Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 121 of 126
Found at i:36285061 original size:29 final size:30
Alignment explanation
Indices: 36285028--36285086 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
36285018 TTTAGTTCAA
*
36285028 TGTGTAATGTTATACATG-AGTTTTGATTT
1 TGTGTAATGTTATACATGAAATTTTGATTT
* *
36285057 TGTGTGATTTTATACATGAAATTTTGATTT
1 TGTGTAATGTTATACATGAAATTTTGATTT
36285087 GATTCAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (30 bp):
TGTGTAATGTTATACATGAAATTTTGATTT
Found at i:36285256 original size:31 final size:31
Alignment explanation
Indices: 36285211--36285297 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
36285201 ATTTTTTTAA
*
36285211 ATGTGTACAAATGAATCAAAATCAAAGTTTT
1 ATGTATACAAATGAATCAAAATCAAAGTTTT
*
36285242 ATGTATACATATGAA-CTAAAATTC-AAGTTTT
1 ATGTATACAAATGAATC-AAAA-TCAAAGTTTT
* *
36285273 ATGTCTATAAATGAATC-AAATCAAA
1 ATGTATACAAATGAATCAAAATCAAA
36285298 ATTTATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 2 0.04
30 6 0.13
31 36 0.77
32 3 0.06
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (31 bp):
ATGTATACAAATGAATCAAAATCAAAGTTTT
Found at i:36286766 original size:17 final size:17
Alignment explanation
Indices: 36286746--36286845 Score: 91
Period size: 17 Copynumber: 6.0 Consensus size: 17
36286736 TAATTTAGAG
* *
36286746 TTTAAATTGATTTTAAA
1 TTTAAATTAAATTTAAA
*
36286763 TTT-ATTTAAATTTAAA
1 TTTAAATTAAATTTAAA
**
36286779 TTTATCTTAAATTTAAA
1 TTTAAATTAAATTTAAA
36286796 TTT-AATT--ATTTAAA
1 TTTAAATTAAATTTAAA
**
36286810 TTTACCTTAAATTTAAA
1 TTTAAATTAAATTTAAA
36286827 TTTAAATTTAAATTATAAA
1 TTTAAA-TTAAATT-TAAA
36286846 ACAAATTTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 15 0.23
17 28 0.42
18 7 0.11
19 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAAATTAAATTTAAA
Found at i:36286775 original size:6 final size:6
Alignment explanation
Indices: 36286757--36286845 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
36286747 TTAAATTGAT
36286757 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* *
36286804 TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
36286846 ACAAATTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
4 6 0.09
5 5 0.07
6 47 0.67
7 6 0.09
8 6 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:36286788 original size:11 final size:11
Alignment explanation
Indices: 36286774--36286824 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
36286764 TTATTTAAAT
36286774 TTAAATTTATC
1 TTAAATTTATC
**
36286785 TTAAATTTAAA
1 TTAAATTTATC
*
36286796 TTTAA-TTAT-
1 TTAAATTTATC
*
36286805 TTAAATTTACC
1 TTAAATTTATC
36286816 TTAAATTTA
1 TTAAATTTA
36286825 AATTTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 22 0.69
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTATC
Found at i:36286810 original size:37 final size:38
Alignment explanation
Indices: 36286757--36286842 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 38
36286747 TTAAATTGAT
*
36286757 TTTAAATTTATTTAAATTTAAATT-TATCTTAAATTTAAA
1 TTTAAA-TTATTTAAATTTAAATTAAAT-TTAAATTTAAA
**
36286796 TTT-AATTATTTAAATTTACCTTAAATTTAAATTTAAA
1 TTTAAATTATTTAAATTTAAATTAAATTTAAATTTAAA
36286833 TTTAAATTAT
1 TTTAAATTAT
36286843 AAAACAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 29 0.69
38 10 0.24
39 3 0.07
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTAAATTATTTAAATTTAAATTAAATTTAAATTTAAA
Found at i:36288926 original size:59 final size:57
Alignment explanation
Indices: 36288863--36289154 Score: 218
Period size: 59 Copynumber: 5.0 Consensus size: 57
36288853 TTGCATTTTA
* * * *
36288863 ACCCCAAATTTTTAGAAAATTCCATTTTTGACCTCGAAACTT-CCAAAAATTACCATTAT
1 ACCCCAAA-CTTTACAAAATTCCATTTTTAACCCCG--ACTTACCAAAAATTACCATTAT
* * *
36288922 ACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
1 A-CCCCAAACTTTACAAAATTCCATTTTTAACCCCGACTT-ACCAAAAATTACCATTAT
* * * * *
36288981 ACCCTCGAACTCTCCAAAATTCCATTTTTTAATCCCGATTTCACC-AAAATTACCATT-T
1 ACCC-CAAACTTTACAAAATTCCA-TTTTTAACCCCGACTT-ACCAAAAATTACCATTAT
* * ** * *
36289039 CACCCCCAAACTTT-CTAAGATTCTATTTTTAACCCTAATTTCACC-AAAATTACCATTTT
1 -A-CCCCAAACTTTAC-AAAATTCCATTTTTAACCCCGACTT-ACCAAAAATTACCATTAT
* * *
36289098 ACCCCTAAA-TTTTCTAAAATTCCATTTTTAACCCCAATTTTACCAAAAATTACCATT
1 ACCCC-AAACTTTAC-AAAATTCCATTTTTAACCCCGA-CTTACCAAAAATTACCATT
36289155 TTGCCCCAGG
Statistics
Matches: 200, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
57 10 0.05
58 62 0.31
59 99 0.50
60 29 0.14
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.35
Consensus pattern (57 bp):
ACCCCAAACTTTACAAAATTCCATTTTTAACCCCGACTTACCAAAAATTACCATTAT
Found at i:36288937 original size:30 final size:28
Alignment explanation
Indices: 36288835--36289161 Score: 112
Period size: 29 Copynumber: 11.1 Consensus size: 28
36288825 GTTTATAGGT
** * *
36288835 CCCCAAACAATCCAGAAATTGCATTTTAA
1 CCCCAAACTTTCCA-AAATTCCATTTTAC
* **
36288864 CCCCAAATTTTTAGAAAATTCCATTTTTGAC
1 CCCCAAA-CTTTCCAAAATTCCA-TTTT-AC
* * *
36288895 CTCGAAAC-TTCCAAAAATTACCATTATAC
1 CCCCAAACTTTCC-AAAATT-CCATTTTAC
*
36288924 CCCCAAACTTTCCAAAATTCCATTTTTAA
1 CCCCAAACTTTCCAAAATTCCA-TTTTAC
*
36288953 CCCC-GA-TTTCACCAAAAATTACCATTTTAC
1 CCCCAAACTTT--CC-AAAATT-CCATTTTAC
* * * *
36288983 CCTCGAACTCTCCAAAATTCCATTTTTTAA
1 CCCCAAACTTTCCAAAATTCCA--TTTTAC
* * *
36289013 TCCC-GA-TTTCACCAAAATTACCATTTCAC
1 CCCCAAACTTT--CCAAAATT-CCATTTTAC
* * *
36289042 CCCCAAACTTTCTAAGATTCTATTTTTA-
1 CCCCAAACTTTCCAAAATTCCA-TTTTAC
* *
36289070 ACCCTAA-TTTCACCAAAATTACCATTTTAC
1 CCCCAAACTTT--CCAAAATT-CCATTTTAC
* * * *
36289100 CCCTAAATTTTCTAAAATTCCATTTTTAA
1 CCCCAAACTTTCCAAAATTCCA-TTTTAC
* *
36289129 CCCC-AATTTTACCAAAAATTACCATTTTGC
1 CCCCAAACTTT-CC-AAAATT-CCATTTTAC
36289159 CCC
1 CCC
36289162 AGGGTATCCA
Statistics
Matches: 219, Mismatches: 49, Indels: 59
0.67 0.15 0.18
Matches are distributed among these distances:
27 6 0.03
28 25 0.11
29 91 0.42
30 70 0.32
31 25 0.11
32 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (28 bp):
CCCCAAACTTTCCAAAATTCCATTTTAC
Found at i:36289087 original size:58 final size:59
Alignment explanation
Indices: 36288905--36289161 Score: 338
Period size: 59 Copynumber: 4.4 Consensus size: 59
36288895 CTCGAAACTT
* *
36288905 CCAAAAATTACCATTATACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* * * * *
36288964 CCAAAAATTACCATTTTACCCTCGAACTCTCCAAAATTCCATTTTTTAATCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTTAACCCCAATTTCA
* * * * *
36289024 CC-AAAATTACCATTTCACCCCCAAACTTTCTAAGATTCTATTTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* * * *
36289082 CC-AAAATTACCATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCCAATTTTA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
*
36289140 CCAAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
36289162 AGGGTATCCA
Statistics
Matches: 173, Mismatches: 23, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
58 68 0.39
59 86 0.50
60 19 0.11
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
Found at i:36289161 original size:29 final size:28
Alignment explanation
Indices: 36288908--36289162 Score: 121
Period size: 29 Copynumber: 8.7 Consensus size: 28
36288898 GAAACTTCCA
* *
36288908 AAAATTACCATTATACCCCCAAACTTT-CC
1 AAAATTACCATTTTA-CCCC-AATTTTACC
* *
36288937 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTT-ACCCCAATTTTACC
* *
36288966 AAAAATTACCATTTTACCCTCGAACTCT-CC
1 -AAAATTACCATTTTACCC-C-AATTTTACC
* * *
36288996 AAAATT-CCATTTTTTAATCCCGATTTCACC
1 AAAATTACCA--TTTT-ACCCCAATTTTACC
* * *
36289026 AAAATTACCATTTCACCCCCAAACTTT-CT
1 AAAATTACCATTTTA-CCCC-AATTTTACC
* * * *
36289055 AAGATT-CTATTTTTAACCCTAATTTCACC
1 AAAATTACCA-TTTT-ACCCCAATTTTACC
*
36289084 AAAATTACCATTTTACCCCTAAATTTT-CT
1 AAAATTACCATTTTACCCC--AATTTTACC
36289113 AAAATT-CCATTTTTAACCCCAATTTTACC
1 AAAATTACCA-TTTT-ACCCCAATTTTACC
*
36289142 AAAAATTACCATTTTGCCCCA
1 -AAAATTACCATTTTACCCCA
36289163 GGGTATCCAA
Statistics
Matches: 168, Mismatches: 33, Indels: 50
0.67 0.13 0.20
Matches are distributed among these distances:
28 29 0.17
29 72 0.43
30 53 0.32
31 14 0.08
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCAATTTTACC
Found at i:36297351 original size:47 final size:47
Alignment explanation
Indices: 36297298--36297393 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 47
36297288 CTTCTAAAAT
36297298 TTTTCTA-ATTT-TTTAT-TTTTTATAAAATTTTTAAATAATTTTAA-TAA
1 TTTTCTATATTTCTTTATATTTTT-T--AATTTTTAAA-AATTTTAATTAA
*
36297345 TTTTCTATATTTCTTTGTATTTTTTAATTTTTAAAAATTTTAATTAA
1 TTTTCTATATTTCTTTATATTTTTTAATTTTTAAAAATTTTAATTAA
36297392 TT
1 TT
36297394 ATTGATGTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
46 8 0.18
47 22 0.50
48 4 0.09
49 5 0.11
50 5 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (47 bp):
TTTTCTATATTTCTTTATATTTTTTAATTTTTAAAAATTTTAATTAA
Found at i:36299964 original size:108 final size:107
Alignment explanation
Indices: 36299827--36300032 Score: 297
Period size: 108 Copynumber: 1.9 Consensus size: 107
36299817 ATTTTTACGG
* * * **
36299827 GTATTTTTACAAATACATACCAATACCATTTGATATAGTGATGACACTAATAATTTTTAAAAAAA
1 GTATTTTTACAAATACATACCAATACCATTTGATACAGTGACGACACCAATAACATTT-AAAAAA
*
36299892 AACATGATAGATGTTGCATGATTGACCAAAAAGTAATTCACGA
