Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 86 of 103
Found at i:31767683 original size:30 final size:30
Alignment explanation
Indices: 31767647--31767705 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
31767637 TTTAACTCTT
31767647 AAAAAATACCATGATATTAATTACAAATAA
1 AAAAAATACCATGATATTAATTACAAATAA
*
31767677 AAAAAATACCATGATATTGATTACAAATA
1 AAAAAATACCATGATATTAATTACAAATA
31767706 TAATATACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAAAATACCATGATATTAATTACAAATAA
Found at i:31769518 original size:12 final size:12
Alignment explanation
Indices: 31769481--31769526 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
31769471 TAATTAATGC
31769481 TAAATATAA--A
1 TAAATATAACTA
31769491 TAAACTAATAAGCTA
1 TAAA-T-ATAA-CTA
31769506 TAAATATAACTA
1 TAAATATAACTA
31769518 TAAATATAA
1 TAAATATAA
31769527 AATATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 4 0.13
11 1 0.03
12 16 0.52
13 4 0.13
14 1 0.03
15 5 0.16
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (12 bp):
TAAATATAACTA
Found at i:31769531 original size:19 final size:19
Alignment explanation
Indices: 31769481--31769527 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
31769471 TAATTAATGC
31769481 TAAATATAAATA-AACTAA
1 TAAATATAAATATAACTAA
*
31769499 TAAGCTATAAATATAACT-A
1 TAA-ATATAAATATAACTAA
31769518 TAAATATAAA
1 TAAATATAAA
31769528 ATATTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
19 12 0.48
20 4 0.16
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAATATAAATATAACTAA
Found at i:31774536 original size:40 final size:38
Alignment explanation
Indices: 31774457--31774536 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
31774447 ATTTGCATTG
*
31774457 GAGAAGGATGATTTGTAGAGGAAAAGAGAGAGGACAGA
1 GAGAAGGATGATTTGCAGAGGAAAAGAGAGAGGACAGA
*
31774495 GAGAAGGGTGATTTGCAGAAGGAAAA-AGAGAGGACAGA
1 GAGAAGGATGATTTGCAG-AGGAAAAGAGAGAGGACAGA
31774533 GAGA
1 GAGA
31774537 TTAATTAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 32 0.82
39 7 0.18
ACGTcount: A:0.45, C:0.04, G:0.40, T:0.11
Consensus pattern (38 bp):
GAGAAGGATGATTTGCAGAGGAAAAGAGAGAGGACAGA
Found at i:31780117 original size:13 final size:13
Alignment explanation
Indices: 31780101--31780125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31780091 AAATATACTT
31780101 TTTTTATATATTC
1 TTTTTATATATTC
31780114 TTTTTATATATT
1 TTTTTATATATT
31780126 TAATAGGTGT
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATATATTC
Found at i:31783967 original size:30 final size:30
Alignment explanation
Indices: 31783933--31783993 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
31783923 CACAATAAGT
31783933 TCATTTCCTAAGGTAGAAAGAAGCACAAAA
1 TCATTTCCTAAGGTAGAAAGAAGCACAAAA
31783963 TCATTTCCTAAGGTAGAAAGAAGCACAAAA
1 TCATTTCCTAAGGTAGAAAGAAGCACAAAA
31783993 T
1 T
31783994 TACTTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (30 bp):
TCATTTCCTAAGGTAGAAAGAAGCACAAAA
Found at i:31788248 original size:63 final size:63
Alignment explanation
Indices: 31788149--31788272 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
31788139 ATTAGCATAG
* * * * *
31788149 AAACATATAAATCTGTAGGAAGATATTGTTGAGGAAATCCATGCTAACACAACCATATTAAAC
1 AAACATATAAATCTATAAGAAGATATTCTAGAGGAAATCCATGCCAACACAACCATATTAAAC
* *
31788212 AAACATGTATATCTATAAGAAGATATTCTAGAGGAAATCCATGCCAACACAACCATATTAA
1 AAACATATAAATCTATAAGAAGATATTCTAGAGGAAATCCATGCCAACACAACCATATTAA
31788273 GCCTCTTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (63 bp):
AAACATATAAATCTATAAGAAGATATTCTAGAGGAAATCCATGCCAACACAACCATATTAAAC
Found at i:31796050 original size:16 final size:17
Alignment explanation
Indices: 31796029--31796061 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31796019 AAAAAAAATA
*
31796029 TTTTGATAA-TTTTTTC
1 TTTTGAAAAGTTTTTTC
31796045 TTTTGAAAAGTTTTTTC
1 TTTTGAAAAGTTTTTTC
31796062 CCAACGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTTGAAAAGTTTTTTC
Found at i:31796267 original size:21 final size:21
Alignment explanation
Indices: 31796242--31796283 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31796232 AAAAGCTAAT
31796242 AAATATTCTTATTTCACTGGA
1 AAATATTCTTATTTCACTGGA
*
31796263 AAATATTCTTATTTCATTGGA
1 AAATATTCTTATTTCACTGGA
31796284 GTAATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (21 bp):
AAATATTCTTATTTCACTGGA
Found at i:31796727 original size:2 final size:2
Alignment explanation
Indices: 31796716--31796765 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
31796706 TTGCTCTACT
31796716 TA TA -A TA TA TA TA TA TA TA T- TA TA TA TA -A 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
31796755 TA TA T- TA TA TA
1 TA TA TA TA TA TA
31796766 AGTCGAGTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31796746 original size:24 final size:24
Alignment explanation
Indices: 31796716--31796765 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
31796706 TTGCTCTACT
31796716 TATAATATATATATATATATTATA
1 TATAATATATATATATATATTATA
31796740 TATAATATATATATATATATTATA
1 TATAATATATATATATATATTATA
31796764 TA
1 TA
31796766 AGTCGAGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAATATATATATATATATTATA
Found at i:31797222 original size:2 final size:2
Alignment explanation
Indices: 31797215--31797258 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
31797205 NNNNNNNNNN
31797215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31797256 AT A
1 AT A
31797259 AGTAGAGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31797446 original size:2 final size:2
Alignment explanation
Indices: 31797439--31797484 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
31797429 TTACTCTACT
31797439 TA TA TA TA TA TA TA TA -A TA TA TA T- TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31797478 TA TA TA T
1 TA TA TA T
31797485 TGTACACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31797460 original size:13 final size:13
Alignment explanation
Indices: 31797438--31797484 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
31797428 ATTACTCTAC
31797438 TTATATATATATA
1 TTATATATATATA
31797451 -TATA-ATATATA
1 TTATATATATATA
31797462 TTATATATATATA
1 TTATATATATATA
31797475 TTATATATAT
1 TTATATATAT
31797485 TGTACACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.22
12 8 0.25
13 17 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATATATATA
Found at i:31797467 original size:22 final size:22
Alignment explanation
Indices: 31797441--31797485 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
31797431 ACTCTACTTA
31797441 TATATATATATATAATATATAT
1 TATATATATATATAATATATAT
*
31797463 TATATATATATATTATATATAT
1 TATATATATATATAATATATAT
31797485 T
1 T
31797486 GTACACTTAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATATATATATAATATATAT
Found at i:31798432 original size:22 final size:24
Alignment explanation
Indices: 31798391--31798434 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
31798381 AAAAAAAACA
31798391 AACAATAAATAGCAAAAAGAAATC
1 AACAATAAATAGCAAAAAGAAATC
*
31798415 AACAA-AAATA-CATAAAGAAA
1 AACAATAAATAGCAAAAAGAAA
31798435 ATGGAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (24 bp):
AACAATAAATAGCAAAAAGAAATC
Found at i:31800184 original size:13 final size:12
Alignment explanation
Indices: 31800159--31800192 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
31800149 AAATACTTAA
31800159 ATAAAAAAT-AC
1 ATAAAAAATAAC
31800170 ATAATAAAATAAC
1 ATAA-AAAATAAC
31800183 ATAAAAAATA
1 ATAAAAAATA
31800193 GTTCATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 11 0.52
13 6 0.29
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAAAAAATAAC
Found at i:31803880 original size:13 final size:13
Alignment explanation
Indices: 31803864--31803888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31803854 TATAGTGATT
31803864 TATTTTTTTTCTA
1 TATTTTTTTTCTA
31803877 TATTTTTTTTCT
1 TATTTTTTTTCT
31803889 TTCCTTCTTT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTTTCTA
Found at i:31809906 original size:13 final size:13
Alignment explanation
Indices: 31809888--31809925 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
31809878 TTTCAGAAAA
31809888 TTTATAAAATCAT
1 TTTATAAAATCAT
31809901 TTTATAAAATCAT
1 TTTATAAAATCAT
31809914 TTTATAAAATCA
1 TTTATAAAATCA
31809926 CAATTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:31826994 original size:21 final size:21
Alignment explanation
Indices: 31826969--31827008 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31826959 GTTCCTTGCA
31826969 TTCTTCAGTTTGTCAACTTCC
1 TTCTTCAGTTTGTCAACTTCC
* *
31826990 TTCTTGAGTTTTTCAACTT
1 TTCTTCAGTTTGTCAACTT
31827009 TCTTATCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.23, G:0.10, T:0.53
Consensus pattern (21 bp):
TTCTTCAGTTTGTCAACTTCC
Found at i:31827402 original size:6 final size:6
Alignment explanation
Indices: 31827391--31827418 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31827381 TATAACTTTA
31827391 TAAAAT TAAAAT TAAAAT TAAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAA
31827419 TAAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAAAT
Found at i:31827427 original size:18 final size:18
Alignment explanation
