Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold168
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: 2098754
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 14 of 16
Found at i:1573938 original size:5 final size:5
Alignment explanation
Indices: 1573892--1573921 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1573882 CTAATTATTT
1573892 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1573922 AAAATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1576547 original size:14 final size:14
Alignment explanation
Indices: 1576530--1576561 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1576520 TAAAAATAAA
1576530 AAATTATTAAAATT
1 AAATTATTAAAATT
1576544 AAATTATTAAAATT
1 AAATTATTAAAATT
1576558 AAAT
1 AAAT
1576562 AAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTATTAAAATT
Found at i:1576560 original size:20 final size:20
Alignment explanation
Indices: 1576535--1576593 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
1576525 ATAAAAAATT
1576535 ATTAAAATTAAATTATTAAA
1 ATTAAAATTAAATTATTAAA
* *
1576555 ATT-AAATAAAATTAATAAA
1 ATTAAAATTAAATTATTAAA
*
1576574 A-TATAATTAATATTGATTAA
1 ATTAAAATTAA-ATT-ATTAA
1576594 TCTAATTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.65
20 6 0.19
21 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTAAAATTAAATTATTAAA
Found at i:1578417 original size:15 final size:15
Alignment explanation
Indices: 1578392--1578427 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1578382 TTTTTATTAT
*
1578392 TTAACATTAATTTACA
1 TTAA-ATTAATTTAAA
1578408 TTAAATTAATTTAAA
1 TTAAATTAATTTAAA
1578423 TTAAA
1 TTAAA
1578428 AATTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAATTAATTTAAA
Found at i:1581078 original size:30 final size:31
Alignment explanation
Indices: 1581034--1581149 Score: 87
Period size: 30 Copynumber: 3.6 Consensus size: 31
1581024 ATAATTTAAA
1581034 AATTT-TAAATTTTAAATT-TATATTTAATTT
1 AATTTATAAATTTTAAATTAT-TATTTAATTT
*
1581064 AATTTATAAA-TTTAAATTATTATTTATTTT
1 AATTTATAAATTTTAAATTATTATTTAATTT
* * * *
1581094 TATTTAAAAAATATTAAA-AATTATTTTAATATT
1 AATTT-ATAAATTTTAAATTATTA-TTTAAT-TT
*
1581127 AATATTTATATATTTTATAATTA
1 -A-ATTTATAAATTTTA-AATTA
1581150 AATTTAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
30 26 0.40
31 13 0.20
32 10 0.15
33 2 0.03
34 7 0.11
35 6 0.09
36 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AATTTATAAATTTTAAATTATTATTTAATTT
Found at i:1581092 original size:24 final size:23
Alignment explanation
Indices: 1581041--1581095 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1581031 AAAAATTTTA
*
1581041 AATTTTAAATTTATATTTAATTT
1 AATTTTAAATTTAAATTTAATTT
*
1581064 AATTTATAAATTTAAATTATTATTT
1 AATTT-TAAATTTAAATT-TAATTT
*
1581089 ATTTTTA
1 AATTTTA
1581096 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 13 0.48
25 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTAAATTTAAATTTAATTT
Found at i:1581140 original size:22 final size:21
Alignment explanation
Indices: 1581115--1581155 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1581105 TATTAAAAAT
1581115 TATTTTA-ATATTAATATTTATA
1 TATTTTATA-ATTAA-ATTTATA
1581137 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1581156 AAAATCTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 12 0.67
23 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1581464 original size:16 final size:16
Alignment explanation
Indices: 1581419--1581483 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
1581409 TTACATATTA
1581419 AAAATAAATTTAAATTT
1 AAAAT-AATTTAAATTT
**
1581436 ATAAA-AAAATAAATTT
1 A-AAATAATTTAAATTT
* * *
1581452 CAAATGATTTAAATAT
1 AAAATAATTTAAATTT
1581468 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
1581484 GAATCTGTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
15 3 0.08
16 29 0.81
17 1 0.03
18 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:1583341 original size:62 final size:62
Alignment explanation
Indices: 1583244--1583369 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
1583234 TGTTTGCCAG
*
1583244 ATAATTTGTGTTGTGGTTCCTTGTTTGGTAACTATAAGCAGGTAGACTAATTAAACTCTAGA
1 ATAATTTGTGGTGTGGTTCCTTGTTTGGTAACTATAAGCAGGTAGACTAATTAAACTCTAGA
1583306 ATAATTTGTGGTGTGGTTCCTTGTTTGGTAACTATAAGCAGGTAGACTAATTAAACTCTAGA
1 ATAATTTGTGGTGTGGTTCCTTGTTTGGTAACTATAAGCAGGTAGACTAATTAAACTCTAGA
1583368 AT
1 AT
1583370 TTGTTTCCTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.38
Consensus pattern (62 bp):
ATAATTTGTGGTGTGGTTCCTTGTTTGGTAACTATAAGCAGGTAGACTAATTAAACTCTAGA
Found at i:1583802 original size:80 final size:80
Alignment explanation
Indices: 1583669--1583822 Score: 272
Period size: 80 Copynumber: 1.9 Consensus size: 80
1583659 GTCCTCGGGC
* *
1583669 CAAAGAAATGTTGTTTATCTTAGGTAAAATTTGTGAAATAATGGATGCTAAAGGGATTGGATCAT
1 CAAAGAAATGCTGTTTATCTTAGGTAAAATTTGTGAAATAATGGATGCTAAAGGGATTGGATCAA
*
1583734 GTATTTACCACGCCT
66 GCATTTACCACGCCT
*
1583749 CAAAGAAATGCTGTTTATCTTAGGTAAAATTTGTGAAATAATTGATGCTAAAGGGATTGGATCAA
1 CAAAGAAATGCTGTTTATCTTAGGTAAAATTTGTGAAATAATGGATGCTAAAGGGATTGGATCAA
1583814 GCATTTACC
66 GCATTTACC
1583823 GGGGCGTGGC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (80 bp):
CAAAGAAATGCTGTTTATCTTAGGTAAAATTTGTGAAATAATGGATGCTAAAGGGATTGGATCAA
GCATTTACCACGCCT
Found at i:1586830 original size:2 final size:2
Alignment explanation
Indices: 1586823--1586862 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1586813 ATAAAGAGTG
1586823 AT AT AT 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 AT AT AT
1586863 TCTGTTTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1590776 original size:2 final size:2
Alignment explanation
Indices: 1590771--1590818 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1590761 TGTGTGTGTG
1590771 AT AT AT AT 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 AT AT AT AT
1590813 AT AT AT
1 AT AT AT
1590819 GGTGTCAGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1592449 original size:14 final size:14
Alignment explanation
Indices: 1592430--1592462 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1592420 TGCTTAGAAA
1592430 TTTTAAA-ATTTTT
1 TTTTAAAGATTTTT
1592443 CTTTTAAAGATTTTT
1 -TTTTAAAGATTTTT
1592458 TTTTA
1 TTTTA
1592463 CGTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTTAAAGATTTTT
Found at i:1592486 original size:18 final size:19
Alignment explanation
Indices: 1592454--1592489 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1592444 TTTTAAAGAT
*
1592454 TTTTTTTTACGTAAAATTA
1 TTTTTTTTACATAAAATTA
1592473 TTTTTTTT-CATAAAATT
1 TTTTTTTTACATAAAATT
1592490 CAGAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTTTTACATAAAATTA
Found at i:1596970 original size:2 final size:2
Alignment explanation
Indices: 1596965--1596993 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1596955 CATGAATGAA
1596965 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 A
1596994 CATAATTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1603837 original size:13 final size:13
Alignment explanation
Indices: 1603819--1603846 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1603809 TTTAATTTTA
1603819 ATTTAATTAATTT
1 ATTTAATTAATTT
1603832 ATTTAATTAATTT
1 ATTTAATTAATTT
