Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 134 of 138
Found at i:19203809 original size:2 final size:2
Alignment explanation
Indices: 19203796--19203838 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
19203786 TTTTGTCACT
* * * *
19203796 TA TA TA TG TA TA TA TA TG TG TA TG 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
19203838 T
1 T
19203839 TAAAGAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19208056 original size:12 final size:12
Alignment explanation
Indices: 19208030--19208069 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
19208020 ATCTATCCCA
* *
19208030 GCATTTGCGTTT
1 GCATTTGCATAT
19208042 GCATTTGCATAT
1 GCATTTGCATAT
*
19208054 GCATATGCATAT
1 GCATTTGCATAT
19208066 GCAT
1 GCAT
19208070 GCAGCTGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (12 bp):
GCATTTGCATAT
Found at i:19211084 original size:17 final size:17
Alignment explanation
Indices: 19211062--19211113 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
19211052 ATTGGTAATC
19211062 AATTTTATATTTAAATA
1 AATTTTATATTTAAATA
* * *
19211079 AATTTTAAAATTAATTA
1 AATTTTATATTTAAATA
*
19211096 AAATTTAT-TTTAAA-A
1 AATTTTATATTTAAATA
19211111 AAT
1 AAT
19211114 CTTTTAGTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 3 0.11
16 4 0.15
17 20 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTATATTTAAATA
Found at i:19212023 original size:15 final size:15
Alignment explanation
Indices: 19211980--19212027 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
19211970 CTGACAAAGT
*
19211980 TAAAAAT-ATATATAA
1 TAAAAATAATA-AAAA
*
19211995 TAAATAAAAATAAAAA
1 TAAA-AATAATAAAAA
19212011 TAAAAATAATAAAAA
1 TAAAAATAATAAAAA
19212026 TA
1 TA
19212028 TATAAAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 16 0.57
16 9 0.32
17 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAATAATAAAAA
Found at i:19212027 original size:6 final size:6
Alignment explanation
Indices: 19211980--19212019 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
19211970 CTGACAAAGT
* *
19211980 TAAAAA TATATA TAATAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAA-AAA TAAAAA TAAAAA TAAAAA TAA
19212020 TAAAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
TAAAAA
Found at i:19212083 original size:39 final size:40
Alignment explanation
Indices: 19212006--19212086 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 40
19211996 AAATAAAAAT
* *
19212006 AAAAATAAAAATAATAAAAATATATAAAAGATTGACCAAA
1 AAAAATAAAAATAATAAAAATAGAAAAAAGATTGACCAAA
*
19212046 AAAATATAAAAATAA-AAAATTACGAAAAAAGA-T-ACCAAA
1 AAAA-ATAAAAATAATAAAAATA-GAAAAAAGATTGACCAAA
19212085 AA
1 AA
19212087 TGCCTTTGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 8 0.22
40 11 0.31
41 17 0.47
ACGTcount: A:0.72, C:0.06, G:0.05, T:0.17
Consensus pattern (40 bp):
AAAAATAAAAATAATAAAAATAGAAAAAAGATTGACCAAA
Found at i:19213114 original size:3 final size:3
Alignment explanation
Indices: 19213108--19213149 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
19213098 AAAAAAAAGA
19213108 AAT AAT AAT AAT AAT -AT AA- AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19213150 TTAAAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19215514 original size:21 final size:19
Alignment explanation
Indices: 19215468--19215552 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
19215458 ATCAAAACAT
19215468 AATTTAAA-TAACTTGA-A
1 AATTTAAATTAACTTGAGA
*
19215485 AACTTAAATTAAACTTGCAGA
1 AATTTAAATT-AACTTG-AGA
19215506 AATTTAAATTAACTTGAAAGA
1 AATTTAAATTAACTTG--AGA
* *
19215527 AA-TTGAATTAAATTGA-A
1 AATTTAAATTAACTTGAGA
19215544 AACTTTAAA
1 AA-TTTAAA
19215553 AAACAAATGC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
17 10 0.18
18 2 0.04
19 10 0.18
20 18 0.33
21 15 0.27
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (19 bp):
AATTTAAATTAACTTGAGA
Found at i:19221396 original size:114 final size:114
Alignment explanation
Indices: 19221195--19221419 Score: 328
Period size: 114 Copynumber: 2.0 Consensus size: 114
19221185 CTAGAAGTAC
* * *
19221195 AATGGTTCATTGGGCCTAAGCTTAGACAATATTAGGGATAGGGAAAGGAACTTATTGAACTCTTC
1 AATGGTTCATTGGGCCTAAGCTTAGAAAATATTAGGGAGAGGGAAAGGAACTCATTGAACTCTTC
19221260 AAAAGCTTATGGACATTATGGTGTCCACTAAAAATCTAAAATGTTCCTT
66 AAAAGCTTATGGACATTATGGTGTCCACTAAAAATCTAAAATGTTCCTT
* * * * *
19221309 AATGGTTCATTGGGCCTAAGCTTAGAAAATATTAGAGGCGA-GGAGAGGAGCTCCTTGAGCTCTT
1 AATGGTTCATTGGGCCTAAGCTTAGAAAATATTAG-GGAGAGGGAAAGGAACTCATTGAACTCTT
* *
19221373 C-AAAGACTTGTGGACATTGTGGTGTCCACTAAAAATCTAAAATGTTC
65 CAAAAG-CTTATGGACATTATGGTGTCCACTAAAAATCTAAAATGTTC
19221420 TTGAATATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
113 4 0.04
114 92 0.93
115 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (114 bp):
AATGGTTCATTGGGCCTAAGCTTAGAAAATATTAGGGAGAGGGAAAGGAACTCATTGAACTCTTC
AAAAGCTTATGGACATTATGGTGTCCACTAAAAATCTAAAATGTTCCTT
Found at i:19227409 original size:30 final size:30
Alignment explanation
Indices: 19227347--19227409 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
19227337 GATCAGTGAG
*
19227347 AAAATTTGAAAATTTCAGTTGGAAATCAAT
1 AAAATTTGAAAATTTCAGTTGAAAATCAAT
*
19227377 AAAATTTGTAAATTTCA-TTGCCAAAATC-AT
1 AAAATTTGAAAATTTCAGTTG--AAAATCAAT
19227407 AAA
1 AAA
19227410 GAACATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.10
30 21 0.72
31 5 0.17
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (30 bp):
AAAATTTGAAAATTTCAGTTGAAAATCAAT
Found at i:19229552 original size:9 final size:9
Alignment explanation
Indices: 19229538--19229562 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19229528 AAACTCAATG
19229538 AAAATTTTT
1 AAAATTTTT
19229547 AAAATTTTT
1 AAAATTTTT
19229556 AAAATTT
1 AAAATTT
19229563 AAGCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:19233632 original size:34 final size:34
Alignment explanation
Indices: 19233593--19233659 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
19233583 ACAGAAACAT
*
19233593 AACAAA-TAAGACAGGAAGTTTAGGGATTTGACCC
1 AACAAATTAA-ACAAGAAGTTTAGGGATTTGACCC
*
19233627 AACAAATTAAATAAGAAGTTTAGGGATTTGACC
1 AACAAATTAAACAAGAAGTTTAGGGATTTGACC
19233660 TAAAATGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.90
35 3 0.10
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (34 bp):
AACAAATTAAACAAGAAGTTTAGGGATTTGACCC
Found at i:19252712 original size:28 final size:28
Alignment explanation
Indices: 19252679--19252748 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
19252669 AAATATTGTA
*
19252679 GTTTGTTAAATGGTATTGTATGATATTG
1 GTTTGTTGAATGGTATTGTATGATATTG
19252707 GTTTGTTGAATGGTATTGTATGATATTG
1 GTTTGTTGAATGGTATTGTATGATATTG
*
19252735 GTTTGCTGAATGGT
1 GTTTGTTGAATGGT
19252749 GTTTTTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.49
Consensus pattern (28 bp):
GTTTGTTGAATGGTATTGTATGATATTG
Found at i:19255907 original size:35 final size:35
Alignment explanation
Indices: 19255861--19255937 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
19255851 TGTCACATAC
*
19255861 CAAATGTTTTCTGGGCATAAACCTACAACTT-ACTT
1 CAAATATTTTCTGGGCATAAACCTACAA-TTAACTT
* *
19255896 CAAATATTTTCTGGGTATAAATCTACAATTAACTT
1 CAAATATTTTCTGGGCATAAACCTACAATTAACTT
*
19255931 CACATAT
1 CAAATAT
19255938 ATAATTAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (35 bp):
CAAATATTTTCTGGGCATAAACCTACAATTAACTT
Found at i:19256251 original size:63 final size:61
Alignment explanation
Indices: 19256029--19256384 Score: 239
Period size: 63 Copynumber: 5.7 Consensus size: 61
19256019 TTGAATGGGG
* * * ** * * * * **
19256029 TTATTGAAGGCGTTTCTAGCTAAAAACGCCTTTAATAATCCCCTCCATAATTTTTTGTATCGA
1 TTATTGAAGGCATTTTTGGCTAAAAATACCTTCAATAAT-CTCTTCA-AATTTTTTGAAAGGA
* ** * * * * ** *
19256092 TTATTGAAGGCGTTTTTAACAAAAAACATCTTCAATAAT-TCTTCATAAAAATTTATTGAGTGAA
1 TTATTGAAGGCATTTTTGGCTAAAAATACCTTCAATAATCTCTTC----AAATTTTTTGAAAGGA
* *
19256156 TTATTGAAGGCATTTTTGGCTAAAAA-AACTTCAATAATCTCTTCCAAATTTTTTCAAAGGA
1 TTATTGAAGGCATTTTTGGCTAAAAATACCTTCAATAATCTCTT-CAAATTTTTTGAAAGGA
* * * * * * *
19256217 TTATTGAAGGTATTTTTTTGATAAAAATACCTTCAATAATCCCCTTAAAATTTTTTGTAAGGT
1 TTATTGAAGGCA-TTTTTGGCTAAAAATACCTTCAATAAT-CTCTTCAAATTTTTTGAAAGGA
* * * *
19256280 TTATTAAAGGCATTTTTGGCTAAAAATACCTTCAATATTCTCTCTTCATAATTTTATGAATGGA
1 TTATTGAAGGCATTTTTGGCTAAAAATACCTTCAATA--ATCTCTTCA-AATTTTTTGAAAGGA
** * *
19256344 TTATTGAAGGTGTTTTTAGCTAGAAAATACCTTAAATAATC
1 TTATTGAAGGCATTTTTGGCTA-AAAATACCTTCAATAATC
19256385 CTTTACAAAT
Statistics
Matches: 231, Mismatches: 49, Indels: 26
0.75 0.16 0.08
Matches are distributed among these distances:
61 25 0.11
62 35 0.15
63 85 0.37
64 70 0.30
65 16 0.07
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (61 bp):
TTATTGAAGGCATTTTTGGCTAAAAATACCTTCAATAATCTCTTCAAATTTTTTGAAAGGA
Found at i:19256371 original size:127 final size:124
Alignment explanation
Indices: 19256156--19256385 Score: 318
Period size: 127 Copynumber: 1.8 Consensus size: 124
19256146 ATTGAGTGAA
* *
19256156 TTATTGAAGGCATTTTTGGCTAAAAAAACTTCAATAATCTCTTCCAAATTTTTTCAAAGGATTAT
1 TTATTAAAGGCATTTTTGGCTAAAAAAACTTCAATAATCTCTTCCAAATTTTATCAAAGGATTAT
* * *
19256221 TGAAGGTATTTTTTTGATAAAAATACCTTCAATAATCCCCTTAAAATTTTTTGTAAGGT
66 TGAAGGTAGTTTTTAGATAAAAATACCTTAAATAATCCCCTTAAAATTTTTTGTAAGGT
* * * * *
19256280 TTATTAAAGGCATTTTTGGCTAAAAATACCTTCAATATTCTCTCTTCATAATTTTATGAATGGAT