65 AACATGATAGATGTTGCATGATTAACCAAAAAGTAATTCACGA
* *
36299935 GTATTTTTTCAAATACATA-TAAGTACCATTTGATACAGTGACGACACCAATAACATTTAAAAAA
1 GTATTTTTACAAATACATACCAA-TACCATTTGATACAGTGACGACACCAATAACATTTAAAAAA
* *
36299999 AACATGATAGATGTTGTATGATTAACTAAAAAGT
65 AACATGATAGATGTTGCATGATTAACCAAAAAGT
36300033 GAAGTAATAC
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
107 39 0.45
108 48 0.55
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (107 bp):
GTATTTTTACAAATACATACCAATACCATTTGATACAGTGACGACACCAATAACATTTAAAAAAA
ACATGATAGATGTTGCATGATTAACCAAAAAGTAATTCACGA
Found at i:36306128 original size:32 final size:32
Alignment explanation
Indices: 36306087--36306148 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
36306077 CATCTATTTT
36306087 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
36306119 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
36306149 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:36307899 original size:18 final size:18
Alignment explanation
Indices: 36307876--36307915 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
36307866 TATTCAATTT
36307876 TATTATTATTCTAATAAA
1 TATTATTATTCTAATAAA
36307894 TATTATTATTCTAATAAA
1 TATTATTATTCTAATAAA
36307912 TATT
1 TATT
36307916 GGAATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATTATTCTAATAAA
Found at i:36308060 original size:21 final size:21
Alignment explanation
Indices: 36308036--36308077 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
36308026 AGTAAATTAC
36308036 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
36308057 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
36308078 CAAGATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:36320115 original size:2 final size:2
Alignment explanation
Indices: 36320110--36320137 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36320100 TTTCCATCCC
36320110 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
36320138 TTCGTGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:36326745 original size:12 final size:12
Alignment explanation
Indices: 36326719--36326760 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
36326709 TCTCTTCTGC
36326719 TCTGGTCT-G-G
1 TCTGGTCTGGTG
36326729 TCTGGTCTGGTG
1 TCTGGTCTGGTG
36326741 TCTGGTCTGGTG
1 TCTGGTCTGGTG
36326753 TCTGGTCT
1 TCTGGTCT
36326761 CACTTGGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
12 21 0.70
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.43
Consensus pattern (12 bp):
TCTGGTCTGGTG
Found at i:36327558 original size:2 final size:2
Alignment explanation
Indices: 36327551--36327576 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36327541 ATTTCTTAGC
36327551 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
36327577 GTGTGTGGAG
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:36331305 original size:16 final size:17
Alignment explanation
Indices: 36331275--36331308 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
36331265 TAAAATTAAC
*
36331275 TTTTTAATATTTTTATT
1 TTTTTAATATATTTATT
36331292 TTTTTAATA-ATTTATT
1 TTTTTAATATATTTATT
36331308 T
1 T
36331309 AATCCAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTAATATATTTATT
Found at i:36338522 original size:161 final size:161
Alignment explanation
Indices: 36338257--36338742 Score: 963
Period size: 161 Copynumber: 3.0 Consensus size: 161
36338247 CTACTTTGTT
36338257 AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
1 AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
36338322 TTCACTTTTGGAGGGATTTATAAAGTCTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
66 TTCACTTTTGGAGGGATTTATAAAGTCTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
36338387 AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
131 AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
36338418 AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
1 AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
36338483 TTCACTTTTGGAGGGATTTATAAAGTCTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
66 TTCACTTTTGGAGGGATTTATAAAGTCTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
36338548 AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
131 AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
36338579 AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
1 AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
*
36338644 TTCACTTTTGGAGGGATTTATAAAGTTTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
66 TTCACTTTTGGAGGGATTTATAAAGTCTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
36338709 AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
131 AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
36338740 AGG
1 AGG
36338743 ATTGCGTTTT
Statistics
Matches: 324, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 324 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (161 bp):
AGGTTATTGTTTTGTAGAAAGGATAGAAAATGAGAAGAGTGAAAATGATAGAGGTGTTTTGTTTC
TTCACTTTTGGAGGGATTTATAAAGTCTAATGGTGGGAAATCTTTCATTGTGCTTATTCACGGTA
AAAGTCTCATGGAGGCCCTTTTACGAAGAGC
Found at i:36345525 original size:9 final size:9
Alignment explanation
Indices: 36345507--36345541 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
36345497 TTTTTTTTTA
*
36345507 TTTAATTTC
1 TTTAAATTC
36345516 TTTAAATTC
1 TTTAAATTC
*
36345525 TTTAAAATC
1 TTTAAATTC
36345534 TTTAAATT
1 TTTAAATT
36345542 AATAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAAATTC
Found at i:36345613 original size:29 final size:32
Alignment explanation
Indices: 36345542--36345614 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 32
36345532 TCTTTAAATT
*
36345542 AATAAAAATAAAATTATACTTTAATCTTCTTAA
1 AATAATAA-AAAATTATACTTTAATCTTCTTAA
*
36345575 AATAATAAAAAATTA-A-TTTAAT-TTTTTAA
1 AATAATAAAAAATTATACTTTAATCTTCTTAA
*
36345604 AATTATAAAAA
1 AATAATAAAAA
36345615 TATAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 16 0.43
30 6 0.16
31 1 0.03
32 7 0.19
33 7 0.19
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAATAAAAAATTATACTTTAATCTTCTTAA
Found at i:36349937 original size:29 final size:31
Alignment explanation
Indices: 36349856--36349938 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 31
36349846 GCTAACAATT
36349856 GGACTTAAATT-TGAAATTTG-AAAAGTATAG
1 GGAC-TAAATTCTGAAATTTGTAAAAGTATAG
* *
36349886 AGACTAAATTCCTGAAA-AT-TAAAA-TATAG
1 GGACTAAATT-CTGAAATTTGTAAAAGTATAG
36349915 GGACTAAATTCT-AAATTTGTAAAA
1 GGACTAAATTCTGAAATTTGTAAAA
36349939 AATATAGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 25 0.57
30 8 0.18
31 5 0.11
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.31
Consensus pattern (31 bp):
GGACTAAATTCTGAAATTTGTAAAAGTATAG
Found at i:36350686 original size:20 final size:20
Alignment explanation
Indices: 36350661--36350702 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
36350651 TGGTCCCGGA
36350661 AAATGTTATTTTTTTTATAC
1 AAATGTTATTTTTTTTATAC
36350681 AAATGTTATTTTTTTTATAC
1 AAATGTTATTTTTTTTATAC
36350701 AA
1 AA
36350703 TATTGAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
AAATGTTATTTTTTTTATAC
Found at i:36355439 original size:14 final size:14
Alignment explanation
Indices: 36355420--36355446 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36355410 TTATTTAAAT
36355420 TTAGTATATATTTG
1 TTAGTATATATTTG
36355434 TTAGTATATATTT
1 TTAGTATATATTT
36355447 TGCCTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTAGTATATATTTG
Found at i:36359329 original size:28 final size:29
Alignment explanation
Indices: 36359278--36359348 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
36359268 GAAAAAAGCC
*
36359278 AAATTTATTACTTTTAAATAATT-AAAT-T
1 AAATTTATTA-TTTTAAAGAATTAAAATGT
* *
36359306 AAAATTTATTATTTTAGAGGATTAAAATGT
1 -AAATTTATTATTTTAAAGAATTAAAATGT
*
36359336 AATTTTATTATTT
1 AAATTTATTATTT
36359349 ATTAACTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.25
29 26 0.72
30 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (29 bp):
AAATTTATTATTTTAAAGAATTAAAATGT
Found at i:36359934 original size:17 final size:18
Alignment explanation
Indices: 36359906--36359939 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
36359896 ATTTAATTAA
36359906 ATAAATTATTAAAAAATT
1 ATAAATTATTAAAAAATT
36359924 ATAAA-TATTAAAAAAT
1 ATAAATTATTAAAAAAT
36359940 AGAAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAATTATTAAAAAATT
Found at i:36366511 original size:87 final size:87
Alignment explanation
Indices: 36366353--36366555 Score: 289
Period size: 87 Copynumber: 2.3 Consensus size: 87
36366343 ATATGATATG
* * * * * *
36366353 CAAGGGCAAGTCATACCATGTTACTTATGATCAGTTAACAAATCAGTAAATTGTCCCTATTGTGA
1 CAAGGGCAAGTCATAACATGTTACTTATGATCAGTAAACAAATCAGTAAATAGCCCCGATTGGGA
36366418 TATGAACAATCGAAACCGTATA
66 TATGAACAATCGAAACCGTATA
* *
36366440 CAAGGGCAAGTCAAAACATGTTACTTATGATCAGTAAACGAATCAGTAAATAGCCCCGATTGGGA
1 CAAGGGCAAGTCATAACATGTTACTTATGATCAGTAAACAAATCAGTAAATAGCCCCGATTGGGA
* * *
36366505 TTTGAACAATCGAATCCGTATG
66 TATGAACAATCGAAACCGTATA
* *
36366527 CAAGGGAAAGTCATATCATGTTACTTATG
1 CAAGGGCAAGTCATAACATGTTACTTATG
36366556 TATGATCTGT
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 102 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (87 bp):