Indices: 31827391--31827429 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31827381 TATAACTTTA
*
31827391 TAAAATTAAAATTAAAAT
1 TAAAATTAAAATAAAAAT
31827409 TAAAATT-AAATAAATAAT
1 TAAAATTAAAATAAA-AAT
31827427 TAA
1 TAA
31827430 TGTAGGTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTAAAATAAAAAT
Found at i:31828688 original size:33 final size:33
Alignment explanation
Indices: 31828649--31828714 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31828639 GGTATGCAAC
* *
31828649 ATATCATAATTGATGATAATGTAACATGCTAAT
1 ATATCATAATTAATGATAACGTAACATGCTAAT
* *
31828682 ATATCATAATTAATGATGACGTAACGTGCTAAT
1 ATATCATAATTAATGATAACGTAACATGCTAAT
31828715 TTTGCATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (33 bp):
ATATCATAATTAATGATAACGTAACATGCTAAT
Found at i:31829731 original size:15 final size:17
Alignment explanation
Indices: 31829713--31829779 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
31829703 TTAAGTTTGA
31829713 AAATA-TAA-ATTTAAT
1 AAATATTAATATTTAAT
31829728 AAATATTAATATTTAATTT
1 AAATATTAATATTTAA--T
* **
31829747 AAATATTAAAAAAATAA-
1 AAATATT-AATATTTAAT
31829764 AAATATTAATATTTAA
1 AAATATTAATATTTAA
31829780 GTTGAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
15 5 0.12
16 9 0.22
17 13 0.32
19 8 0.20
20 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTAATATTTAAT
Found at i:31829801 original size:36 final size:35
Alignment explanation
Indices: 31829690--31829814 Score: 100
Period size: 35 Copynumber: 3.5 Consensus size: 35
31829680 TTTTAAAAAA
* *
31829690 TAAAAAAATT-ATA-TTAAGTTTG-AAAATATAAATT
1 TAAAAATATTAATATTTAAG-TTGAAAAAAAT-AATT
* **
31829724 TAATAAATATTAATATTTAA-TTTAAATATTAAA-AAAA
1 TAA-AAATATTAATATTTAAGTTGAAA-A--AAATAATT
31829761 TAAAAATATTAATATTTAAGTTGAAAAAAATTAATT
1 TAAAAATATTAATATTTAAGTTGAAAAAAA-TAATT
31829797 T-AAAATATTAATATTTAA
1 TAAAAATATTAATATTTAA
31829815 ATTATACAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
34 6 0.08
35 25 0.34
36 25 0.34
37 15 0.21
39 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (35 bp):
TAAAAATATTAATATTTAAGTTGAAAAAAATAATT
Found at i:31829849 original size:73 final size:71
Alignment explanation
Indices: 31829684--31829850 Score: 171
Period size: 71 Copynumber: 2.3 Consensus size: 71
31829674 CAAATTTTTT
* *
31829684 AAAAAATAAAAAAAT-TATATTAAGTTTGAAAATATAAATTTAATAAATATTAATATTTAATTTA
1 AAAAAATAAAAATATATAT-TTAAGTTTGAAAAAATAAATTTAATAAATATTAATATTTAATTTA
* *
31829748 AATATTA
65 AACACTA
*
31829755 AAAAAATAAAAATATTAATATTTAAG-TTGAAAAAAATTAATTT-A-AAATATTAATATTTAAAT
1 AAAAAATAAAAATA-T-ATATTTAAGTTTG-AAAAAATAAATTTAATAAATATTAATATTT-AAT
31829817 TATACAACACTA
62 T-TA-AACACTA
* *
31829829 TTAAAATTAAAAATATATATTT
1 -AAAAAATAAAAATATATATTT
31829851 TAATGAAACC
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
71 27 0.33
72 9 0.11
73 24 0.30
74 9 0.11
75 12 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (71 bp):
AAAAAATAAAAATATATATTTAAGTTTGAAAAAATAAATTTAATAAATATTAATATTTAATTTAA
ACACTA
Found at i:31837781 original size:170 final size:169
Alignment explanation
Indices: 31837497--31837838 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 169
31837487 ATAATAAGTA
31837497 AATTAAATTTATTTTTTTATTTTTATGTTTCTTTCATTTAGCATTTTGTTATACTTTTGGACAGA
1 AATTAAATTTATTTTTTTATTTTTATGTTTCTTTCATTTAGCATTTTGTTATACTTTTGGACAGA
31837562 ACTTTGAATAAAGGTTCATTAGGTAAAGTTCCTAAAGCATTTCATATAAGAAAGATTAAATTACA
66 ACTTTGAATAAAGGTTCATTAGGTAAAGTTCCTAAAGCATTTCATATAAGAAAGATTAAATTACA
31837627 TTTGATAATAAAAAATAGTAATATTTTGATATAAAATTG
131 TTTGATAATAAAAAATAGTAATATTTTGATATAAAATTG
31837666 AANTTAAATTTATTTTTTTATTTTTATGTTTCTTTCATTTAGCATTTTGTTATACTTTTGGACAG
1 AA-TTAAATTTATTTTTTTATTTTTATGTTTCTTTCATTTAGCATTTTGTTATACTTTTGGACAG
31837731 AACTTTGAATAAAGGTTCATTAGGTAAAGTTCCTAAAGCATTTCATATAAGAAAGATTAAATTAC
65 AACTTTGAATAAAGGTTCATTAGGTAAAGTTCCTAAAGCATTTCATATAAGAAAGATTAAATTAC
31837796 ATTTGATAATAAAAAATAGTAATATTTTGATATAAAATTG
130 ATTTGATAATAAAAAATAGTAATATTTTGATATAAAATTG
31837836 AAT
1 AAT
31837839 CAATGTTGTT
Statistics
Matches: 172, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
169 3 0.02
170 169 0.98
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (169 bp):
AATTAAATTTATTTTTTTATTTTTATGTTTCTTTCATTTAGCATTTTGTTATACTTTTGGACAGA
ACTTTGAATAAAGGTTCATTAGGTAAAGTTCCTAAAGCATTTCATATAAGAAAGATTAAATTACA
TTTGATAATAAAAAATAGTAATATTTTGATATAAAATTG
Found at i:31843647 original size:27 final size:25
Alignment explanation
Indices: 31843608--31843664 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
31843598 TATTAACATT
*
31843608 AAAATTATCAATTATTAATATTTTAA
1 AAAATTATAAATTATTAATA-TTTAA
31843634 ATAAATTATAAATTATTAATATTTAA
1 A-AAATTATAAATTATTAATATTTAA
31843660 AAAAT
1 AAAAT
31843665 AAAATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.14
26 7 0.24
27 18 0.62
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAATTATAAATTATTAATATTTAA
Found at i:31843671 original size:27 final size:27
Alignment explanation
Indices: 31843617--31843824 Score: 87
Period size: 27 Copynumber: 7.1 Consensus size: 27
31843607 TAAAATTATC
*
31843617 AATTATTAATATTTTAAATAAATTATA
1 AATTATTAATATTTTAAATAAATAATA
* *
31843644 AATTATTAATATTTAAAAAATAAAATAAAA
1 AATTATTAATATTT--TAAAT-AAATAATA
* * *
31843674 AATTATCACAATAACATTTAAAT-TATAAATA
1 AATTAT--TAAT-A-TTTTAAATAAAT-AATA
*
31843705 AAATATTAATATTTTAAAATATTAATAATTA
1 AATTATTAATATTTT-AAATA--AATAA-TA
* * * *
31843736 AATTATGAATAAAATATTAACATTTAAATTATC
1 AATTAT---TAATATTTTAA-A--TAAATAATA
* * *
31843769 AATTGTTAATAATTTAAATAAATTATA
1 AATTATTAATATTTTAAATAAATAATA
* *
31843796 AATTAGTAATA-TTTAAATAATAAAATA
1 AATTATTAATATTTTAAATAA-ATAATA
31843823 AA
1 AA
31843825 ATCAAAATAA
Statistics
Matches: 135, Mismatches: 26, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
26 9 0.07
27 40 0.30
28 5 0.04
29 8 0.06
30 24 0.18
31 17 0.13
32 7 0.05
33 9 0.07
34 14 0.10
36 2 0.01
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (27 bp):
AATTATTAATATTTTAAATAAATAATA
Found at i:31843759 original size:152 final size:152
Alignment explanation
Indices: 31843435--31843825 Score: 557
Period size: 152 Copynumber: 2.5 Consensus size: 152
31843425 TCAAACTTCT
* * * ** *
31843435 AATAAAATATTAAAATTTAAATGATCAATAATTAATATTTTAAGCAAATTATAAATTATTAATTT
1 AATAAAATATTAACATTTAAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAT
* * * *
31843500 TTATAAAATATAATAAAAAATAAATAATGATAATAACATTTTAATTATAAATAAAATATTAATAT
66 TTA-AAAA-ATAA-AATAAA-AAATAATCACAATAACATTTAAATTATAAATAAAATATTAATAT
* * *
31843565 TTTGAAATGTTAATGATTAAATTATA
127 TTTAAAATATTAATAATTAAATTATA
* *
31843591 AATACAATATTAACATTAAAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAT
1 AATAAAATATTAACATTTAAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAT
*
31843656 TTAAAAAATAAAATAAAAAATTATCACAATAACATTTAAATTATAAATAAAATATTAATATTTTA
66 TTAAAAAATAAAATAAAAAATAATCACAATAACATTTAAATTATAAATAAAATATTAATATTTTA
*
31843721 AAATATTAATAATTAAATTATG
131 AAATATTAATAATTAAATTATA
* * *
31843743 AATAAAATATTAACATTTAAATTATCAATTGTTAATAATTTAAATAAATTATAAATTAGTAATAT
1 AATAAAATATTAACATTTAAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAT
*
31843808 TTAAATAATAAAATAAAA
66 TTAAAAAATAAAATAAAA
31843826 TCAAAATAAT
Statistics
Matches: 212, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
152 139 0.66
153 5 0.02
154 4 0.02
155 4 0.02
156 60 0.28
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (152 bp):
AATAAAATATTAACATTTAAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAT
TTAAAAAATAAAATAAAAAATAATCACAATAACATTTAAATTATAAATAAAATATTAATATTTTA
AAATATTAATAATTAAATTATA
Found at i:31843790 original size:42 final size:42
Alignment explanation
Indices: 31843691--31843771 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
31843681 ACAATAACAT
* *
31843691 TTAAATTATAAATAAAATATTAATATTTTAAAATATTAATAA
1 TTAAATTATAAATAAAATATTAACATTTTAAAATATCAATAA
* *
31843733 TTAAATTATGAATAAAATATTAACA-TTTAAATTATCAAT
1 TTAAATTATAAATAAAATATTAACATTTTAAAATATCAAT
31843772 TGTTAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (42 bp):
TTAAATTATAAATAAAATATTAACATTTTAAAATATCAATAA
Found at i:31848717 original size:3 final size:3
Alignment explanation
Indices: 31848709--31848737 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31848699 CAAATACCCA
31848709 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31848738 CTGACATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31852015 original size:152 final size:152
Alignment explanation
Indices: 31851739--31852047 Score: 528
Period size: 152 Copynumber: 2.0 Consensus size: 152
31851729 CTTGTATTCT
* *
31851739 CATCATTATCAGCAGTGAAATCTTAACATAACAAGATGATCATAAACAAAATTAACAGTAAGTGA
1 CATCACTATCAGCAGTGAAATCATAACATAACAAGATGATCATAAACAAAATTAACAGTAAGTGA
* *
31851804 AAAGGCAAAATTCAACTTATTGTGTACTTTCAAACACACTTCGCAAAACTTGTTAACCAAAACAA
66 AAAGGCAAAATTCAACTTATTGTGAACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
*
31851869 GCATATACTAAAATAACGAGCA
131 GCATATACTAAAATAACAAGCA
* *
31851891 CATCACTATCAGTAGTGAAATCATAACATAACAAGATGATCATAAACAATATTAACAGTAAGTGA
1 CATCACTATCAGCAGTGAAATCATAACATAACAAGATGATCATAAACAAAATTAACAGTAAGTGA
* *
31851956 AAAGGCAAGATTCAGCTTATTGTGAACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