1603845 AT
1 AT
1603847 AATTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTAATTAATTT
Found at i:1603936 original size:35 final size:35
Alignment explanation
Indices: 1603875--1603969 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
1603865 ATTGATTGAA
* * *
1603875 TAAATTAATAATTAAATTAAA-AAATATTATTTTATT
1 TAAATAAATAA-TAACTTAAATAAATATTA-TTTAAT
*
1603911 TAAATATAATAA-AAC-TCAATAAATATTATTTAAT
1 TAAATA-AATAATAACTTAAATAAATATTATTTAAT
1603945 TAAATAAATAATAACTTAAATAAAT
1 TAAATAAATAATAACTTAAATAAAT
1603970 TAATTAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
33 5 0.10
34 17 0.34
35 18 0.36
36 5 0.10
37 5 0.10
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (35 bp):
TAAATAAATAATAACTTAAATAAATATTATTTAAT
Found at i:1603965 original size:16 final size:18
Alignment explanation
Indices: 1603935--1603983 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
1603925 CTCAATAAAT
*
1603935 ATTATTTAA-TTAAATAA
1 ATTAATTAACTTAAATAA
1603952 A-TAA-TAACTTAAATAA
1 ATTAATTAACTTAAATAA
*
1603968 ATTAATTAATTTAAAT
1 ATTAATTAACTTAAAT
1603984 TATAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 4 0.15
18 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATTAACTTAAATAA
Found at i:1603982 original size:34 final size:35
Alignment explanation
Indices: 1603875--1603983 Score: 109
Period size: 34 Copynumber: 3.1 Consensus size: 35
1603865 ATTGATTGAA
* * * *
1603875 TAAATTAATAATTAAATTAAAAAATATTATTTTATT
1 TAAATAAATAA-TAACTTAAATAATATTATTTAATT
*
1603911 TAAATATAATAA-AAC-TCAATAAATATTATTTAA-T
1 TAAATA-AATAATAACTTAAAT-AATATTATTTAATT
*
1603945 TAAATAAATAATAACTTAAATAA-ATTAATTAATT
1 TAAATAAATAATAACTTAAATAATATTATTTAATT
1603979 TAAAT
1 TAAAT
1603984 TATAAAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
33 13 0.21
34 21 0.34
35 17 0.28
36 5 0.08
37 5 0.08
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAATAAATAATAACTTAAATAATATTATTTAATT
Found at i:1605816 original size:17 final size:17
Alignment explanation
Indices: 1605796--1605840 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1605786 AAATAATAAT
*
1605796 ATTTATCGAATATTCAA
1 ATTTATCAAATATTCAA
*
1605813 ATTTATTAAATATTCAA
1 ATTTATCAAATATTCAA
*
1605830 ATTTATTAAAT
1 ATTTATCAAAT
1605841 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTTATCAAATATTCAA
Found at i:1608995 original size:20 final size:22
Alignment explanation
Indices: 1608972--1609013 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1608962 AAATATTTTA
*
1608972 ATATAAAT-TT-ATTATAAAAT
1 ATATAAATATTAATAATAAAAT
1608992 ATATAAATATTAATAATAAAAT
1 ATATAAATATTAATAATAAAAT
1609014 TAAATTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAATATTAATAATAAAAT
Found at i:1617524 original size:87 final size:88
Alignment explanation
Indices: 1617373--1617550 Score: 268
Period size: 87 Copynumber: 2.0 Consensus size: 88
1617363 GATATTATTC
* * *
1617373 AAACCCAAATGGCCAAATTTGAAGATGGCCCAAAGCAACCCATGTGCTTCTCTAATGGCCAGCAA
1 AAACCCAAATGGCCAAATTTGAAGACGGCCCAAAGCAACCCATGTGCTGCTCTAATGGACAGCAA
*
1617438 GCTCTACCAAATGTAACCTAAGA
66 GCTCTACCAAACGTAACCTAAGA
* * *
1617461 AAACCCAAATGGCCAAATTTGAAGACGG-CCAAAGCAGCCCATTTGCTGCTCTAATGGATAGCAA
1 AAACCCAAATGGCCAAATTTGAAGACGGCCCAAAGCAACCCATGTGCTGCTCTAATGGACAGCAA
* *
1617525 GCTCTGCCAAACGTAACCTGAGA
66 GCTCTACCAAACGTAACCTAAGA
1617548 AAA
1 AAA
1617551 TTTATCCAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 54 0.67
88 27 0.33
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (88 bp):
AAACCCAAATGGCCAAATTTGAAGACGGCCCAAAGCAACCCATGTGCTGCTCTAATGGACAGCAA
GCTCTACCAAACGTAACCTAAGA
Found at i:1619504 original size:63 final size:63
Alignment explanation
Indices: 1619405--1619530 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
1619395 ATTGAGATCA
1619405 AAAGGAAGAGAATGGAAGAAATGGTAGATTTTACCAAGACAATAGATCTAGAGAAAGAGGCTT
1 AAAGGAAGAGAATGGAAGAAATGGTAGATTTTACCAAGACAATAGATCTAGAGAAAGAGGCTT
* *
1619468 AAAGGAAGAGAATGGAAGAAATGGTGGATTTTACCAAGACAATAGATCTAGAGAAAGGGGCTT
1 AAAGGAAGAGAATGGAAGAAATGGTAGATTTTACCAAGACAATAGATCTAGAGAAAGAGGCTT
1619531 TCTTTTGTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.44, C:0.08, G:0.29, T:0.19
Consensus pattern (63 bp):
AAAGGAAGAGAATGGAAGAAATGGTAGATTTTACCAAGACAATAGATCTAGAGAAAGAGGCTT
Found at i:1621814 original size:2 final size:2
Alignment explanation
Indices: 1621807--1621842 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1621797 CTGCAAAATG
1621807 AT 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 AT
1621843 TTTAAAGGAT
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):
AT
Found at i:1622582 original size:15 final size:15
Alignment explanation
Indices: 1622564--1622623 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1622554 TATATAAATT
1622564 TATTTTATTATTTTA
1 TATTTTATTATTTTA
* *
1622579 TATTTTA-TCTTTCA
1 TATTTTATTATTTTA
*
1622593 TATATTTATGTATATTA
1 TAT-TTTAT-TATTTTA
1622610 TATTTTAATTATTT
1 TATTTT-ATTATTT
1622624 GTTAATAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
14 8 0.23
15 11 0.31
16 7 0.20
17 9 0.26
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTTTATTATTTTA
Found at i:1623857 original size:25 final size:26
Alignment explanation
Indices: 1623845--1623899 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1623835 AAATATTATT
*
1623845 TCAAATT-AAATTAAAATATGAAAAT
1 TCAAATTCAAATTAAAAAATGAAAAT
*
1623870 TCAAATTCAAATT-AAAAATTAAAAT
1 TCAAATTCAAATTAAAAAATGAAAAT
1623895 T-AAAT
1 TCAAAT
1623900 GAATTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (26 bp):
TCAAATTCAAATTAAAAAATGAAAAT
Found at i:1623887 original size:19 final size:18
Alignment explanation
Indices: 1623847--1623899 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
1623837 ATATTATTTC
*
1623847 AAATTAAATTAAAATATGA
1 AAATTAAATT-AAATATAA
1623866 AAATTCAAATTCAAAT-TAA
1 AAATT-AAATT-AAATATAA
1623885 AAATTAAAATTAAAT
1 AAATT-AAATTAAAT
1623900 GAATTATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 17 0.57
20 9 0.30
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
AAATTAAATTAAATATAA
Found at i:1623893 original size:6 final size:6
Alignment explanation
Indices: 1623847--1623898 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
1623837 ATATTATTTC
* *
1623847 AAATT- AAATTA AAATATGA AAATTC AAATTC AAATTAA AAATTA AAATTA
1 AAATTA AAATTA AAAT-T-A AAATTA AAATTA AAATT-A AAATTA AAATTA
1623897 AA
1 AA
1623899 TGAATTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 5 0.12
6 24 0.59
7 7 0.17
8 5 0.12
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (6 bp):
AAATTA
Found at i:1623894 original size:13 final size:13
Alignment explanation
Indices: 1623847--1623898 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
1623837 ATATTATTTC
1623847 AAATT-AAATTAA
1 AAATTAAAATTAA
* *
1623859 AATATGAAAATT-C
1 AA-ATTAAAATTAA
*
1623872 AAATTCAAATTAA
1 AAATTAAAATTAA
1623885 AAATTAAAATTAA
1 AAATTAAAATTAA
1623898 A
1 A
1623899 TGAATTATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
12 9 0.29
13 17 0.55
14 5 0.16
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (13 bp):
AAATTAAAATTAA
Found at i:1624169 original size:32 final size:32
Alignment explanation