CAAGGGCAAGTCATAACATGTTACTTATGATCAGTAAACAAATCAGTAAATAGCCCCGATTGGGA
TATGAACAATCGAAACCGTATA
Found at i:36367594 original size:23 final size:24
Alignment explanation
Indices: 36367562--36367616 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
36367552 TTAGTCATTC
*
36367562 TAAATA-TTAATTTTTTTC-A-AT
1 TAAATATTTAACTTTTTTCGAGAT
36367583 TAAATTATTTAACTTTTTTCGAGAT
1 TAAA-TATTTAACTTTTTTCGAGAT
36367608 TAAATATTT
1 TAAATATTT
36367617 TAATCACTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 11 0.38
24 6 0.21
25 6 0.21
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (24 bp):
TAAATATTTAACTTTTTTCGAGAT
Found at i:36371709 original size:25 final size:24
Alignment explanation
Indices: 36371681--36371734 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
36371671 AAGTACAAAC
* *
36371681 TATTAAAATAATAAATTTATATTTT
1 TATTAAAATAA-AAATATATAATTT
*
36371706 TATTATAATAAAAATATATAATTT
1 TATTAAAATAAAAATATATAATTT
*
36371730 AATTA
1 TATTA
36371735 CGGACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTAAAATAAAAATATATAATTT
Found at i:36373069 original size:19 final size:20
Alignment explanation
Indices: 36373045--36373092 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
36373035 GTTTAAAATA
*
36373045 TTAAAA-AAATTAGACTCGT
1 TTAAAATAAATAAGACTCGT
* *
36373064 TTAAAATAAGTAAGACTTGT
1 TTAAAATAAATAAGACTCGT
36373084 TTAAAATAA
1 TTAAAATAA
36373093 GTTTATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (20 bp):
TTAAAATAAATAAGACTCGT
Found at i:36373085 original size:20 final size:20
Alignment explanation
Indices: 36373056--36373094 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36373046 TAAAAAAATT
36373056 AGACTCGTTTAAAATAAGTA
1 AGACTCGTTTAAAATAAGTA
*
36373076 AGACTTGTTTAAAATAAGT
1 AGACTCGTTTAAAATAAGT
36373095 TTATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (20 bp):
AGACTCGTTTAAAATAAGTA
Found at i:36375698 original size:14 final size:14
Alignment explanation
Indices: 36375645--36375698 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
36375635 ATACACAAAT
*
36375645 ATATTAAAATCTATAA
1 ATATAAAAAT-TA-AA
*
36375661 ATATAAAATATTAAG
1 ATATAAAA-ATTAAA
*
36375676 ATATTAAAATTAAA
1 ATATAAAAATTAAA
36375690 ATATAAAAA
1 ATATAAAAA
36375699 GAGAAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 13 0.41
15 8 0.25
16 9 0.28
17 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATAAAAATTAAA
Found at i:36376398 original size:73 final size:73
Alignment explanation
Indices: 36376279--36376837 Score: 838
Period size: 73 Copynumber: 7.7 Consensus size: 73
36376269 TCCTAACCCC
* * * *
36376279 AGCTC-AAGTTGGGGTTGGTTAAGCAACATCAGCAGCAATGGACAATGGTGCAGGAAAGCTTGTT
1 AGCTCGAA-TTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTT
36376343 CTTTTTACA
65 CTTTTTACA
* *
36376352 AGCTCGAATTGGGGCTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
1 AGCTCGAATTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
36376417 TTTTTACA
66 TTTTTACA
* * * *
36376425 AGCTC-AAGTTGGGGTTGGCTGGGCAGCACCAGCAGAAATGGACAATGGTGCAGGAAAGCTTGTT
1 AGCTCGAA-TTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTT
36376489 CTTTTTACA
65 CTTTTTACA
* *
36376498 AGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
1 AGCTCGAATTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
36376563 TTTTTACA
66 TTTTTACA
* * *
36376571 AGCTC-AAGTTGGGGTTGGCTGGGCAGCACCCGCAGCAATGGACAATGGTGCAGAAAAGCTTGTT
1 AGCTCGAA-TTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTT
36376635 CTTTTTACA
65 CTTTTTACA
* * *
36376644 AGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTT
1 AGCTCGAATTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
36376709 TTTTTACA
66 TTTTTACA
* * *
36376717 AGCTC-AAGTTGGGGTTGGCTGAGAAACACCCGCAGCAATGGACAATGATGCAGAAAAGCTTGTT
1 AGCTCGAA-TTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTT
36376781 CTTTTTACA
65 CTTTTTACA
* * *
36376790 AGCTCGAGTTGGGGTTGGCTGAGCAACACCGGCAGCAATGGGCAATGG
1 AGCTCGAATTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGG
36376838 GCAATGGGCA
Statistics
Matches: 441, Mismatches: 38, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
72 4 0.01
73 432 0.98
74 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (73 bp):
AGCTCGAATTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
TTTTTACA
Found at i:36376465 original size:146 final size:146
Alignment explanation
Indices: 36376279--36376837 Score: 938
Period size: 146 Copynumber: 3.8 Consensus size: 146
36376269 TCCTAACCCC
* * * *
36376279 AGCTCAAGTTGGGGTTGGTTAAGCAACATCAGCAGCAATGGACAATGGTGCAGGAAAGCTTGTTC
1 AGCTCAAGTTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
* *
36376344 TTTTTACAAGCTCGAATTGGGGCTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
66 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
36376409 GCTTGTTCTTTTTACA
131 GCTTGTTCTTTTTACA
* * * *
36376425 AGCTCAAGTTGGGGTTGGCTGGGCAGCACCAGCAGAAATGGACAATGGTGCAGGAAAGCTTGTTC
1 AGCTCAAGTTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
36376490 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
66 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
36376555 GCTTGTTCTTTTTACA
131 GCTTGTTCTTTTTACA
* * *
36376571 AGCTCAAGTTGGGGTTGGCTGGGCAGCACCCGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
1 AGCTCAAGTTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
36376636 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
66 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
*
36376701 GCTTGTTTTTTTTACA
131 GCTTGTTCTTTTTACA
* * *
36376717 AGCTCAAGTTGGGGTTGGCTGAGAAACACCCGCAGCAATGGACAATGATGCAGAAAAGCTTGTTC
1 AGCTCAAGTTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
* * *
36376782 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACACCGGCAGCAATGGGCAATGG
66 TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGG
36376838 GCAATGGGCA
Statistics
Matches: 394, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
146 394 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (146 bp):
AGCTCAAGTTGGGGTTGGCTGAGCAACACCAGCAGCAATGGACAATGGTGCAGAAAAGCTTGTTC
TTTTTACAAGCTCGAGTTGGGGTTGGCTGAGCAACATCAGCAGCAATGGACAATGGTGCAGAAAA
GCTTGTTCTTTTTACA
Found at i:36376836 original size:7 final size:7
Alignment explanation
Indices: 36376824--36376879 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
36376814 AACACCGGCA
36376824 GCAATGG
1 GCAATGG
36376831 GCAATGG
1 GCAATGG
36376838 GCAATGG
1 GCAATGG
36376845 GCAATGG
1 GCAATGG
36376852 GCAATGG
1 GCAATGG
36376859 GCAATGG
1 GCAATGG
36376866 GCAATGG
1 GCAATGG
36376873 GCAATGG
1 GCAATGG
36376880 TACAAATGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (7 bp):
GCAATGG
Found at i:36378636 original size:36 final size:36
Alignment explanation
Indices: 36378588--36378658 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
36378578 TGCCCCACTA
* *
36378588 AATTCATTCTCTCTATATTAATTCTCAACAAATATG
1 AATTCATGCTCTCTACATTAATTCTCAACAAATATG
* *
36378624 AATTCATGCTCTCTACATTATTTCTCAATAAATAT
1 AATTCATGCTCTCTACATTAATTCTCAACAAATAT
36378659 TGCATTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (36 bp):
AATTCATGCTCTCTACATTAATTCTCAACAAATATG
Found at i:36396991 original size:51 final size:51
Alignment explanation
Indices: 36396936--36397039 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
36396926 TTTTCTCTTT
** * * * *
36396936 TCTTTTCCGGTAACTATTAACTCACTTATCATATGTTATCTTCTAAACACG
1 TCTTTTCCAATAACTACTAACTCACTTATAATATATTATATTCTAAACACG
* * * *
36396987 TCTTTTTCAATGATTACTAACTCACTTATAATGTATTATATTCTAAACACG
1 TCTTTTCCAATAACTACTAACTCACTTATAATATATTATATTCTAAACACG
36397038 TC
1 TC
36397040 GACATTTCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (51 bp):
TCTTTTCCAATAACTACTAACTCACTTATAATATATTATATTCTAAACACG
Found at i:36405540 original size:25 final size:25
Alignment explanation
Indices: 36405510--36405564 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
36405500 ATGATAGCAA
* *
36405510 AACAGTGAG-AAGACAACAAGAAAAT
1 AACAGTAAGAAAG-CAACAAAAAAAT
36405535 AACAGTAAGAAAGCAACAAAAAAAT
1 AACAGTAAGAAAGCAACAAAAAAAT
36405560 AACAG
1 AACAG
36405565 ACTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.64, C:0.13, G:0.16, T:0.07
Consensus pattern (25 bp):
AACAGTAAGAAAGCAACAAAAAAAT
Found at i:36408243 original size:18 final size:18
Alignment explanation
Indices: 36408220--36408256 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36408210 ACGATTCATA
36408220 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
36408238 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
36408256 T
1 T
36408257 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:36408587 original size:17 final size:18
Alignment explanation
Indices: 36408553--36408588 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36408543 TGAATTTCTA
36408553 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
36408571 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
36408588 T
1 T
36408589 AACTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:36417710 original size:31 final size:32
Alignment explanation
Indices: 36417671--36417746 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
36417661 AGTTTTGGAT
* *
36417671 CAAAATTAAAATTTTAA-AATTAAAAAG-ATA
1 CAAAATTAAAAATTGAACAATTAAAAAGTATA