66 AAAGGCAAAATTCAACTTATTGTGAACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
*
31852021 GCATATACTACAATAACAAGCA
131 GCATATACTAAAATAACAAGCA
31852043 CATCA
1 CATCA
31852048 GCATGTTAAT
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 147 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (152 bp):
CATCACTATCAGCAGTGAAATCATAACATAACAAGATGATCATAAACAAAATTAACAGTAAGTGA
AAAGGCAAAATTCAACTTATTGTGAACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
GCATATACTAAAATAACAAGCA
Found at i:31855195 original size:61 final size:61
Alignment explanation
Indices: 31855089--31855211 Score: 185
Period size: 61 Copynumber: 2.0 Consensus size: 61
31855079 CTCTAGCACC
*
31855089 CGAATGTGAAACTGAAAACAAAGTAAAATTTCAGCAAAATCATCATCAAAGACACCAACTG
1 CGAATGTGAAACTGAAAACAAAGTAAAATTTCAGCAAAATAATCATCAAAGACACCAACTG
* * * *
31855150 CGAATGTGAAACTGAAAACAAAG-AACAATTTTAGTAACATAATCATCAAAGAGACCAACTG
1 CGAATGTGAAACTGAAAACAAAGTAA-AATTTCAGCAAAATAATCATCAAAGACACCAACTG
31855211 C
1 C
31855212 AACCAAGCCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 2 0.04
61 54 0.96
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.19
Consensus pattern (61 bp):
CGAATGTGAAACTGAAAACAAAGTAAAATTTCAGCAAAATAATCATCAAAGACACCAACTG
Found at i:31859978 original size:30 final size:31
Alignment explanation
Indices: 31859942--31860003 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
31859932 CGTTTTAGAG
31859942 AGAGAAACAA-TTT-TTATATATATATATAT
1 AGAGAAACAATTTTATTATATATATATATAT
31859971 NAGAGAAACAATTTTATTATATATATATATAT
1 -AGAGAAACAATTTTATTATATATATATATAT
31860003 A
1 A
31860004 TATATAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 10 0.33
31 4 0.13
32 16 0.53
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.40
Consensus pattern (31 bp):
AGAGAAACAATTTTATTATATATATATATAT
Found at i:31863577 original size:15 final size:16
Alignment explanation
Indices: 31863545--31863577 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31863535 AATAATTCGT
*
31863545 TAAATTTATAAAATAA
1 TAAATTTATAAAAAAA
31863561 TAAATTT-TAAAAAAA
1 TAAATTTATAAAAAAA
31863576 TA
1 TA
31863578 TATAAGTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATTTATAAAAAAA
Found at i:31869914 original size:25 final size:25
Alignment explanation
Indices: 31869880--31869929 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
31869870 GTTTTCCATA
* *
31869880 GATTTATCATTTCATCTACGAATGG
1 GATTTATCATTTCATCCACAAATGG
31869905 GATTTATCATTTCATCCACAAATGG
1 GATTTATCATTTCATCCACAAATGG
31869930 CAGAAGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (25 bp):
GATTTATCATTTCATCCACAAATGG
Found at i:31876807 original size:53 final size:51
Alignment explanation
Indices: 31876722--31876825 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 51
31876712 ATGTCAGTGA
*
31876722 TCGACGTTCAGATCATGATTGGTGTATGTTGTCAATTACGGACAAGTCTTGAG
1 TCGACGTTCAGATCATGATTGGTGTATGTTGTCAATTACAGAC-A-TCTTGAG
* *
31876775 TCGATGTTCATATCATGATTGGTGTATGTTGTCAATTACAGACATCTTGAG
1 TCGACGTTCAGATCATGATTGGTGTATGTTGTCAATTACAGACATCTTGAG
31876826 GTTTATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 7 0.15
52 1 0.02
53 40 0.83
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (51 bp):
TCGACGTTCAGATCATGATTGGTGTATGTTGTCAATTACAGACATCTTGAG
Found at i:31879535 original size:2 final size:2
Alignment explanation
Indices: 31879528--31879558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31879518 CTCAGCATTT
31879528 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
31879559 CAANNNNNNN
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:31879664 original size:2 final size:2
Alignment explanation
Indices: 31879657--31879683 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31879647 CAGCATTTAT
31879657 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 T
31879684 CAAGCAATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31881593 original size:21 final size:20
Alignment explanation
Indices: 31881567--31881606 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31881557 TTTTTTATTA
31881567 CTTCTTACTTTTATTTCTTTT
1 CTTCTT-CTTTTATTTCTTTT
*
31881588 CTTCTTTTTTTATTT-TTTT
1 CTTCTTCTTTTATTTCTTTT
31881607 TAACTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (20 bp):
CTTCTTCTTTTATTTCTTTT
Found at i:31881883 original size:26 final size:27
Alignment explanation
Indices: 31881816--31881873 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
31881806 ACATAGTTTT
* *
31881816 GAAAAAAAGTAAAAAAAATAAAAAAGAA
1 GAAAAGAA-TAAAAGAAATAAAAAAGAA
*
31881844 GAAAAGAATAAAAGAAAT-AAAAGGAA
1 GAAAAGAATAAAAGAAATAAAAAAGAA
31881870 GAAA
1 GAAA
31881874 TAATCAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 11 0.41
27 9 0.33
28 7 0.26
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (27 bp):
GAAAAGAATAAAAGAAATAAAAAAGAA
Found at i:31893470 original size:34 final size:34
Alignment explanation
Indices: 31893432--31893512 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
31893422 AAAAAAGAAA
31893432 GAAAAAGAATATTGTTAATAGTTTGTAGAAATTT
1 GAAAAAGAATATTGTTAATAGTTTGTAGAAATTT
31893466 GAAAAAGAATATTGTTAATAGTTTGTAGAAATTT
1 GAAAAAGAATATTGTTAATAGTTTGTAGAAATTT
31893500 GAAAAAGAATATT
1 GAAAAAGAATATT
31893513 TATAGAAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (34 bp):
GAAAAAGAATATTGTTAATAGTTTGTAGAAATTT
Found at i:31905557 original size:30 final size:31
Alignment explanation
Indices: 31905521--31905597 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
31905511 ACTTGTAAAC
31905521 TAAA-TTTTATTCAATTT-AGT-CTTCATATTT
1 TAAATTTTTATTCAATTTGA-TCCTT-ATATTT
* *
31905551 TTAATTTTTTTTC-ATTTGATCCTTATATTT
1 TAAATTTTTATTCAATTTGATCCTTATATTT
31905581 TAAATTTTTATTCAATT
1 TAAATTTTTATTCAATT
31905598 AAGTGTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 25 0.64
31 14 0.36
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (31 bp):
TAAATTTTTATTCAATTTGATCCTTATATTT
Found at i:31905938 original size:25 final size:25
Alignment explanation
Indices: 31905908--31905956 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
31905898 TTGAAAAAAA
31905908 AAGGGTCTATGTATAGAGATTAAAG
1 AAGGGTCTATGTATAGAGATTAAAG
31905933 AAGGGTCTATGTATAGAGATTAAA
1 AAGGGTCTATGTATAGAGATTAAA
31905957 TGTTGAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.27, T:0.29
Consensus pattern (25 bp):
AAGGGTCTATGTATAGAGATTAAAG
Found at i:31907059 original size:7 final size:7
Alignment explanation
Indices: 31907047--31907084 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
31907037 GAAAGCAAAG
31907047 AAAAGAA
1 AAAAGAA
31907054 AAAAGAA
1 AAAAGAA
31907061 AAAA-AA
1 AAAAGAA
* *
31907067 AGAAGAG
1 AAAAGAA
31907074 AAAAGAA
1 AAAAGAA
31907081 AAAA
1 AAAA
31907085 TGGGGGCGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:31917067 original size:28 final size:26
Alignment explanation
Indices: 31917036--31917095 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
31917026 GTTATGACAT
* *
31917036 TTTTTAATATAATATTTTGATATTATTA
1 TTTTTAACATAAAATTTTG-TATT-TTA
*
31917064 TTTTTTACATAAAATTTTGTATTTTA
1 TTTTTAACATAAAATTTTGTATTTTA
*
31917090 ATTTTA
1 TTTTTA
31917096 TTTTAAGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 7 0.26
27 4 0.15
28 16 0.59
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTTAACATAAAATTTTGTATTTTA
Found at i:31920030 original size:20 final size:20
Alignment explanation
Indices: 31920005--31920051 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
31919995 TTTTTGATCC
31920005 ATTTGACTTATTGGAGTATA-
1 ATTTGACTTATTGGAGTA-AG
31920025 ATTTGACTTATTGGAGTAAG
1 ATTTGACTTATTGGAGTAAG
31920045 ATTTGAC
1 ATTTGAC
31920052 GTTTAGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTAAG
Found at i:31924365 original size:58 final size:57
Alignment explanation
Indices: 31924276--31924395 Score: 204
Period size: 58 Copynumber: 2.1 Consensus size: 57
31924266 TAAGTCTCAT
*
31924276 CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCATACTA
1 CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
* *
31924333 CTTTGCATTGCATAGCATTTATTAAATTGCATAAAATAAATTTATCACATGCAAACTA
1 CTTTGCA-TGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
31924391 CTTTG
1 CTTTG
31924396 GATGATTATG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 7 0.12
58 52 0.88
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (57 bp):
CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
Found at i:31926011 original size:180 final size:176
Alignment explanation
Indices: 31925644--31926137 Score: 491
Period size: 180 Copynumber: 2.7 Consensus size: 176
31925634 CTGTATCTTT
* *
31925644 AGGAATTTAATTCCAATAAAATTTATCCTGATAGATAACTCACGCAACTATTCCATAATAAATTT
1 AGGAATTTAATTCCAATAAAA-TTATCCTGATAGATAACTCATGGAACTATTCC-TAATAAATTT
* * *
31925709 TTAGGATTTTAGGAGGTG-ATTTGGCCAT-TC-AAAAAATTAAAAAACCGTGACCTTTATCTGCA
64 TCAGGATTTTAGGAGGTGTTTTTGG-C-TGTCAAAAAAATT-CAAAACCGTGACCTTTATCTGCA
* * *
31925771 GGAGGCAGAATTGGTTTTTGAGACCTTTTGAAATTCTTTGTGACTAAAACTT
126 -GAGGCAGAATTGGTTTTTGAGACCTTTTGAAACTATTTGTGACTAAAACTC
* *
31925823 AAGAATTTAATTCCTAATAAAATTCATCCTGATATATAACTCATGGAACTATTCCTGAATAAATT
1 AGGAATTTAATTCC-AATAAAATT-ATCCTGATAGATAACTCATGGAACTATTCCT-AATAAATT
