanation
Indices: 10504361--10504443 Score: 157
Period size: 25 Copynumber: 3.3 Consensus size: 25
10504351 TTCTCTGTAA
10504361 TTTCTTTGATAACTGGGGCTTTAGT
1 TTTCTTTGATAACTGGGGCTTTAGT
10504386 TTTCTTTGATAACTGGGGCTTTAGT
1 TTTCTTTGATAACTGGGGCTTTAGT
10504411 TTTCTTTGATAACTGGGGCTTTAGT
1 TTTCTTTGATAACTGGGGCTTTAGT
10504436 TTTGCTTT
1 TTT-CTTT
10504444 TTTCGTTTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 53 0.93
26 4 0.07
ACGTcount: A:0.14, C:0.12, G:0.23, T:0.51
Consensus pattern (25 bp):
TTTCTTTGATAACTGGGGCTTTAGT
Found at i:10504761 original size:49 final size:47
Alignment explanation
Indices: 10504689--10504783 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 47
10504679 TGTATGGTAG
* *
10504689 TTGTTATAATTAGTTATTTCATTACTTTCTTTTTACAGATTATTCTTTA
1 TTGTTATAATTAGTTATTCCATTAC-TT-TTTTCACAGATTATTCTTTA
*
10504738 TTGTTATAATTAGTTATTCCATTACTTTTTTCCCAGATTATTCTTT
1 TTGTTATAATTAGTTATTCCATTACTTTTTTCACAGATTATTCTTT
10504784 CATATAGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 17 0.40
48 2 0.05
49 24 0.56
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (47 bp):
TTGTTATAATTAGTTATTCCATTACTTTTTTCACAGATTATTCTTTA
Found at i:10513741 original size:12 final size:12
Alignment explanation
Indices: 10513724--10513749 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10513714 GAACTTGGAT
10513724 GAGGATGAGGAA
1 GAGGATGAGGAA
10513736 GAGGATGAGGAA
1 GAGGATGAGGAA
10513748 GA
1 GA
10513750 TCCTTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (12 bp):
GAGGATGAGGAA
Found at i:10523956 original size:21 final size:22
Alignment explanation
Indices: 10523913--10523957 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
10523903 ATACAAATTT
10523913 AATAAATGAAAAATATGTATAAA
1 AATAAATGAAAAATA-GTATAAA
10523936 AATAAATGAAAAATA-TATAAA
1 AATAAATGAAAAATAGTATAAA
10523957 A
1 A
10523958 CTATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
23 15 0.68
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AATAAATGAAAAATAGTATAAA
Found at i:10525416 original size:4 final size:4
Alignment explanation
Indices: 10525407--10525445 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
10525397 GAACCTTTTC
10525407 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
10525446 ATCAAAGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:10533487 original size:16 final size:18
Alignment explanation
Indices: 10533466--10533503 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
10533456 CCATCAAAAC
10533466 AAATT-GAAAAATT-TAA
1 AAATTGGAAAAATTATAA
*
10533482 AAATTGGGAAAATTATAA
1 AAATTGGAAAAATTATAA
10533500 AAAT
1 AAAT
10533504 ATATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAATTGGAAAAATTATAA
Found at i:10533637 original size:17 final size:18
Alignment explanation
Indices: 10533606--10533642 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
10533596 TCTAGACATA
10533606 TATATTTTTTAATAATTT
1 TATATTTTTTAATAATTT
10533624 TATATTTTTT-ATAATTT
1 TATATTTTTTAATAATTT
10533641 TA
1 TA
10533643 AAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATATTTTTTAATAATTT
Found at i:10536705 original size:22 final size:22
Alignment explanation
Indices: 10536670--10536731 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
10536660 AATAAAATGA
*
10536670 AATTTATTTAATTACTATATATT
1 AATTT-TTAAATTACTATATATT
* *
10536693 AATTTTTAAATTATTATATTTT
1 AATTTTTAAATTACTATATATT
* *
10536715 TATTTTTATAATGACTA
1 AATTTTTA-AATTACTA
10536732 AATTTATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTTAAATTACTATATATT
Found at i:10544806 original size:3 final size:3
Alignment explanation
Indices: 10544798--10544832 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
10544788 TTTTCTACAT
*
10544798 TTC TTC TTC TTC TTC TCC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
10544833 TTGACTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:10545513 original size:2 final size:2
Alignment explanation
Indices: 10545501--10545533 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10545491 AGAATACGGG
10545501 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10545534 TAAAGAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10546555 original size:16 final size:16
Alignment explanation
Indices: 10546534--10546569 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10546524 AGACCAGCTA
10546534 CAGCATGAAATTGCTC
1 CAGCATGAAATTGCTC
*
10546550 CAGCATGAAATTGGTC
1 CAGCATGAAATTGCTC
10546566 CAGC
1 CAGC