*
36417701 CAAATATTAAAAATTGAACAATTCAAAAGTATA
1 CAAA-ATTAAAAATTGAACAATTAAAAAGTATA
36417734 -AAAATTAAAAATT
1 CAAAATTAAAAATT
36417747 ATTACATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 4 0.10
31 21 0.52
32 12 0.30
33 3 0.08
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (32 bp):
CAAAATTAAAAATTGAACAATTAAAAAGTATA
Found at i:36417744 original size:7 final size:7
Alignment explanation
Indices: 36417672--36417747 Score: 53
Period size: 7 Copynumber: 10.0 Consensus size: 7
36417662 GTTTTGGATC
36417672 AAAATTA
1 AAAATTA
* *
36417679 AAATTTT
1 AAAATTA
36417686 AAAATTA
1 AAAATTA
*
36417693 AAAAGATA
1 AAAA-TTA
36417701 CAAATATTA
1 -AAA-ATTA
36417710 AAAATTGA
1 AAAATT-A
*
36417718 ACAATTCA
1 AAAATT-A
*
36417726 AAAGTATA
1 AAAAT-TA
36417734 AAAATTA
1 AAAATTA
36417741 AAAATTA
1 AAAATTA
36417748 TTACATTAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
7 26 0.49
8 20 0.38
9 6 0.11
10 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (7 bp):
AAAATTA
Found at i:36420297 original size:5 final size:6
Alignment explanation
Indices: 36420267--36420305 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
36420257 AATAAAAAAA
**
36420267 GAGGGG AGAGGGG CTGGGG GAGGGG GAGGGG GAGGGG GA
1 GAGGGG -GAGGGG GAGGGG GAGGGG GAGGGG GAGGGG GA
36420306 ACGCACTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.03, G:0.77, T:0.03
Consensus pattern (6 bp):
GAGGGG
Found at i:36427955 original size:17 final size:17
Alignment explanation
Indices: 36427935--36427993 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
36427925 TCTGCATGAT
*
36427935 TAAACAATTCAATAATA
1 TAAATAATTCAATAATA
* *
36427952 TAAATAGTACAA-AATA
1 TAAATAATTCAATAATA
36427968 TGAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
36427988 TAAATA
1 TAAATA
36427994 GTATATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
17 14 0.42
19 9 0.27
20 5 0.15
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:36431694 original size:57 final size:58
Alignment explanation
Indices: 36431604--36431722 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 58
36431594 AAAAGGAGTT
* **
36431604 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTGAATTTA
*
36431662 GTTTATGAGT-TT-TTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGAATTTA
1 GTTTATGAGTGTTATTT-AAGAATAAAATTATATTTGGGTTTAAAAATATTTGAATTTA
36431719 GTTT
1 GTTT
36431723 GTTGATGAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
56 3 0.05
57 43 0.77
58 10 0.18
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTGAATTTA
Found at i:36431967 original size:23 final size:23
Alignment explanation
Indices: 36431924--36431968 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
36431914 AAAAAAATTC
**
36431924 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
36431947 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
36431969 ATTCAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:36447078 original size:36 final size:36
Alignment explanation
Indices: 36447033--36447101 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
36447023 TCAAAGTATA
36447033 ATGTCGAATAAAAAGGGTAATCTTTGAATTTCGTGT
1 ATGTCGAATAAAAAGGGTAATCTTTGAATTTCGTGT
* *
36447069 ATGTTGAATAAAAGGGGTAATCTTTGAATTTCG
1 ATGTCGAATAAAAAGGGTAATCTTTGAATTTCG
36447102 AGCGTTGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (36 bp):
ATGTCGAATAAAAAGGGTAATCTTTGAATTTCGTGT
Found at i:36456456 original size:2 final size:2
Alignment explanation
Indices: 36456449--36456500 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
36456439 TCAGGGCATA
* *
36456449 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AC 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
36456491 AT AT AT AT AT
1 AT AT AT AT AT
36456501 TAAATTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:36457339 original size:15 final size:16
Alignment explanation
Indices: 36457304--36457345 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
36457294 TTTTTTAAAT
36457304 ATATT-TTATATTAAG
1 ATATTATTATATTAAG
36457319 AT-TTATTAT-TTAAG
1 ATATTATTATATTAAG
36457333 ATATTATT-TATTA
1 ATATTATTATATTA
36457346 TTTAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
ATATTATTATATTAAG
Found at i:36459532 original size:162 final size:162
Alignment explanation
Indices: 36459342--36459801 Score: 785
Period size: 162 Copynumber: 2.8 Consensus size: 162
36459332 AGTTTTCAAG
*
36459342 TTAGTCCTTTGGCTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
* *
36459407 TCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAAATACAA
66 TCTAGTCCCTGCCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTACAA
*
36459472 AATTGACCCTGGAATCTTTTGAGATTTTTAAA
131 AATTGACCCTGAAATCTTTTGAGATTTTTAAA
* * * *
36459504 TTAGTCCTTAGACTGTTTGATTGCACCAGAGGCTGCCATGTGTCACTTTTTGGCTTATTTATGTG
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
36459569 TCTAGTCCCTGCCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTACAA
66 TCTAGTCCCTGCCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTACAA
*
36459634 AATTGACCCTGAAATTTTTTGAGATTTTTAAA
131 AATTGACCCTGAAATCTTTTGAGATTTTTAAA
*
36459666 TTAGTCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
* * **
36459731 TCTAGTCCCTACCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACA
66 TCTAGTCCCTGCCA-TTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTACA
36459796 AAATTG
130 AAATTG
36459802 GCTCAAGAAT
Statistics
Matches: 279, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
162 226 0.81
163 53 0.19
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
TCTAGTCCCTGCCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTACAA
AATTGACCCTGAAATCTTTTGAGATTTTTAAA
Found at i:36459955 original size:28 final size:27
Alignment explanation
Indices: 36459923--36460016 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
36459913 CCGAAATTTA
36459923 CCATTTTACCCTTAAACTTCCCAAAATT
1 CCATTTTACCC-TAAACTTCCCAAAATT
* * * *
36459951 CCATTTTTAACCTCAATTTCACCAAAAAATA
1 CCA-TTTTACCCTAAACTTC-CC--AAAATT
* *
36459982 CCATTTTACCCCCAAACTTTCCAAAATT
1 CCATTTTA-CCCTAAACTTCCCAAAATT
36460010 CCATTTT
1 CCATTTT
36460017 TAACCTCGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 21 0.41
29 9 0.18
30 7 0.14
31 14 0.27
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (27 bp):
CCATTTTACCCTAAACTTCCCAAAATT
Found at i:36459958 original size:29 final size:28
Alignment explanation
Indices: 36459926--36460077 Score: 81
Period size: 29 Copynumber: 5.1 Consensus size: 28
36459916 AAATTTACCA
36459926 TTTTACCCTTAAACTTCCCAAAATTCCAT
1 TTTTACCC-TAAACTTCCCAAAATTCCAT
* * * *
36459955 TTTTAACCTCAATTTCACCAAAAAATACCA-
1 TTTTACCCTAAACTTC-CC--AAAATTCCAT
* *
36459985 TTTTACCCCCAAACTTTCCAAAATTCCAT
1 TTTTA-CCCTAAACTTCCCAAAATTCCAT
* ** * *
36460014 TTTTAACCTCGATTTCACCAAAAATTACCCT
1 TTTTACCCTAAACTTC-CC-AAAATT-CCAT
* ** *
36460045 TTTATCCCCCGAACTTTCCAAAATTCCAT
1 TTT-TACCCTAAACTTCCCAAAATTCCAT
36460074 TTTT
1 TTTT
36460078 GACCTCGATT
Statistics
Matches: 89, Mismatches: 25, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
28 20 0.22
29 22 0.25
30 19 0.21
31 22 0.25
32 6 0.07
ACGTcount: A:0.32, C:0.30, G:0.01, T:0.36
Consensus pattern (28 bp):
TTTTACCCTAAACTTCCCAAAATTCCAT
Found at i:36460048 original size:30 final size:30
Alignment explanation
Indices: 36459945--36460107 Score: 110
Period size: 30 Copynumber: 5.5 Consensus size: 30
36459935 TAAACTTCCC
*
36459945 AAAATT-CCATTTTTAACCTCAATTTCACCA
1 AAAATTACCA-TTTTAACCTCGATTTCACCA
* * * *
36459975 AAAAATACCATTTTACCCCCAAACTTT--CC-
1 AAAATTACCATTTTAACCTC-GA-TTTCACCA
36460004 AAAATT-CCATTTTTAACCTCGATTTCACCA
1 AAAATTACCA-TTTTAACCTCGATTTCACCA
* * *
36460034 AAAATTACCCTTTTATCCCCCGAACTTT--CC-
1 AAAATTACCATTTTA-ACCTCG-A-TTTCACCA
*
36460064 AAAATT-CCATTTTTGACCTCGATTTCACCA
1 AAAATTACCA-TTTTAACCTCGATTTCACCA
36460094 AAAATTACCATTTT
1 AAAATTACCATTTT
36460108 GCCCTCGGGT
Statistics
Matches: 103, Mismatches: 14, Indels: 32
0.69 0.09 0.21
Matches are distributed among these distances:
27 6 0.06
28 5 0.05
29 23 0.22
30 46 0.45
31 16 0.16
32 4 0.04
33 3 0.03
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTAACCTCGATTTCACCA
Found at i:36460083 original size:60 final size:59
Alignment explanation
Indices: 36459920--36460107 Score: 295
Period size: 59 Copynumber: 3.2 Consensus size: 59
36459910 TATCCGAAAT
** * *
36459920 TTACCATTTTACCCTTAAACTTCCCAAAATTCCATTTTTAACCTCAATTTCACCAAAAA
1 TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
*
36459979 ATACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
1 TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
* * *
36460038 TTACCCTTTTATCCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAAA
1 TTACCATTTTA-CCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
36460098 TTACCATTTT
1 TTACCATTTT
36460108 GCCCTCGGGT
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 63 0.53
60 55 0.47
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.36
Consensus pattern (59 bp):
TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
Found at i:36460108 original size:30 final size:29
Alignment explanation
Indices: 36459945--36460107 Score: 106
Period size: 31 Copynumber: 5.4 Consensus size: 29