1 TTATTAAAGGCATTTTTGGCTAAAAA-AACTTCAATAATCTCT-TCCA-AATTTTATCAAAGGAT
*
19256345 TATTGAAGGT-GTTTTTAGCTAGAAAATACCTTAAATAATCC
63 TATTGAAGGTAGTTTTTAGATA-AAAATACCTTAAATAATCC
19256386 TTTACAAATA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
124 25 0.27
125 14 0.15
126 11 0.12
127 41 0.45
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (124 bp):
TTATTAAAGGCATTTTTGGCTAAAAAAACTTCAATAATCTCTTCCAAATTTTATCAAAGGATTAT
TGAAGGTAGTTTTTAGATAAAAATACCTTAAATAATCCCCTTAAAATTTTTTGTAAGGT
Found at i:19256677 original size:62 final size:60
Alignment explanation
Indices: 19256611--19256789 Score: 184
Period size: 63 Copynumber: 2.9 Consensus size: 60
19256601 TTTCTGGTAA
*
19256611 AAAAATACCTTCAATAATCGTCTTCATTTTTTATGAGGGGATTATTCAAAGCGTTGTCTACC
1 AAAAATACCTTCAATAATC-TCTTCATTTTTTATGAGGGGATTATTCAAAGCGTTGTATA-C
* * * * *
19256673 AAAAATACCTTCAATAATCCTCTATCCA-TTTTTATAAAGGCATTATTCAAAGTGTTTTATAC
1 AAAAATACCTTCAATAAT-CTCT-T-CATTTTTTATGAGGGGATTATTCAAAGCGTTGTATAC
* * *
19256735 AAAAA-ACGTCTTCAATAATCACTTCAATTTTTTA-GAGAGGATTATTCAAGGCGTT
1 AAAAATAC--CTTCAATAATCTCTTC-ATTTTTTATGAGGGGATTATTCAAAGCGTT
19256790 TTAGTCGATA
Statistics
Matches: 97, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
60 1 0.01
61 19 0.20
62 36 0.37
63 39 0.40
64 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (60 bp):
AAAAATACCTTCAATAATCTCTTCATTTTTTATGAGGGGATTATTCAAAGCGTTGTATAC
Found at i:19257466 original size:14 final size:15
Alignment explanation
Indices: 19257437--19257467 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19257427 AGATAATAAG
19257437 ATAAATATTAAGTAA
1 ATAAATATTAAGTAA
19257452 ATAAATATT-AGTAA
1 ATAAATATTAAGTAA
19257466 AT
1 AT
19257468 TTTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
ATAAATATTAAGTAA
Found at i:19257520 original size:16 final size:18
Alignment explanation
Indices: 19257493--19257525 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19257483 GTAAATGTAT
19257493 TATTATTTTTAA-ATAAC
1 TATTATTTTTAATATAAC
19257510 TATTA-TTTTAATATAA
1 TATTATTTTTAATATAA
19257526 AGATTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTTTTAATATAAC
Found at i:19269176 original size:20 final size:20
Alignment explanation
Indices: 19269153--19269192 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19269143 TTTGCATACT
19269153 TTATTTTGTTTTGTTGCACA
1 TTATTTTGTTTTGTTGCACA
19269173 TTATTTTGTTTTGTTGCACA
1 TTATTTTGTTTTGTTGCACA
19269193 AACAGTCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (20 bp):
TTATTTTGTTTTGTTGCACA
Found at i:19272757 original size:37 final size:37
Alignment explanation
Indices: 19272716--19272812 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
19272706 AAAAAAAAAG
* *
19272716 TAGTGAAAGTGTTT-TCTAGAGAAAATAGGAGAATAAA
1 TAGTGAAAGTGTTTCTCTA-AAAAAAAAGGAGAATAAA
* * *
19272753 TAGTGGAAGTGTTTCTTTAAAAAAAAAGGAGAATAAG
1 TAGTGAAAGTGTTTCTCTAAAAAAAAAGGAGAATAAA
* * *
19272790 TAATAAAAGTGTTTCCCTAAAAA
1 TAGTGAAAGTGTTTCTCTAAAAA
19272813 TTAGGAGAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
37 46 0.94
38 3 0.06
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (37 bp):
TAGTGAAAGTGTTTCTCTAAAAAAAAAGGAGAATAAA
Found at i:19273239 original size:3 final size:3
Alignment explanation
Indices: 19273231--19273263 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
19273221 ATTTATTTAT
*
19273231 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19273264 CTACTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:19273723 original size:19 final size:18
Alignment explanation
Indices: 19273681--19273723 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
19273671 CTCCTTTTTT
19273681 TTTTTTTTACTATTTGAC
1 TTTTTTTTACTATTTGAC
19273699 TATTTTTTTAGGCTATTTGA-
1 T-TTTTTTTA--CTATTTGAC
19273719 TTTTT
1 TTTTT
19273724 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 12 0.55
20 1 0.05
21 8 0.36
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTTTTTTACTATTTGAC
Found at i:19275272 original size:160 final size:160
Alignment explanation
Indices: 19274999--19275333 Score: 431
Period size: 160 Copynumber: 2.1 Consensus size: 160
19274989 TAATCCAAAT
* * * *
19274999 TGTAACTTTTTTCACATATATCAATCATGAAAACCATGTCAATCATTTGAACAAGTTTAATATCA
1 TGTAA-TTTTTTCACACATATCAATCATGAAAACCAAGTCAATCATTCGAACAAATTTAATATCA
* * ** * *
19275064 TTTATTTAAGCTATCTAAACTTCTAAAACAAAACAATAACTGTAAATTTGTATTTTTACCTTTTA
65 TATATTGAAGCTATCTAAACTTCTAAAACAAAACAATAACAATAAATTTGCATTTTTACCTCTTA
*
19275129 ACGG-TGCAAAAGTCCTAAACAGACATAAAC
130 ACGGATGAAAAAGTCCTAAACAGACATAAAC
* *
19275159 TGTAATTTTTTCACACATATCAATCATGAAAACTAAGTTCAATGATTCGAACAAATTTAATATCA
1 TGTAATTTTTTCACACATATCAATCATGAAAACCAAG-TCAATCATTCGAACAAATTTAATATCA
* * *
19275224 TATATTGAAGCTATCTAAACTGT-TAAAATAGAACAATAACAATAAATTTGCATTTTTTCCTCTT
65 TATATTGAAGCTATCTAAACT-TCTAAAACAAAACAATAACAATAAATTTGCATTTTTACCTCTT
* * *
19275288 AACGGCATGAAAAAGTTCTAAATAGACATAAAG
129 AACGG-ATGAAAAAGTCCTAAACAGACATAAAC
* *
19275321 TGCAAGTTTTTCA
1 TGTAATTTTTTCA
19275334 TTTAGTGCTT
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
159 29 0.19
160 87 0.58
161 1 0.01
162 33 0.22
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.35
Consensus pattern (160 bp):
TGTAATTTTTTCACACATATCAATCATGAAAACCAAGTCAATCATTCGAACAAATTTAATATCAT
ATATTGAAGCTATCTAAACTTCTAAAACAAAACAATAACAATAAATTTGCATTTTTACCTCTTAA
CGGATGAAAAAGTCCTAAACAGACATAAAC
Found at i:19279214 original size:3 final size:3
Alignment explanation
Indices: 19279206--19279359 Score: 128
Period size: 3 Copynumber: 53.7 Consensus size: 3
19279196 TAGTCAATTT
* * * * *
19279206 TTA TTA TTA CTA TTA CTA TTA TTA TTT TTA TTA TTA ATA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
19279254 TTTG TTA TTA TTG GTA TTA TTA ATA TCA -TA TTA TTA -TA TTA -TA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
19279297 TTA -TA TT- TTCA TTA TTA TTA -TA TTA -TA GTA -TA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19279338 TTA TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
19279360 CTTCTTTCCT
Statistics
Matches: 120, Mismatches: 20, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
2 17 0.14
3 100 0.83
4 3 0.03
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19279293 original size:5 final size:5
Alignment explanation
Indices: 19279285--19279358 Score: 71
Period size: 5 Copynumber: 14.2 Consensus size: 5
19279275 AATATCATAT
* *
19279285 TATTA TATTA TATTA TATTT TCATTA TTATTA TATTA TAGTA TATTA TTATTA
1 TATTA TATTA TATTA TATTA T-ATTA -TATTA TATTA TATTA TATTA -TATTA
19279338 TTATTA TTATTA T-TT- TATTA T
1 -TATTA -TATTA TATTA TATTA T
19279359 TCTTCTTTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 30 0.50
6 24 0.40
7 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:19280203 original size:26 final size:25
Alignment explanation
Indices: 19280164--19280246 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 25
19280154 CCGATTATAG
19280164 TTTTTA-TTTT-ATTTTTTATTTTA
1 TTTTTATTTTTCATTTTTTATTTTA
*
19280187 TTTTTATTTTATCATTTTATATTTTAA
1 TTTTTATTTT-TCATTTTTTATTTT-A
*
19280214 GTTTTTA--TTTCATTTTTATAATTTA
1 -TTTTTATTTTTCATTTTT-TATTTTA
19280239 -TTTTATTT
1 TTTTTATTT
19280247 GGCTAATTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
23 11 0.22
24 3 0.06
25 10 0.20
26 18 0.37
27 1 0.02
28 6 0.12
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTTCATTTTTTATTTTA
Found at i:19280212 original size:7 final size:7
Alignment explanation
Indices: 19280158--19280239 Score: 56
Period size: 6 Copynumber: 12.6 Consensus size: 7
19280148 CCTAACCCGA
19280158 TTATAGTT
1 TTATA-TT
19280166 TT-TATT
1 TTATATT
19280172 TTAT-TT
1 TTATATT
19280178 TT-TA-T
1 TTATATT
19280183 TT-TATT
1 TTATATT
19280189 TT-TATT
1 TTATATT
19280195 TTATCATT
1 TTAT-ATT
19280203 TTATATT
1 TTATATT
19280210 TTA-AGTT
1 TTATA-TT
19280217 TT-TATT
1 TTATATT
*
19280223 TCAT-TT
1 TTATATT
*
19280229 TTATAAT
1 TTATATT
19280236 TTAT
1 TTAT
19280240 TTTATTTGGC
Statistics
Matches: 62, Mismatches: 3, Indels: 19
0.74 0.04 0.23
Matches are distributed among these distances:
5 6 0.10
6 26 0.42
7 21 0.34
8 9 0.15
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (7 bp):
TTATATT
Found at i:19290916 original size:45 final size:44
Alignment explanation
Indices: 19290856--19290958 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
19290846 TCACTTGAAC
*
19290856 AAAAAAA-A-TTCAAGTTAAAAACCCAAAAGCACGACTTAAGAAA
1 AAAAAAAGAGTTCAAGTTAAAAACCCAAAAGCACAACTTAAG-AA
* * * *
19290899 AAAAAAAGAGTTCAAGTTAAAAACCCGAAAGGATAACTTGAGAA
1 AAAAAAAGAGTTCAAGTTAAAAACCCAAAAGCACAACTTAAGAA
19290943 AAAAAAAGTAGTTCAA
1 AAAAAAAG-AGTTCAA
19290959 TCTGAAAACC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
43 7 0.13
44 11 0.21
45 34 0.65
ACGTcount: A:0.58, C:0.13, G:0.14, T:0.16
Consensus pattern (44 bp):
AAAAAAAGAGTTCAAGTTAAAAACCCAAAAGCACAACTTAAGAA
Found at i:19293280 original size:6 final size:6
Alignment explanation
Indices: 19293265--19293349 Score: 57
Period size: 6 Copynumber: 13.5 Consensus size: 6
19293255 GATCGTAGGT
* * * *
19293265 TTTTTC TTTTTA TTTTTTA ATTTTA ATTTTA TTTTATCA TTTTATA TTTTAA
1 TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTT-T-A TTTT-TA TTTTTA
*
19293317 GTTTTTA -TTTGA TTTTTA TTATTTA -TTTTA TTT