31925888 TTCAGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTGACCTTTATCTGCAGA
63 TTCAGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTGACCTTTATCTGCAGA
* **** * *
31925953 GGCAG-TTTCGG-TTTTGTCTTTCTTTTGAAGCTATTTGGTGGCATAAAA-TC
128 GGCAGAATT-GGTTTTTG-AGACCTTTTGAAACTATTT-GTGAC-TAAAACTC
* * * * ** *
31926003 AGGAATTTAATTTCCAATTAAATTTTCCTTGATAGAAAACTTATGGAAAAATT-CTATAGTAATT
1 AGGAATTTAA-TTCCAATAAAATTATCC-TGATAGATAACTCATGGAACTATTCCTA-A-TAAAT
*** * **
31926067 TTTCAGGATTTTAGGAAACGTTTTTAGCTGTCAAAAAAAATTCAAAACCGTGA-CTTGCTGCTGC
62 TTTCAGGATTTTAGGAGGTGTTTTTGGCTGTC-AAAAAAATTCAAAACCGTGACCTTTAT-CTGC
31926131 AGAGGCA
125 AGAGGCA
31926138 ACAACAGTTT
Statistics
Matches: 267, Mismatches: 32, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
178 8 0.03
179 44 0.16
180 162 0.61
181 53 0.20
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (176 bp):
AGGAATTTAATTCCAATAAAATTATCCTGATAGATAACTCATGGAACTATTCCTAATAAATTTTC
AGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTGACCTTTATCTGCAGAGGC
AGAATTGGTTTTTGAGACCTTTTGAAACTATTTGTGACTAAAACTC
Found at i:31926176 original size:23 final size:23
Alignment explanation
Indices: 31926147--31926193 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
31926137 AACAACAGTT
31926147 TTGACTCTACCAACTCAGTTTTA
1 TTGACTCTACCAACTCAGTTTTA
31926170 TTGACTCTACCAACTCAGTTTTA
1 TTGACTCTACCAACTCAGTTTTA
31926193 T
1 T
31926194 GAAGGCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (23 bp):
TTGACTCTACCAACTCAGTTTTA
Found at i:31928898 original size:49 final size:50
Alignment explanation
Indices: 31928802--31928914 Score: 147
Period size: 49 Copynumber: 2.3 Consensus size: 50
31928792 GAACTTAGTT
* * *
31928802 TTGATCACGAACTTGCTTGATCTTCGCTTTAAGGGTCTTCACGACTTAATC
1 TTGATCACGAAC-TACTTGATCTTCGCTTCAAGGATCTTCACGACTTAATC
* * *
31928853 TTGATCACGAAC-ACTTGATTTTTGCTTCAAGGATCTTGACGACTTAATC
1 TTGATCACGAACTACTTGATCTTCGCTTCAAGGATCTTCACGACTTAATC
*
31928902 CTGATCACGAACT
1 TTGATCACGAACT
31928915 TCGTTGTCGC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 42 0.78
51 12 0.22
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (50 bp):
TTGATCACGAACTACTTGATCTTCGCTTCAAGGATCTTCACGACTTAATC
Found at i:31929011 original size:18 final size:18
Alignment explanation
Indices: 31928968--31929011 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
31928958 TTGATATCTG
31928968 AAATG-CTCTCAATCTTC
1 AAATGCCTCTCAATCTTC
* * *
31928985 GAATACCTCTCAATCTTT
1 AAATGCCTCTCAATCTTC
31929003 AAATGCCTC
1 AAATGCCTC
31929012 CAAATGATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.34
Consensus pattern (18 bp):
AAATGCCTCTCAATCTTC
Found at i:31933449 original size:192 final size:190
Alignment explanation
Indices: 31933117--31933499 Score: 748
Period size: 192 Copynumber: 2.0 Consensus size: 190
31933107 TAAATTATTC
31933117 AATTATTTAAATATTTAATTCATTGCTAATACATAACCAATTAAAAGAACAGATTTATTACTTAT
1 AATTATTTAAATATTTAATTCATTGCTAATACATAACCAATTAAAAGAACAGATTTATTACTTAT
31933182 TTACTTATATTATAACACATTCCATTAATTTAACTAAGTACCCTAACACATTCTTTAATTGCCCT
66 TTACTTATATTATAACACATTCCATTAATTTAACTAAGTACCCTAACACATTCTTTAATTGCCCT
31933247 AACTACAACCTTAATTAATTTAACTACTTTTAAATTTTATTAAATTTACCCATTTAGTTT
131 AACTACAACCTTAATTAATTTAACTACTTTTAAATTTTATTAAATTTACCCATTTAGTTT
31933307 ANATTATTTTAAATATTTAATTCATTGCTAATACATAACCAATTAAAAGAACAGATTTATTACTT
1 A-ATTA-TTTAAATATTTAATTCATTGCTAATACATAACCAATTAAAAGAACAGATTTATTACTT
31933372 ATTTACTTATATTATAACACATTCCATTAATTTAACTAAGTACCCTAACACATTCTTTAATTGCC
64 ATTTACTTATATTATAACACATTCCATTAATTTAACTAAGTACCCTAACACATTCTTTAATTGCC
31933437 CTAACTACAACCTTAATTAATTTAACTACTTTTAAATTTTATTAAATTTACCCATTTAGTTT
129 CTAACTACAACCTTAATTAATTTAACTACTTTTAAATTTTATTAAATTTACCCATTTAGTTT
31933499 A
1 A
31933500 TTGCTTACCC
Statistics
Matches: 191, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
190 1 0.01
191 4 0.02
192 186 0.97
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.42
Consensus pattern (190 bp):
AATTATTTAAATATTTAATTCATTGCTAATACATAACCAATTAAAAGAACAGATTTATTACTTAT
TTACTTATATTATAACACATTCCATTAATTTAACTAAGTACCCTAACACATTCTTTAATTGCCCT
AACTACAACCTTAATTAATTTAACTACTTTTAAATTTTATTAAATTTACCCATTTAGTTT
Found at i:31936813 original size:16 final size:16
Alignment explanation
Indices: 31936767--31936814 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
31936757 TATTTTGTTG
*
31936767 ATTAATTAATTTATTT-
1 ATTAATT-ACTTATTTA
*
31936783 ATTAATTACTCATTTA
1 ATTAATTACTTATTTA
*
31936799 ATTAATTTCTTATTTA
1 ATTAATTACTTATTTA
31936815 CTTATATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAATTACTTATTTA
Found at i:31936824 original size:24 final size:24
Alignment explanation
Indices: 31936773--31936824 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
31936763 GTTGATTAAT
* *
31936773 TAATTTATTTATTAATTACTCATT
1 TAATTAATTTATTAATTACTCATA
* * *
31936797 TAATTAATTTCTTATTTACTTATA
1 TAATTAATTTATTAATTACTCATA
31936821 TAAT
1 TAAT
31936825 AACACATTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATTAATTTATTAATTACTCATA
Found at i:31937012 original size:259 final size:268
Alignment explanation
Indices: 31936606--31937166 Score: 833
Period size: 275 Copynumber: 2.1 Consensus size: 268
31936596 TTGCCCTAAC
* * *
31936606 TACAACCTTAATTAATTTAACTACTTTTAAATTTTATTAAATTTACCCATTTAGTTTATTGCTTA
1 TACAACCTTAATTAATTTAACTAATTTTAAATTTTATTAAACTTACCCATTTAATTTATTGCTTA
*
31936671 CCCCTAAACCTTAGTTAAGTTAATCTAAGTTTTAAATTATTCTAAATTTACTAATTTAATTTATT
66 CCCCTAAACCTTAATTAAGTTAATCTAAGTTTTAAATTATTCTAAATTTACTAATTTAATTTATT
* *
31936736 GATTAATTACTAATACATG-A-TT-A-TT-TTGTTGAT-TA-ATTAA-TT-T-ATTT-ATTAATT
131 GATTAATTAATAATACATGTATTTAATTTCTTATTGATATATATTAATTTCTCATTTAATTAATT
31936790 ACTCATTTAATTAATTTCTTATTTACTTATATAATAACACATTCCATTCCTAAACCCTAATTATA
196 ACTCATTTAATTAATTTCTTATTTACTTATATAATAACACATTCCATTCCTAAACCCTAATTATA
*
31936855 CCGTATAA
261 CCCTATAA
*
31936863 TACAACCTTAATTAATGAATGTAACTAATTTTAAATTTTATTAAACTTGCCCATTTAATTTATTG
1 TACAACCTTAATTAAT---T-TAACTAATTTTAAATTTTATTAAACTTACCCATTTAATTTATTG
* * *
31936928 CTTA-CCCTAAACCTTAATTAAGTTAATCTAAGTTTT-AATTTTTTTAAATTTACTAGTTTAATT
62 CTTACCCCTAAACCTTAATTAAGTTAATCTAAGTTTTAAATTATTCTAAATTTACTAATTTAATT
31936991 TATTGATTAATTAATAATACATGATTATTTTAATTTCTTATTGATATATTGATTAATTTCTCATT
127 TATTGATTAATTAATAATACATG--TA-TTTAATTTCTTATTGATATA-T-ATTAATTTCTCATT
* *
31937056 TAATTAATTTCTCATTTAATTAATTTCTTATTTACTTATATAATAACACATTCCATTCCTAAACT
187 TAATTAATTACTCATTTAATTAATTTCTTATTTACTTATATAATAACACATTCCATTCCTAAACC
31937121 CTAATTATACCCTATAA
252 CTAATTATACCCTATAA
31937138 TACAACCTTAATTAATTTAACTAATTTTA
1 TACAACCTTAATTAATTTAACTAATTTTA
31937167 CTGATACAAT
Statistics
Matches: 271, Mismatches: 13, Indels: 26
0.87 0.04 0.08
Matches are distributed among these distances:
257 16 0.06
259 46 0.17
260 32 0.12
261 44 0.16
262 1 0.00
264 2 0.01
265 1 0.00
266 2 0.01
267 7 0.03
268 2 0.01
271 17 0.06
272 3 0.01
273 1 0.00
274 4 0.01
275 93 0.34
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (268 bp):
TACAACCTTAATTAATTTAACTAATTTTAAATTTTATTAAACTTACCCATTTAATTTATTGCTTA
CCCCTAAACCTTAATTAAGTTAATCTAAGTTTTAAATTATTCTAAATTTACTAATTTAATTTATT
GATTAATTAATAATACATGTATTTAATTTCTTATTGATATATATTAATTTCTCATTTAATTAATT
ACTCATTTAATTAATTTCTTATTTACTTATATAATAACACATTCCATTCCTAAACCCTAATTATA
CCCTATAA
Found at i:31937063 original size:16 final size:16
Alignment explanation
Indices: 31937042--31937089 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
31937032 TGATATATTG
31937042 ATTAATTTCTCATTTA
1 ATTAATTTCTCATTTA
31937058 ATTAATTTCTCATTTA
1 ATTAATTTCTCATTTA
*
31937074 ATTAATTTCTTATTTA
1 ATTAATTTCTCATTTA
31937090 CTTATATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAATTTCTCATTTA
Found at i:31940541 original size:64 final size:62
Alignment explanation
Indices: 31940466--31940640 Score: 190
Period size: 63 Copynumber: 2.8 Consensus size: 62
31940456 ATTATGAGTA
* * * * * *
31940466 AAATTAAAAAATTTTAAGAAAAATAAAAATATGTTAGAAAATTTTAAAAATTTTTG-TAGAGGTG
1 AAATTATAAAATTTT-A-AAAAATAAAAATAAGTTATAAAAATTTAAAAATTATTGAAAG-GGTG
** ***
31940530 AAATTATAAAATTTTTAAAAAGCAAAGGCAAGTTATAAAAATTTAAAAATTATTGAAAGGGTG
1 AAATTATAAAA-TTTTAAAAAATAAAAATAAGTTATAAAAATTTAAAAATTATTGAAAGGGTG
*
31940593 AAATTATAAAAATTTTAAAAAATAAAAATAAATTATAAAAATTTAAAA
1 AAATTAT-AAAATTTTAAAAAATAAAAATAAGTTATAAAAATTTAAAA
31940641 GTTAATGGGG
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
63 70 0.77
64 17 0.19
65 4 0.04
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.32
Consensus pattern (62 bp):
AAATTATAAAATTTTAAAAAATAAAAATAAGTTATAAAAATTTAAAAATTATTGAAAGGGTG
Found at i:31942367 original size:15 final size:14
Alignment explanation
Indices: 31942328--31942368 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
31942318 CTATTTTGTG
*
31942328 TTATCATTATAAAA
1 TTATAATTATAAAA
31942342 TTATAACTTATAAAA
1 TTATAA-TTATAAAA
31942357 TTATTAATTATA
1 TTA-TAATTATA
31942369 CTAATTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 16 0.67
16 3 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (14 bp):
TTATAATTATAAAA
Found at i:31942625 original size:18 final size:18
Alignment explanation
Indices: 31942602--31942636 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31942592 TTCAGGAGAC
31942602 GACCCCCACTGCTGACAT
1 GACCCCCACTGCTGACAT