36459935 TAAACTTCCC
*
36459945 AAAATTCCATTTTTAACCTCAATTTCACCAA
1 AAAATTCCATTTTT-ACCTCGATTTCACC-A
* * *
36459976 AAAATACCA-TTTTACCCCCAAACTTT--CC-
1 AAAATTCCATTTTTA-CCTC-GA-TTTCACCA
36460004 AAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTT-ACCTCGATTTCACCA
* * *
36460034 AAAATTACCCTTTTATCCCCCGAACTTT--CC-
1 AAAATT-CCATTTT-TACCTCG-A-TTTCACCA
36460064 AAAATTCCATTTTTGACCTCGATTTCACCA
1 AAAATTCCATTTTT-ACCTCGATTTCACCA
36460094 AAAATTACCATTTT
1 AAAATT-CCATTTT
36460108 GCCCTCGGGT
Statistics
Matches: 104, Mismatches: 11, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
27 6 0.06
28 11 0.11
29 22 0.21
30 28 0.27
31 29 0.28
32 5 0.05
33 3 0.03
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCTCGATTTCACCA
Found at i:36460114 original size:30 final size:30
Alignment explanation
Indices: 36459920--36460114 Score: 108
Period size: 30 Copynumber: 6.6 Consensus size: 30
36459910 TATCCGAAAT
** *
36459920 TTACCATTTTACCCTTAAACTTC-CC-AAAA
1 TTACCATTTTACCC-TCGATTTCACCAAAAA
* *
36459949 TT-CCATTTTTAACCTCAATTTCACCAAAAA
1 TTACCA-TTTTACCCTCGATTTCACCAAAAA
* * *
36459979 ATACCATTTTACCCCCAAACTTT--CC-AAAA
1 TTACCATTTTACCCTC-GA-TTTCACCAAAAA
*
36460008 TT-CCATTTTTAACCTCGATTTCACCAAAAA
1 TTACCA-TTTTACCCTCGATTTCACCAAAAA
* *
36460038 TTACCCTTTTATCCCCCGAACTTT--CC-AAAA
1 TTACCATTTTA-CCCTCG-A-TTTCACCAAAAA
36460068 TT-CCATTTTTGA-CCTCGATTTCACCAAAAA
1 TTACCA-TTTT-ACCCTCGATTTCACCAAAAA
*
36460098 TTACCATTTTGCCCTCG
1 TTACCATTTTACCCTCG
36460115 GGTACCCAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
27 6 0.05
28 14 0.11
29 34 0.26
30 51 0.40
31 17 0.13
32 4 0.03
33 3 0.02
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (30 bp):
TTACCATTTTACCCTCGATTTCACCAAAAA
Found at i:36461939 original size:15 final size:16
Alignment explanation
Indices: 36461921--36461950 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36461911 CTTCCCTATT
36461921 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
36461936 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
36461951 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:36461955 original size:22 final size:22
Alignment explanation
Indices: 36461916--36461976 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
36461906 TTCGACTTCC
* *
36461916 CTATTTTCTATTT-CTTTTAGTT
1 CTATTTTCT-TTTATTTTTAATT
36461938 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
36461960 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
36461977 CCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:36464035 original size:18 final size:19
Alignment explanation
Indices: 36463997--36464034 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
36463987 TATCTATTAA
*
36463997 TTAATTTTAATAAATACTT
1 TTAATTTTAAAAAATACTT
36464016 TTAA-TTTAAAAAATA-TT
1 TTAATTTTAAAAAATACTT
36464033 TT
1 TT
36464035 TTGGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATTTTAAAAAATACTT
Found at i:36476319 original size:19 final size:19
Alignment explanation
Indices: 36476281--36476321 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
36476271 TTTAGCAATG
* *
36476281 TTTTTATTTCAAAAATATT
1 TTTTTATTCCAAAAACATT
*
36476300 TTTTTATTCCAAAAGCATT
1 TTTTTATTCCAAAAACATT
36476319 TTT
1 TTT
36476322 GAAAAGCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTTATTCCAAAAACATT
Found at i:36477351 original size:15 final size:16
Alignment explanation
Indices: 36477326--36477359 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
36477316 AAATTACAAT
36477326 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
36477342 TTTA-TATTTTCATAA
1 TTTATTATTTTAATAA
36477357 TTT
1 TTT
36477360 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:36480656 original size:16 final size:16
Alignment explanation
Indices: 36480637--36480704 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
36480627 AAAATTCAAT
36480637 AAATTA-AAAATATATA
1 AAATTATAAAATAT-TA
*
36480653 AAATTATTAAATATTA
1 AAATTATAAAATATTA
* *
36480669 AAATAATATAATA-TA
1 AAATTATAAAATATTA
* *
36480684 AATATTTTTAAAAAATTA
1 AA-A-TTATAAAATATTA
36480702 AAA
1 AAA
36480705 AAAATATAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
15 4 0.10
16 19 0.47
17 13 0.32
18 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTATAAAATATTA
Found at i:36480671 original size:25 final size:25
Alignment explanation
Indices: 36480621--36480679 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
36480611 TAAGATGATT
*
36480621 ATATAAAAAATTCAATAAATTAAAA
1 ATATATAAAATTCAATAAATTAAAA
* *
36480646 ATATATAAAATT-ATTAAATATTAAA
1 ATATATAAAATTCAATAAAT-TAAAA
36480671 ATAATATAA
1 AT-ATATAA
36480680 TATAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 17 0.59
26 6 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATATAAAATTCAATAAATTAAAA
Found at i:36485885 original size:3 final size:3
Alignment explanation
Indices: 36485877--36485905 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
36485867 GTTAATTTGT
36485877 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36485906 TAAGATCCAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36490055 original size:20 final size:20
Alignment explanation
Indices: 36490030--36490068 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36490020 AAGGATTAGG
36490030 GTTTAAGATTTAAGGTTCGA
1 GTTTAAGATTTAAGGTTCGA
* *
36490050 GTTTAAGTTTTAGGGTTCG
1 GTTTAAGATTTAAGGTTCG
36490069 GGATTTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (20 bp):
GTTTAAGATTTAAGGTTCGA
Found at i:36491008 original size:2 final size:2
Alignment explanation
Indices: 36491003--36491027 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36490993 CAAAAAACTA
36491003 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
36491028 CAAATAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36496649 original size:9 final size:9
Alignment explanation
Indices: 36496637--36496661 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
36496627 TTTCTCTTGT
36496637 CTCTCCCAA
1 CTCTCCCAA
36496646 CTCTCCCAA
1 CTCTCCCAA
36496655 CTCTCCC
1 CTCTCCC
36496662 TCTCTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.60, G:0.00, T:0.24
Consensus pattern (9 bp):
CTCTCCCAA
Found at i:36500574 original size:19 final size:19
Alignment explanation
Indices: 36500550--36500590 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
36500540 CCTAAAAATT
*
36500550 TAAAAATATATATC-AAAAA
1 TAAAAAAATA-ATCTAAAAA
36500569 TAAAAAAATAATCTAAAAA
1 TAAAAAAATAATCTAAAAA
36500588 TAA
1 TAA
36500591 TGTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAAATAATCTAAAAA
Found at i:36501324 original size:57 final size:57
Alignment explanation
Indices: 36501257--36501371 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
36501247 GTAGTTAAGG
36501257 GGGGTTTGCAGGGACTTCGACCCCCTAAAATGAAAAATTATCCATTTAGGCCATTTA
1 GGGGTTTGCAGGGACTTCGACCCCCTAAAATGAAAAATTATCCATTTAGGCCATTTA
*
36501314 GGGGTTTGCAGGGACTTCGACCTCCTAAAATGAAAAATTATCCATTTAGGCCATTTA
1 GGGGTTTGCAGGGACTTCGACCCCCTAAAATGAAAAATTATCCATTTAGGCCATTTA
36501371 G
1 G
36501372 AAATTTTAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (57 bp):
GGGGTTTGCAGGGACTTCGACCCCCTAAAATGAAAAATTATCCATTTAGGCCATTTA
Found at i:36504470 original size:163 final size:163
Alignment explanation
Indices: 36504195--36504520 Score: 625
Period size: 163 Copynumber: 2.0 Consensus size: 163
36504185 GAAAGGTGAA
*
36504195 TTTTGCTACGAGTTTCGTGGTAACCAATCTCTGTTATTGATTTGAGTGGACCTTAAGAACAACTG
1 TTTTCCTACGAGTTTCGTGGTAACCAATCTCTGTTATTGATTTGAGTGGACCTTAAGAACAACTG
36504260 CAAAACAACTTAAACAACAACCATCGGCATTAAGGTAATGAGAAAGGATTGTATGAAATAGTTAC
66 CAAAACAACTTAAACAACAACCATCGGCATTAAGGTAATGAGAAAGGATTGTATGAAATAGTTAC
36504325 TTTTTTTCATTTGTTTAATGCCACATCAGCATG
131 TTTTTTTCATTTGTTTAATGCCACATCAGCATG
36504358 TTTTCCTACGAGTTTCGTGGTAACCAATCTCTGTTATTGATTTGAGTGGACCTTAAGAACAACTG
1 TTTTCCTACGAGTTTCGTGGTAACCAATCTCTGTTATTGATTTGAGTGGACCTTAAGAACAACTG
*
36504423 CAAAACAACTTAAACAACAACCATCGGCATTAAGGTAATGGGAAAGGATTGTATGAAATAGTTAC
66 CAAAACAACTTAAACAACAACCATCGGCATTAAGGTAATGAGAAAGGATTGTATGAAATAGTTAC
*
36504488 TTTTTTTCATTTGTTTAATGCCATATCAGCATG
131 TTTTTTTCATTTGTTTAATGCCACATCAGCATG
36504521 CTGATGTGGC
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 160 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (163 bp):
TTTTCCTACGAGTTTCGTGGTAACCAATCTCTGTTATTGATTTGAGTGGACCTTAAGAACAACTG
CAAAACAACTTAAACAACAACCATCGGCATTAAGGTAATGAGAAAGGATTGTATGAAATAGTTAC
TTTTTTTCATTTGTTTAATGCCACATCAGCATG
Found at i:36505287 original size:39 final size:39
Alignment explanation
Indices: 36505233--36505311 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
36505223 TTATATGAGG
36505233 TTTGTCAAGGTAAGGGTTGCCAAATCTATTGAAAACCGT
1 TTTGTCAAGGTAAGGGTTGCCAAATCTATTGAAAACCGT
*
36505272 TTTGTCAAGGTAAGGGTTGCCAAATCTATTGAAAATCGT
1 TTTGTCAAGGTAAGGGTTGCCAAATCTATTGAAAACCGT
36505311 T
1 T
36505312 CTCAGAGGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (39 bp):
TTTGTCAAGGTAAGGGTTGCCAAATCTATTGAAAACCGT
Found at i:36522606 original size:22 final size:23
Alignment explanation
Indices: 36522576--36522619 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
36522566 ACGGTTTTTT
**
36522576 TTTTCAAAAATTTTATATTATTC
1 TTTTCAAAAAAGTTATATTATTC