Indices: 1624121--1624200 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1624111 TTTAATAATT
*
1624121 TATA-TTATATTTATATAAAATTCAATATTTTAA
1 TATATTTATA-TTATATAAAATTCAA-ATATTAA
* *
1624154 TA-ATTTATATTATATAAACTTTAAATATTAA
1 TATATTTATATTATATAAAATTCAAATATTAA
*
1624185 TATATTCATATTATAT
1 TATATTTATATTATAT
1624201 TTTTAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.20
32 26 0.63
33 7 0.17
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATATTATATAAAATTCAAATATTAA
Found at i:1625946 original size:32 final size:32
Alignment explanation
Indices: 1625900--1625961 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1625890 ATTATTTAAA
1625900 TTTAATTATAAATATTAATATAAA-AATAAATT
1 TTTAATTATAAATATT-ATATAAATAATAAATT
* * *
1625932 TTTAATTGTTAATATTATTTAAATAATAAA
1 TTTAATTATAAATATTATATAAATAATAAA
1625962 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
TTTAATTATAAATATTATATAAATAATAAATT
Found at i:1628719 original size:3 final size:3
Alignment explanation
Indices: 1628713--1628747 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1628703 TATTTAAAGT
1628713 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1628748 TAAAAGAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1630534 original size:2 final size:2
Alignment explanation
Indices: 1630529--1630575 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1630519 ATTTCTTGGC
1630529 AT AT AT AT 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 AT AT AT AT
1630571 AT AT A
1 AT AT A
1630576 GAACACTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1631844 original size:24 final size:23
Alignment explanation
Indices: 1631816--1631862 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1631806 TACAACATAA
*
1631816 AAAAATTAAAATATAACTTGACATG
1 AAAAA-TAAAATA-AAATTGACATG
*
1631841 AAAAATAATATAAAATTGACAT
1 AAAAATAAAATAAAATTGACAT
1631863 AAATAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (23 bp):
AAAAATAAAATAAAATTGACATG
Found at i:1632185 original size:27 final size:28
Alignment explanation
Indices: 1632154--1632206 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1632144 AAAAATAAGT
*
1632154 TATAATATATCAAATTTTA-TATAAATA
1 TATAATATATCAAATTTAATTATAAATA
* *
1632181 TATAATATTTTAAATTTAATTATAAA
1 TATAATATATCAAATTTAATTATAAA
1632207 AATAACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TATAATATATCAAATTTAATTATAAATA
Found at i:1632263 original size:21 final size:20
Alignment explanation
Indices: 1632202--1632265 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
1632192 AAATTTAATT
**
1632202 ATAAAAATAACATTTAATATA
1 ATAAAAATAA-AAATAATATA
*
1632223 ATACGAATATAAAAAT-ATATA
1 ATA--AAAATAAAAATAATATA
1632244 ATAAAAATAAAAATAAATATA
1 ATAAAAATAAAAAT-AATATA
1632265 A
1 A
1632266 ATTGCCAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 10 0.29
21 17 0.49
22 2 0.06
23 6 0.17
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (20 bp):
ATAAAAATAAAAATAATATA
Found at i:1633146 original size:3 final size:3
Alignment explanation
Indices: 1633138--1633175 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1633128 ATTTATTTTA
1633138 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1633176 AAGAATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1633562 original size:15 final size:16
Alignment explanation
Indices: 1633531--1633571 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1633521 ATTTACTAAT
1633531 TAGTAAAATAGGTTAGA
1 TAGTAAAA-AGGTTAGA
1633548 TAGTAAAAA-GTTAGA
1 TAGTAAAAAGGTTAGA
*
1633563 TAATAAAAA
1 TAGTAAAAA
1633572 ACATTCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 1 0.04
17 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (16 bp):
TAGTAAAAAGGTTAGA
Found at i:1633791 original size:13 final size:12
Alignment explanation
Indices: 1633773--1633810 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1633763 ATAAAGATAA
1633773 TAAATTTAATAT
1 TAAATTTAATAT
1633785 CTAAATTTAATAT
1 -TAAATTTAATAT
1633798 T-AATTTATATAT
1 TAAATTTA-ATAT
1633810 T
1 T
1633811 TAGTACAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 6 0.25
13 12 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATTTAATAT
Found at i:1637769 original size:27 final size:27
Alignment explanation
Indices: 1637738--1637797 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1637728 ATTATTACAG
* * *
1637738 TAAACGTGTAATAAAAGAGAATTATTT
1 TAAACATGTAATAAAAGAAAACTATTT
*
1637765 TAAACATGTAATAAAAGAAAACTGTTT
1 TAAACATGTAATAAAAGAAAACTATTT
1637792 TAAACA
1 TAAACA
1637798 CGTGTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.30
Consensus pattern (27 bp):
TAAACATGTAATAAAAGAAAACTATTT
Found at i:1637930 original size:18 final size:18
Alignment explanation
Indices: 1637904--1637966 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
1637894 ATTATTTGAG
1637904 TTTAATTAAAAATTAAAA
1 TTTAATTAAAAATTAAAA
* *
1637922 TTTATTTAATAATT-AAA
1 TTTAATTAAAAATTAAAA
* * *
1637939 TTAAATTTAAATTTAAATA
1 TTTAATTAAAAATTAAA-A
1637958 TTTTAATTA
1 -TTTAATTA
1637967 TTAAAAAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
17 12 0.36
18 14 0.42
19 1 0.03
20 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAAATTAAAA
Found at i:1637931 original size:22 final size:21
Alignment explanation
Indices: 1637904--1637947 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1637894 ATTATTTGAG
1637904 TTTAATTAA-AAATTAAAATTTA
1 TTTAA-TAATAAATTA-AATTTA
1637926 TTTAATAATTAAATTAAATTTA
1 TTTAATAA-TAAATTAAATTTA
1637948 AATTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.15
22 11 0.55
23 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATAATAAATTAAATTTA
Found at i:1637949 original size:36 final size:35
Alignment explanation
Indices: 1637907--1638006 Score: 85
Period size: 37 Copynumber: 2.7 Consensus size: 35
1637897 ATTTGAGTTT
*
1637907 AATTAAAAATTAAAATTTATTTAATAATTAAATT-A
1 AATTAAAAATTAAAATTTATTTAATAA-AAAATTAA
* * * *
1637942 AATTTAAATTTAAATATTTTAATTATTAAAAAATTAA
1 AATTAAAAATTAAA-A-TTTATTTAATAAAAAATTAA
1637979 AATTAAATATATCTAAAATTTGATTTAA
1 AATTAAA-A-AT-TAAAATTT-ATTTAA
1638007 ATAGATGATA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
35 12 0.24
36 6 0.12
37 17 0.35
38 4 0.08
39 6 0.12
40 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (35 bp):
AATTAAAAATTAAAATTTATTTAATAAAAAATTAA
Found at i:1638617 original size:24 final size:24
Alignment explanation
Indices: 1638590--1638637 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1638580 TTGTTAAAAT
*
1638590 AATTTT-TTATAATTAATTAAGTAC
1 AATTTTGTTATAAAT-ATTAAGTAC
1638614 AATTTTGTTATAAATATTAAGTAC
1 AATTTTGTTATAAATATTAAGTAC
1638638 GCTCAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (24 bp):
AATTTTGTTATAAATATTAAGTAC
Found at i:1639404 original size:3 final size:3
Alignment explanation
Indices: 1639398--1639423 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1639388 ATAATAATAA
1639398 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1639424 CCTCAATTTG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1640989 original size:19 final size:20
Alignment explanation
Indices: 1640967--1641016 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1640957 TAATAATATT
1640967 TGATATAAATATAT-AAATA
1 TGATATAAATATATAAAATA
*