1 -TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTT
19293350 GGCTGATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.12
6 29 0.45
7 21 0.32
8 7 0.11
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:19293294 original size:19 final size:18
Alignment explanation
Indices: 19293272--19293346 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 18
19293262 GGTTTTTTCT
19293272 TTTTATTTTTTAATTTTAA
1 TTTTATTTTTT-ATTTTAA
*
19293291 TTTTATTTTATCATTTTATA
1 TTTTATTTT-TTATTTTA-A
* * *
19293311 TTTTAAGTTTTTATTTGAT
1 TTTT-ATTTTTTATTTTAA
*
19293330 TTTTATTATTTATTTTA
1 TTTTATTTTTTATTTTA
19293347 TTTGGCTGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
18 10 0.22
19 19 0.42
20 12 0.27
21 4 0.09
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATTTTTTATTTTAA
Found at i:19293333 original size:26 final size:24
Alignment explanation
Indices: 19293278--19293350 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
19293268 TTCTTTTTAT
*
19293278 TTTTTA-ATTTTAATTTTATTTTA
1 TTTTTATATTTTAATTTTATTTGA
19293301 TCATTTTATATTTTAAGTTTTTATTTGA
1 T--TTTTATATTTTAA--TTTTATTTGA
19293329 TTTTTAT-TATTT-ATTTTATTTG
1 TTTTTATAT-TTTAATTTTATTTG
19293351 GCTGATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
23 10 0.23
25 7 0.16
26 16 0.37
28 10 0.23
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTTTATATTTTAATTTTATTTGA
Found at i:19298318 original size:90 final size:90
Alignment explanation
Indices: 19298165--19298332 Score: 257
Period size: 90 Copynumber: 1.9 Consensus size: 90
19298155 AGTTACAAGA
* *
19298165 ATGGTTATTTATGGAATGACTTAGCAGGCAATGACATTATTCCTCTATCAGATTGAGCTAAATAT
1 ATGGTTATTTATGGAATGACTTAGCAGACAATGACATTATTCCTCTATCAGATTGAACTAAATAT
*
19298230 GTACTTAAAGGCTCAGATTTAGTTG
66 GTACTCAAAGGCTCAGATTTAGTTG
* ** *
19298255 ATGGTTATTTATGGAATGACTTAGCAGACAATGATATTATTTTTCTATTAGA-TGAAACTAAATA
1 ATGGTTATTTATGGAATGACTTAGCAGACAATGACATTATTCCTCTATCAGATTG-AACTAAATA
19298319 TGTACTCAAAGGCT
65 TGTACTCAAAGGCT
19298333 TATAATTGGT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
89 2 0.03
90 68 0.97
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (90 bp):
ATGGTTATTTATGGAATGACTTAGCAGACAATGACATTATTCCTCTATCAGATTGAACTAAATAT
GTACTCAAAGGCTCAGATTTAGTTG
Found at i:19298650 original size:21 final size:21
Alignment explanation
Indices: 19298629--19298675 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
19298619 AAGAATGAGA
*
19298629 AAAAGAAAAGGAATAAGAAGAAG
1 AAAA-AAAA-GAAAAAGAAGAAG
*
19298652 AAAAAAAAGAAAAAGAATAAG
1 AAAAAAAAGAAAAAGAAGAAG
19298673 AAA
1 AAA
19298676 TGGAAGAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 4 0.18
23 4 0.18
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AAAAAAAAGAAAAAGAAGAAG
Found at i:19301833 original size:13 final size:13
Alignment explanation
Indices: 19301815--19301839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19301805 TGAATTTAGA
19301815 TATTTTATTAAAT
1 TATTTTATTAAAT
19301828 TATTTTATTAAA
1 TATTTTATTAAA
19301840 AATTTCATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTTATTAAAT
Found at i:19302000 original size:2 final size:2
Alignment explanation
Indices: 19301993--19302026 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19301983 AAACACCTTA
19301993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19302027 TTTATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19305486 original size:14 final size:15
Alignment explanation
Indices: 19305454--19305496 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
19305444 CTTGTATTTT
19305454 CAAA-CATATTTTCA
1 CAAATCATATTTTCA
*
19305468 CAAATCATATTTTTA
1 CAAATCATATTTTCA
*
19305483 -AAATCAGATTTTCA
1 CAAATCATATTTTCA
19305497 TATTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (15 bp):
CAAATCATATTTTCA
Found at i:19306087 original size:2 final size:2
Alignment explanation
Indices: 19306080--19306110 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19306070 AAGAAAAATC
19306080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19306111 CTACATGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19309376 original size:12 final size:12
Alignment explanation
Indices: 19309356--19309385 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19309346 GAACATAAAG
*
19309356 AAATTTGGTCCA
1 AAATCTGGTCCA
19309368 AAATCTGGTCCA
1 AAATCTGGTCCA
19309380 AAATCT
1 AAATCT
19309386 TTTGCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (12 bp):
AAATCTGGTCCA
Found at i:19309840 original size:22 final size:22
Alignment explanation
Indices: 19309812--19309856 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
19309802 TTATTTAGTA
*
19309812 TATGACAAGCTGTTAATAAAGT
1 TATGACAAGCTGTTAAAAAAGT
19309834 TATGACAAGCTGTTAAAAAAGT
1 TATGACAAGCTGTTAAAAAAGT
19309856 T
1 T
19309857 TCACCCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (22 bp):
TATGACAAGCTGTTAAAAAAGT
Found at i:19318495 original size:2 final size:2
Alignment explanation
Indices: 19318488--19318518 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19318478 TGTCTTTTAT
19318488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19318519 CAATATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19323718 original size:20 final size:20
Alignment explanation
Indices: 19323695--19323745 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
19323685 CTAATTAATT
19323695 TTTTTATTTTTTAATA-TATA
1 TTTTTATTTTTTAATAGTA-A
* *
19323715 TTTTTATATTTTATTAGTAA
1 TTTTTATTTTTTAATAGTAA
19323735 TTTATTATTTT
1 TTT-TTATTTT
19323746 ACCCTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTTTAATAGTAA
Found at i:19324090 original size:52 final size:52
Alignment explanation
Indices: 19324027--19324158 Score: 183
Period size: 52 Copynumber: 2.5 Consensus size: 52
19324017 AATTTCAAGA
* *
19324027 GAAAGAGGATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAG
1 GAAAG-GGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAG
* * * *
19324080 GAAAGTGATTCTTAATAGGCAAGTTTTACTTACAGGAGAAGAATTCTAAGAG
1 GAAAGGGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAG
* *
19324132 GAGAGGGATTCTTAATGGGCAAGTTTG
1 GAAAGGGATTCTTAATAGGCAAGTTTG
19324159 TATGGTTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
52 64 0.93
53 5 0.07
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (52 bp):
GAAAGGGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAG
Found at i:19326899 original size:2 final size:2
Alignment explanation
Indices: 19326892--19326927 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19326882 TCATACATAC
*
19326892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19326928 TGAGGGTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19331138 original size:14 final size:14
Alignment explanation
Indices: 19331121--19331162 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
19331111 ATAAAGTACA
19331121 AAAATGCTGAAAAT
1 AAAATGCTGAAAAT
* *
19331135 AAAA--CTTAAAAG
1 AAAATGCTGAAAAT
19331147 AAAATGCTGAAAAT
1 AAAATGCTGAAAAT
19331161 AA
1 AA
19331163 GATAATTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (14 bp):
AAAATGCTGAAAAT
Found at i:19332749 original size:24 final size:24
Alignment explanation
Indices: 19332717--19332773 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
19332707 ACAGTTTCAA
* **
19332717 ACAACTTATATAAACCTTTTAAGC
1 ACAAATTATATAAACAATTTAAGC
*
19332741 ACAAATTATATAAATAATTTAAGC
1 ACAAATTATATAAACAATTTAAGC
*
19332765 ACAATTTAT
1 ACAAATTAT
19332774 CAATAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (24 bp):
ACAAATTATATAAACAATTTAAGC
Found at i:19342800 original size:16 final size:15
Alignment explanation
Indices: 19342772--19342847 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
19342762 ATGAAAAGTG
*
19342772 AAAAATAAA-TAAACA
1 AAAAAAAAAGTAAA-A
19342787 AAAAAAAAAGTAAATGA
1 AAAAAAAAAGTAAA--A
19342804 AAAGAAAAAAG-AGAAA
1 AAA-AAAAAAGTA-AAA
19342820 AAAAAAAAA--AAAA
1 AAAAAAAAAGTAAAA
*
19342833 AATAAAAAAG-AAAA
1 AAAAAAAAAGTAAAA
19342847 A
1 A
19342848 CAAATTGATG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
13 11 0.21
14 6 0.11
15 14 0.26
16 8 0.15
17 5 0.09
18 9 0.17
ACGTcount: A:0.84, C:0.01, G:0.08, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAGTAAAA
Found at i:19342800 original size:20 final size:18
Alignment explanation
Indices: 19342772--19342847 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 18
19342762 ATGAAAAGTG
19342772 AAAAA-TAAATAAACAAAAA
1 AAAAAGTAAA-AAA-AAAAA
*
19342791 AAAAAGTAAATGAAAAGAAA
1 AAAAAGTAAA--AAAAAAAA
* *
19342811 AAAGAGAAAAAAAAAAAA
1 AAAAAGTAAAAAAAAAAA
*
19342829 AAAAAATAAAAAAGAAAAA
1 AAAAAGTAAAAAA-AAAAA
19342848 CAAATTGATG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
18 17 0.37
19 10 0.22
20 16 0.35
21 3 0.07
ACGTcount: A:0.84, C:0.01, G:0.08, T:0.07
Consensus pattern (18 bp):
AAAAAGTAAAAAAAAAAA
Found at i:19342815 original size:7 final size:7
Alignment explanation
Indices: 19342803--19342847 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
19342793 AAAGTAAATG
19342803 AAAAGAA
1 AAAAGAA
19342810 AAAAGAGA
1 AAAAGA-A
19342818 AAAA-AA
1 AAAAGAA
*
19342824 AAAAAAA
1 AAAAGAA
*
19342831 AAAATAA
1 AAAAGAA
19342838 AAAAGAA
1 AAAAGAA
19342845 AAA
1 AAA
19342848 CAAATTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.15