36522599 TTTT-AAAAAAGTTATATTATT
1 TTTTCAAAAAAGTTATATTATT
36522620 GTGGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTCAAAAAAGTTATATTATTC
Found at i:36525326 original size:16 final size:16
Alignment explanation
Indices: 36525301--36525335 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
36525291 TGACTCCTTA
*
36525301 AAAATAATAAAAATTT
1 AAAATAATAAAAATAT
*
36525317 AAAATTATAAAAATAT
1 AAAATAATAAAAATAT
36525333 AAA
1 AAA
36525336 CTATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATAAAAATAT
Found at i:36526932 original size:54 final size:53
Alignment explanation
Indices: 36526874--36527006 Score: 128
Period size: 53 Copynumber: 2.5 Consensus size: 53
36526864 AATCCGGTAC
* *
36526874 TTGAATTTGATAATTATTTTTATATTATAATTT-AAATTTTTTTTAAGTTGGAT-T
1 TTGAATTTGATAATTATTTTTATATTAGAATTTGAAA--TTTTTTAAGTT-AATCT
* * * *
36526928 TTGAA-TTCAGTTATTATTTTTATATTGGAGTTTGAAATTTTTTAAGTTAATCT
1 TTGAATTTGA-TAATTATTTTTATATTAGAATTTGAAATTTTTTAAGTTAATCT
* * *
36526981 TTGATTTTGACAATTACTTTTATATT
1 TTGAATTTGATAATTATTTTTATATT
36527007 GAGGTTTAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
52 2 0.03
53 32 0.50
54 27 0.42
55 3 0.05
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (53 bp):
TTGAATTTGATAATTATTTTTATATTAGAATTTGAAATTTTTTAAGTTAATCT
Found at i:36527583 original size:15 final size:16
Alignment explanation
Indices: 36527556--36527608 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 16
36527546 TTTATATAAA
*
36527556 AATAAATTTAAAATAT
1 AATAAATTTAAAATAC
36527572 AATAAA-TTAAAATAC
1 AATAAATTTAAAATAC
36527587 AATACAAATATTAAAATA-
1 AAT--AAAT-TTAAAATAC
36527605 AATA
1 AATA
36527609 TTTTCCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 11 0.34
16 7 0.22
17 3 0.09
18 3 0.09
19 8 0.25
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATTTAAAATAC
Found at i:36528824 original size:7 final size:7
Alignment explanation
Indices: 36528812--36528863 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
36528802 AAAACAAGTT
*
36528812 TGGGAAG
1 TGGGAAA
*
36528819 TGGGAAG
1 TGGGAAA
*
36528826 TGGGAAG
1 TGGGAAA
36528833 TGGGAAA
1 TGGGAAA
36528840 TGGGAAA
1 TGGGAAA
36528847 TGGGAAA
1 TGGGAAA
36528854 TGGGAAA
1 TGGGAAA
36528861 TGG
1 TGG
36528864 ATTGAGGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (7 bp):
TGGGAAA
Found at i:36531634 original size:24 final size:24
Alignment explanation
Indices: 36531589--36531634 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
36531579 CAATATAAGT
* * **
36531589 TTTAGTCCCTGAATTTGGCAACAC
1 TTTAGTACCTGAACTTAACAACAC
36531613 TTTAGTACCTGAACTTAACAAC
1 TTTAGTACCTGAACTTAACAAC
36531635 TGGGTCCGTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (24 bp):
TTTAGTACCTGAACTTAACAACAC
Found at i:36534402 original size:51 final size:51
Alignment explanation
Indices: 36534341--36534453 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
36534331 ATTGGTATAA
* * * **
36534341 TAATAAATTTAACC-CTCAAAATTTATACATTTTGTCAGTTTGGTCTTGATT
1 TAATAAATTTAACCAAT-AAAATTTACACATTTTGTCAATTTAATCTTGATT
* * *
36534392 TAATAAATTTAGCCAATAATATTTACATATTTTGTCAATTTAATCTTGATT
1 TAATAAATTTAACCAATAAAATTTACACATTTTGTCAATTTAATCTTGATT
*
36534443 TAACAAATTTA
1 TAATAAATTTA
36534454 TCTCGCAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 51 0.98
52 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (51 bp):
TAATAAATTTAACCAATAAAATTTACACATTTTGTCAATTTAATCTTGATT
Found at i:36539208 original size:29 final size:30
Alignment explanation
Indices: 36539169--36539228 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
36539159 TTTATTTTTT
* *
36539169 AAAATTAAATTT-ATTTTCAACCTTTAAAA
1 AAAATAAAATTTAATTATCAACCTTTAAAA
*
36539198 AAAATAAAATTTAATTATCAACTTTTAAAA
1 AAAATAAAATTTAATTATCAACCTTTAAAA
36539228 A
1 A
36539229 GAATCGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAATAAAATTTAATTATCAACCTTTAAAA
Found at i:36548176 original size:90 final size:90
Alignment explanation
Indices: 36548030--36548200 Score: 202
Period size: 90 Copynumber: 1.9 Consensus size: 90
36548020 ATGAACTTTC
* * * * * **
36548030 TTTTTATCCAAGTTTGTCCTTAAACTTGATAGTTGTTCCCATATTGGAGGTTTGAACTACGA-AA
1 TTTTTATCCAAGTTAGTCCCTAAACTAGATAATTGTTCCCATACTGGAGGCCTGAACT-CGATAA
* *
36548094 TTGTTCCCACATTGGGGCTTAAACTT
65 ATGTTCCCACACTGGGGCTTAAACTT
* * *
36548120 TTTTTGTCCAAGTTAGTCCCTAAACTAGGTAATTGCTTCCCATACTGG-GGCCTGAACTTGATAA
1 TTTTTATCCAAGTTAGTCCCTAAACTAGATAATTG-TTCCCATACTGGAGGCCTGAACTCGATAA
36548184 ATGTTCCCACACTGGGG
65 ATGTTCCCACACTGGGG
36548201 ACTGAACTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 2 0.03
90 54 0.81
91 11 0.16
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (90 bp):
TTTTTATCCAAGTTAGTCCCTAAACTAGATAATTGTTCCCATACTGGAGGCCTGAACTCGATAAA
TGTTCCCACACTGGGGCTTAAACTT
Found at i:36550831 original size:83 final size:80
Alignment explanation
Indices: 36550607--36550914 Score: 336
Period size: 81 Copynumber: 3.8 Consensus size: 80
36550597 AAAAAAATTT
*
36550607 AATCAAGACCAAAAGGTTAAACTTTTCATACAAACCCCACAATTTCCCT-ATCAATTCAAATAAT
1 AATCAAGACCAAAAGGTTAAACTTTTCATACAAA-CCCACAATTTCCCTCA-CAATCCAAATAA-
* *
36550671 AAACCAAAACTTGGTCTT
63 AAATCAAAACTTGGTCTC
* * * ** *
36550689 AATTAAGACCAAAAGGTTAAACATTTCATACAAACCCCCAATTTCCCAAACAATTCAAATAACAA
1 AATCAAGACCAAAAGGTTAAACTTTTCATACAAACCCACAATTTCCCTCACAATCCAAATAA-AA
*
36550754 ATCAGAACTTGGTCTC
65 ATCAAAACTTGGTCTC
* * *
36550770 AATCAAGGCCAAAAGGTTTAAACTTTTTCATACAAACCCTCAATTTCCTTCACAATCCAAATAAA
1 AATCAAGACCAAAAGG-TTAAAC-TTTTCATACAAACCCACAATTTCCCTCACAATCCAAATAAA
* *
36550835 CAATCAAAATTTGGTTTC
64 -AATCAAAACTTGGTCTC
* * * * *
36550853 AATCAA-AGCC-AAAGTTTGAACTTTTAATAC-AACCCACAATTTCCTTCACGATCCAAATAAAA
1 AATCAAGA-CCAAAAGGTTAAACTTTTCATACAAACCCACAATTTCCCTCACAATCCAAATAAAA
36550915 GGTTAAACTT
Statistics
Matches: 196, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 29 0.15
80 8 0.04
81 58 0.30
82 44 0.22
83 56 0.29
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.27
Consensus pattern (80 bp):
AATCAAGACCAAAAGGTTAAACTTTTCATACAAACCCACAATTTCCCTCACAATCCAAATAAAAA
TCAAAACTTGGTCTC
Found at i:36553853 original size:35 final size:34
Alignment explanation
Indices: 36553814--36553923 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 34
36553804 CCAAACCCAT
**
36553814 TTTAAATTTATTTT-AAGATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAG-TTAAATTTAATTT-AAA
*
36553849 TTTAAATTTATTTTAAAGTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAAGTTAAATTTAATTTAAA
* * *
36553883 TTTAAATTTATTTACAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTT-TAAAGTTAAATTTAATT-TAAA
36553918 TTTAAA
1 TTTAAA
36553924 AATAAAAGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
34 18 0.28
35 44 0.68
36 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAGTTAAATTTAATTTAAA
Found at i:36553857 original size:6 final size:6
Alignment explanation
Indices: 36553846--36553892 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
36553836 ATTTGTTTTA
* * *
36553846 AAATTT AAATTT -ATTTT AAAGTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
36553892 A
1 A
36553893 TTTACAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:36553881 original size:52 final size:52
Alignment explanation
Indices: 36553815--36553923 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
36553805 CAAACCCATT
* * * *
36553815 TTAAATTTATTTTAAGATTAAATTTGTTTTA-AAATTTAAATTTATTTTAAAG
1 TTAAATTTAATTTAAGATTAAATTT-ATTTACAAATTTAAAATTATTATAAAG
* *
36553867 TTAAATTTAATTTAAGTTTAAATTTATTTACAAATTTAAAATTATTATAAAT
1 TTAAATTTAATTTAAGATTAAATTTATTTACAAATTTAAAATTATTATAAAG
36553919 TTAAA
1 TTAAA
36553924 AATAAAAGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 4 0.08
52 46 0.92
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (52 bp):
TTAAATTTAATTTAAGATTAAATTTATTTACAAATTTAAAATTATTATAAAG
Found at i:36553924 original size:17 final size:17
Alignment explanation
Indices: 36553814--36553923 Score: 98
Period size: 17 Copynumber: 6.4 Consensus size: 17
36553804 CCAAACCCAT
*
36553814 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTATAA-A
* *
36553832 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTAT-AAA
*
36553849 TTTAAATTTATTTTAAA
1 TTTAAATTTATTATAAA
* *
36553866 GTTAAATTTAATT-TAAG
1 TTTAAATTT-ATTATAAA
*
36553883 TTTAAATTTATTTACAAA
1 TTTAAATTTA-TTATAAA
*
36553901 TTTAAAATTATTATAAA
1 TTTAAATTTATTATAAA
36553918 TTTAAA
1 TTTAAA
36553924 AATAAAAGTC
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
16 1 0.01
17 49 0.63
18 28 0.36
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTATAAA
Found at i:36554614 original size:12 final size:12
Alignment explanation
Indices: 36554577--36554622 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
36554567 CATACCATTT
*
36554577 ATTATTATTATT
1 ATTATTATTATC
36554589 ATTATTATTATC
1 ATTATTATTATC
36554601 ATTATTACTT-TC
1 ATTATTA-TTATC
36554613 ATT-TTATTAT
1 ATTATTATTAT
36554623 TTTTTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 2 0.06
11 4 0.13
12 23 0.74
13 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:36554623 original size:3 final size:3
Alignment explanation
Indices: 36554575--36554607 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
36554565 CCCATACCAT
*