1640986 TGATATAAA-AAATAAAATA
1 TGATATAAATATATAAAATA
1641005 TGATAT-AATATA
1 TGATATAAATATA
1641017 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (20 bp):
TGATATAAATATATAAAATA
Found at i:1641070 original size:50 final size:48
Alignment explanation
Indices: 1641008--1641129 Score: 121
Period size: 50 Copynumber: 2.6 Consensus size: 48
1640998 TAAAATATGA
* * *
1641008 TATAATATAAATAT-TTTAATATTTTAAAAT-TTGTTTAATATAAATTAT
1 TATAATATAAATATATATAA-AATATAAAATATT-TTTAATATAAATTAT
1641056 TATAATATTAAAATATATATAAAATATAAAATATTTTTAATATAAA-TA-
1 TATAATA-T-AAATATATATAAAATATAAAATATTTTTAATATAAATTAT
*
1641104 TAAAATTATAAA-ATATA-AAAATATAA
1 TATAA-TATAAATATATATAAAATATAA
1641130 TACGGATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
45 9 0.14
46 5 0.08
47 3 0.05
48 12 0.18
49 5 0.08
50 25 0.38
51 6 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (48 bp):
TATAATATAAATATATATAAAATATAAAATATTTTTAATATAAATTAT
Found at i:1641097 original size:16 final size:16
Alignment explanation
Indices: 1641010--1641101 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 16
1641000 AAATATGATA
1641010 TAATAT-AAATA-TTT
1 TAATATAAAATATTTT
1641024 TAATATTTTAAAAT-TTGTT
1 TAATA---TAAAATATT-TT
* *
1641043 TAATATAAATTA-TTA
1 TAATATAAAATATTTT
*
1641058 TAATATTAAAATATATATA
1 TAATA-TAAAATAT-T-TT
*
1641077 AAATATAAAATATTTT
1 TAATATAAAATATTTT
1641093 TAATATAAA
1 TAATATAAA
1641102 TATAAAATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 5 0.08
15 6 0.10
16 21 0.34
17 2 0.03
18 14 0.23
19 13 0.21
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
TAATATAAAATATTTT
Found at i:1641105 original size:6 final size:7
Alignment explanation
Indices: 1641072--1641129 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
1641062 ATTAAAATAT
1641072 ATATAAA
1 ATATAAA
1641079 ATATAAA
1 ATATAAA
**
1641086 ATATTTTTA
1 ATA--TAAA
1641095 ATAT-AA
1 ATATAAA
1641101 ATATAAA
1 ATATAAA
1641108 ATTATAAA
1 A-TATAAA
1641116 ATATAAAA
1 ATAT-AAA
1641124 ATATAA
1 ATATAA
1641130 TACGGATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.12
7 19 0.44
8 14 0.33
9 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
ATATAAA
Found at i:1641117 original size:15 final size:15
Alignment explanation
Indices: 1641070--1641129 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1641060 ATATTAAAAT
1641070 ATATATAAAATATAAA
1 ATATA-AAAATATAAA
***
1641086 ATATTTTTAATAT-AA
1 ATA-TAAAAATATAAA
*
1641101 ATATAAAATTATAAA
1 ATATAAAAATATAAA
1641116 ATATAAAAATATAA
1 ATATAAAAATATAA
1641130 TACGGATATA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 5 0.15
15 20 0.59
16 8 0.24
17 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAAAATATAAA
Found at i:1641126 original size:29 final size:29
Alignment explanation
Indices: 1641044--1641129 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
1641034 AAATTTGTTT
*
1641044 AATAT-AAATTATTATAATATTAAAATAT-
1 AATATAAAATTA-TAAAATATTAAAATATA
**
1641072 -ATATAAAA-TATAAAATATTTTTAATATA
1 AATATAAAATTATAAAATA-TTAAAATATA
*
1641100 AATATAAAATTATAAAATATAAAAATATA
1 AATATAAAATTATAAAATATTAAAATATA
1641129 A
1 A
1641130 TACGGATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
26 6 0.13
27 13 0.28
28 3 0.06
29 16 0.34
30 9 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATAAAATTATAAAATATTAAAATATA
Found at i:1641129 original size:23 final size:23
Alignment explanation
Indices: 1641070--1641129 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 23
1641060 ATATTAAAAT
**
1641070 ATATATAAAATATAAAATAT-TT
1 ATATATAAAATATAAAATATAAA
*
1641092 TTA-ATATAAATATAAAATTATAAA
1 ATATATA-AAATATAAAA-TATAAA
1641116 ATATA-AAAATATAA
1 ATATATAAAATATAA
1641130 TACGGATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.10
22 12 0.40
23 11 0.37
24 3 0.10
25 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATATAAAATATAAAATATAAA
Found at i:1650768 original size:13 final size:13
Alignment explanation
Indices: 1650747--1650780 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1650737 TTGATCCTTC
*
1650747 CTTTCTTTTTTTT
1 CTTTTTTTTTTTT
1650760 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
1650773 -TTTTTTTT
1 CTTTTTTTT
1650781 GAATTTCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:1667935 original size:3 final size:3
Alignment explanation
Indices: 1667927--1667953 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1667917 AATTTTCCGA
1667927 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1667954 GAAAAAGAGG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1674690 original size:28 final size:28
Alignment explanation
Indices: 1674641--1674717 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
1674631 TAATATTATC
1674641 ATATTTA-ATTGTATTAAT-TTTTTTAATT
1 ATATTTATATT-TA-TAATATTTTTTAATT
*
1674669 ATATTTATATTTATAATATTTTTTTATT
1 ATATTTATATTTATAATATTTTTTAATT
*
1674697 -T-TTTAT-TTTAATATTATTTTT
1 ATATTTATATTT-ATAATATTTTT
1674718 ACCAATTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.07
26 15 0.34
27 5 0.11
28 18 0.41
29 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (28 bp):
ATATTTATATTTATAATATTTTTTAATT
Found at i:1674696 original size:23 final size:24
Alignment explanation
Indices: 1674667--1674718 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
1674657 ATTTTTTTAA
1674667 TTATATTTATATTTATAATATT-TTT
1 TTAT-TTTATATTT-TAATATTATTT
*
1674692 TTATTTTTTATTTTAATATTATTT
1 TTATTTTATATTTTAATATTATTT
1674716 TTA
1 TTA
1674719 CCAATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 14 0.56
25 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTTTATATTTTAATATTATTT
Found at i:1674701 original size:26 final size:29
Alignment explanation
Indices: 1674657--1674717 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
1674647 AATTGTATTA
1674657 ATTTTTTTAATTATATTTATATTT-ATAAT
1 ATTTTTTTAATTATATTTAT-TTTAATAAT
*
1674686 ATTTTTTT-ATT-T-TTTATTTTAATATT
1 ATTTTTTTAATTATATTTATTTTAATAAT
1674712 ATTTTT
1 ATTTTT
1674718 ACCAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 15 0.50
27 1 0.03
28 3 0.10
29 8 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (29 bp):
ATTTTTTTAATTATATTTATTTTAATAAT
Found at i:1674864 original size:24 final size:24
Alignment explanation
Indices: 1674805--1674873 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
1674795 AAATTTAACA
*
1674805 TAATTTTTATATAAATTATAAATCTT
1 TAATTTTTAT-TAAATAATAAA-CTT
*
1674831 TAA-TTGTATTAAATAATATAA-TT
1 TAATTTTTATTAAATAATA-AACTT
*
1674854 TAATTTTTATT-ATTAATAAA
1 TAATTTTTATTAAATAATAAA
1674874 TTAAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.05
23 11 0.30
24 14 0.38
25 7 0.19
26 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TAATTTTTATTAAATAATAAACTT
Found at i:1675190 original size:31 final size:31
Alignment explanation
Indices: 1675148--1675210 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1675138 TAATTGATCA
* *
1675148 TATTGTAGATGTTATTTCTCTTGCCAATACT
1 TATTGTAGATGTGATTTCCCTTGCCAATACT
* *
1675179 TATTGTGGATGTGATTTCCCTTGCTAATACT
1 TATTGTAGATGTGATTTCCCTTGCCAATACT
1675210 T
1 T
1675211 GGGACCTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (31 bp):
TATTGTAGATGTGATTTCCCTTGCCAATACT
Found at i:1676329 original size:3 final size:3