7 24 0.71
8 5 0.15
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:19342852 original size:17 final size:17
Alignment explanation
Indices: 19342772--19342852 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
19342762 ATGAAAAGTG
*
19342772 AAAAATAAATAAACAAAA
1 AAAAAAAAATAAA-AAAA
*
19342790 AAAAAAGTAAATGAAAAGAA
1 AAAAAA--AAAT-AAAAAAA
* *
19342810 AAAAGAGAA-AAAAAAA
1 AAAAAAAAATAAAAAAA
*
19342826 AAAAAAAAATAAAAAAG
1 AAAAAAAAATAAAAAAA
*
19342843 AAAAACAAAT
1 AAAAAAAAAT
19342853 TGATGGGTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
16 13 0.26
17 15 0.30
18 7 0.14
20 12 0.24
21 3 0.06
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAA
Found at i:19344380 original size:22 final size:22
Alignment explanation
Indices: 19344355--19344419 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
19344345 TTTAAACAAA
** *
19344355 AATCTTTAAAATTTTGGTTGTG
1 AATCTTTAAAATTTTGAATGAG
*
19344377 AATCTCTAAAATTTTTGAATGAG
1 AATCTTTAAAA-TTTTGAATGAG
*
19344400 AATCTTTGAAATTTTGAATG
1 AATCTTTAAAATTTTGAATG
19344420 TAAAATCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (22 bp):
AATCTTTAAAATTTTGAATGAG
Found at i:19344426 original size:23 final size:23
Alignment explanation
Indices: 19344353--19344426 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
19344343 TTTTTAAACA
**
19344353 AAAATCTTTAAAATTTTGGTTGT
1 AAAATCTTTAAAATTTTGAATGT
* *
19344376 -GAATCTCTAAAATTTTTGAATG-
1 AAAATCTTTAAAA-TTTTGAATGT
* *
19344398 AGAATCTTTGAAATTTTGAATGT
1 AAAATCTTTAAAATTTTGAATGT
19344421 AAAATC
1 AAAATC
19344427 ATAAAGTTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (23 bp):
AAAATCTTTAAAATTTTGAATGT
Found at i:19344486 original size:22 final size:24
Alignment explanation
Indices: 19344461--19344524 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
19344451 AAAGGCTTTG
19344461 AAATTTTGGATGTGAAATA-C-TA
1 AAATTTTGGATGTGAAATATCTTA
* *
19344483 AAATTTTTTGA-ATGAAA-ATCTTTA
1 AAA-TTTTGGATGTGAAATATC-TTA
19344507 AAATTTTGGATGTGAAAT
1 AAATTTTGGATGTGAAAT
19344525 CATAAAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
21 1 0.03
22 9 0.28
23 12 0.38
24 10 0.31
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.41
Consensus pattern (24 bp):
AAATTTTGGATGTGAAATATCTTA
Found at i:19344491 original size:24 final size:24
Alignment explanation
Indices: 19344464--19344538 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 24
19344454 GGCTTTGAAA
19344464 TTTTGGATGTGAAATAC-TAAAATT
1 TTTTGGATGTGAAAT-CTTAAAATT
* *
19344488 TTTTGAATG-AAAATCTTTAAAA--
1 TTTTGGATGTGAAATC-TTAAAATT
*
19344510 TTTTGGATGTGAAATCATAAAGATT
1 TTTTGGATGTGAAATCTTAAA-ATT
19344535 TTTT
1 TTTT
19344539 AATAAGAACC
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 13 0.32
23 10 0.25
24 13 0.32
25 4 0.10
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (24 bp):
TTTTGGATGTGAAATCTTAAAATT
Found at i:19344526 original size:99 final size:91
Alignment explanation
Indices: 19344331--19344615 Score: 268
Period size: 99 Copynumber: 3.0 Consensus size: 91
19344321 CTCTGGGCAT
* * * * * *
19344331 AATCACTAAAG-TTTTTTAAACAAAAATCTTTAAAATTTTGGTTGTGAATCTCTAAAA-TTTTTG
1 AATCA-TAAAGATTTTTT-AATAAGAACCTTTGAAATTTTGGATGTGAAT-ACTAAAATTTTTTG
* *
19344394 AATGAGAATCTTTGAAATTTTGAATGTAA
63 AATGAGAATCTTTGAAATTTTGGATGTGA
* ** *
19344423 AATCATAAAGTTGTTTTTTTTTTCAATGAAAGGCTTTGAAATTTTGGATGTGAAATACTAAAATT
1 AATCATAAA---GATTTTTTAAT-AA-G-AA-CCTTTGAAATTTTGGATGTG-AATACTAAAATT
* *
19344488 TTTTGAATGAAAATCTTTAAAATTTTGGATGTGA
58 TTTTGAATGAGAATCTTTGAAATTTTGGATGTGA
* * *
19344522 AATCATAAAGATTTTTTAATAAGAACCTTTGAAATTTTGGATGTGGAATGCTAAATTTTTTTTTA
1 AATCATAAAGATTTTTTAATAAGAACCTTTGAAATTTTGGATGT-GAATACTAAA-ATTTTTTGA
* *
19344587 ATGCGAGTCTTTGAAATTTTGGATGTGA
64 ATGAGAATCTTTGAAATTTTGGATGTGA
19344615 A
1 A
19344616 TCCCTAAGTT
Statistics
Matches: 158, Mismatches: 23, Indels: 23
0.77 0.11 0.11
Matches are distributed among these distances:
91 4 0.03
92 31 0.20
93 35 0.22
94 2 0.01
95 10 0.06
96 8 0.05
97 2 0.01
98 23 0.15
99 43 0.27
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (91 bp):
AATCATAAAGATTTTTTAATAAGAACCTTTGAAATTTTGGATGTGAATACTAAAATTTTTTGAAT
GAGAATCTTTGAAATTTTGGATGTGA
Found at i:19344602 original size:47 final size:45
Alignment explanation
Indices: 19344438--19344615 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
19344428 TAAAGTTGTT
**
19344438 TTTTTTTTCAATGAAAGGCTTTGAAATTTTGGATGTGAAATACTAAA
1 TTTTTTTT-AATGAAAATCTTTGAAATTTTGGATGTGAAAT-CTAAA
* * *
19344485 ATTTTTTGAATGAAAATCTTTAAAATTTTGGATGTGAAATCATAAA
1 TTTTTTTTAATGAAAATCTTTGAAATTTTGGATGTGAAATC-TAAA
** * *
19344531 GATTTTTTAAT-AAGAACCTTTGAAATTTTGGATGTGGAATGCTAAA
1 TTTTTTTTAATGAA-AATCTTTGAAATTTTGGATGTGAAAT-CTAAA
** *
19344577 TTTTTTTTTAATGCGAGTCTTTGAAATTTTGGATGTGAA
1 -TTTTTTTTAATGAAAATCTTTGAAATTTTGGATGTGAA
19344616 TCCCTAAGTT
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
45 3 0.03
46 68 0.63
47 37 0.34
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
TTTTTTTTAATGAAAATCTTTGAAATTTTGGATGTGAAATCTAAA
Found at i:19344796 original size:14 final size:14
Alignment explanation
Indices: 19344777--19344804 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19344767 TACTAACAAA
19344777 AATTTTTTTAATCT
1 AATTTTTTTAATCT
19344791 AATTTTTTTAATCT
1 AATTTTTTTAATCT
19344805 TGTATGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTTTTAATCT
Found at i:19345168 original size:18 final size:18
Alignment explanation
Indices: 19345145--19345202 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
19345135 TTTTAAGAAC
* *
19345145 CTTTACGAATCTTGAAGT
1 CTTTACAAATCTTGAAAT
19345163 CTTTACAAATCTTGAAAT
1 CTTTACAAATCTTGAAAT
19345181 CTTTGA-AAATCTT-AGAAT
1 CTTT-ACAAATCTTGA-AAT
19345199 CTTT
1 CTTT
19345203 GTGAATCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (18 bp):
CTTTACAAATCTTGAAAT
Found at i:19345209 original size:54 final size:54
Alignment explanation
Indices: 19345091--19345209 Score: 123
Period size: 55 Copynumber: 2.2 Consensus size: 54
19345081 AATGATGGAA
* * * *
19345091 CTTTGTGAATCTGAAACCTTTATAAAACTTGGAACCTTTGCAAATTTTAAGAAC
1 CTTTGTGAATCTGAAACCTTTACAAAACTTGAAACCTTTGAAAATCTTAAGAAC
** ** * * *
19345145 CTTTACGAATCTTGAAGTCTTTACAAATCTTGAAATCTTTGAAAATCTT-AGAAT
1 CTTTGTGAATC-TGAAACCTTTACAAAACTTGAAACCTTTGAAAATCTTAAGAAC
19345199 CTTTGTGAATC
1 CTTTGTGAATC
19345210 CAAGGACTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
54 22 0.43
55 29 0.57
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (54 bp):
CTTTGTGAATCTGAAACCTTTACAAAACTTGAAACCTTTGAAAATCTTAAGAAC
Found at i:19349123 original size:61 final size:61
Alignment explanation
Indices: 19349022--19349142 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
19349012 TGGTTTGAGA
** * * * * *
19349022 AAACCTACATTCAATGTGTGTTGAGTAAGTTTGATATGCACTGGTGTTTTCCTAGTAAGGC
1 AAACCTACATTCAACATATGTTGAGTAAGTTTAATATGCACTAGTCTTTCCCTAGTAAGGC
* *
19349083 AAACCTACATTCAGCATATGTTGAGTAAGTTTAATGTGCACTAGTCTTTCCCTAGTAAGG
1 AAACCTACATTCAACATATGTTGAGTAAGTTTAATATGCACTAGTCTTTCCCTAGTAAGG
19349143 TGCTTGTTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (61 bp):
AAACCTACATTCAACATATGTTGAGTAAGTTTAATATGCACTAGTCTTTCCCTAGTAAGGC
Found at i:19359535 original size:15 final size:16
Alignment explanation
Indices: 19359515--19359551 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
19359505 ATGCTTAAGC
*
19359515 TCATTTTTTTTTC-AT
1 TCATTTTTCTTTCTAT
19359530 TCATTTTTCTTTCTAT
1 TCATTTTTCTTTCTAT
19359546 TCATTT
1 TCATTT
19359552 GTAGAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTCTTTCTAT
Found at i:19369980 original size:16 final size:16
Alignment explanation
Indices: 19369958--19369997 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
19369948 AGTTCATAAA
*
19369958 ATTATTTTTAATTTAT
1 ATTATTTTTAATTCAT
* *
19369974 TTTATTTTTCATTCAT
1 ATTATTTTTAATTCAT
19369990 ATTATTTT
1 ATTATTTT
19369998 GCTCATATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATTTTTAATTCAT
Found at i:19385997 original size:15 final size:16
Alignment explanation
Indices: 19385977--19386013 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
19385967 ATGCTTAAGC
*
19385977 TCATTTTTTTTTC-AT
1 TCATTTTTCTTTCGAT
19385992 TCATTTTTCTTTCGAT
1 TCATTTTTCTTTCGAT
19386008 TCATTT
1 TCATTT
19386014 GTAGAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.14, C:0.16, G:0.03, T:0.68
Consensus pattern (16 bp):
TCATTTTTCTTTCGAT
Found at i:19394840 original size:2 final size:2
Alignment explanation
Indices: 19394835--19394870 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19394825 TGTGTGTGTG
19394835 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
19394871 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19394875 original size:2 final size:2
Alignment explanation
Indices: 19394870--19394917 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
19394860 ATATATATAT
*
19394870 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19394912 AG AG AG
1 AG AG AG
19394918 TCATTTGATC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19396514 original size:16 final size:16
Alignment explanation
Indices: 19396492--19396531 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
19396482 AGTTCATAAA
*
19396492 ATTATTTTTAATTTAT
1 ATTATTTTTAATTCAT