36554575 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36554608 CTTTCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:36555977 original size:30 final size:30
Alignment explanation
Indices: 36555848--36555991 Score: 125
Period size: 30 Copynumber: 4.8 Consensus size: 30
36555838 CAAAAATGGT
36555848 ATTTTGAA-CCCAAAACTTTCTAAAAATTAC
1 ATTTT-AACCCCAAAACTTTCTAAAAATTAC
* * * *
36555878 ATTTTAACCCTAAAA--TTCTCCAAAATCAT
1 ATTTTAACCCCAAAACTTTCT-AAAAATTAC
** * *
36555907 ATTTTAACCTTAAAACCTTT-TGAAAATTAT
1 ATTTTAACCCCAAAA-CTTTCTAAAAATTAC
36555937 ATTTTAACCCCAAAACTTTCTAAAAATTAC
1 ATTTTAACCCCAAAACTTTCTAAAAATTAC
* * **
36555967 ATTTTTACCCCCAAGTTTTCTAAAA
1 ATTTTAACCCCAAAACTTTCTAAAA
36555992 TTCCGTTTCT
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
28 4 0.04
29 26 0.28
30 60 0.65
31 1 0.01
32 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCCAAAACTTTCTAAAAATTAC
Found at i:36556294 original size:59 final size:59
Alignment explanation
Indices: 36555956--36556330 Score: 368
Period size: 59 Copynumber: 6.4 Consensus size: 59
36555946 CCAAAACTTT
* * * * * *
36555956 CTAAAAATTA-CATTTTTACCCCC-AAGTTTTCTAAAATTCCGTTTCTACCCCCGATTTCA
1 CTAAAAATTACCA-TTTTACCCCCGAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTTA
* * ** * *
36556015 C-CAAAATTACCATTTTACCCCTGAACTTTTTAAAATTCCATTTTTAATCTCGATTTTA
1 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTA
* * * * * **
36556073 CCAAAAATTACCATTTCACCCCTGAACTTTCCAAAATTTCATTTTTGACCCTAATTTTA
1 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTA
* * *
36556132 CAAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCTCGATTTTA
1 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTA
* * * **
36556190 CCAAAAATTACTATTTTACACTTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTA
1 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTA
* * * * *
36556249 CTAAAAATTACCGTTTTACCCCCGAACTTTTCAAAA-TCTCTTTTTTGA-CCCAATTTTAA
1 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-CATTTTTAACCCCGATTTT-A
*
36556308 CT-AAAATTACCATTTTCCCCCCG
1 CTAAAAATTACCATTTTACCCCCG
36556331 GGTATTCAAA
Statistics
Matches: 264, Mismatches: 46, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
58 121 0.46
59 143 0.54
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.38
Consensus pattern (59 bp):
CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTA
Found at i:36556305 original size:117 final size:115
Alignment explanation
Indices: 36555983--36556323 Score: 387
Period size: 117 Copynumber: 2.9 Consensus size: 115
36555973 ACCCCCAAGT
* * * * * * * *
36555983 TTTCTAAAATTCCGTTTCTACCCCCGATTTCACCAAAATTACCATTTTACCCCTGAACTTTTTAA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTTACAAAAATTACCATTTTACCCCCGAACTTTTCAA
* * *
36556048 AATTCCATTTTTAATCTCGATTTTACCAAAAATTACCATTTCACCCCTGAAC
66 AATT-CATTTTTAA-CCCGATTTTACCAAAAATTACCATTTTACACCTGAAC
* * ** * *
36556100 TTTCCAAAATTTCATTTTTGACCCTAATTTTACAAAAAATTACCATTTTACCCTCGAACTTTCCA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTTAC-AAAAATTACCATTTTACCCCCGAACTTTTCA
* *
36556165 AAATTCCA-TTTTAACCTCGATTTTACCAAAAATTACTATTTTACACTTGAAC
65 AAATT-CATTTTTAACC-CGATTTTACCAAAAATTACCATTTTACACCTGAAC
*
36556217 TTTCCAAAATTCCATTTTTAACCCCGATTTTACTAAAAATTACCGTTTTACCCCCGAACTTTTCA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTTAC-AAAAATTACCATTTTACCCCCGAACTTTTCA
* * * * *
36556282 AAATCTCTTTTTTGACCCAATTTTAACTAAAATTACCATTTT
65 AAAT-TCATTTTTAACCCGATTTTACCAAAAATTACCATTTT
36556324 CCCCCCGGGT
Statistics
Matches: 187, Mismatches: 33, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
116 1 0.01
117 144 0.77
118 42 0.22
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (115 bp):
TTTCCAAAATTCCATTTTTAACCCCGATTTTACAAAAATTACCATTTTACCCCCGAACTTTTCAA
AATTCATTTTTAACCCGATTTTACCAAAAATTACCATTTTACACCTGAAC
Found at i:36563419 original size:4 final size:4
Alignment explanation
Indices: 36563410--36563445 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
36563400 CTGGTATGCA
36563410 TATG TATG TATG TATG T-TG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
36563446 TTTTTAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:36563432 original size:15 final size:15
Alignment explanation
Indices: 36563412--36563441 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36563402 GGTATGCATA
36563412 TGTATGTATGTATGT
1 TGTATGTATGTATGT
36563427 TGTATGTATGTATGT
1 TGTATGTATGTATGT
36563442 ATGTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (15 bp):
TGTATGTATGTATGT
Found at i:36563434 original size:19 final size:19
Alignment explanation
Indices: 36563410--36563446 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
36563400 CTGGTATGCA
36563410 TATGTATGTATGTATGTTG
1 TATGTATGTATGTATGTTG
36563429 TATGTATGTATGTATGTT
1 TATGTATGTATGTATGTT
36563447 TTTTAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (19 bp):
TATGTATGTATGTATGTTG
Found at i:36564912 original size:97 final size:97
Alignment explanation
Indices: 36564734--36564923 Score: 213
Period size: 97 Copynumber: 2.0 Consensus size: 97
36564724 TATAGAAGTT
** * * * * * * *
36564734 TTTGGGATGAGAATAAAACGTGTTTTATAGGATGTGTTCTCTCTGTCAGATCAAAGAAAACGCGT
1 TTTGGGATGAGAATAAAACGCCTCTTATAAGACGTATTCTCTCTATCAAATCAAAGAAAACACGT
36564799 CTTATAAGACTCGTTTTCTTTTT-TCTCTTTAA
66 CTTATAAGACTCGTTTT-TTTTTCTCTCTTTAA
* * *
36564831 TTTGGGATGAGAATAAAACGCCTCTTATAAGACGTATTTTTTCTATCAAATCAATGAAAACACGT
1 TTTGGGATGAGAATAAAACGCCTCTTATAAGACGTATTCTCTCTATCAAATCAAAGAAAACACGT
* * *
36564896 CTTGTATGA-TGTGTTTTTTTTTCTCTCT
66 CTTATAAGACT-CGTTTTTTTTTCTCTCT
36564924 CTAAAAACAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
96 6 0.08
97 70 0.92
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (97 bp):
TTTGGGATGAGAATAAAACGCCTCTTATAAGACGTATTCTCTCTATCAAATCAAAGAAAACACGT
CTTATAAGACTCGTTTTTTTTTCTCTCTTTAA
Found at i:36565588 original size:4 final size:4
Alignment explanation
Indices: 36565568--36565604 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
36565558 AACCCAATTC
*
36565568 TATT TTTT TATTT TATT TATT TATT TATT TATT TATT
1 TATT TATT TA-TT TATT TATT TATT TATT TATT TATT
36565605 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TATT
Found at i:36565659 original size:63 final size:63
Alignment explanation
Indices: 36565583--36565756 Score: 223
Period size: 63 Copynumber: 2.8 Consensus size: 63
36565573 TTTTATTTTA
* *
36565583 TTTA-TTTATTTATTTATTTATTATTATT-T-TTATGAACATAAATAAATATAATATAATATTAA
1 TTTATTTTA-TTATTTATTTATTATTATTATAATAT-AA-ATAAATAAATATAAAATAATATTAA
36565645 T
63 T
*
36565646 TTTATTTTATTATTTATTTATTATT-TTATGAATATAAATAAATAAATGTAAAATAATATTAAT
1 TTTATTTTATTATTTATTTATTATTATTAT-AATATAAATAAATAAATATAAAATAATATTAAT
* *
36565709 TTTGTTTTATTATTTATTTATTATTATAAATAA-ATAAATAAATAAATA
1 TTTATTTTATTATTTATTTATTATTAT-TATAATATAAATAAATAAATA
36565757 ACAAACCAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
62 2 0.02
63 83 0.84
64 9 0.09
65 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (63 bp):
TTTATTTTATTATTTATTTATTATTATTATAATATAAATAAATAAATATAAAATAATATTAAT
Found at i:36565683 original size:59 final size:58
Alignment explanation
Indices: 36565587--36565756 Score: 201
Period size: 59 Copynumber: 2.9 Consensus size: 58
36565577 ATTTTATTTA
36565587 TTTA-TTTATTTATTTA-TTATTATTTTTATGAACATAAATAAATATAATATAATATTAAT
1 TTTATTTTA-TTATTTATTTATTA-TTTTATGAA-ATAAATAAATATAATATAATATTAAT
*
36565646 TTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAAT
1 TTTATTTTATTATTTATTTATTATTTTATGAA-ATAAATAAAT--A--TAATATAATATTAAT
*
36565709 TTTGTTTTATTATTTATTTATTA--TTAT-AAATAAATAAATA-AATA-AATA
1 TTTATTTTATTATTTATTTATTATTTTATGAAATAAATAAATATAATATAATA
36565757 ACAAACCAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
53 4 0.04
54 3 0.03
57 1 0.01
59 40 0.40
60 12 0.12
61 5 0.05
63 36 0.36
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (58 bp):
TTTATTTTATTATTTATTTATTATTTTATGAAATAAATAAATATAATATAATATTAAT
Found at i:36570785 original size:25 final size:25
Alignment explanation
Indices: 36570757--36570804 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
36570747 AAAAATTAAA
*
36570757 AAAAGAAAAAAAGACAAAGAAAAGG
1 AAAAGAAAAAAAGAAAAAGAAAAGG
*
36570782 AAAAGAAGAAAAGAAAAAGAAAA
1 AAAAGAAAAAAAGAAAAAGAAAA
36570805 AGGGGAGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (25 bp):
AAAAGAAAAAAAGAAAAAGAAAAGG
Found at i:36570800 original size:14 final size:14
Alignment explanation
Indices: 36570773--36570802 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36570763 AAAAAAGACA
*
36570773 AAGAAAAGGAAAAG
1 AAGAAAAGAAAAAG
36570787 AAGAAAAGAAAAAG
1 AAGAAAAGAAAAAG
36570801 AA
1 AA
36570803 AAAGGGGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAAAG
Found at i:36570806 original size:20 final size:21
Alignment explanation
Indices: 36570756--36570806 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
36570746 AAAAAATTAA
36570756 AAAAAGAAAAA-AAGACAAAG
1 AAAAAGAAAAAGAAGACAAAG
*
36570776 -AAAAGGAAAAGAAGA-AAAG
1 AAAAAGAAAAAGAAGACAAAG
36570795 AAAAAGAAAAAG
1 AAAAAGAAAAAG
36570807 GGGAGGTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGACAAAG
Found at i:36571249 original size:12 final size:12
Alignment explanation