Alignment explanation
Indices: 1676321--1676346 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1676311 TGACAAATTA
1676321 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1676347 AATTTAAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1676467 original size:25 final size:24
Alignment explanation
Indices: 1676439--1676495 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 24
1676429 ATTATTAATA
1676439 TTAATATTAATACATAAAATA-AAAT
1 TTAAT-TTAA-ACATAAAATATAAAT
*
1676464 TTAATTTAAATATAAAATATAAA-
1 TTAATTTAAACATAAAATATAAAT
1676487 -TAATTTAAA
1 TTAATTTAAA
1676496 ATTTAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.30
23 9 0.30
24 7 0.23
25 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAATTTAAACATAAAATATAAAT
Found at i:1676511 original size:16 final size:15
Alignment explanation
Indices: 1676452--1676513 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
1676442 ATATTAATAC
*
1676452 ATAAAATAAAATTTA
1 ATAATATAAAATTTA
*
1676467 ATTTAAATATAAAATATAA
1 A--T-AATATAAAAT-TTA
*
1676486 ATAATTTAAAATTTA
1 ATAATATAAAATTTA
1676501 ATGAATATAAAAT
1 AT-AATATAAAAT
1676514 AATATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
15 5 0.14
16 18 0.49
17 2 0.05
18 9 0.24
19 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAATATAAAATTTA
Found at i:1677246 original size:26 final size:26
Alignment explanation
Indices: 1677217--1677288 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 26
1677207 ATATTCTATA
* *
1677217 TAAAGATATTTATTTTA-ATTTGTATT
1 TAAA-ATATTTATATTATATTTATATT
*
1677243 TAAAATA-TTATATTATATTTATTTT
1 TAAAATATTTATATTATATTTATATT
*
1677268 TAAATATATTTTTATATATAT
1 TAAA-ATATTTATAT-TATAT
1677289 AAAAATCACG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 7 0.18
25 14 0.37
26 7 0.18
27 5 0.13
28 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (26 bp):
TAAAATATTTATATTATATTTATATT
Found at i:1678923 original size:6 final size:6
Alignment explanation
Indices: 1678912--1678968 Score: 71
Period size: 6 Copynumber: 9.2 Consensus size: 6
1678902 TTTTTTTAAA
*
1678912 ATATTT ATATTT ATTATTT ATGTATTT ATATTT ATATTT ATATTT A-ATAT
1 ATATTT ATATTT A-TATTT A--TATTT ATATTT ATATTT ATATTT ATATTT
1678962 ATATTT A
1 ATATTT A
1678969 AATATGAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.09
6 29 0.64
7 6 0.13
8 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:1678937 original size:21 final size:20
Alignment explanation
Indices: 1678913--1678968 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
1678903 TTTTTTAAAA
1678913 TATTTATATTTATTATTTATG
1 TATTTATATTTA-TATTTATG
1678934 TATTTATATTTATATTTA--
1 TATTTATATTTATATTTATG
*
1678952 TATTTA-ATATATATTTA
1 TATTTATATTTATATTTA
1678969 AATATGAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 10 0.29
18 6 0.18
20 6 0.18
21 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTATATTTATATTTATG
Found at i:1682860 original size:45 final size:45
Alignment explanation
Indices: 1682792--1682966 Score: 188
Period size: 45 Copynumber: 3.9 Consensus size: 45
1682782 TGAAATCTGC
* * * * **
1682792 CATAGACATCCCACAAGCTGAATTACTACCCAGGGAATCAAATAT
1 CATAGGCATCCCATAAGCAGAATTACTGCCCTTGGAATCAAATAT
* * *
1682837 CATAGGCATCCCATAAGCAGAATTAGTGCCCTTGGAATTAGATAT
1 CATAGGCATCCCATAAGCAGAATTACTGCCCTTGGAATCAAATAT
* * * *
1682882 TATGGGCATCCCATAAGCAGAATTACTGCACTTGGAATCACATAT
1 CATAGGCATCCCATAAGCAGAATTACTGCCCTTGGAATCAAATAT
* ** * *
1682927 CACAGGCATTTCATCAGCAGAATTTCTGCCCTTGGAATCA
1 CATAGGCATCCCATAAGCAGAATTACTGCCCTTGGAATCA
1682967 GATACTTGGT
Statistics
Matches: 107, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 107 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (45 bp):
CATAGGCATCCCATAAGCAGAATTACTGCCCTTGGAATCAAATAT
Found at i:1682957 original size:90 final size:90
Alignment explanation
Indices: 1682798--1682970 Score: 220
Period size: 90 Copynumber: 1.9 Consensus size: 90
1682788 CTGCCATAGA
* * * *
1682798 CATCCCACAAGCTGAATTACTACCCAGGGAATCAAATATCATAGGCATCCCATAAGCAGAATTAG
1 CATCCCACAAGCAGAATTACTACACAGGGAATCAAATATCACAGGCATCCCATAAGCAGAATTAC
*
1682863 TGCCCTTGGAATTAGATATTATGGG
66 TGCCCTTGGAATCAGATATTATGGG
* * ** * ** * *
1682888 CATCCCATAAGCAGAATTACTGCACTTGGAATCACATATCACAGGCATTTCATCAGCAGAATTTC
1 CATCCCACAAGCAGAATTACTACACAGGGAATCAAATATCACAGGCATCCCATAAGCAGAATTAC
1682953 TGCCCTTGGAATCAGATA
66 TGCCCTTGGAATCAGATA
1682971 CTTGGTTTCT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (90 bp):
CATCCCACAAGCAGAATTACTACACAGGGAATCAAATATCACAGGCATCCCATAAGCAGAATTAC
TGCCCTTGGAATCAGATATTATGGG
Found at i:1685010 original size:22 final size:22
Alignment explanation
Indices: 1684966--1685017 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1684956 TTCACAAATT
* *
1684966 ATAATAAAATTTTAAATTTAAA
1 ATAATAAATTTTTAAATTAAAA
1684988 ATAATAAATTTTTATAA-TAAAA
1 ATAATAAATTTTTA-AATTAAAA
1685010 ATAA-AAAT
1 ATAATAAAT
1685018 GAACATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 21 0.78
23 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATAAATTTTTAAATTAAAA
Found at i:1688087 original size:2 final size:2
Alignment explanation
Indices: 1688080--1688110 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1688070 AGTTAACGAA
*
1688080 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1688111 GTTTTATACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1700687 original size:2 final size:2
Alignment explanation
Indices: 1700682--1700708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1700672 TATTATATAT
1700682 AC 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 AC A
1700709 TCAGGGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1713229 original size:14 final size:14
Alignment explanation
Indices: 1713203--1713241 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1713193 TATGAAAAAA
1713203 ATAAAAA-AATAAT
1 ATAAAAATAATAAT
1713216 -TAAAATATAATAAT
1 ATAAAA-ATAATAAT
1713230 ATAAAAATAATA
1 ATAAAAATAATA
1713242 TTAGTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.22
13 1 0.04
14 12 0.52
15 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:1720446 original size:21 final size:22
Alignment explanation
Indices: 1720406--1720446 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1720396 GTAAAGTAGT
*
1720406 GAAAAGGGAGGAGGTTACGGCG
1 GAAAAGGGAGGAGGTGACGGCG
*
1720428 GAAAA-GGAGGTGGTGACGG
1 GAAAAGGGAGGAGGTGACGG
1720447 TGGCGGCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.07, G:0.51, T:0.10
Consensus pattern (22 bp):
GAAAAGGGAGGAGGTGACGGCG
Found at i:1727913 original size:2 final size:2
Alignment explanation
Indices: 1727906--1727936 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1727896 GCCCACATGT
1727906 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1727937 TACTGTGTTT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1729502 original size:3 final size:3
Alignment explanation
Indices: 1729496--1729526 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1729486 ATTAATAGTG
1729496 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1729527 TTTGAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1730718 original size:23 final size:23
Alignment explanation