10546570 TGGAACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (16 bp):
CAGCATGAAATTGCTC
Found at i:10551406 original size:23 final size:23
Alignment explanation
Indices: 10551380--10551455 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
10551370 ATAAGTGTCA
10551380 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
10551403 CACTGAAATGTAGTC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
10551426 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
10551449 CACTGAT
1 CACTGAT
10551456 CAATAACACT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
22 2 0.04
23 43 0.93
24 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:10555220 original size:21 final size:21
Alignment explanation
Indices: 10555179--10555222 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10555169 AAATTTCAAA
**
10555179 GTTGGTATCGATATTTAATTG
1 GTTGGTATCGATACATAATTG
10555200 GTTGGTATCGATACCAT-ATTG
1 GTTGGTATCGATA-CATAATTG
10555221 GT
1 GT
10555223 ACTTTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (21 bp):
GTTGGTATCGATACATAATTG
Found at i:10557747 original size:24 final size:24
Alignment explanation
Indices: 10557720--10557774 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
10557710 CTATATGTTG
* *
10557720 CCTTAGTGGCGTATTGTGTTTGGC
1 CCTTAGTGGCGTACTCTGTTTGGC
*
10557744 CCTTA-TGGTGTACTCTGTTTGGC
1 CCTTAGTGGCGTACTCTGTTTGGC
10557767 CCTT-GTGG
1 CCTTAGTGG
10557775 TGAATTATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.07, C:0.20, G:0.31, T:0.42
Consensus pattern (24 bp):
CCTTAGTGGCGTACTCTGTTTGGC
Found at i:10561602 original size:12 final size:12
Alignment explanation
Indices: 10561585--10561615 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10561575 CTCTAGTTTT
10561585 CACACGGCCTAG
1 CACACGGCCTAG
*
10561597 CACACGGCCTGG
1 CACACGGCCTAG
10561609 CACACGG
1 CACACGG
10561616 GCGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.29, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:10563320 original size:23 final size:23
Alignment explanation
Indices: 10563293--10563414 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
10563283 AGTGTTATTG
*
10563293 ATCAGTGGTAGCTTCAGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
*
10563315 ATTCAGTGGTAGCTACGGCTACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
* *
10563339 ATCAGTGGTAGATTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
10563362 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
10563385 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
10563408 ATCAGTG
1 ATCAGTG
10563415 TGGCACTTAT
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
22 1 0.01
23 85 0.98
24 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:10563346 original size:46 final size:46
Alignment explanation
Indices: 10563293--10563414 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
10563283 AGTGTTATTG
*
10563293 ATCAGTGGTAGCTTCAGCTACAATTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
* * *
10563339 ATCAGTGGTAGATTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
10563385 ATCAGTGGTAGCTTCGGCTAC-ATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACAAT-TCAGTG
10563415 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.01
46 67 0.99
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
Found at i:10566081 original size:25 final size:25
Alignment explanation
Indices: 10566036--10566114 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
10566026 GTCATTAGCA
* *
10566036 TTACCGATTC-CAGCTCTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
10566060 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
* * * *
10566085 TTACCGTTATTCAGCTCGGAAGAGC
1 TTACCGATACTCAGCTCGTATGAGC
10566110 TTACC
1 TTACC
10566115 ATTTATCGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 9 0.19
25 39 0.81
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Found at i:10567266 original size:12 final size:12
Alignment explanation
Indices: 10567251--10567283 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
10567241 CTCCAGTTTT
10567251 CACACGGCCTAG
1 CACACGGCCTAG
*
10567263 CACACGGCCTGG
1 CACACGGCCTAG
10567275 CACACGGCC
1 CACACGGCC
10567284 GTGTGAGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.45, G:0.27, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:10568664 original size:18 final size:17
Alignment explanation
Indices: 10568613--10568665 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