31942620 GACCCCCACTGCTGACA
1 GACCCCCACTGCTGACA
31942637 CCCCTGCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.46, G:0.17, T:0.14
Consensus pattern (18 bp):
GACCCCCACTGCTGACAT
Found at i:31942883 original size:27 final size:27
Alignment explanation
Indices: 31942850--31943186 Score: 306
Period size: 27 Copynumber: 12.5 Consensus size: 27
31942840 GCCCCCGCTA
*
31942850 CCACCCTC-GCTCCTGGTCGAGCCACTC
1 CCACCC-CAGCTCCCGGTCGAGCCACTC
** *
31942877 CCACCCTC-GCTCCCGACCGAGCCGCTC
1 CCACCC-CAGCTCCCGGTCGAGCCACTC
*
31942904 CCACCCTC-GTTCCCGGTCGAGCCACTC
1 CCACCC-CAGCTCCCGGTCGAGCCACTC
* * ** **
31942931 GCACCCCAGCTCTCGACCGAGCCGTTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
*
31942958 CCACCCTC-GCTCCAGGTCGAGCCACTC
1 CCACCC-CAGCTCCCGGTCGAGCCACTC
* * ** *
31942985 GCACCCCAGCTCTCGACCGAGCCGCTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
*
31943012 CCACCCTC-GCTCCCGGTCAAGCCACTC
1 CCACCC-CAGCTCCCGGTCGAGCCACTC
* ** *
31943039 GCACCCCAGCTCCCGACCGAGCCGCTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
*
31943066 CCACCCCTGCTCCCGGTCGAGCCACTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
*
31943093 GCACCCCAGCTCCCGGTCGAGCCACTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
* * ** **
31943120 GCACCCCAGCTCCTGACCGAGCCGTTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
*
31943147 CCACCCCTGCTCCCGGTCGAGCCACTC
1 CCACCCCAGCTCCCGGTCGAGCCACTC
*
31943174 GCACCCCAGCTCC
1 CCACCCCAGCTCC
31943187 TGACGGAGCC
Statistics
Matches: 245, Mismatches: 60, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
26 3 0.01
27 240 0.98
28 2 0.01
ACGTcount: A:0.13, C:0.53, G:0.20, T:0.14
Consensus pattern (27 bp):
CCACCCCAGCTCCCGGTCGAGCCACTC
Found at i:31942908 original size:54 final size:54
Alignment explanation
Indices: 31942844--31943266 Score: 417
Period size: 54 Copynumber: 7.8 Consensus size: 54
31942834 GCTCCTGCCC
*
31942844 CCGCTACCACCCTCGCTCCTGGTCGAGCCACTCCCACCCTC-GCTCCCGACCGAG
1 CCGCTCCCACCCTCGCTCCTGGTCGAGCCACTCCCACCC-CAGCTCCCGACCGAG
* * * *
31942898 CCGCTCCCACCCTCGTTCCCGGTCGAGCCACTCGCACCCCAGCTCTCGACCGAG
1 CCGCTCCCACCCTCGCTCCTGGTCGAGCCACTCCCACCCCAGCTCCCGACCGAG
* * * *
31942952 CCGTTCCCACCCTCGCTCCAGGTCGAGCCACTCGCACCCCAGCTCTCGACCGAG
1 CCGCTCCCACCCTCGCTCCTGGTCGAGCCACTCCCACCCCAGCTCCCGACCGAG
* * *
31943006 CCGCTCCCACCCTCGCTCCCGGTCAAGCCACTCGCACCCCAGCTCCCGACCGAG
1 CCGCTCCCACCCTCGCTCCTGGTCGAGCCACTCCCACCCCAGCTCCCGACCGAG
* * **
31943060 CCGCTCCCACCC-CTGCTCCCGGTCGAGCCACTCGCACCCCAGCTCCCGGTCGAG
1 CCGCTCCCACCCTC-GCTCCTGGTCGAGCCACTCCCACCCCAGCTCCCGACCGAG
* * ** ** * **
31943114 CCACTCGCACCC-CAGCTCCTGACCGAGCCGTTCCCACCCCTGCTCCCGGTCGAG
1 CCGCTCCCACCCTC-GCTCCTGGTCGAGCCACTCCCACCCCAGCTCCCGACCGAG
* * * * * * *
31943168 CCACTCGCACCC-CAGCTCCT-GACGGAGCCGCTTCCACAGCC-GCTCCCAACCGAG
1 CCGCTCCCACCCTC-GCTCCTGGTC-GAGCCACTCCCAC-CCCAGCTCCCGACCGAG
* * * * *
31943222 CCGTTCCCACCCCCGCTCCTGGCCGAGCCGCTCCCACCCCTGCTC
1 CCGCTCCCACCCTCGCTCCTGGTCGAGCCACTCCCACCCCAGCTC
31943267 TTGGCCGACA
Statistics
Matches: 323, Mismatches: 39, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
53 5 0.02
54 313 0.97
55 5 0.02
ACGTcount: A:0.13, C:0.53, G:0.20, T:0.14
Consensus pattern (54 bp):
CCGCTCCCACCCTCGCTCCTGGTCGAGCCACTCCCACCCCAGCTCCCGACCGAG
Found at i:31942990 original size:81 final size:81
Alignment explanation
Indices: 31942867--31943266 Score: 387
Period size: 81 Copynumber: 4.9 Consensus size: 81
31942857 CGCTCCTGGT
*
31942867 CGAGCCACTCCCACCCTC-GCTCCCGACCGAGCCGCTCCCA-CCCTCGTTCCCGGTCGAGCCACT
1 CGAGCCACTCCCACCC-CAGCTCCCGACCGAGCCGCTCCCACCCCT-GCTCCCGGTCGAGCCACT
*
31942930 CGCACCCCAGCTCTCGAC
64 CGCACCCCAGCTCCCGAC
** * ** * * * * ** *
31942948 CGAGCCGTTCCCACCCTC-GCTCCAGGTCGAGCCACTCGCACCCCAGCTCTCGACCGAGCCGCTC
1 CGAGCCACTCCCACCC-CAGCTCCCGACCGAGCCGCTCCCACCCCTGCTCCCGGTCGAGCCACTC
* **
31943012 CCACCCTC-GCTCCCGGT
65 GCACCC-CAGCTCCCGAC
* *
31943029 CAAGCCACTCGCACCCCAGCTCCCGACCGAGCCGCTCCCACCCCTGCTCCCGGTCGAGCCACTCG
1 CGAGCCACTCCCACCCCAGCTCCCGACCGAGCCGCTCCCACCCCTGCTCCCGGTCGAGCCACTCG
**
31943094 CACCCCAGCTCCCGGT
66 CACCCCAGCTCCCGAC
* * *
31943110 CGAGCCACTCGCACCCCAGCTCCTGACCGAGCCGTTCCCACCCCTGCTCCCGGTCGAGCCACTCG
1 CGAGCCACTCCCACCCCAGCTCCCGACCGAGCCGCTCCCACCCCTGCTCCCGGTCGAGCCACTCG
*
31943175 CACCCCAGCTCCTGAC
66 CACCCCAGCTCCCGAC
* * * * * * * * * *
31943191 GGAGCCGCTTCCACAGCC-GCTCCCAACCGAGCCGTTCCCACCCCCGCTCCTGGCCGAGCCGCTC
1 CGAGCCACTCCCAC-CCCAGCTCCCGACCGAGCCGCTCCCACCCCTGCTCCCGGTCGAGCCACTC
* *
31943255 CCACCCCTGCTC
65 GCACCCCAGCTC
31943267 TTGGCCGACA
Statistics
Matches: 263, Mismatches: 51, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
80 2 0.01
81 255 0.97
82 6 0.02
ACGTcount: A:0.14, C:0.53, G:0.20, T:0.13
Consensus pattern (81 bp):
CGAGCCACTCCCACCCCAGCTCCCGACCGAGCCGCTCCCACCCCTGCTCCCGGTCGAGCCACTCG
CACCCCAGCTCCCGAC
Found at i:31943274 original size:27 final size:27
Alignment explanation
Indices: 31942844--31943266 Score: 291
Period size: 27 Copynumber: 15.7 Consensus size: 27
31942834 GCTCCTGCCC
* * *
31942844 CCGCTACCA-CCCTCGCTCCTGGTCGAG
1 CCGCTCCCACCCCT-GCTCCCGGCCGAG
* *
31942871 CCACTCCCA-CCCTCGCTCCCGACCGAG
1 CCGCTCCCACCCCT-GCTCCCGGCCGAG
* *
31942898 CCGCTCCCA-CCCTCGTTCCCGGTCGAG
1 CCGCTCCCACCCCT-GCTCCCGGCCGAG
* * * * *
31942925 CCACTCGCACCCCAGCTCTCGACCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* * *
31942952 CCGTTCCCA-CCCTCGCTCCAGGTCGAG
1 CCGCTCCCACCCCT-GCTCCCGGCCGAG
* * * * *
31942979 CCACTCGCACCCCAGCTCTCGACCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* *
31943006 CCGCTCCCA-CCCTCGCTCCCGGTCAAG
1 CCGCTCCCACCCCT-GCTCCCGGCCGAG
* * * *
31943033 CCACTCGCACCCCAGCTCCCGACCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
*
31943060 CCGCTCCCACCCCTGCTCCCGGTCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* * * *
31943087 CCACTCGCACCCCAGCTCCCGGTCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* * * * *
31943114 CCACTCGCACCCCAGCTCCTGACCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* *
31943141 CCGTTCCCACCCCTGCTCCCGGTCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* * * * * *
31943168 CCACTCGCACCCCAGCTCCTGACGGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
* * **
31943195 CCGCTTCCACAGCC-GCTCCCAACCGAG
1 CCGCTCCCAC-CCCTGCTCCCGGCCGAG
* * *
31943222 CCGTTCCCACCCCCGCTCCTGGCCGAG
1 CCGCTCCCACCCCTGCTCCCGGCCGAG
31943249 CCGCTCCCACCCCTGCTC
1 CCGCTCCCACCCCTGCTC
31943267 TTGGCCGACA
Statistics
Matches: 303, Mismatches: 86, Indels: 14
0.75 0.21 0.03
Matches are distributed among these distances:
26 8 0.03
27 284 0.94
28 11 0.04
ACGTcount: A:0.13, C:0.53, G:0.20, T:0.14
Consensus pattern (27 bp):
CCGCTCCCACCCCTGCTCCCGGCCGAG
Found at i:31944506 original size:2 final size:2
Alignment explanation
Indices: 31944499--31944534 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
31944489 TTCGAGAAGA
*
31944499 AT AT AT AT GT AT A- 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 AT AT A
31944535 GATTGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31944755 original size:28 final size:27
Alignment explanation
Indices: 31944715--31944771 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
31944705 TAAAATAGAC
**
31944715 ATAAAATACAAAATTTTATA-TAAAAA
1 ATAAAATACAAAACATTATATTAAAAA
31944741 ATAATAATATCAAAACATTATATTAAAAA
1 ATAA-AATA-CAAAACATTATATTAAAAA
31944770 AT
1 AT
31944772 GTCAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 4 0.15
28 10 0.38
29 8 0.31
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAATACAAAACATTATATTAAAAA
Found at i:31951974 original size:52 final size:52
Alignment explanation
Indices: 31951877--31952010 Score: 146
Period size: 52 Copynumber: 2.6 Consensus size: 52
31951867 TTCTTAGTTA
* * * **
31951877 GAAAAAAAAACCTTTTAGTATTTTGAGCATTTTGAAATTTTTTTTGATACAC
1 GAAAAAAAAAACTTTTAGCATTTTGAGCATTTTGAAAGTGATTTTGATACAC
* * *
31951929 GAAAAAAAAAACTTTTAAGCGTTTTGAGCATTTTG-GAGTGATTTTGATATAC
1 GAAAAAAAAAACTTTT-AGCATTTTGAGCATTTTGAAAGTGATTTTGATACAC
** *
31951981 G-ATGAAAAAACATTTAGCATTTTGAGCATT
1 GAAAAAAAAAACTTTTAGCATTTTGAGCATT
31952011 CCTTACTAGG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 14 0.20
51 11 0.16
52 28 0.41
53 16 0.23
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (52 bp):
GAAAAAAAAAACTTTTAGCATTTTGAGCATTTTGAAAGTGATTTTGATACAC
Found at i:31952267 original size:22 final size:22
Alignment explanation
Indices: 31952211--31952271 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
31952201 TTGCATGACT
*
31952211 TAGGTATTGTGTGACTGGTTGA
1 TAGGTATTGTGTGACTGATTGA
**
31952233 TAAAATATTGTGTGACTGATTGA
1 T-AGGTATTGTGTGACTGATTGA
*
31952256 TAGGGATTGTGTGACT
1 TAGGTATTGTGTGACT
31952272 TAGGCATTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.25, C:0.05, G:0.31, T:0.39
Consensus pattern (22 bp):
TAGGTATTGTGTGACTGATTGA
Found at i:31952300 original size:23 final size:23
Alignment explanation
Indices: 31952273--31952337 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
31952263 TGTGTGACTT
* * *
31952273 AGGCATTGCGTGATTGGTTGATA
1 AGGCATTACGTAACTGGTTGATA
31952296 AGGCATTACGTAACTGGTTGATA
1 AGGCATTACGTAACTGGTTGATA
* * *
31952319 GGGCATTACATGACTGGTT
1 AGGCATTACGTAACTGGTT
31952338 TTTAAGTCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.32