Indices: 1730686--1730739 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1730676 AAAATTCAAC
1730686 AATTTAA-ATATTCTAAATGATAAA-
1 AATTTAATA-ATT-TAAAT-ATAAAT
*
1730710 AATTTAATAATTTAAATTTAAAT
1 AATTTAATAATTTAAATATAAAT
1730733 AATTTAA
1 AATTTAA
1730740 ATATCAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.15
23 12 0.44
24 10 0.37
25 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTAATAATTTAAATATAAAT
Found at i:1730735 original size:15 final size:14
Alignment explanation
Indices: 1730709--1730741 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
1730699 TAAATGATAA
1730709 AAATTTAATAATTT
1 AAATTTAATAATTT
1730723 AAATTTAAATAATTT
1 AAATTT-AATAATTT
1730738 AAAT
1 AAAT
1730742 ATCAAATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTTAATAATTT
Found at i:1730886 original size:2 final size:2
Alignment explanation
Indices: 1730879--1730920 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
1730869 AAACTATGTC
*
1730879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
1730921 GCATATGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1731602 original size:2 final size:2
Alignment explanation
Indices: 1731595--1731638 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1731585 AAATAGGGGC
1731595 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1731637 GA
1 GA
1731639 ACAGGCGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1733131 original size:23 final size:19
Alignment explanation
Indices: 1733090--1733128 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1733080 CATCTGAGCG
1733090 AGCACGGAGTGAAAAACTT
1 AGCACGGAGTGAAAAACTT
1733109 AGCACGGAGTGAAAAACTT
1 AGCACGGAGTGAAAAACTT
1733128 A
1 A
1733129 CTTCAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (19 bp):
AGCACGGAGTGAAAAACTT
Found at i:1738848 original size:4 final size:4
Alignment explanation
Indices: 1738839--1738901 Score: 71
Period size: 4 Copynumber: 16.8 Consensus size: 4
1738829 CTATTTTTAT
*
1738839 ATAC ATAC ATAC AT-- ATAT ATAC ATAC ATAC ATAC AT-- ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
1738883 ATAC ATAT ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATA
1738902 TATATATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
2 4 0.08
4 48 0.92
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAC
Found at i:1738906 original size:4 final size:4
Alignment explanation
Indices: 1738836--1738914 Score: 59
Period size: 4 Copynumber: 19.8 Consensus size: 4
1738826 TGCCTATTTT
* * * * * * * * *
1738836 TATA TACA TACA TACA TATA TATA CATA CATA CATA CATA TACA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
1738884 TACA TATA TATA TACA TATA TATA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TAT
1738915 TCTTCTAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (4 bp):
TATA
Found at i:1738911 original size:14 final size:14
Alignment explanation
Indices: 1738836--1738907 Score: 80
Period size: 14 Copynumber: 5.4 Consensus size: 14
1738826 TGCCTATTTT
1738836 TATATACATACATA
1 TATATACATACATA
* *
1738850 CATATATATAC--A
1 TATATACATACATA
*
1738862 TACATACATACATA
1 TATATACATACATA
*
1738876 TACATACATACATA
1 TATATACATACATA
1738890 TATAT--ATACATA
1 TATATACATACATA
1738902 TATATA
1 TATATA
1738908 TATATATTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
12 21 0.43
14 28 0.57
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
TATATACATACATA
Found at i:1738914 original size:18 final size:18
Alignment explanation
Indices: 1738836--1738911 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
1738826 TGCCTATTTT
1738836 TATATACATACATACATA
1 TATATACATACATACATA
1738854 TATATACATACATACATA
1 TATATACATACATACATA
*
1738872 CATATACATACATACATA
1 TATATACATACATACATA
*
1738890 TATAT--ATACATATATA
1 TATATACATACATACATA
1738906 TATATA
1 TATATA
1738912 TATTCTTCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.28
18 39 0.72
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (18 bp):
TATATACATACATACATA
Found at i:1739594 original size:104 final size:104
Alignment explanation
Indices: 1739414--1739625 Score: 370
Period size: 104 Copynumber: 2.0 Consensus size: 104
1739404 TTTGTTAAGC
* *
1739414 AGCTTAGGACAACCTAAGACTTAAGAGTGTCCTTATGCATGATTGATCTCGAGAAAAATAACTTG
1 AGCTTAGGACAACCTAAGACTTAAGAGTCTCCTTACGCATGATTGATCTCGAGAAAAATAACTTG
* *
1739479 AAACGAAAAGCCAGTGCCAATAAGCATACATCTTGTAAA
66 AAACCAAAAGCCAGTGCCAATAAGCATACATCTTCTAAA
*
1739518 AGCTTAGGACAACCTAAGACTTAAGAGTCTTCTTACGCATGATTGATCTCGAGAAAAATAACTTG
1 AGCTTAGGACAACCTAAGACTTAAGAGTCTCCTTACGCATGATTGATCTCGAGAAAAATAACTTG
*
1739583 AAACCAAAAGCCAGTGCCAATAAGCATACATCTTCTAAC
66 AAACCAAAAGCCAGTGCCAATAAGCATACATCTTCTAAA
1739622 AGCT
1 AGCT
1739626 CTAATATGGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (104 bp):
AGCTTAGGACAACCTAAGACTTAAGAGTCTCCTTACGCATGATTGATCTCGAGAAAAATAACTTG
AAACCAAAAGCCAGTGCCAATAAGCATACATCTTCTAAA
Found at i:1742837 original size:18 final size:19
Alignment explanation
Indices: 1742811--1742891 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 19
1742801 CGTTTATTCG
*
1742811 TATTTTATT-TATATATTT
1 TATTATATTATATATATTT
*
1742829 TATTATATTATAAAATATTT
1 TATTATATTAT-ATATATTT
*
1742849 TA-TAT-TTATATAAATTT
1 TATTATATTATATATATTT
* *
1742866 TAATATGTTA-ATA-ATTT
1 TATTATATTATATATATTT
1742883 ATATTATAT
1 -TATTATAT
1742892 AAATTTTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 12 0.23
18 24 0.46
19 7 0.13
20 9 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TATTATATTATATATATTT
Found at i:1742848 original size:20 final size:18
Alignment explanation
Indices: 1742823--1742867 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
1742813 TTTTATTTAT
1742823 ATATTTTATTATATTATAAA
1 ATATTTTA-TAT-TTATAAA
*
1742843 ATATTTTATATTTATATA
1 ATATTTTATATTTATAAA
1742861 A-ATTTTA
1 ATATTTTA
1742868 ATATGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 3 0.12
20 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTTATATTTATAAA
Found at i:1742851 original size:17 final size:17
Alignment explanation
Indices: 1742825--1742899 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
1742815 TTATTTATAT
1742825 ATTTTATTATATTATAAAA
1 ATTTTA-TAT-TTATAAAA
*
1742844 TATTTTATATTTATATAA
1 -ATTTTATATTTATAAAA
* *
1742862 ATTTTAATATGT-TAATA
1 ATTTT-ATATTTATAAAA
*
1742879 A-TTTATA-TTATATAA
1 ATTTTATATTTATAAAA
1742894 ATTTTA
1 ATTTTA
1742900 AAATATTGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 1 0.02
15 7 0.16
16 7 0.16
17 9 0.20
18 12 0.27
19 3 0.07
20 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATAAAA
Found at i:1742930 original size:33 final size:32
Alignment explanation
Indices: 1742854--1742931 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
1742844 TATTTTATAT
* * *
1742854 TTATATAAATTTTAATATGTTAATAATTTATA
1 TTATATAAATTTTAAAATATTAATAATTCATA
*
1742886 TTATATAAATTTTAAAATATTGATATATTCATA
1 TTATATAAATTTTAAAATATTAATA-ATTCATA
* *
1742919 TTATGTTAATTTT
1 TTATATAAATTTT
1742932 TTTATATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 22 0.56
33 17 0.44
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (32 bp):
TTATATAAATTTTAAAATATTAATAATTCATA
Found at i:1748822 original size:47 final size:48
Alignment explanation
Indices: 1748722--1748825 Score: 174