10568603 TCGTACCTTA
10568613 GGTGAGCTCACATCTTT
1 GGTGAGCTCACATCTTT
*
10568630 GGTGAGCTCACAACTTT
1 GGTGAGCTCACATCTTT
*
10568647 GGATGAGCTCGCATCTTT
1 GG-TGAGCTCACATCTTT
10568665 G
1 G
10568666 CGATTTGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (17 bp):
GGTGAGCTCACATCTTT
Found at i:10569576 original size:2 final size:2
Alignment explanation
Indices: 10569569--10569593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10569559 TGAGTCAGGC
10569569 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10569594 GGTTTGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10571136 original size:25 final size:24
Alignment explanation
Indices: 10571090--10571144 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
10571080 CTATATTTAA
10571090 ATATAAATTCAAAACCCAAAACTAG
1 ATATAAATTCAAAACCCAAAACT-G
* *
10571115 ATATAAA-TCATAAACTCGAAACTG
1 ATATAAATTCA-AAACCCAAAACTG
10571139 A-ATAAA
1 ATATAAA
10571145 AAATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 17 0.63
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.22
Consensus pattern (24 bp):
ATATAAATTCAAAACCCAAAACTG
Found at i:10571927 original size:22 final size:22
Alignment explanation
Indices: 10571899--10572005 Score: 142
Period size: 22 Copynumber: 4.9 Consensus size: 22
10571889 TTTATTGTTC
*
10571899 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
10571921 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
10571943 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
10571965 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
10571987 AAACATGAGAGCTTAGTAC
1 AAACATGAGAGCTTAGTAC
10572006 CTATACCAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:10575094 original size:23 final size:22
Alignment explanation
Indices: 10575023--10575113 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 22
10575013 ATCAACTATT
10575023 AATATTTTAA-TAT-TAAATAT-
1 AATA-TTTAAGTATATAAATATG
*
10575043 -ATATTATAAGTTATATTAAATAATA
1 AATATT-TAAG-TATA-TAAAT-ATG
10575068 AATACTTTATAGTATA-AAATATG
1 AATA-TTTA-AGTATATAAATATG
*
10575091 AATATTTAATTATATAAATATG
1 AATATTTAAGTATATAAATATG
10575113 A
1 A
10575114 GTAAGGTAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
18 2 0.03
19 6 0.10
21 8 0.14
22 12 0.21
23 11 0.19
24 6 0.10
26 9 0.16
27 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (22 bp):
AATATTTAAGTATATAAATATG
Found at i:10576698 original size:27 final size:29
Alignment explanation
Indices: 10576668--10576723 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
10576658 ACAATTCAAA
*
10576668 ATACA-TTTTTTTA-TATTATACATATAT
1 ATACACTTTTTTTAGTATTATAAATATAT
10576695 ATACACGTTTTTTTAGTTATTATAAATAT
1 ATACAC-TTTTTTTAG-TATTATAAATAT
10576724 TTCTCTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
29 8 0.33
31 11 0.46
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.54
Consensus pattern (29 bp):
ATACACTTTTTTTAGTATTATAAATATAT
Found at i:10581126 original size:21 final size:21
Alignment explanation
Indices: 10581086--10581127 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10581076 AAGTGATGTG
*
10581086 AAAAAATGAAAAGATGAAAAT
1 AAAAAATGAAAAGATAAAAAT
10581107 AAAAAATGAAAA-AGTAAAAAT
1 AAAAAATGAAAAGA-TAAAAAT
10581128 GGAGAGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (21 bp):
AAAAAATGAAAAGATAAAAAT
Found at i:10582638 original size:132 final size:132
Alignment explanation
Indices: 10582401--10583067 Score: 1018
Period size: 132 Copynumber: 5.0 Consensus size: 132
10582391 TAGACAGCGA
* *
10582401 AGCAGATC-AAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCGAAA-ATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAA
* * *
10582465 TTCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTATGCAGTA
65 TTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTA
10582529 GTGG
129 GTGG
*
10582533 AGCAGATCGAAAATGGCAGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAAATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
*
10582598 TCTACTTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
10582663 GG
131 GG
* *
10582665 AGCAGATCGAAGATGGCGGATTTTACCCCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAAATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
* *
10582730 TCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
10582795 GG
131 GG
* **
10582797 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGCGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAAATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