* *
19396508 TTTATTTTTCATTCAT
1 ATTATTTTTAATTCAT
19396524 ATTATTTT
1 ATTATTTT
19396532 GCTCATATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATTTTTAATTCAT
Found at i:19400058 original size:85 final size:86
Alignment explanation
Indices: 19399917--19400081 Score: 192
Period size: 85 Copynumber: 1.9 Consensus size: 86
19399907 AATGCCTTCT
* * * *
19399917 TAAAGGCTTAACTCGACAAAATAGCTCGACTTAAGAGCTTAGATTCAATTCGGCT-AAAAGAGCT
1 TAAAGGCTTAACTCAACAAAACAGCTCGACTTAAGAGCTTAGATTCAACTCAGCTAAAAAGAGCT
*
19399981 CGGATCTACAAAATATATTCA
66 CAGATCTACAAAATATATTCA
* * * *
19400002 TAAAGGTTTAACTCAACAAAACAGCTTGGCTTAAGAG-TTCGGACTT-AACTCAGCTAAAAAGAG
1 TAAAGGCTTAACTCAACAAAACAGCTCGACTTAAGAGCTT-AGA-TTCAACTCAGCTAAAAAGAG
* *
19400065 TTCAGATCTATAAAATA
64 CTCAGATCTACAAAATA
19400082 CCTTTACAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
84 2 0.03
85 41 0.62
86 23 0.35
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (86 bp):
TAAAGGCTTAACTCAACAAAACAGCTCGACTTAAGAGCTTAGATTCAACTCAGCTAAAAAGAGCT
CAGATCTACAAAATATATTCA
Found at i:19402822 original size:33 final size:33
Alignment explanation
Indices: 19402758--19402833 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
19402748 GATGTAAAAC
*
19402758 TGGTTTTCATATCATGCCACCATTTATGAATAA
1 TGGTTTTCATATCATGCCACCATATATGAATAA
* *
19402791 TGGTTTTCATA-CTATGCTACCGATATA-GAATAG
1 TGGTTTTCATATC-ATGCCACC-ATATATGAATAA
*
19402824 TAGTTTTCAT
1 TGGTTTTCAT
19402834 TCCATTAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 32 0.86
34 4 0.11
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (33 bp):
TGGTTTTCATATCATGCCACCATATATGAATAA
Found at i:19409959 original size:13 final size:13
Alignment explanation
Indices: 19409920--19409966 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
19409910 AGCACGTTAT
19409920 TATTATAGTATAA
1 TATTATAGTATAA
*
19409933 TATGTTATAATATAA
1 TA--TTATAGTATAA
*
19409948 TATTATAGTATAG
1 TATTATAGTATAA
19409961 TATTAT
1 TATTAT
19409967 TATTATTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (13 bp):
TATTATAGTATAA
Found at i:19409969 original size:3 final size:3
Alignment explanation
Indices: 19409961--19410068 Score: 68
Period size: 3 Copynumber: 36.0 Consensus size: 3
19409951 TATAGTATAG
* * *
19409961 TAT TAT TAT TAT TAGT T-T TAT TA- TAGT AAT TAT ATAG TA- CAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT
19410006 TAT TA- TAT TAT TAT TAT TAT TAT TA- TAGT TCGA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T T--AT TAT TAT TAT TAT
*
19410051 TCA- TAT TAT TAT CAT TAT
1 T-AT TAT TAT TAT TAT TAT
19410069 ACTATATTTA
Statistics
Matches: 84, Mismatches: 7, Indels: 28
0.71 0.06 0.24
Matches are distributed among these distances:
2 11 0.13
3 64 0.76
4 8 0.10
6 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:19410088 original size:19 final size:20
Alignment explanation
Indices: 19410056--19410094 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
19410046 ATTATTCATA
* *
19410056 TTATTATCATTATACTATAT
1 TTATTATCACTATAATATAT
19410076 TTATTAT-ACTATAATATAT
1 TTATTATCACTATAATATAT
19410095 CAATACTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTATCACTATAATATAT
Found at i:19410106 original size:3 final size:3
Alignment explanation
Indices: 19410098--19410129 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19410088 AATATATCAA
*
19410098 TAC TAC TAC TAC TAT TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
19410130 TTATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
TAC
Found at i:19410946 original size:5 final size:5
Alignment explanation
Indices: 19410938--19411010 Score: 55
Period size: 5 Copynumber: 15.0 Consensus size: 5
19410928 TTTTTTTCAT
* * *
19410938 TTTTA TTTTA -TTT- TTTGA TTCTA TTTTA -TTTA -TTTA TTTATT TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA
* *
19410985 ATTTA ATTTA TTTTTA TTTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTTA TTTTA
19411011 CTGGTTTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 13 0.24
5 34 0.62
6 8 0.15
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:19410952 original size:11 final size:11
Alignment explanation
Indices: 19410931--19411009 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 11
19410921 GGTTTTCTTT
19410931 TTTTCATTTTTA
1 TTTT-ATTTTTA
19410943 TTTTATTTTTTGA
1 TTTTA-TTTTT-A
*
19410956 TTCTA-TTTTA
1 TTTTATTTTTA
19410966 -TTTATTTATTTA
1 TTTTA-TT-TTTA
19410978 TTTT-TTAATTTA
1 TTTTATT--TTTA
*
19410990 ATTTATTTTTA
1 TTTTATTTTTA
19411001 TTTTATTTT
1 TTTTATTTT
19411010 ACTGGTTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
9 3 0.05
10 1 0.02
11 20 0.36
12 21 0.38
13 10 0.18
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:19410962 original size:18 final size:17
Alignment explanation
Indices: 19410939--19411008 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
19410929 TTTTTTCATT
19410939 TTTATTTTATTT-TTTGA
1 TTTATTTTATTTATTT-A
19410956 TTCTATTTTATTTATTTA
1 TT-TATTTTATTTATTTA
*
19410974 TTTATTTT-TTAATTTAA
1 TTTATTTTATTTATTT-A
19410991 TTTATTTTTATTTTATTT
1 TTTA-TTTTA-TTTATTT
19411009 TACTGGTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.13
17 13 0.29
18 17 0.38
19 3 0.07
20 6 0.13
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:19410971 original size:4 final size:4
Alignment explanation
Indices: 19410939--19410997 Score: 50
Period size: 4 Copynumber: 13.8 Consensus size: 4
19410929 TTTTTTCATT
19410939 TTTA TTTTA TTT- TTTGA TTCTA TTTTA TTTA TTTA TTTA TTT- TTTAA
1 TTTA -TTTA TTTA TTT-A TT-TA -TTTA TTTA TTTA TTTA TTTA TTT-A
19410986 TTTAA TTTA TTT
1 TTT-A TTTA TTT
19410998 TTATTTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
3 6 0.12
4 22 0.46
5 17 0.35
6 3 0.06
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:19411005 original size:16 final size:17
Alignment explanation
Indices: 19410959--19410999 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
19410949 TTTTTGATTC
*
19410959 TATTTTATTTATTT-ATT
1 TATTTT-TTAATTTAATT
19410976 TATTTTTTAATTTAATT
1 TATTTTTTAATTTAATT
19410993 TATTTTT
1 TATTTTT
19411000 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTTAATTTAATT
Found at i:19423121 original size:13 final size:13
Alignment explanation
Indices: 19423103--19423132 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19423093 GTATCATATG
19423103 TTATAATATAATA
1 TTATAATATAATA
*
19423116 TTATAATATAGTA
1 TTATAATATAATA
19423129 TTAT
1 TTAT
19423133 TATTAGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TTATAATATAATA
Found at i:19423141 original size:12 final size:12
Alignment explanation
Indices: 19423114--19423190 Score: 59
Period size: 12 Copynumber: 6.3 Consensus size: 12
19423104 TATAATATAA
*
19423114 TATTATAATATAG
1 TATTATTAT-TAG
19423127 TATTATTATTAG
1 TATTATTATTAG
19423139 TATTATTA-TAG
1 TATTATTATTAG
* *
19423150 TAATTATGCAATA-
1 T-ATTAT-TATTAG
* *
19423163 CATTATTATTAT
1 TATTATTATTAG
*
19423175 TATTATTATTAT
1 TATTATTATTAG
19423187 TATT
1 TATT
19423191 TGATATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
11 7 0.13
12 36 0.67
13 9 0.17
14 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:19423172 original size:3 final size:3
Alignment explanation
Indices: 19423164--19423255 Score: 63
Period size: 3 Copynumber: 32.7 Consensus size: 3
19423154 TATGCAATAC
* *
19423164 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TG A-T ATT ATT ATC ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
19423209 ACT A-T ATTT ATT A-T ACT -TT AAT A-T ATC AAT ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19423251 ATT AT
1 ATT AT
19423256 GATTTTTAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
2 11 0.15
3 58 0.82
4 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:19423215 original size:19 final size:19
Alignment explanation
Indices: 19423175--19423222 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
19423165 TTATTATTAT
* *
19423175 TATTATTATTATTATTTGA
1 TATTATTATCATTATCTGA
19423194 TATTATTATCATTATACT-A
1 TATTATTATCATTAT-CTGA
19423213 TATTTATTAT
1 TA-TTATTAT
19423223 ACTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTATTATCATTATCTGA
Found at i:19424139 original size:16 final size:16
Alignment explanation
Indices: 19424083--19424129 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
19424073 TGTTTATTTA
19424083 TTCATTTATTTTTTAAT
1 TTCATTTA-TTTTTAAT
19424100 TTCATTTATTTTTAAT
1 TTCATTTATTTTTAAT
19424116 TTCATTTATTTTTA
1 TTCATTTATTTTTA
19424130 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCATTTATTTTTAAT
Found at i:19424944 original size:19 final size:19
Alignment explanation
Indices: 19424920--19424956 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
19424910 AGTTTCATGA
19424920 ATTAGATTCGATCAAGTGG
1 ATTAGATTCGATCAAGTGG
19424939 ATTAGATTCGATCAAGTG
1 ATTAGATTCGATCAAGTG
19424957 ACCAATCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTAGATTCGATCAAGTGG
Found at i:19425806 original size:40 final size:39
Alignment explanation
Indices: 19425727--19425807 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
19425717 AAATCCAAAT
* * *
19425727 TTTGATTTTAATGCCCAAGTTTATTGTTTTTAGGATTAA
1 TTTGATTTTAAGGCCCAAGTTTATTATTTTTAGAATTAA
19425766 TTTGATTTTAAGGCCCAA-TGTTATTTATTTTTA-AATTTAA