Period size: 47 Copynumber: 2.2 Consensus size: 48
1748712 TATTTATTGA
1748722 TATCCGTATGATTTGATTTTAAGGACTTCTCCCTTAGCTCCGAATTTGT
1 TATCC-TATGATTTGATTTTAAGGACTTCTCCCTTAGCTCCGAATTTGT
* *
1748771 TATCCTATGATTTGATTTTGAGGACTTCT-CCTTAGCTCTGAATTTGT
1 TATCCTATGATTTGATTTTAAGGACTTCTCCCTTAGCTCCGAATTTGT
1748818 TATCCTAT
1 TATCCTAT
1748826 AAAAATTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
47 25 0.47
48 23 0.43
49 5 0.09
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.45
Consensus pattern (48 bp):
TATCCTATGATTTGATTTTAAGGACTTCTCCCTTAGCTCCGAATTTGT
Found at i:1752300 original size:8 final size:8
Alignment explanation
Indices: 1752287--1752311 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1752277 CATTGAACAG
1752287 AAAATAGT
1 AAAATAGT
1752295 AAAATAGT
1 AAAATAGT
1752303 AAAATAGT
1 AAAATAGT
1752311 A
1 A
1752312 TCAAGTTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAAATAGT
Found at i:1758426 original size:12 final size:13
Alignment explanation
Indices: 1758408--1758443 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1758398 ATCTGTTTTT
1758408 GATATTAATTTAA
1 GATATTAATTTAA
*
1758421 -ATATTAATATAA
1 GATATTAATTTAA
1758433 GATATTAATTT
1 GATATTAATTT
1758444 GACATTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
GATATTAATTTAA
Found at i:1759064 original size:15 final size:16
Alignment explanation
Indices: 1759044--1759078 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1759034 TTAAAAAAAA
1759044 ATTAAAT-ATATTCAT
1 ATTAAATAATATTCAT
1759059 ATTAAATACATATTCAT
1 ATTAAATA-ATATTCAT
1759076 ATT
1 ATT
1759079 TGACACTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
17 11 0.61
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAAATAATATTCAT
Found at i:1760029 original size:21 final size:21
Alignment explanation
Indices: 1760003--1760048 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1759993 TGGAATGAAC
1760003 ATTCCCCTATTAGGTTTACTT
1 ATTCCCCTATTAGGTTTACTT
1760024 ATTCCCCTATTAGGTTTACTT
1 ATTCCCCTATTAGGTTTACTT
1760045 ATTC
1 ATTC
1760049 GTTGAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.48
Consensus pattern (21 bp):
ATTCCCCTATTAGGTTTACTT
Found at i:1762075 original size:2 final size:2
Alignment explanation
Indices: 1762068--1762100 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1762058 GCGTGCGCGT
1762068 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1762101 TGACTACCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1765485 original size:4 final size:4
Alignment explanation
Indices: 1765476--1765501 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1765466 GTTAGTCCAA
1765476 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1765502 GGATGGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1765657 original size:2 final size:2
Alignment explanation
Indices: 1765650--1765682 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1765640 GGATAGGAGC
1765650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1765683 ATGTTCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1771045 original size:19 final size:19
Alignment explanation
Indices: 1771021--1771063 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1771011 TTTAAAATAT
1771021 AATATTATATAAATATA-AA
1 AATATTATA-AAATATATAA
* *
1771040 AATATTTTAAAATTTATAA
1 AATATTATAAAATATATAA
1771059 AATAT
1 AATAT
1771064 AAATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTATAAAATATATAA
Found at i:1771092 original size:23 final size:24
Alignment explanation
Indices: 1771002--1771101 Score: 63
Period size: 23 Copynumber: 4.3 Consensus size: 24
1770992 ATATAAAAAA
* *
1771002 ATTATAATTTTTAAAATATAATATT
1 ATTAAAATTTATAAAATAT-ATATT
1771027 A-TATAAA--TAT-AAA-A-ATATT
1 ATTA-AAATTTATAAAATATATATT
*
1771046 -TTAAAATTTATAAAATATAAATT
1 ATTAAAATTTATAAAATATATATT
* *
1771069 ATTAATATTT-TAAAATTTATATT
1 ATTAAAATTTATAAAATATATATT
1771092 AATATAAAAT
1 -AT-TAAAAT
1771102 AATTTTTATA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
18 3 0.05
19 7 0.12
20 3 0.05
21 4 0.07
22 4 0.07
23 17 0.29
24 12 0.21
25 8 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTAAAATTTATAAAATATATATT
Found at i:1771096 original size:33 final size:32
Alignment explanation
Indices: 1771000--1771099 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 32
1770990 TGATATAAAA
*
1771000 AAATTATAAT-TTTTAAAATATAATATT-ATAT
1 AAATTATAATATTTTAAAAT-TTATATTAATAT
* *
1771031 AAATATAAAAATATTTTAAAATTTATA-AAATAT
1 AAAT-T-ATAATATTTTAAAATTTATATTAATAT
1771064 AAATTATTAATATTTTAAAATTTATATTAATAT
1 AAATTA-TAATATTTTAAAATTTATATTAATAT
1771097 AAA
1 AAA
1771100 ATAATTTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 5 0.09
32 20 0.34
33 24 0.41
34 9 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATTATAATATTTTAAAATTTATATTAATAT
Found at i:1771160 original size:10 final size:10
Alignment explanation
Indices: 1771120--1771177 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
1771110 TATAATTATA
1771120 ATATACTAAA-
1 ATATA-TAAAT
*
1771130 ATATTTAAAT
1 ATATATAAAT
1771140 ATGATATAAAT
1 AT-ATATAAAT
*
1771151 ATAAATAAAT
1 ATATATAAAT
*
1771161 ATATATATAT
1 ATATATAAAT
1771171 ATATATA
1 ATATATA
1771178 TATGTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 4 0.10
10 28 0.68
11 9 0.22
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
ATATATAAAT
Found at i:1771166 original size:2 final size:2
Alignment explanation
Indices: 1771138--1771180 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1771128 AAATATTTAA
* * *
1771138 AT AT GAT AT AA AT AT AA AT AA 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 AT AT AT AT
1771181 GTAAAAGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1782351 original size:2 final size:2
Alignment explanation
Indices: 1782346--1782376 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1782336 AGTGTGTGTG
1782346 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
1782377 GTAACATGGA
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:1785539 original size:2 final size:2
Alignment explanation
Indices: 1785532--1785573 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1785522 CTGATAGTCT
1785532 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
1785574 GTCAATGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1788736 original size:2 final size:2
Alignment explanation
Indices: 1788729--1788763 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1788719 TATCAGCATG
1788729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1788764 GTTTCAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1789497 original size:2 final size:2
Alignment explanation
Indices: 1789492--1789537 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1789482 TGTGTGTGTG
1789492 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
1789534 TA TA
1 TA TA
1789538 ATTGGTGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1791124 original size:52 final size:52
Alignment explanation
Indices: 1791044--1791145 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
1791034 CAAGAAGAAA
*
1791044 TATATATACGGTTCGTTAGTCATCCATGTTAAGCCCTTTGAAAACTAATAGT
1 TATATATACGGTTCGTTAGTCATCCATGTTAAGCCCATTGAAAACTAATAGT