* * *
10582862 TCTACTTCCCTGGGCAGCAGCGAAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCTGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
10582927 GG
131 GG
* *
10582929 AGCAGATC-AAAGATGGCGGATTTTACCTCCCT-AAGATTACAGTGGAGTACATTGAAACCAGTA
1 AGCAGATCGAAA-ATGGCGGATTTTACCTCCCTGAAG-TTGCAGTGGAGTACATTGAAGCCAGTA
* * * ** ** *
10582992 ATTCTATTTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTGAAGTTGC
64 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCT-AAGCAGT
10583057 AGTGG
128 AGTGG
10583062 AGCAGA
1 AGCAGA
10583068 CAGAAGTATA
Statistics
Matches: 497, Mismatches: 33, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
131 3 0.01
132 474 0.95
133 20 0.04
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (132 bp):
AGCAGATCGAAAATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
GG
Found at i:10582784 original size:44 final size:44
Alignment explanation
Indices: 10582736--10582916 Score: 118
Period size: 44 Copynumber: 4.1 Consensus size: 44
10582726 TAATTCTACT
10582736 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTACC
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTACC
** * * ** * ** * *
10582780 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTACC
** * * * * *
10582824 TCCCTGCGGTTGCAGTGGAGTACATTGAAG---CCAGTAAT-TCTACT
1 TCCCTG-GGCAGCAGCGGAATAGATTGAAGATTTCAG--ATCT-TACC
* *
10582868 TCCCTGGGCAGCAGCGAAATAGATTGAAGATTTCAGATCTTGCC
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTACC
10582912 TCCCT
1 TCCCT
10582917 AAGCTGTAGT
Statistics
Matches: 98, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
42 2 0.02
43 18 0.18
44 58 0.59
45 17 0.17
46 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (44 bp):
TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTACC
Found at i:10583061 original size:45 final size:46
Alignment explanation
Indices: 10583011--10583148 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 46
10583001 CCCTGGGCAA
*
10583011 CAGTGGAATAGATTGAAGATTA-CAGATCTTATCTCCCTGAAGTTG
1 CAGTGGAGTAGATTGAAGATTACCAGATCTTATCTCCCTGAAGTTG
* ** * *
10583056 CAGTGGAGCAGACAGAAG-TATACCA-ATCCTATCTCCTTGAAGTTG
1 CAGTGGAGTAGATTGAAGAT-TACCAGATCTTATCTCCCTGAAGTTG
* * * * * *
10583101 CAATGGAGTGGATT-AA-AATAGCAGATCTCATCTCTCTGAAGTTG
1 CAGTGGAGTAGATTGAAGATTACCAGATCTTATCTCCCTGAAGTTG
10583145 CAGT
1 CAGT
10583149 AAAGCAGATC
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
43 4 0.06
44 22 0.31
45 43 0.61
46 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (46 bp):
CAGTGGAGTAGATTGAAGATTACCAGATCTTATCTCCCTGAAGTTG
Found at i:10594904 original size:38 final size:39
Alignment explanation
Indices: 10594852--10594934 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
10594842 ATTTGTCAGC
* *
10594852 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTA
* * *
10594890 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTA
10594929 TTACTG
1 TTACTG
10594935 TTACCAACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 14 0.36
39 25 0.64
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (39 bp):
TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTA
Found at i:10594933 original size:39 final size:39
Alignment explanation
Indices: 10594852--10595017 Score: 127
Period size: 45 Copynumber: 4.0 Consensus size: 39
10594842 ATTTGTCAGC
* * * * *
10594852 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
10594890 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
* *
10594929 TTACTGTTACCAACTCGGCACTTTTTGTGTCGAATACTGTTACCGTTA
1 TTACTG------ATTCGGCACTTTGTGTGTCGAATACTGTTA-C--TA
* * *
10594977 CTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACT
1 ---TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACT
10595018 GCTACCGTTA
Statistics
Matches: 103, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
38 14 0.14
39 25 0.24
42 1 0.01
44 1 0.01
45 54 0.52
46 1 0.01
48 2 0.02
51 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
Found at i:10594948 original size:45 final size:45
Alignment explanation
Indices: 10594879--10595028 Score: 194
Period size: 45 Copynumber: 3.3 Consensus size: 45
10594869 ATGTGCCGAC
**
10594879 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
* * *
10594924 TACTATTACTGTTACCAACTCGGCACTTTTTGTGTCGAATACTGT
1 TACTGTTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
* * *
10594969 TACCGTTACTGTTA-CAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCA-ATTCGGCACTTTGTGTGTCGAATACTGT