1 TTTGATTTTAAGGCCCAAGT-TTA-TTATTTTTAGAA-TTAA
19425806 TT
1 TT
19425808 ATTTTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.03
39 21 0.58
40 14 0.39
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.53
Consensus pattern (39 bp):
TTTGATTTTAAGGCCCAAGTTTATTATTTTTAGAATTAA
Found at i:19427763 original size:3 final size:3
Alignment explanation
Indices: 19427757--19427782 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19427747 CTTCTTCTTC
19427757 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
19427783 TTAAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:19428056 original size:19 final size:22
Alignment explanation
Indices: 19428034--19428082 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
19428024 TTTCATTTTT
*
19428034 TTAATTATAT-ATAA-AT-AAA
1 TTAATAATATAATAATATAAAA
19428053 TTAATAATATAATAATATAAAA
1 TTAATAATATAATAATATAAAA
19428075 TTAA-AATA
1 TTAATAATA
19428083 ACAAAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 4 0.15
21 6 0.23
22 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATAATATAATAATATAAAA
Found at i:19428091 original size:27 final size:27
Alignment explanation
Indices: 19428035--19428091 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
19428025 TTCATTTTTT
* * * *
19428035 TAATTATATATAAATAAATTAATAATA
1 TAATAATATATAAATAAAATAACAAAA
19428062 TAATAATATA-AAATTAAAATAACAAAA
1 TAATAATATATAAA-TAAAATAACAAAA
19428089 TAA
1 TAA
19428092 CAAAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAATAATATATAAATAAAATAACAAAA
Found at i:19432211 original size:63 final size:62
Alignment explanation
Indices: 19432106--19432625 Score: 287
Period size: 63 Copynumber: 8.2 Consensus size: 62
19432096 ATTTGAAAAA
* * ** * *
19432106 AGGATTATTGAAGGTGTTTTAGGCAAAAAAATACCTTTAATAATCCTCTTACATTTTTTAGAG
1 AGGATTATTAAAGGTATTTTTTGTAAAAAAATACCTTCAATAATCCTCTTA-ATTTTTTAGAG
* * *
19432169 AGGATTATTAAAGGTATTTTTTGTAAAAAAATACTTTCAATAATTCTCTTAAATTTTGATA-AG
1 AGGATTATTAAAGGTATTTTTTGTAAAAAAATACCTTCAATAATCCTCTT-AATTTT-TTAGAG
* ** * * *
19432232 -GAGATTATTTAAGGCGTTTTTTG-ACAAAAAATGCCTTCAATAATCCCCTTTAATTTTTTTGA-
1 AG-GATTATTAAAGGTATTTTTTGTA-AAAAAATACCTTCAATAATCCTC-TTAATTTTTTAGAG
* * * ** * *
19432294 AGGGATTATTGAAGGTATTTTCTG--CAAAAATGTCTTCAATAATCC-CTTTAAATTTTAATGAG
1 A-GGATTATTAAAGGTATTTTTTGTAAAAAAATACCTTCAATAATCCTC-TTAATTTTTTA-GAG
* * * * * * * * *
19432356 AAGATTATTGAGGGCATTTTTTTTTTATCAAAAACACCTTCAATAATCCCTTTTAATTTTTTGGA
1 AGGATTATTAAAGG--TATTTTTTGTA-AAAAAATACCTTCAATAAT-CCTCTTAATTTTTTAGA
19432421 G
62 G
* * * *
19432422 -GAGATTATTAATGGCT-TTTTTTGGT-CAAAAATGCCTTCAATAATCC-CATCCAATTTTTTAG
1 AG-GATTATTAAAGG-TATTTTTT-GTAAAAAAATACCTTCAATAATCCTC-T-TAATTTTTTAG
19432483 AG
61 AG
* * * * * *
19432485 GGGATTATTGAAGGTATTTTTTGTAAAAAAAACACCTTTAATAAT-CTCTTTCATTTTTTATA-
1 AGGATTATTAAAGGTATTTTTTGT-AAAAAAATACCTTCAATAATCCTC-TTAATTTTTTAGAG
* * * * ** *
19432547 AGGGATTATTAAAGGTGTTTTGTG-CAAACAACGCCTTCAATAATCCCTTTGTAATTTTTTATGA
1 A-GGATTATTAAAGGTATTTTTTGTAAAAAAATACCTTCAATAAT-CCTCT-TAATTTTTTA-GA
19432611 G
62 G
19432612 A-GATTATTAAAGGT
1 AGGATTATTAAAGGT
19432626 GTTTCAAGCA
Statistics
Matches: 355, Mismatches: 70, Indels: 64
0.73 0.14 0.13
Matches are distributed among these distances:
60 10 0.03
61 48 0.14
62 11 0.03
63 213 0.60
64 31 0.09
65 3 0.01
66 29 0.08
67 10 0.03
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (62 bp):
AGGATTATTAAAGGTATTTTTTGTAAAAAAATACCTTCAATAATCCTCTTAATTTTTTAGAG
Found at i:19432504 original size:129 final size:127
Alignment explanation
Indices: 19432265--19432594 Score: 334
Period size: 127 Copynumber: 2.6 Consensus size: 127
19432255 ACAAAAAATG
*
19432265 CCTTCAATAATCCCCTTTAATTTTTTTGAAGGGATTATTGAAGGTATTTTCTGCAAAAATGTCTT
1 CCTTCAATAATCCCCTTTAATTTTTTTGAAGGGATTATTGAAGGTATTTTCTGCAAAAATGCCTT
** *
19432330 CAATAATCCCTTTAAATTTTAATGAGAAGATTATTGAGGGCATTTTTTTTTTATCAAAAACA
66 CAATAATCCCTCCAAATTTTAATGAGAAGATTATTGAAGGCATTTTTTTTTTATCAAAAACA
* * *
19432392 CCTTCAATAATCCCTTTTAA-TTTTTTGGAGGAGATTATT-AATGGCT-TTTTTTGGTCAAAAAT
1 CCTTCAATAATCCCCTTTAATTTTTTTGAAGG-GATTATTGAA-GG-TATTTTCT-G-CAAAAAT
* * ** * * **
19432454 GCCTTCAATAATCCCATCCAATTTTTTA-GAGGGGATTATTGAAGG--TATTTTTTGTAAAAAAA
61 GCCTTCAATAATCCC-TCCAAATTTTAATGAGAAGATTATTGAAGGCATTTTTTTTTTATCAAAA
19432516 ACA
125 ACA
* * * * * * *
19432519 CCTTTAATAAT-CTCTTTCATTTTTTAT-AAGGGATTATTAAAGGTGTTTTGTGCAAACAACGCC
1 CCTTCAATAATCCCCTTTAATTTTTT-TGAAGGGATTATTGAAGGTATTTTCTGCAAA-AATGCC
19432582 TTCAATAATCCCT
64 TTCAATAATCCCT
19432595 TTGTAATTTT
Statistics
Matches: 170, Mismatches: 22, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
124 5 0.03
125 19 0.11
126 31 0.18
127 69 0.41
128 3 0.02
129 35 0.21
130 8 0.05
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (127 bp):
CCTTCAATAATCCCCTTTAATTTTTTTGAAGGGATTATTGAAGGTATTTTCTGCAAAAATGCCTT
CAATAATCCCTCCAAATTTTAATGAGAAGATTATTGAAGGCATTTTTTTTTTATCAAAAACA
Found at i:19432625 original size:126 final size:125
Alignment explanation
Indices: 19432108--19432625 Score: 410
Period size: 126 Copynumber: 4.1 Consensus size: 125
19432098 TTGAAAAAAG
* * ** * * *
19432108 GATTATTGAAGGT-GTTTTAGGCAAAAAAATACCTTTAATAATCCTC-TTACA-TTTTTTAGAGA
1 GATTATTGAAGGTATTTTTTGTAAAAAAAACACCTTCAATAATCCCCTTTA-ATTTTTTTA-AG-
* * * * * *
19432170 GGATTATTAAAGGTATTTTTTGTAAAAAAATACTTTCAATAAT-TCTCTTAAATTTTGATAAGGA
63 GGATTATTAAAGGTATTTTTTGT-CAAAAATGCCTTCAATAATCCCT-TTAAATTTTTATGAGGA
* ** * **
19432234 GATTATTTAAGGCGTTTTTTG-ACAAAAAATGCCTTCAATAATCCCCTTTAATTTTTTTGAAGGG
1 GATTATTGAAGGTATTTTTTGTAAAAAAAACACCTTCAATAATCCCCTTTAATTTTTTT-AAGGG
* * * * *
19432298 ATTATTGAAGGTATTTTCTG-CAAAAATGTCTTCAATAATCCCTTTAAATTTTAATGAGAA
65 ATTATTAAAGGTATTTTTTGTCAAAAATGCCTTCAATAATCCCTTTAAATTTTTATGAGGA
* * * ** * **
19432358 GATTATTGAGGGCATTTTTTTTTTATCAAAAACACCTTCAATAATCCCTTTTAATTTTTTGGAGG
1 GATTATTGAAGG--TATTTTTTGTAAAAAAAACACCTTCAATAATCCCCTTTAATTTTTTTAAGG
* * **
19432423 AGATTATTAATGGCT-TTTTTTGGTCAAAAATGCCTTCAATAATCCCATCCAATTTTT-TAGAGG
64 -GATTATTAAAGG-TATTTTTT-GTCAAAAATGCCTTCAATAATCCCTTTAAATTTTTAT-GAGG
*
19432486 G
125 A
* * *
19432487 GATTATTGAAGGTATTTTTTGTAAAAAAAACACCTTTAATAAT-CTCTTTCATTTTTTATAAGGG
1 GATTATTGAAGGTATTTTTTGTAAAAAAAACACCTTCAATAATCCCCTTTAATTTTTT-TAAGGG
* * * *
19432551 ATTATTAAAGGTGTTTTGTG-CAAACAACGCCTTCAATAATCCCTTTGTAATTTTTTATGA-GA
65 ATTATTAAAGGTATTTTTTGTCAAA-AATGCCTTCAATAATCCC-TT-TAAATTTTTATGAGGA
*
19432613 GATTATTAAAGGT
1 GATTATTGAAGGT
19432626 GTTTCAAGCA
Statistics
Matches: 312, Mismatches: 61, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
124 43 0.14
125 21 0.07
126 102 0.33
127 99 0.32
128 5 0.02
129 42 0.13
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (125 bp):
GATTATTGAAGGTATTTTTTGTAAAAAAAACACCTTCAATAATCCCCTTTAATTTTTTTAAGGGA
TTATTAAAGGTATTTTTTGTCAAAAATGCCTTCAATAATCCCTTTAAATTTTTATGAGGA
Found at i:19433291 original size:63 final size:63
Alignment explanation
Indices: 19433205--19433347 Score: 211
Period size: 62 Copynumber: 2.3 Consensus size: 63
19433195 TTTTTGCTTG
** * *
19433205 AAATGCCTTCAATAAT-CTTTCATAAAAAATTGCAAGGGATTATTGAAGGCA-TTTTCTG-CACA
1 AAATGCCTTCAATAATCCCCTCATAAAAAA-TGAAAGGGATTATTGAAGGCAGTTTT-TGACAAA
19433267 AAATGCCTTCAATAATCCCCTCATAAAAAATGAAAGGGATTATTGAAGGCAGTTTTTGACAAA
1 AAATGCCTTCAATAATCCCCTCATAAAAAATGAAAGGGATTATTGAAGGCAGTTTTTGACAAA
19433330 AAATGCCTTCAATAATCC
1 AAATGCCTTCAATAATCC
19433348 TCTACAATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
62 38 0.51
63 36 0.49
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (63 bp):
AAATGCCTTCAATAATCCCCTCATAAAAAATGAAAGGGATTATTGAAGGCAGTTTTTGACAAA
Found at i:19433371 original size:62 final size:62
Alignment explanation
Indices: 19433053--19433379 Score: 175
Period size: 62 Copynumber: 5.3 Consensus size: 62
19433043 TATTGACAAG
* * * * * * *
19433053 GAGATTTATTGAAGGC-GTTTTTGACTAAAAACGTCTTCAATAGTCTTCTACAACTTTTTAGG
1 GAGA-TTATTGAAGGCAGTTTTTGACAAAAAATGCCTTCAATAATCCTCTACAAATTTTTAGA
* * * * * ***
19433115 GAAATTATTGAATGCATTTTTTTACAAAAAACGCCTTCAATAAT--TGCT-TTTATTTTTATGA
1 GAGATTATTGAAGGCAGTTTTTGACAAAAAATGCCTTCAATAATCCT-CTACAAATTTTTA-GA
* * * *** * * * **
19433176 GTAGATTATTCAAGGAATTTTTTTG-CTTGAAATGCCTTCAATAATCTTTCATAAAAAATTGCA-
1 G-AGATTATTGAAGGCA-GTTTTTGACAAAAAATGCCTTCAATAATC-CTC-TACAAATTTTTAG
19433239 A
62 A
* * * * *** * *
19433240 GGGATTATTGAAGGCA-TTTTCTG-CACAAAATGCCTTCAATAATCCCCTCATAAAAAATGAAA
1 GAGATTATTGAAGGCAGTTTT-TGACAAAAAATGCCTTCAATAATCCTCT-ACAAATTTTTAGA
* *
19433302 GGGATTATTGAAGGCAGTTTTTGACAAAAAATGCCTTCAATAATCCTCTACAATTTTTTAGA
1 GAGATTATTGAAGGCAGTTTTTGACAAAAAATGCCTTCAATAATCCTCTACAAATTTTTAGA
*
19433364 GAAATTATTGAAGGCA
1 GAGATTATTGAAGGCA
19433380 TTTGCAATAG
Statistics
Matches: 199, Mismatches: 51, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
60 8 0.04
61 25 0.13
62 112 0.56
63 45 0.23
64 3 0.02
65 2 0.01
66 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (62 bp):
GAGATTATTGAAGGCAGTTTTTGACAAAAAATGCCTTCAATAATCCTCTACAAATTTTTAGA
Found at i:19437002 original size:30 final size:30
Alignment explanation
Indices: 19436968--19437030 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
19436958 ATTTAGGTAT
19436968 AAATTAAGAA-TTAAAA-TCTTATTCAAATAC
1 AAATTAA-AAGTTAAAAGT-TTATTCAAATAC
**
19436998 AAATTAAAAGTTAAAAGTTTATTTGAATAC
1 AAATTAAAAGTTAAAAGTTTATTCAAATAC
19437028 AAA
1 AAA