* * *
1791096 TATATATACGGTTCGTTGGTCATTCATGTTAAGGCCATTGAAAACTAATA
1 TATATATACGGTTCGTTAGTCATCCATGTTAAGCCCATTGAAAACTAATA
1791146 ATTAAAGATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (52 bp):
TATATATACGGTTCGTTAGTCATCCATGTTAAGCCCATTGAAAACTAATAGT
Found at i:1791349 original size:2 final size:2
Alignment explanation
Indices: 1791342--1791375 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1791332 ACCGCCTGAA
1791342 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
1791376 TATGAAAAAG
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:1795978 original size:11 final size:11
Alignment explanation
Indices: 1795950--1795994 Score: 51
Period size: 10 Copynumber: 4.2 Consensus size: 11
1795940 TTATTGATAC
1795950 TTTATTATATT-
1 TTTATT-TATTA
1795961 TTT-TTTATTA
1 TTTATTTATTA
1795971 TTTATTTATTTA
1 TTTATTTA-TTA
1795983 TTTA-TTATTA
1 TTTATTTATTA
1795993 TT
1 TT
1795995 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.13
10 10 0.32
11 10 0.32
12 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:1797011 original size:8 final size:8
Alignment explanation
Indices: 1796998--1797090 Score: 68
Period size: 8 Copynumber: 11.4 Consensus size: 8
1796988 TAGATCATTA
1796998 ATTTATAT
1 ATTTATAT
1797006 ATTTATATT
1 ATTTATA-T
1797015 ATAATTATAT
1 AT--TTATAT
* *
1797025 -TTGAAAT
1 ATTTATAT
1797032 ATTATATAT
1 ATT-TATAT
1797041 ATTTATAT
1 ATTTATAT
*
1797049 AAATTTTTAT
1 --ATTTATAT
*
1797059 ATTTTTAT
1 ATTTATAT
1797067 A-TTATAT
1 ATTTATAT
1797074 ATTTAT-T
1 ATTTATAT
1797081 -TTTATAT
1 ATTTATAT
1797088 ATT
1 ATT
1797091 ATGTTTCAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
6 5 0.07
7 12 0.17
8 29 0.42
9 10 0.14
10 8 0.12
11 5 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:1797060 original size:27 final size:27
Alignment explanation
Indices: 1797030--1797092 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1797020 TATATTTGAA
1797030 ATATTATATATATT-TATATAAATTTTT
1 ATATT-TATATATTATATATAAATTTTT
* **
1797057 ATATTTTTATATTATATATTTATTTTT
1 ATATTTATATATTATATATAAATTTTT
1797084 ATATATTAT
1 ATAT-TTAT
1797093 GTTTCAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.23
27 20 0.67
28 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATTTATATATTATATATAAATTTTT
Found at i:1800556 original size:2 final size:2
Alignment explanation
Indices: 1800549--1800574 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1800539 GTTGTGAAAG
1800549 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
1800575 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1800579 original size:4 final size:4
Alignment explanation
Indices: 1800572--1800669 Score: 134
Period size: 4 Copynumber: 25.8 Consensus size: 4
1800562 TATATATATA
1800572 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
1800620 TATG TATG TTTG TATG -ATG TATG TA-- TATT TATA TATG TA-- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1800663 TATG TAT
1 TATG TAT
1800670 ATGCGTACAT
Statistics
Matches: 85, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
2 4 0.05
3 3 0.04
4 78 0.92
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1801942 original size:3 final size:3
Alignment explanation
Indices: 1801932--1801960 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1801922 AATTAATATT
1801932 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1801961 TATATGCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1807093 original size:2 final size:2
Alignment explanation
Indices: 1807088--1807116 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1807078 ATACATACAT
1807088 AC AC 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 AC AC A
1807117 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1807295 original size:2 final size:2
Alignment explanation
Indices: 1807277--1807313 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1807267 ACCTATGATT
* *
1807277 TA TA CA TA TA CA 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 TA TA TA T
1807314 CAGATGATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1807423 original size:182 final size:182
Alignment explanation
Indices: 1807116--1807492 Score: 736
Period size: 182 Copynumber: 2.1 Consensus size: 182
1807106 ACACACACAC
1807116 ATATATATATATATATCAGATGATGGGTCACCATTAATGTATACAAAATACATATCATCAAACAG
1 ATATATATATATATATCAGATGATGGGTCACCATTAATGTATACAAAATACATATCATCAAACAG
*
1807181 TGTTAATCTGAACATTATAAGGGTCAAATTTTTTCACTAAATTATGTGTTTGATTCCCTTCAAAA
66 TGTTAATCTGAACATTATAAGGGTCAAATTTTTTCACTAAATGATGTGTTTGATTCCCTTCAAAA
*
1807246 TATTTGCCCATTAAAGTGCAGACCTATGATTTATACATATACATATATATAT
131 TATTTGCCCATTAAAGTGCAGACCTATGATTTATACATATACATATACATAT
1807298 ATATATATATATATATCAGATGATGGGTCACCATTAATGTATACAAAATACATATCATCAAACAG
1 ATATATATATATATATCAGATGATGGGTCACCATTAATGTATACAAAATACATATCATCAAACAG
1807363 TGTTAATCTGAACATTATAAGGGTCAAATTTTTTCACTAAATGATGTGTTTGATTCCCTTCAAAA
66 TGTTAATCTGAACATTATAAGGGTCAAATTTTTTCACTAAATGATGTGTTTGATTCCCTTCAAAA
1807428 TATTTGCCCATTAAAGTGCAGACCTATGATTTATACATATACATATACATAT
131 TATTTGCCCATTAAAGTGCAGACCTATGATTTATACATATACATATACATAT
1807480 ATATATATATATA
1 ATATATATATATA
1807493 AACTGGAAAA
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 193 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (182 bp):
ATATATATATATATATCAGATGATGGGTCACCATTAATGTATACAAAATACATATCATCAAACAG
TGTTAATCTGAACATTATAAGGGTCAAATTTTTTCACTAAATGATGTGTTTGATTCCCTTCAAAA
TATTTGCCCATTAAAGTGCAGACCTATGATTTATACATATACATATACATAT
Found at i:1807470 original size:6 final size:6
Alignment explanation
Indices: 1807459--1807492 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1807449 ACCTATGATT
* *
1807459 TATACA TATACA TATACA TATATA TATATA TATA
1 TATACA TATACA TATACA TATACA TATACA TATA
1807493 AACTGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (6 bp):
TATACA
Found at i:1808232 original size:48 final size:49
Alignment explanation
Indices: 1808136--1808235 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 49
1808126 TAATTCAGGG
1808136 ATTGTACTGTGTGGCTCATCTCATTTAAGTTGAAAAAAAAGGAAAGAGTA
1 ATTGTACTGTGTGGCTCATCTCA-TTAAGTTGAAAAAAAAGGAAAGAGTA
*
1808186 ATTGTACTGTGTGGTTCATCTCA-TAAGTT-AAAAAAAAGGGAAAGAGTA
1 ATTGTACTGTGTGGCTCATCTCATTAAGTTGAAAAAAAA-GGAAAGAGTA
1808234 AT
1 AT
1808236 CCAAACAGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
47 8 0.17
48 18 0.38
50 22 0.46
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (49 bp):
ATTGTACTGTGTGGCTCATCTCATTAAGTTGAAAAAAAAGGAAAGAGTA
Found at i:1812155 original size:2 final size:2
Alignment explanation
Indices: 1812148--1812184 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1812138 AGCAACCTTG
*
1812148 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1812185 GCCATGAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1812361 original size:29 final size:29
Alignment explanation
Indices: 1812328--1812385 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1812318 AGTAAGGTTA
1812328 AGAAGATATTCAAAGAAGCTGATAATATG
1 AGAAGATATTCAAAGAAGCTGATAATATG
1812357 AGAAGATATTCAAAGAAGCTGATAATATG
1 AGAAGATATTCAAAGAAGCTGATAATATG
1812386 GCAAATGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (29 bp):
AGAAGATATTCAAAGAAGCTGATAATATG
Done.