Consensus pattern (23 bp):
AGGCATTACGTAACTGGTTGATA
Found at i:31952317 original size:61 final size:61
Alignment explanation
Indices: 31952206--31952321 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
31952196 AGCCATTGCA
* * * ** *
31952206 TGACTTAGGTATTGTGTGACTGGTTGATAAAATATTGTGTGACTGATTGATAGGGATTGTG
1 TGACTTAGGCATTGCGTGACTGGTTGATAAAACATTACGTAACTGATTGATAGGGATTGTG
* ** *
31952267 TGACTTAGGCATTGCGTGATTGGTTGATAAGGCATTACGTAACTGGTTGATAGGG
1 TGACTTAGGCATTGCGTGACTGGTTGATAAAACATTACGTAACTGATTGATAGGG
31952322 CATTACATGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (61 bp):
TGACTTAGGCATTGCGTGACTGGTTGATAAAACATTACGTAACTGATTGATAGGGATTGTG
Found at i:31952410 original size:22 final size:22
Alignment explanation
Indices: 31952385--31952435 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
31952375 GTCTAAGTCA
31952385 TGCAATGTTT-AAAATCCAATCT
1 TGCAATGTTTAAAAAT-CAATCT
31952407 TGCAATGTTTAAAAATCAATCT
1 TGCAATGTTTAAAAATCAATCT
*
31952429 CGCAATG
1 TGCAATG
31952436 CCTAAAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (22 bp):
TGCAATGTTTAAAAATCAATCT
Found at i:31952441 original size:22 final size:23
Alignment explanation
Indices: 31952395--31952443 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
31952385 TGCAATGTTT
* **
31952395 AAAATCCAATCTTGCAATGTTTA
1 AAAATCCAATCTCGCAATGCCTA
31952418 AAAAT-CAATCTCGCAATGCCTA
1 AAAATCCAATCTCGCAATGCCTA
31952440 AAAA
1 AAAA
31952444 CTAGTGATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (23 bp):
AAAATCCAATCTCGCAATGCCTA
Found at i:31956063 original size:24 final size:24
Alignment explanation
Indices: 31956030--31956084 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
31956020 AAAAAAAGAG
* *
31956030 AAAAAG-GAAAGAAAAAGAGAGGT
1 AAAAAGAGAAAGAAAAAAACAGGT
31956053 AAAAAGAGAAAGAAAAAAACAGGT
1 AAAAAGAGAAAGAAAAAAACAGGT
*
31956077 AGAAAGAG
1 AAAAAGAG
31956085 GTTCGAATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (24 bp):
AAAAAGAGAAAGAAAAAAACAGGT
Found at i:31956068 original size:12 final size:12
Alignment explanation
Indices: 31956028--31956069 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
31956018 GGAAAAAAAG
31956028 AGAAAAAG-GAA
1 AGAAAAAGAGAA
31956039 AGAAAAAGAG-A
1 AGAAAAAGAGAA
*
31956050 GGTAAAAAGAGAA
1 AG-AAAAAGAGAA
31956063 AGAAAAA
1 AGAAAAA
31956070 AACAGGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 14 0.54
13 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:31957772 original size:30 final size:30
Alignment explanation
Indices: 31957723--31957793 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
31957713 AATAAAACAT
*
31957723 TTAA-ATTTTTAATTATAAA-TTATAAGAAA
1 TTAATATTTTAAATTATAAATTTA-AAGAAA
* **
31957752 TTAATATTTTAAATTTTAAATTTAAAGTTA
1 TTAATATTTTAAATTATAAATTTAAAGAAA
31957782 TTAATATTTTAA
1 TTAATATTTTAA
31957794 TGTTTTGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.11
30 29 0.81
31 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TTAATATTTTAAATTATAAATTTAAAGAAA
Found at i:31957873 original size:16 final size:16
Alignment explanation
Indices: 31957826--31957894 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
31957816 AAATTGCAAA
*
31957826 TAAAATATTAATATTTT
1 TAAAATTTTAA-ATTTT
*
31957843 TAAAAAATGTT-AATTTT
1 T--AAAATTTTAAATTTT
*
31957860 TAAAATTTTAAATTAT
1 TAAAATTTTAAATTTT
*
31957876 TAATATTTTAAATTTT
1 TAAAATTTTAAATTTT
31957892 TAA
1 TAA
31957895 TGGAAATAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.16
16 22 0.50
17 7 0.16
18 1 0.02
19 7 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TAAAATTTTAAATTTT
Found at i:31957977 original size:18 final size:21
Alignment explanation
Indices: 31957942--31957983 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
31957932 AAAAAATAAA
*
31957942 AAATTATATTAATATTTT-AT
1 AAATTATATAAATATTTTAAT
31957962 AAATTAT-TAAAT-TTTTAAT
1 AAATTATATAAATATTTTAAT
31957981 AAA
1 AAA
31957984 AATACAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTATATAAATATTTTAAT
Found at i:31958715 original size:52 final size:50
Alignment explanation
Indices: 31958556--31958758 Score: 160
Period size: 52 Copynumber: 3.9 Consensus size: 50
31958546 GGAAACCAAA
* * *
31958556 ACAGTGAGACCTCCCCACAAATTGGAGGAAAAATCATCTACCAT--CATC
1 ACAGTGGGACCTCCCCACAAATTGGAGGATATATCATCTACCATAACATC
* * * * * *
31958604 AACAGTGGGACCTCTCCACGAAAATGGTAGGAGTATATCATTTACCTTAA-TTT
1 -ACAGTGGGACCTCCCCAC-AAATTGG-AGGA-TATATCATCTACCATAACATC
* * *
31958657 ATAGTGGGACCTCCCCACAAATTGGCAGGGATATAGCACCTACCATAACATC
1 ACAGTGGGACCTCCCCACAAATTGG-A-GGATATATCATCTACCATAACATC
* * *
31958709 ACAGTGGGACCTCCCCGCAAAATGGGTAAGAATATGATCATCTACCATAA
1 ACAGTGGGACCTCCCCAC-AAATTGG--AGGATAT-ATCATCTACCATAA
31958759 AGGTTCCCAC
Statistics
Matches: 118, Mismatches: 26, Indels: 15
0.74 0.16 0.09
Matches are distributed among these distances:
49 16 0.14
50 6 0.05
51 24 0.20
52 47 0.40
53 12 0.10
54 13 0.11
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (50 bp):
ACAGTGGGACCTCCCCACAAATTGGAGGATATATCATCTACCATAACATC
Found at i:31961416 original size:35 final size:35
Alignment explanation
Indices: 31961345--31961593 Score: 234
Period size: 35 Copynumber: 7.1 Consensus size: 35
31961335 CACTTGATTA
* * *
31961345 AAATTGTTTAATTAAG---TTGTGCTTAATTAATC
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
31961377 AAATTGTTTAATTAAGTCATTGAGACTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
31961412 AAATTATTTAATTAAATCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
**** * * * *
31961447 AAATTAAACAACTAAGTTATTGAGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
31961482 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * ** *
31961518 AAAATTGTTTAGTTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * * *
31961554 AAGTTATTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
31961589 AAATT
1 AAATT
31961594 AAACAATTAA
Statistics
Matches: 175, Mismatches: 37, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
32 16 0.09
35 105 0.60
36 51 0.29
37 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:31961520 original size:71 final size:70
Alignment explanation
Indices: 31961386--31961614 Score: 269
Period size: 71 Copynumber: 3.2 Consensus size: 70
31961376 CAAATTGTTT
* * * *
31961386 AATTAAGTCATTGAGACTAATTAATTAAATTATTTAATTAAATCATTGGGCCTAATTAATTAAAT
1 AATTAAGTTATTGAGCCTAATTAATTAAATTATTTAATTAAGTCATTGGGCCTAATTGATTAAAT
31961451 TAAAC
66 TAAAC
* * *
31961456 AACTAAGTTATTGAGCCTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAA
1 AATTAAGTTATTGAGCCTAATTAATTAAA-TTATTTAATTAAGTCATTGGGCCTAATTGATT-AA
****
31961521 ATTGTTT
64 ATTAAAC
* * * * * * *
31961528 AGTTAAATTGTTGGGCTTAATTAATTAAGTTATTTAATTAAGTTATTGGGCCTAATTGATTAAAT
1 AATTAAGTTATTGAGCCTAATTAATTAAATTATTTAATTAAGTCATTGGGCCTAATTGATTAAAT
31961593 TAAAC
66 TAAAC
31961598 AATTAAGTTAATTGAGC
1 AATTAAGTT-ATTGAGC
31961615 TTCTTAAGAA
Statistics
Matches: 127, Mismatches: 29, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
70 37 0.29
71 64 0.50
72 26 0.20
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (70 bp):
AATTAAGTTATTGAGCCTAATTAATTAAATTATTTAATTAAGTCATTGGGCCTAATTGATTAAAT
TAAAC
Found at i:31961564 original size:13 final size:13
Alignment explanation
Indices: 31961548--31961574 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31961538 TTGGGCTTAA
31961548 TTAATTAAGTTAT
1 TTAATTAAGTTAT
31961561 TTAATTAAGTTAT
1 TTAATTAAGTTAT
31961574 T
1 T
31961575 GGGCCTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTAATTAAGTTAT
Found at i:31961570 original size:107 final size:106
Alignment explanation
Indices: 31961380--31961593 Score: 293
Period size: 107 Copynumber: 2.0 Consensus size: 106
31961370 ATTAATCAAA
31961380 TTGTTTAATTAAGTCATTGAGACTAATTAATTAAATTATTTAATTAAATCATTGGGCCTAATTAA
1 TTGTTTAATTAAGTCATTGAGACTAATTAATTAAATTATTTAATTAAATCATTGGGCCTAATTAA
31961445 TTAAATTAAACAACTAAGTTATTGAGCCTAATTGATTAAAT
66 TTAAATTAAACAACTAAGTTATTGAGCCTAATTGATTAAAT
* * * * * ** *
31961486 TTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAGTTAAATTGTTGGGCTTAATTA
1 TTGTTTAATTAAGTCATTGAGACTAATTAATT-AAATTATTTAATTAAATCATTGGGCCTAATTA
* *** * *
31961551 ATTAAGTTATTTAATTAAGTTATTGGGCCTAATTGATTAAAT
65 ATTAAATTAAACAACTAAGTTATTGAGCCTAATTGATTAAAT
31961593 T
1 T
31961594 AAACAATTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
106 29 0.31
107 64 0.69
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (106 bp):
TTGTTTAATTAAGTCATTGAGACTAATTAATTAAATTATTTAATTAAATCATTGGGCCTAATTAA
TTAAATTAAACAACTAAGTTATTGAGCCTAATTGATTAAAT
Found at i:31962644 original size:30 final size:31
Alignment explanation
Indices: 31962571--31962679 Score: 113
Period size: 30 Copynumber: 3.6 Consensus size: 31
31962561 TTTTTCAATT
*
31962571 TTTTCTTCTTTTTCAATTT-GATCCTCTAAAC-
1 TTTTCTTCTTTTTCAATTTAG-TCC-CTTAACA
*
31962602 TCTTTATTC-TTTTCAATTTAGTCCCTTAACA
1 T-TTTCTTCTTTTTCAATTTAGTCCCTTAACA
*
31962633 TTTTCTTCTTTTT-AATTTAGTCCC-TCA-A
1 TTTTCTTCTTTTTCAATTTAGTCCCTTAACA
*
31962661 TTTTTTTCTTTTTCAATTT
1 TTTTCTTCTTTTTCAATTT
31962680 TATCCCTCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
28 13 0.19
29 7 0.10
30 22 0.32
31 19 0.28
32 7 0.10