* *
10595014 TACTGCTACCGTTAC
1 TACTGTTACTGTTAC
10595029 TGATTACTGT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 2 0.02
45 87 0.98
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:10595438 original size:11 final size:11
Alignment explanation
Indices: 10595424--10595490 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
10595414 ATTTTTTTTA
10595424 TTTTAAAATAT
1 TTTTAAAATAT
10595435 TTTTAAAATACT
1 TTTTAAAATA-T
**
10595447 TTTTTTAAT-T
1 TTTTAAAATAT
*
10595457 TTTT----TAA
1 TTTTAAAATAT
10595464 TTTTAAAATAT
1 TTTTAAAATAT
10595475 TTTTAAAATACT
1 TTTTAAAATA-T
10595487 TTTT
1 TTTT
10595491 TTAATTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
10 5 0.11
11 22 0.49
12 13 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:10595451 original size:40 final size:40
Alignment explanation
Indices: 10595375--10595520 Score: 231
Period size: 40 Copynumber: 3.6 Consensus size: 40
10595365 AAATATATTT
* * *
10595375 ATTTTTTAAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
10595414 ATTTTTTTTATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
10595454 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
10595494 ATTTTTTTAATTTTAAAAATACTTTTT
1 ATTTTTTTAATTTT-AAAATA-TTTTT
10595521 TTAATTTTTT
Statistics
Matches: 99, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
39 28 0.28
40 60 0.61
41 6 0.06
42 5 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:10595467 original size:30 final size:30
Alignment explanation
Indices: 10595433--10595545 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
10595423 ATTTTAAAAT
10595433 ATTTTTAAAATACTTTTTTTAATTTTTTTA
1 ATTTTTAAAATACTTTTTTTAATTTTTTTA
*
10595463 A-TTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTA
1 ATTTTTAAAATA---CT----T--TTTT--TAATTTTTTTA
*
10595503 ATTTTAAAAATACTTTTTTTAATTTTTTTAA
1 ATTTTTAAAATACTTTTTTTAATTTTTTT-A
10595534 ATTTTTAAAATA
1 ATTTTTAAAATA
10595546 AAAATGGGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 25
0.69 0.04 0.26
Matches are distributed among these distances:
29 10 0.15
30 11 0.17
31 12 0.18
32 5 0.08
34 1 0.02
36 1 0.02
38 5 0.08
40 12 0.18
41 9 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTTAAAATACTTTTTTTAATTTTTTTA
Found at i:10595493 original size:31 final size:30
Alignment explanation
Indices: 10595455--10595545 Score: 128
Period size: 31 Copynumber: 3.0 Consensus size: 30
10595445 CTTTTTTTAA
**
10595455 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTTTAA-ATTTTTAAAATAC
* *
10595486 TTTTTTTAATTTTTTTAATTTTAAAAATAC
1 TTTTTTTAATTTTTTAAATTTTTAAAATAC
10595516 TTTTTTTAATTTTTTTAAATTTTTAAAATA
1 TTTTTTTAA-TTTTTTAAATTTTTAAAATA
10595546 AAAATGGGCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.40
31 32 0.60
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTTTAATTTTTTAAATTTTTAAAATAC
Found at i:10595529 original size:79 final size:77
Alignment explanation
Indices: 10595375--10595542 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 77
10595365 AAATATATTT
* * *
10595375 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTAATTTTTTTTATTTTAAAATATTTTTA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATATTTTT-
*
10595440 AAATACTTTTTTTA
65 -AATAATTTTTTTA
*
10595454 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAAATACTTT
1 ATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTTTTAATTTT-AAAATA-TTT
*
10595519 TT-TTAATTTTTTTA
63 TTAATAATTTTTTTA
*
10595533 AATTTTTAAA
1 ATTTTTTAAA
10595543 ATAAAAATGG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
79 47 0.60
80 20 0.26
81 6 0.08
82 5 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (77 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATATTTTTA
ATAATTTTTTTA
Found at i:10595530 original size:40 final size:39
Alignment explanation
Indices: 10595375--10595539 Score: 215
Period size: 40 Copynumber: 4.2 Consensus size: 39
10595365 AAATATATTT
* * * *
10595375 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
*
10595414 ATTTTTTTTATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTTTA
10595454 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTTTA
** *
10595494 ATTTTTTTAATTTTAAAAATACTTTTTTTAAT-TTTTTTAA
1 ATTTTTTTAATTTT-AAAATA-TTTTTAAAATATTTTTTTA
10595534 ATTTTT
1 ATTTTT
10595540 AAAATAAAAA
Statistics
Matches: 114, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 27 0.24
40 73 0.64
41 6 0.05
42 8 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
Done.