19437031 GATCAAGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 2 0.07
30 26 0.90
31 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (30 bp):
AAATTAAAAGTTAAAAGTTTATTCAAATAC
Found at i:19442954 original size:21 final size:24
Alignment explanation
Indices: 19442910--19442963 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
19442900 ATGGTTATAC
*
19442910 TAAAAGATCTATTTATATATTTAA
1 TAAAAAATCTATTTATATATTTAA
19442934 -AAAAAATCTATTTATA-A-TTAA
1 TAAAAAATCTATTTATATATTTAA
19442955 TAAACAAAT
1 TAAA-AAAT
19442964 ATAAATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 19 0.70
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (24 bp):
TAAAAAATCTATTTATATATTTAA
Found at i:19443143 original size:20 final size:21
Alignment explanation
Indices: 19443118--19443159 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
19443108 TTAATAACAA
19443118 AATTAAATCTATTTA-CCAAT
1 AATTAAATCTATTTATCCAAT
*
19443138 AATTAAATCTTTTTATCCAAT
1 AATTAAATCTATTTATCCAAT
19443159 A
1 A
19443160 TGGAATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAAATCTATTTATCCAAT
Found at i:19447140 original size:20 final size:20
Alignment explanation
Indices: 19447115--19447194 Score: 97
Period size: 20 Copynumber: 3.9 Consensus size: 20
19447105 ATTAAACAAA
* *
19447115 TAACAAGGAGATTTAAAACT
1 TAACAAGGAAATGTAAAACT
19447135 TAACAAGGAAATGTAAAACTAT
1 TAACAAGGAAATGTAAAAC--T
*
19447157 TAACAGGGAAATGTAAAACT
1 TAACAAGGAAATGTAAAACT
* *
19447177 AAACAAGGAAATATAAAA
1 TAACAAGGAAATGTAAAA
19447195 TTTGGGTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 33 0.63
22 19 0.37
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (20 bp):
TAACAAGGAAATGTAAAACT
Found at i:19452872 original size:3 final size:3
Alignment explanation
Indices: 19452864--19452907 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
19452854 AAAGTTATGC
** *
19452864 ATA ATA ATA ATA ATA ATA ATA ATA ATA GCA ATA ATA ATA TTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
19452908 GATGGTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19467715 original size:29 final size:28
Alignment explanation
Indices: 19467673--19467786 Score: 93
Period size: 29 Copynumber: 3.9 Consensus size: 28
19467663 TGTAAATAAT
*
19467673 AAAATATCACAAAAATTTTCAAAATTTTG
1 AAAATATCAAAAAAATTTT-AAAATTTTG
* * * *
19467702 AAAATTTCAAAAAATTTTTAAAAAATTCG
1 AAAATATCAAAAAAATTTT-AAAATTTTG
* *
19467731 CAAAACATAAAAAAAATTTTAAAATTTTG
1 -AAAATATCAAAAAAATTTTAAAATTTTG
* * *
19467760 AAATAAATTAAAAAATATTTGAAAATT
1 AAA-ATATCAAAAAA-ATTTTAAAATT
19467787 CAAAATATGA
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 3 0.04
29 39 0.58
30 25 0.37
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATATCAAAAAAATTTTAAAATTTTG
Found at i:19467815 original size:34 final size:34
Alignment explanation
Indices: 19467764--19467846 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 34
19467754 ATTTTGAAAT
* *
19467764 AAATT-AAAAAATATTTGAAAATTCAAAATATG-A
1 AAATTAAAAAAATATTTGAAAAAT-AAAAAATGAA
*
19467797 AAATTAAAAAAATCTTTGAAAAATAAAAAATGAA
1 AAATTAAAAAAATATTTGAAAAATAAAAAATGAA
19467831 ATAATTAAAAAAATAT
1 A-AATTAAAAAAATAT
19467847 AATGAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 12 0.28
34 18 0.42
35 13 0.30
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (34 bp):
AAATTAAAAAAATATTTGAAAAATAAAAAATGAA
Found at i:19467820 original size:35 final size:33
Alignment explanation
Indices: 19467764--19467846 Score: 98
Period size: 35 Copynumber: 2.5 Consensus size: 33
19467754 ATTTTGAAAT
*
19467764 AAATT-AAAAAATATTTGAAAATTCAAAATATG-A
1 AAATTAAAAAAATATTTGAAAA-T-AAAAAATGAA
*
19467797 AAATTAAAAAAATCTTTGAAAAATAAAAAATGAA
1 AAATTAAAAAAATATTTG-AAAATAAAAAATGAA
19467831 ATAATTAAAAAAATAT
1 A-AATTAAAAAAATAT
19467847 AATGAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
33 12 0.28
34 14 0.33
35 17 0.40
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (33 bp):
AAATTAAAAAAATATTTGAAAATAAAAAATGAA
Found at i:19467982 original size:9 final size:9
Alignment explanation
Indices: 19467958--19467991 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19467948 AAAAAAAAAC
19467958 TAAAAAATT
1 TAAAAAATT
*
19467967 CTTAAAAATT
1 -TAAAAAATT
19467977 TAAAAAATT
1 TAAAAAATT
19467986 TAAAAA
1 TAAAAA
19467992 TTCAAAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAAATT
Found at i:19468051 original size:17 final size:17
Alignment explanation
Indices: 19468026--19468101 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
19468016 TAAAATCCTC
*
19468026 AAAATTAAAAAATATGA
1 AAAAATAAAAAATATGA
* *
19468043 GAAAATAAAAATTACT-A
1 AAAAATAAAAAATA-TGA
19468060 AAAAATAAAAAA-ATGA
1 AAAAATAAAAAATATGA
* *
19468076 AACATATTAAAAAA-ATCA
1 AA-A-AATAAAAAATATGA
19468094 AAAAATAA
1 AAAAATAA
19468102 TTTGAAAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
15 1 0.02
16 8 0.17
17 24 0.51
18 14 0.30
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAAATAAAAAATATGA
Found at i:19468072 original size:25 final size:25
Alignment explanation
Indices: 19468029--19468101 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
19468019 AATCCTCAAA
* *
19468029 ATTAAAAAATATGAGAAAATAAA-A-
1 ATTAAAAAA-ATAAAAAAATAAACAT
19468053 ATTACTAAAAAATAAAAAAATGAAACAT
1 ATTA--AAAAAATAAAAAAAT-AAACAT
*
19468081 ATTAAAAAAATCAAAAAATAA
1 ATTAAAAAAATAAAAAAATAA
19468102 TTTGAAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.10
25 10 0.24
26 22 0.54
27 1 0.02
28 4 0.10
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (25 bp):
ATTAAAAAAATAAAAAAATAAACAT
Found at i:19468730 original size:7 final size:6
Alignment explanation
Indices: 19468702--19468742 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
19468692 AAAAATAGGT
19468702 TAAAAA T-AAAA T-AAAA TCAAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA T--AAAAA TAAAAA TAAAAA TAAAA
19468743 TGAAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 10 0.31
6 17 0.53
8 5 0.16
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:19468734 original size:24 final size:25
Alignment explanation
Indices: 19468702--19468749 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
19468692 AAAAATAGGT
19468702 TAAAAAT-AAAATAAAATCAAAAAA
1 TAAAAATAAAAATAAAATCAAAAAA
*
19468726 TAAAAATAAAAATAAAATGAAAAA
1 TAAAAATAAAAATAAAATCAAAAA
19468750 GGGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (25 bp):
TAAAAATAAAAATAAAATCAAAAAA
Found at i:19469141 original size:9 final size:10
Alignment explanation
Indices: 19469127--19469161 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
19469117 ACTAAACCCA
19469127 AAAAAAAT-T
1 AAAAAAATCT
19469136 AAAAAAATCT
1 AAAAAAATCT
*
19469146 AAAAAAATCC
1 AAAAAAATCT
19469156 AAAAAA
1 AAAAAA
19469162 CCTCCAAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATCT
Found at i:19469243 original size:19 final size:19
Alignment explanation
Indices: 19469219--19469274 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
19469209 TTCACCTTTA
*
19469219 AAAACCCATAATTACACCC-
1 AAAACCCA-AATTAAACCCT
19469238 AAAACCACAAATTAAACCCT
1 AAAACC-CAAATTAAACCCT
19469258 AAAATCCCAAGATTAAA
1 AAAA-CCCAA-ATTAAA
19469275 TTCTAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 15 0.47
20 9 0.28
21 8 0.25
ACGTcount: A:0.54, C:0.29, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAACCCAAATTAAACCCT
Found at i:19469657 original size:18 final size:18
Alignment explanation
Indices: 19469610--19469671 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
19469600 AAATAAAGAA
* *
19469610 AATAAAATAAAAACA-AAA
1 AATATAATAAAAA-ATAAT
*
19469628 AATATTAT-AAAAATAAT
1 AATATAATAAAAAATAAT
*
19469645 AATATAATAAAAAATAGT
1 AATATAATAAAAAATAAT
19469663 AATAATAAT
1 AAT-ATAAT
19469672 GATACTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.03
17 13 0.36
18 17 0.47
19 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AATATAATAAAAAATAAT
Found at i:19470425 original size:186 final size:186
Alignment explanation
Indices: 19470111--19470464 Score: 557
Period size: 186 Copynumber: 1.9 Consensus size: 186
19470101 ATGAAAGGCA
** * *
19470111 AGTCGAGGTCGAAAATGACCAAGATACAATCATGAATCATAAAAATAATTTAGATTGAGCCAAGA
1 AGTCGAGGTAAAAAATGACCAAGATACAATCATGAATCATAAAAATAATTTAGACTAAGCCAAGA
* * *
19470176 TCAAGTGATCGGGCTAAAATCACGAGTCAAAATATAATGACCAGGACCAAGTCGAGGTCAAAAAT
66 TCAAATGATCAGGCTAAAATCACAAGTCAAAATATAATGACCAGGACCAAGTCGAGGTCAAAAAT
*
19470241 AGATGATCAAGACGAAATCACAAATCATAAAAAATGATTAAGATGAAAGGTAACCG
131 AGATGATCAAGACGAAACCACAAATCATAAAAAATGATTAAGATGAAAGGTAACCG
*
19470297 AGTCGAGGTAAAAAATGACCAAGATACAATCATGAATCATGAAAATAATTTAGACTAAGCCAAGA
1 AGTCGAGGTAAAAAATGACCAAGATACAATCATGAATCATAAAAATAATTTAGACTAAGCCAAGA
* *
19470362 TCAAATGATCAGGCTAAAATCACAAGTCAAAATA-AAGTGACCAGGATCGAGTCGAGGTCAAAAA
66 TCAAATGATCAGGCTAAAATCACAAGTCAAAATATAA-TGACCAGGACCAAGTCGAGGTCAAAAA
* ** *
19470426 TAGATGATTAAGACGAAACCATGAATCATAAGAAATGAT
130 TAGATGATCAAGACGAAACCACAAATCATAAAAAATGAT
19470465 CTAGACTGAG
Statistics
Matches: 152, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
185 2 0.01
186 150 0.99
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (186 bp):
AGTCGAGGTAAAAAATGACCAAGATACAATCATGAATCATAAAAATAATTTAGACTAAGCCAAGA
TCAAATGATCAGGCTAAAATCACAAGTCAAAATATAATGACCAGGACCAAGTCGAGGTCAAAAAT