ACGTcount: A:0.18, C:0.20, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTCTTCTTTTTCAATTTAGTCCCTTAACA
Found at i:31962695 original size:31 final size:30
Alignment explanation
Indices: 31962565--31962698 Score: 118
Period size: 31 Copynumber: 4.4 Consensus size: 30
31962555 TCTTTATTTT
*
31962565 TCAATTTTTTCTTCTTTTTCAATTT-GAT-CC
1 TCAAATTTTT-TTCTTTTTCAATTTAG-TCCC
*
31962595 TCTAAACTCTTTATTC-TTTTCAATTTAGTCCC
1 TC-AAA-T-TTTTTTCTTTTTCAATTTAGTCCC
* *
31962627 TTAACATTTTCTTCTTTTT-AATTTAGTCCC
1 TCAA-ATTTTTTTCTTTTTCAATTTAGTCCC
31962657 TC-AATTTTTTTCTTTTTCAATTTTA-TCCC
1 TCAAATTTTTTTCTTTTTCAA-TTTAGTCCC
31962686 TCAATATTTTTTT
1 TCAA-ATTTTTTT
31962699 TCAATTTAAT
Statistics
Matches: 87, Mismatches: 6, Indels: 21
0.76 0.05 0.18
Matches are distributed among these distances:
28 13 0.15
29 9 0.10
30 25 0.29
31 28 0.32
32 9 0.10
33 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.02, T:0.58
Consensus pattern (30 bp):
TCAAATTTTTTTCTTTTTCAATTTAGTCCC
Found at i:31964403 original size:38 final size:38
Alignment explanation
Indices: 31964361--31964433 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
31964351 AAATCTGCTC
* * *
31964361 ATATTGAAGTGCACGTACCATTTGAAAATAAACTCCTT
1 ATATTCAAGCGCACGTACAATTTGAAAATAAACTCCTT
*
31964399 ATATTCAAGCGCACGTGCAATTTGAAAATAAACTC
1 ATATTCAAGCGCACGTACAATTTGAAAATAAACTC
31964434 AACCATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (38 bp):
ATATTCAAGCGCACGTACAATTTGAAAATAAACTCCTT
Found at i:31964587 original size:72 final size:71
Alignment explanation
Indices: 31964501--31964645 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 71
31964491 ACTGAGAGAG
* * * *
31964501 AGCATTTGAGCATTTACATCGTTCGATTCTACCTTAAACTCAAAAGCTAGCAAAGCGTTCAAAGA
1 AGCATTTGAGCATTTACATCATTCGATTCTACCCTAAACTC-AAAGCTAGCAAAACGTTCAAACA
31964566 AGTTCAA
65 AGTTCAA
* * * *
31964573 AGCATTTGAGCATTTACATCATTTGATTTTACCCTAAACTCAAAGCTAGCAAAATGTTCGAACAA
1 AGCATTTGAGCATTTACATCATTCGATTCTACCCTAAACTCAAAGCTAGCAAAACGTTCAAACAA
31964638 GTTCAA
66 GTTCAA
31964644 AG
1 AG
31964646 TAAAGTAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 28 0.43
72 37 0.57
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (71 bp):
AGCATTTGAGCATTTACATCATTCGATTCTACCCTAAACTCAAAGCTAGCAAAACGTTCAAACAA
GTTCAA
Found at i:31968480 original size:13 final size:13
Alignment explanation
Indices: 31968461--31968493 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
31968451 ATTATTATTA
31968461 TTATTTTTTA--T
1 TTATTTTTTACTT
31968472 TTATTTTTTACTT
1 TTATTTTTTACTT
31968485 TTATTTTTT
1 TTATTTTTT
31968494 GTTTGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTATTTTTTACTT
Found at i:31971759 original size:11 final size:11
Alignment explanation
Indices: 31971743--31971775 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31971733 ACCGATTGAA
31971743 GCAAGCAA-TGT
1 GCAAGCAACT-T
31971754 GCAAGCAACTT
1 GCAAGCAACTT
31971765 GCAAGCAACTT
1 GCAAGCAACTT
31971776 ATGTTAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (11 bp):
GCAAGCAACTT
Found at i:31975417 original size:2 final size:2
Alignment explanation
Indices: 31975412--31975436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31975402 TCTCTCTCTC
31975412 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 T
31975437 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31975885 original size:22 final size:22
Alignment explanation
Indices: 31975841--31975896 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
31975831 TAATTTTAAA
* * *
31975841 AATATAAATATAAAGAAATAAT
1 AATATAAACAAAAAGAAAGAAT
*
31975863 AATATAAACAAAAATAAAGAAT
1 AATATAAACAAAAAGAAAGAAT
31975885 AACT-TAAACAAA
1 AA-TATAAACAAA
31975897 TTTAATTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (22 bp):
AATATAAACAAAAAGAAAGAAT
Found at i:31982374 original size:72 final size:72
Alignment explanation
Indices: 31982257--31982401 Score: 236
Period size: 72 Copynumber: 2.0 Consensus size: 72
31982247 TCTCAAACAT
* * *
31982257 AATTCCTTTGAAAAGTTTTGTTAATCTCATACCTTCGATGCATGCTATCCTCATAAAGGCAGTGA
1 AATTCCTTTGAAAAGTTTTGTTAATCTCATACCGTAGATGCATGCTATCCTCATAAAGACAGTGA
31982322 CAGGATC
66 CAGGATC
* * *
31982329 AATTCCTTTGAAAAGTTTTGTTAATTTCATCCCGTAGATGCATGCTATCCTCATGAAGACAGTGA
1 AATTCCTTTGAAAAGTTTTGTTAATCTCATACCGTAGATGCATGCTATCCTCATAAAGACAGTGA
31982394 CAGGATC
66 CAGGATC
31982401 A
1 A
31982402 TGGAGATAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (72 bp):
AATTCCTTTGAAAAGTTTTGTTAATCTCATACCGTAGATGCATGCTATCCTCATAAAGACAGTGA
CAGGATC
Found at i:32021672 original size:2 final size:2
Alignment explanation
Indices: 32021665--32021725 Score: 71
Period size: 2 Copynumber: 33.0 Consensus size: 2
32021655 TTGTTAGGTC
32021665 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32021704 AT A- AT -T ACT AT AT AT AT A- AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT
32021726 TGTCTTTGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
1 6 0.12
2 44 0.85
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32021690 original size:9 final size:9
Alignment explanation
Indices: 32021666--32021725 Score: 68
Period size: 9 Copynumber: 6.6 Consensus size: 9
32021656 TGTTAGGTCA
32021666 TATATATAT
1 TATATATAT
32021675 ATATATATAT
1 -TATATATAT
32021685 TATATATAT
1 TATATATAT
*
32021694 AATATATAT
1 TATATATAT
*
32021703 TATA-ATTAC
1 TATATA-TAT
32021712 TATATATAT
1 TATATATAT
*
32021721 AATAT
1 TATAT
32021726 TGTCTTTGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
8 1 0.02
9 32 0.74
10 10 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
TATATATAT
Found at i:32021715 original size:27 final size:30
Alignment explanation
Indices: 32021665--32021725 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 30
32021655 TTGTTAGGTC
*
32021665 ATATATATATATATATATATTATATATATA
1 ATATATATATATATATATACTATATATATA
32021695 ATATATAT-TATA-AT-TACTATATATATA
1 ATATATATATATATATATACTATATATATA
32021722 ATAT
1 ATAT
32021726 TGTCTTTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 16 0.53
28 2 0.07
29 4 0.13
30 8 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATATATATATATATATACTATATATATA
Found at i:32025334 original size:33 final size:33
Alignment explanation
Indices: 32025291--32025358 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
32025281 AACATGTCAT
*
32025291 ATCATCATCAATTATGATATATCAGCATATCAC
1 ATCATAATCAATTATGATATATCAGCATATCAC
* * *
32025324 ATCATAATCAATTATGATATTTTAGCATGTCAC
1 ATCATAATCAATTATGATATATCAGCATATCAC
32025357 AT
1 AT
32025359 TGTCACTCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (33 bp):
ATCATAATCAATTATGATATATCAGCATATCAC
Found at i:32038955 original size:26 final size:27
Alignment explanation
Indices: 32038926--32038992 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
32038916 TCTAAACTAT
*
32038926 TTATTAAAATAAAATTTTAT-TTTTTA
1 TTATTAAATTAAAATTTTATATTTTTA
* *
32038952 TTATTTTTAATTAAATTTTTATATTTTTA
1 TTA--TTAAATTAAAATTTTATATTTTTA
32038981 TT-TTAAATTAAA
1 TTATTAAATTAAA
32038993 TAAATTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 12 0.35
28 14 0.41
29 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATTAAATTAAAATTTTATATTTTTA
Found at i:32038961 original size:29 final size:30
Alignment explanation
Indices: 32038923--32039003 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
32038913 AACTCTAAAC
32038923 TATTTATTAAAATAAAATTTTAT-TTTTTAT
1 TATTTATT-AAATAAAATTTTATATTTTTAT
* *
32038953 TATTT-TTAATTAAATTTTTATATTTTTAT
1 TATTTATTAAATAAAATTTTATATTTTTAT
* *
32038982 T-TTAAATTAAATAAATTTTTAT
1 TATT-TATTAAATAAAATTTTAT
32039004 GGTTGACGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 14 0.32
29 10 0.23
30 20 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTATTAAATAAAATTTTATATTTTTAT
Found at i:32038972 original size:21 final size:21
Alignment explanation
Indices: 32038946--32038989 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32038936 AAAATTTTAT
32038946 TTTTTATTATTTTTA-ATTAAA
1 TTTTTA-TATTTTTATATTAAA
*
32038967 TTTTTATATTTTTATTTTAAA
1 TTTTTATATTTTTATATTAAA
32038988 TT
1 TT
32038990 AAATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTATATTTTTATATTAAA
Found at i:32038993 original size:26 final size:28
Alignment explanation
Indices: 32038929--32038993 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
32038919 AAACTATTTA
* * *
32038929 TTAAAATAAAATTTTATTTTTTATTATT
1 TTAAATTAAATTTTTATTATTTATTATT
*
32038957 TTTAATTAAATTTTTA-TATTT-TTATT
1 TTAAATTAAATTTTTATTATTTATTATT
32038983 TTAAATTAAAT
1 TTAAATTAAAT
32038994 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 15 0.47
27 4 0.12
28 13 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTAAATTAAATTTTTATTATTTATTATT
Found at i:32049745 original size:20 final size:22
Alignment explanation
Indices: 32049698--32049745 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
32049688 AATGCAAAAT
*
32049698 TATTTTTTTTGTAAAGATTCAA
1 TATTTTTTTTGTAAAGAGTCAA
* *
32049720 TTTTTTTTTTG-AAA-AGTGAA
1 TATTTTTTTTGTAAAGAGTCAA
32049740 TATTTT
1 TATTTT
32049746 ATGATTTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.58
Consensus pattern (22 bp):
TATTTTTTTTGTAAAGAGTCAA
Found at i:32050337 original size:8 final size:7
Alignment explanation