AGATGATCAAGACGAAACCACAAATCATAAAAAATGATTAAGATGAAAGGTAACCG
Found at i:19470478 original size:119 final size:119
Alignment explanation
Indices: 19470309--19471084 Score: 637
Period size: 119 Copynumber: 6.5 Consensus size: 119
19470299 TCGAGGTAAA
* * * * * * *
19470309 AAATGACCAAGA-TACAATCATGAATCATGA-AAATAATTTAGACTAAGCCAAGATCAAATGATC
1 AAATGACCAAGACGA-AACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGATC
* * * *
19470372 AGGCTAAAATCACAAGTCAAAATAAAGTGACCAGGATCGAGTCGAGGTCAAAAAT
65 AGGATAAAACCACAAGTCAAAATAAAATGACCAGGATCGAGTCAAGGTCAAAAAT
* ** *
19470427 AGATGATTAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGACCA
1 AAATGACCAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGATCA
** * * * * *
19470492 AAATAAAACCACCAGTCAAAATAAAGTGACAAGGACCGAGTCAAGGTAAAAAAT
66 GGATAAAACCACAAGTCAAAATAAAATGACCAGGATCGAGTCAAGGTCAAAAAT
* * * * * * * * * * **
19470546 AGATGACTAGGATGAAACCACGAATCATCAGAAATGATTTGGATTGAGCCAAGATCAAATGATTG
1 AAATGACCAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGATCA
* * * * * ** *
19470611 GGATAAAATCACTAGTCAAAACAAAACCGACTAGGATCGAGTTGAGGTAAAAAAT
66 GGATAAAACCACAAGTCAAAATAAAA-TGACCAGGATCGAGTCAAGGTCAAAAAT
* * * *
19470666 AGATGACCGAGA-TAACACCATGAATCATCAGAAATGATCTAGACTGAGCCAAGA-CTAAGTGAT
1 AAATGACCAAGACGAA-ACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATC-AAGTGAT
* * * * * * *
19470729 CAGGACAAAACCATAAGTCAAAATGAAATGACCAAGATCAAGTCAAGATCAAGAAT
64 CAGGATAAAACCACAAGTCAAAATAAAATGACCAGGATCGAGTCAAGGTCAAAAAT
* * * * * * * *
19470785 AAATGATCAGGACGAAACCATGAATTATAATAAATGATCTGGACTAAGCCAAGATTAAGTGATCG
1 AAATGACCAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGATCA
* * * * * ** *
19470850 GGATGAAATCACTAGTCAAAATAAAATGACTAGGA-CTAAGTTGAGGTTAAAAAT
66 GGATAAAACCACAAGTCAAAATAAAATGACCAGGATC-GAGTCAAGGTCAAAAAT
*** * ** * * ** *
19470904 AAATGACTGGGATGAAACCACAAATCATCAGAAATGATCTGGACTGAGTTAAGA-CTAAGTGACC
1 AAATGACCAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATC-AAGTGATC
* * * * ** *
19470968 AGGATGAAACCACGAGTCAAAATAAAACGATCAAAATCGAGTCAAGGTCAAGAAT
65 AGGATAAAACCACAAGTCAAAATAAAATGACCAGGATCGAGTCAAGGTCAAAAAT
* * * *
19471023 AAATGATCGAGACGAAACCATAAATCATAAGAAATGATCTAGACTGAGCCAAGATCACGTGA
1 AAATGACCAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGA
19471085 GTGAATAATG
Statistics
Matches: 516, Mismatches: 131, Indels: 21
0.77 0.20 0.03
Matches are distributed among these distances:
118 23 0.04
119 397 0.77
120 96 0.19
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (119 bp):
AAATGACCAAGACGAAACCATGAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGATCA
GGATAAAACCACAAGTCAAAATAAAATGACCAGGATCGAGTCAAGGTCAAAAAT
Found at i:19470630 original size:238 final size:235
Alignment explanation
Indices: 19470327--19471079 Score: 821
Period size: 238 Copynumber: 3.2 Consensus size: 235
19470317 AAGATACAAT
* * * * * * * *
19470327 CATGAATCATGA-AAATAATTTAGACTAAGCCAAGATCAAATGATCAGGCTAAAATCACAAGTCA
1 CATGAATCATAAGAAATGATCTGGACTGAGCCAAGATCAAATGATCGGGATAAAATCACTAGTCA
* * * * * * *
19470391 AAATAAAGTGACCAGGATCGAGTCGAGGTCAAAAATAGATGATTAAGACGAAACCATGAATCATA
66 AAATAAAATGACTAGGATCGAGTTGAGGTAAAAAATAGATGACTGAGA-GAAACCATGAATCATC
** *
19470456 AGAAATGATCTAGACTGAGCCAAGA-TCAAGTGACCAAAATAAAACCACCAGTCAAAATAAAGTG
130 AGAAATGATCTAGACTGAGCCAAGACT-AAGTGACCAGGATAAAACCACAAGTCAAAATAAA-TG
* * * * *
19470520 A-CAAGGACCGAGTCAAGGTAAAAAATAGATGACTAGGATGAAAC
193 ACCAA-GATCGAGTCAAGGTCAAGAATAAATGA-TAGGACGAAAC
* * * * *
19470564 CACGAATCATCAGAAATGATTTGGATTGAGCCAAGATCAAATGATTGGGATAAAATCACTAGTCA
1 CATGAATCATAAGAAATGATCTGGACTGAGCCAAGATCAAATGATCGGGATAAAATCACTAGTCA
* * * *
19470629 AAACAAAACCGACTAGGATCGAGTTGAGGTAAAAAATAGATGACCGAGATAACACCATGAATCAT
66 AAATAAAA-TGACTAGGATCGAGTTGAGGTAAAAAATAGATGACTGAGAGAA-ACCATGAATCAT
* * *
19470694 CAGAAATGATCTAGACTGAGCCAAGACTAAGTGATCAGGACAAAACCATAAGTCAAAATGAAATG
129 CAGAAATGATCTAGACTGAGCCAAGACTAAGTGACCAGGATAAAACCACAAGTCAAAAT-AAATG
* *
19470759 ACCAAGATCAAGTCAAGATCAAGAATAAATGATCAGGACGAAAC
193 ACCAAGATCGAGTCAAGGTCAAGAATAAATGAT-AGGACGAAAC
* * * * * *
19470803 CATGAATTATAATAAATGATCTGGACTAAGCCAAGATTAAGTGATCGGGATGAAATCACTAGTCA
1 CATGAATCATAAGAAATGATCTGGACTGAGCCAAGATCAAATGATCGGGATAAAATCACTAGTCA
* * * * **
19470868 AAATAAAATGACTAGGA-CTAAGTTGAGGTTAAAAATAAATGACTGGGATGAAACCACAAATCAT
66 AAATAAAATGACTAGGATC-GAGTTGAGGTAAAAAATAGATGACTGAGA-GAAACCATGAATCAT
* ** * * *
19470932 CAGAAATGATCTGGACTGAGTTAAGACTAAGTGACCAGGATGAAACCACGAGTCAAAATAAAACG
129 CAGAAATGATCTAGACTGAGCCAAGACTAAGTGACCAGGATAAAACCACAAGTCAAAAT-AAATG
* * *
19470997 ATCAAAATCGAGTCAAGGTCAAGAATAAATGATCGAGACGAAAC
193 ACCAAGATCGAGTCAAGGTCAAGAATAAATGATAG-GACGAAAC
* *
19471041 CATAAATCATAAGAAATGATCTAGACTGAGCCAAGATCA
1 CATGAATCATAAGAAATGATCTGGACTGAGCCAAGATCA
19471080 CGTGAGTGAA
Statistics
Matches: 430, Mismatches: 76, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
237 12 0.03
238 220 0.51
239 191 0.44
240 7 0.02
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (235 bp):
CATGAATCATAAGAAATGATCTGGACTGAGCCAAGATCAAATGATCGGGATAAAATCACTAGTCA
AAATAAAATGACTAGGATCGAGTTGAGGTAAAAAATAGATGACTGAGAGAAACCATGAATCATCA
GAAATGATCTAGACTGAGCCAAGACTAAGTGACCAGGATAAAACCACAAGTCAAAATAAATGACC
AAGATCGAGTCAAGGTCAAGAATAAATGATAGGACGAAAC
Found at i:19482261 original size:16 final size:15
Alignment explanation
Indices: 19482226--19482267 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
19482216 AAAATGGGTT
*
19482226 AAAAATAAAATAAAAT
1 AAAAATAAAA-AAAAG
19482242 AAAAATAAAAAAATAG
1 AAAAATAAAAAAA-AG
19482258 AAAAA-AAAAA
1 AAAAATAAAAA
19482268 CGTGCGATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAAAAG
Found at i:19482681 original size:21 final size:22
Alignment explanation
Indices: 19482634--19482681 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
19482624 AACCAAACCC
** *
19482634 AGAAAAATCCAAAAAAGTTTTT
1 AGAAAAATCCAAAAAAGAATCT
19482656 A-AAAAATCCAAAAAA-AATCT
1 AGAAAAATCCAAAAAAGAATCT
19482676 AGAAAA
1 AGAAAA
19482682 CCTCTTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 18 0.82
22 1 0.05
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (22 bp):
AGAAAAATCCAAAAAAGAATCT
Found at i:19483073 original size:4 final size:4
Alignment explanation
Indices: 19483064--19483094 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
19483054 AACAAAAAAG
19483064 GAAA GAAA GAAA GAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
19483095 AAAATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:19483386 original size:18 final size:18
Alignment explanation
Indices: 19483360--19483394 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
19483350 TTTGTTTTTT
19483360 TTTTAATTTTTTTCAAAAG
1 TTTTAA-TTTTTTCAAAAG
19483379 TTTT-ATTTTTTCAAAA
1 TTTTAATTTTTTCAAAA
19483395 TTTGATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 1 0.06
19 4 0.25
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAATTTTTTCAAAAG
Found at i:19483402 original size:16 final size:17
Alignment explanation
Indices: 19483367--19483402 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19483357 TTTTTTTAAT
*
19483367 TTTTTTCAAAAGTTTTA
1 TTTTTTCAAAAGTTTGA
19483384 TTTTTTCAAAA-TTTGA
1 TTTTTTCAAAAGTTTGA
19483400 TTT
1 TTT
19483403 AGTTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTTTCAAAAGTTTGA
Found at i:19483565 original size:27 final size:27
Alignment explanation
Indices: 19483535--19483592 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
19483525 AAGTTTCTCA
19483535 TTTTCTAATTTTCTT-AGATCTTTT-AAT
1 TTTTCT-ATTTTCTTCA-ATCTTTTGAAT
* *
19483562 TTTTCTTTTTTCTTCAATTTTTTGAAT
1 TTTTCTATTTTCTTCAATCTTTTGAAT
19483589 TTTT
1 TTTT
19483593 AGATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTCTATTTTCTTCAATCTTTTGAAT
Found at i:19483601 original size:19 final size:19
Alignment explanation
Indices: 19483579--19483637 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
19483569 TTTTCTTCAA
19483579 TTTTTTGAATTTTTAGATT
1 TTTTTTGAATTTTTAGATT
* *
19483598 TTTTATGAATTTTTGGA-T
1 TTTTTTGAATTTTTAGATT
19483616 TTTTTTG--TTTTTA-ATT
1 TTTTTTGAATTTTTAGATT
19483632 TTTTTT
1 TTTTTT
19483638 TTTTTTATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.03
16 12 0.34
18 7 0.20
19 15 0.43
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (19 bp):
TTTTTTGAATTTTTAGATT
Found at i:19486191 original size:25 final size:25
Alignment explanation
Indices: 19486123--19486191 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
19486113 GATGTAAAAA
** *
19486123 TATTTTAT-TATTTATTTAGTTTTT
1 TATTTTATATATTTATTTAAATTGT
*
19486147 TA-TTTATATATATTA-ATAAATTGT
1 TATTTTATATAT-TTATTTAAATTGT
19486171 TATTTTATATATTTATTTAAA
1 TATTTTATATATTTATTTAAA
19486192 ATATTAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
23 5 0.14
24 15 0.42
25 16 0.44
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (25 bp):
TATTTTATATATTTATTTAAATTGT
Found at i:19486202 original size:25 final size:25
Alignment explanation
Indices: 19486148--19486202 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
19486138 TTAGTTTTTT
* *
19486148 ATTTATATATATTAATAAATTGTTA
1 ATTTATATATATTAATAAAATATTA
* *
19486173 TTTTATATAT-TTATTTAAAATATTA
1 ATTTATATATATTA-ATAAAATATTA
19486198 ATTTA
1 ATTTA
19486203 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTATATATATTAATAAAATATTA
Done.