Indices: 32050318--32050351 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
32050308 TTGAAGCAAC
32050318 AAAAGAA
1 AAAAGAA
32050325 AAAAGACA
1 AAAAGA-A
32050333 AAAAGAAA
1 AAAAG-AA
32050341 AAAAGAA
1 AAAAGAA
32050348 AAAA
1 AAAA
32050352 TGATAATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 12 0.48
8 12 0.48
9 1 0.04
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:32059463 original size:12 final size:12
Alignment explanation
Indices: 32059446--32059484 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
32059436 GGAGCCTTAC
*
32059446 ATACATACATAT
1 ATACATATATAT
32059458 ATACATATATAT
1 ATACATATATAT
*
32059470 ATATATATATAT
1 ATACATATATAT
32059482 ATA
1 ATA
32059485 TATGTATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
ATACATATATAT
Found at i:32059465 original size:8 final size:8
Alignment explanation
Indices: 32059443--32059484 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
32059433 GTGGGAGCCT
*
32059443 TACATACA
1 TACATATA
32059451 TACATATA
1 TACATATA
32059459 TACATATA
1 TACATATA
*
32059467 TATATATA
1 TACATATA
*
32059475 TATATATA
1 TACATATA
32059483 TA
1 TA
32059485 TATGTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
TACATATA
Found at i:32059467 original size:2 final size:2
Alignment explanation
Indices: 32059454--32059493 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
32059444 ACATACATAC
* *
32059454 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32059494 GTTTAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32059769 original size:26 final size:26
Alignment explanation
Indices: 32059739--32059792 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
32059729 TTTAAACACA
* *
32059739 TTACTTTTTAATGTATTTCTATCAGT
1 TTACTTTTTAATGTATTCCCATCAGT
*
32059765 TTACTTTTTCATGTATTCCCATCAGT
1 TTACTTTTTAATGTATTCCCATCAGT
32059791 TT
1 TT
32059793 TTATTAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (26 bp):
TTACTTTTTAATGTATTCCCATCAGT
Found at i:32061262 original size:38 final size:39
Alignment explanation
Indices: 32061176--32061278 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 39
32061166 ACCCGGCTCA
*
32061176 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* *
32061216 TGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
32061254 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
32061279 CGGGCACTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 30 0.52
39 3 0.05
40 25 0.43
ACGTcount: A:0.22, C:0.42, G:0.17, T:0.19
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:32061271 original size:19 final size:19
Alignment explanation
Indices: 32061176--32061274 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
32061166 ACCCGGCTCA
32061176 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* * **
32061195 TGCACATAGCCGGCACCATCG
1 TGTACAT-CCCCCCA-CATCG
*
32061216 TGTGCATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* ****
32061235 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
32061254 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
32061273 TG
1 TG
32061275 CACACGGGCA
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 4 0.07
19 30 0.54
20 12 0.21
21 10 0.18
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.20
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:32070219 original size:12 final size:12
Alignment explanation
Indices: 32070202--32070226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32070192 TGAGCAGGCT
32070202 TGCACACACACA
1 TGCACACACACA
32070214 TGCACACACACA
1 TGCACACACACA
32070226 T
1 T
32070227 AAAAACCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.40, G:0.08, T:0.12
Consensus pattern (12 bp):
TGCACACACACA
Found at i:32075958 original size:13 final size:13
Alignment explanation
Indices: 32075933--32075966 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
32075923 TAATTACTAA
*
32075933 TTAATTCAATAAT
1 TTAATTAAATAAT
*
32075946 TTGATTAAATAAT
1 TTAATTAAATAAT
32075959 TTAATTAA
1 TTAATTAA
32075967 GTCCTTAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (13 bp):
TTAATTAAATAAT
Found at i:32076024 original size:35 final size:35
Alignment explanation
Indices: 32075980--32076090 Score: 152
Period size: 35 Copynumber: 3.1 Consensus size: 35
32075970 CTTAAGAAGC
*
32075980 CCAATTAACTTAATTGTTTAATTTAATTAATTAGGT
1 CCAA-TAACTTAATTGATTAATTTAATTAATTAGGT
*
32076016 CCAATAACTTAATTGATTAATTTAATTAATTAAG-
1 CCAATAACTTAATTGATTAATTTAATTAATTAGGT
* * *
32076050 CCTAATGACTTAATTAAATAATTTAATTAATTAGGT
1 CC-AATAACTTAATTGATTAATTTAATTAATTAGGT
32076086 CCAAT
1 CCAAT
32076091 GATTCAATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.03
35 59 0.88
36 6 0.09
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (35 bp):
CCAATAACTTAATTGATTAATTTAATTAATTAGGT
Found at i:32076092 original size:35 final size:35
Alignment explanation
Indices: 32075998--32076119 Score: 158
Period size: 35 Copynumber: 3.5 Consensus size: 35
32075988 CTTAATTGTT
* * *
32075998 TAATTTAATTAATTAGGTCCAATAACTTAATTGAT
1 TAATTTAATTAATTAGGTCCAATGACTTAATTAAA
*
32076033 TAATTTAATTAATTAAG-CCTAATGACTTAATTAAA
1 TAATTTAATTAATTAGGTCC-AATGACTTAATTAAA
32076068 TAATTTAATTAATTAGGTCCAATGA-TTCAATTAAA
1 TAATTTAATTAATTAGGTCCAATGACTT-AATTAAA
* *
32076103 CAATTTAGTTAATTAGG
1 TAATTTAATTAATTAGG
32076120 CACAACTTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
34 4 0.05
35 71 0.92
36 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (35 bp):
TAATTTAATTAATTAGGTCCAATGACTTAATTAAA
Found at i:32084167 original size:20 final size:20
Alignment explanation
Indices: 32084130--32084167 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
32084120 TTGACATTTT
*
32084130 ATTTAACTTTTTCTATATTG
1 ATTTAACTTTTTCAATATTG
32084150 ATTTAA-TTTTATCAATAT
1 ATTTAACTTTT-TCAATAT
32084168 ATTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTAACTTTTTCAATATTG
Found at i:32084528 original size:9 final size:9
Alignment explanation
Indices: 32084516--32084588 Score: 76
Period size: 9 Copynumber: 8.1 Consensus size: 9
32084506 ATATTGTAAT
32084516 TTAATCGTG
1 TTAATCGTG
*
32084525 TTAAACGTG
1 TTAATCGTG
* *
32084534 TTAAACATG
1 TTAATCGTG
32084543 TTAATCGTG
1 TTAATCGTG
*
32084552 TTAAAT-GTA
1 TT-AATCGTG
32084561 TTAATCGTG
1 TTAATCGTG
*
32084570 TTAATCATG
1 TTAATCGTG
*
32084579 TTAAACGTG
1 TTAATCGTG
32084588 T
1 T
32084589 CATTAATCGT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
8 3 0.06
9 47 0.89
10 3 0.06
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (9 bp):
TTAATCGTG
Found at i:32084546 original size:27 final size:27
Alignment explanation
Indices: 32084516--32084588 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
32084506 ATATTGTAAT
32084516 TTAATCGTGTTAAACGTGTTAAACATG
1 TTAATCGTGTTAAACGTGTTAAACATG
* * * *
32084543 TTAATCGTGTTAAATGTATTAATCGTG
1 TTAATCGTGTTAAACGTGTTAAACATG
*
32084570 TTAATCATGTTAAACGTGT
1 TTAATCGTGTTAAACGTGT
32084589 CATTAATCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (27 bp):
TTAATCGTGTTAAACGTGTTAAACATG
Found at i:32092723 original size:2 final size:2
Alignment explanation
Indices: 32092714--32092745 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
32092704 TTTTATTTCG
32092714 TA TA -A 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 TA T
32092746 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32093763 original size:14 final size:14
Alignment explanation
Indices: 32093744--32093777 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
32093734 NNNNNNTGGT
32093744 GAAAAAAAAAAAAG
1 GAAAAAAAAAAAAG
**
32093758 GAAAAAAAGGAAAG
1 GAAAAAAAAAAAAG
32093772 GAAAAA
1 GAAAAA
32093778 TAATTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAAAG
Found at i:32097905 original size:2 final size:2
Alignment explanation
Indices: 32097898--32097930 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32097888 TGCTTTTGAT
32097898 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
32097931 TTTATTTTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:32101511 original size:2 final size:2
Alignment explanation
Indices: 32101504--32101569 Score: 86
Period size: 2 Copynumber: 35.0 Consensus size: 2
32101494 GACATTACAT
*
32101504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TT TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
32101543 TA TT TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32101570 ATAGTAATAT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
1 4 0.07
2 53 0.93
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:32101579 original size:13 final size:15
Alignment explanation
Indices: 32101504--32101580 Score: 69
Period size: 14 Copynumber: 5.5 Consensus size: 15
32101494 GACATTACAT
32101504 TATATATATATATA-
1 TATATATATATATAG
32101518 TATATATATATATA-
1 TATATATATATATAG
*
32101532 TAT-TAT-TTTATTA-
1 TATATATATATA-TAG
* *
32101545 TTTATATATATATAT
1 TATATATATATATAG
32101560 TATATATATA-ATAG
1 TATATATATATATAG
32101574 TA-ATATA
1 TATATATA
32101581 GAAATATTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
12 3 0.06
13 12 0.22
14 27 0.50
15 12 0.22
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
TATATATATATATAG
Done.