Indices: 36571232--36571279 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
36571222 CTCCAATTCC
*
36571232 ATTTTTCTTATT
1 ATTTTTATTATT
36571244 ATTTTTATTTATTT
1 ATTTTTA-TTA-TT
36571258 ATTTATTTATTATT
1 A-TT-TTTATTATT
36571272 ATTTTTAT
1 ATTTTTAT
36571280 GAACATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 11 0.35
13 5 0.16
14 6 0.19
15 5 0.16
16 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:36571492 original size:67 final size:67
Alignment explanation
Indices: 36571240--36571490 Score: 369
Period size: 67 Copynumber: 3.9 Consensus size: 67
36571230 CCATTTTTCT
* *
36571240 TATTATTTTTA-TTTATTTATTTATTTA-TTATTATTTTTATGAACATAAATAAAT--A--TAAA
1 TATTAATTTTATTTTA-TTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATGTAAA
36571299 ATAA
64 ATAA
36571303 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
1 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
36571368 AA
66 AA
36571370 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
1 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
36571435 AA
66 AA
* **
36571437 TATTAATTTTGTTTTATTATTTATTTA-TTATTA-TAAAT-AA-ATAAATAAATAAAT
1 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAAT
36571491 AACAAACCAA
Statistics
Matches: 177, Mismatches: 5, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
63 54 0.31
64 12 0.07
65 4 0.02
66 6 0.03
67 101 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (67 bp):
TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
AA
Found at i:36576764 original size:49 final size:49
Alignment explanation
Indices: 36576702--36576800 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
36576692 TCTTAATCAA
36576702 TTGCATAATGGAAAACTACTCTTCCACTTATGAATTATGTTAATAAGTC
1 TTGCATAATGGAAAACTACTCTTCCACTTATGAATTATGTTAATAAGTC
36576751 TTGCATAATGGAAAACTACTCTTCCACTTATGAATTATGTTAATAAGTC
1 TTGCATAATGGAAAACTACTCTTCCACTTATGAATTATGTTAATAAGTC
36576800 T
1 T
36576801 CTTCCACTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (49 bp):
TTGCATAATGGAAAACTACTCTTCCACTTATGAATTATGTTAATAAGTC
Found at i:36576805 original size:30 final size:30
Alignment explanation
Indices: 36576769--36576830 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
36576759 TGGAAAACTA
36576769 CTCTTCCACTTATGAATTATGTTAATAAGT
1 CTCTTCCACTTATGAATTATGTTAATAAGT
36576799 CTCTTCCACTTATGAATTATGTTAATAAGT
1 CTCTTCCACTTATGAATTATGTTAATAAGT
36576829 CT
1 CT
36576831 TGCATAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.44
Consensus pattern (30 bp):
CTCTTCCACTTATGAATTATGTTAATAAGT
Found at i:36576851 original size:79 final size:79
Alignment explanation
Indices: 36576720--36576879 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
36576710 TGGAAAACTA
36576720 CTCTTCCACTTATGAATTATGTTAATAAGTCTTGCATAATGGAAAACTACTCTTCCACTTATGAA
1 CTCTTCCACTTATGAATTATGTTAATAAGTCTTGCATAATGGAAAACTACTCTTCCACTTATGAA
36576785 TTATGTTAATAAGT
66 TTATGTTAATAAGT
36576799 CTCTTCCACTTATGAATTATGTTAATAAGTCTTGCATAATGGAAAACTACTCTTCCACTTATGAA
1 CTCTTCCACTTATGAATTATGTTAATAAGTCTTGCATAATGGAAAACTACTCTTCCACTTATGAA
36576864 TTATGTTAATAAGT
66 TTATGTTAATAAGT
36576878 CT
1 CT
36576880 TGAAAAGGAG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (79 bp):
CTCTTCCACTTATGAATTATGTTAATAAGTCTTGCATAATGGAAAACTACTCTTCCACTTATGAA
TTATGTTAATAAGT
Found at i:36577204 original size:16 final size:19
Alignment explanation
Indices: 36577166--36577204 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
36577156 ATTTAAAAAA
36577166 TAAAAAACATTACTAACCC
1 TAAAAAACATTACTAACCC
36577185 -AAAAAA-A-TACT-ACCC
1 TAAAAAACATTACTAACCC
36577200 TAAAA
1 TAAAA
36577205 TGATTGCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.21
16 8 0.42
17 1 0.05
18 6 0.32
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (19 bp):
TAAAAAACATTACTAACCC
Found at i:36577672 original size:15 final size:15
Alignment explanation
Indices: 36577652--36577683 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36577642 TTTATCTCGA
*
36577652 AAAAAATAATATTTG
1 AAAAAATAAAATTTG
36577667 AAAAAATAAAATTTG
1 AAAAAATAAAATTTG
36577682 AA
1 AA
36577684 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AAAAAATAAAATTTG
Found at i:36579343 original size:27 final size:28
Alignment explanation
Indices: 36579291--36579345 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
36579281 TCGTATATTT
*
36579291 GAAATTTAGTCTCTTATTTTTATTTCAA
1 GAAATTTAATCTCTTATTTTTATTTCAA
*
36579319 GAAATTTAAT-TCTTCTATTTT-TTTCAA
1 GAAATTTAATCTCTTAT-TTTTATTTCAA
36579346 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (28 bp):
GAAATTTAATCTCTTATTTTTATTTCAA
Found at i:36582445 original size:34 final size:34
Alignment explanation
Indices: 36582407--36582518 Score: 95
Period size: 34 Copynumber: 3.1 Consensus size: 34
36582397 GGATTCAATA
36582407 ATAAAATTAATGTTATTTAAATTAGATCAAATCG
1 ATAAAATTAATGTTATTTAAATTAGATCAAATCG
* * * *
36582441 AT-AAA-TATAT-TGATTCGTAAATTTGTTTATAAGTCG
1 ATAAAATTA-ATGTTATT--TAAATTAGATCA-AA-TCG
36582477 ATAATAAAATTAATGTTATTTAAATTAGATCAAATCG
1 ---ATAAAATTAATGTTATTTAAATTAGATCAAATCG
36582514 ATAAA
1 ATAAA
36582519 TATATTGATT
Statistics
Matches: 59, Mismatches: 8, Indels: 22
0.66 0.09 0.25
Matches are distributed among these distances:
32 6 0.10
33 5 0.08
34 16 0.27
35 2 0.03
36 3 0.05
37 3 0.05
38 2 0.03
39 11 0.19
40 5 0.08
41 6 0.10
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (34 bp):
ATAAAATTAATGTTATTTAAATTAGATCAAATCG
Found at i:36582491 original size:73 final size:73
Alignment explanation
Indices: 36582404--36582550 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
36582394 TTCGGATTCA
36582404 ATAATAAAATTAATGTTATTTAAATTAGATCAAATCGATAAATATATTGATTCGTAAATTTGTTT
1 ATAATAAAATTAATGTTATTTAAATTAGATCAAATCGATAAATATATTGATTCGTAAATTTGTTT
36582469 ATAAGTCG
66 ATAAGTCG
36582477 ATAATAAAATTAATGTTATTTAAATTAGATCAAATCGATAAATATATTGATTCGTAAATTTGTTT
1 ATAATAAAATTAATGTTATTTAAATTAGATCAAATCGATAAATATATTGATTCGTAAATTTGTTT
36582542 ATAAGTCG
66 ATAAGTCG
36582550 A
1 A
36582551 GTTATTCGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (73 bp):
ATAATAAAATTAATGTTATTTAAATTAGATCAAATCGATAAATATATTGATTCGTAAATTTGTTT
ATAAGTCG
Found at i:36582535 original size:34 final size:34
Alignment explanation
Indices: 36582424--36582536 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 34
36582414 TAATGTTATT
36582424 TAAATTAGATCAAATCGATAAATATATTGATTCG
1 TAAATTAGATCAAATCGATAAATATATTGATTCG
* * * * *
36582458 TAAATTTGTTTATAAGTCGATAATAAAATTAATGTTATT--
1 TAAATTAGATCA-AA-TCGAT-A-AATA-T-AT-TGATTCG
36582497 TAAATTAGATCAAATCGATAAATATATTGATTCG
1 TAAATTAGATCAAATCGATAAATATATTGATTCG
36582531 TAAATT
1 TAAATT
36582537 TGTTTATAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
32 4 0.07
33 2 0.03
34 16 0.27
35 5 0.08
36 6 0.10
37 6 0.10
38 5 0.08
39 10 0.17
40 2 0.03
41 4 0.07
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (34 bp):
TAAATTAGATCAAATCGATAAATATATTGATTCG
Found at i:36594685 original size:15 final size:15
Alignment explanation
Indices: 36594667--36594718 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
36594657 TACTACAAAC
36594667 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
36594682 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
36594701 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
36594716 ATT
1 ATT
36594719 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:36594782 original size:16 final size:16
Alignment explanation
Indices: 36594751--36594787 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
36594741 ATGTGAAGAA
36594751 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
36594767 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
36594783 TATTA
1 TATTA
36594788 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:36599630 original size:31 final size:31
Alignment explanation
Indices: 36599550--36599622 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
36599540 TTTTTTGTCC
* * *
36599550 CAATTTGGTACCCGGATTGGGCTTTAACGTT
1 CAATTTGGTACCCGAATTTGACTTTAACGTT
*
36599581 CTATTTGGTACCCGAATTTGACTTTAACGTT
1 CAATTTGGTACCCGAATTTGACTTTAACGTT
36599612 CAATTTGGTAC
1 CAATTTGGTAC
36599623 TTGAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
CAATTTGGTACCCGAATTTGACTTTAACGTT
Found at i:36604935 original size:17 final size:17
Alignment explanation
Indices: 36604915--36604951 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
36604905 TTGGAGATTG
*
36604915 AATTTACTTTAAATTTA
1 AATTTACTTTAAATTAA
*
36604932 AATTTATTTTAAATTAA
1 AATTTACTTTAAATTAA
36604949 AAT
1 AAT
36604952 ATAAAAGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTACTTTAAATTAA
Found at i:36606892 original size:30 final size:29
Alignment explanation
Indices: 36606856--36607208 Score: 259
Period size: 29 Copynumber: 12.1 Consensus size: 29
36606846 CATTAAAGGT
*
36606856 CCCTAAACTATCTAAAAATTCCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* *
36606886 CCCTAAAATTCCAAAAATTCCATTTTAAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * * *
36606915 CTCGAAACTTCCAAAAATTACATTTTAAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * * *
36606944 CCCAAAATTTCAAAAAATTCCATTTTTAA
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
36606973 CCCTAAAAATTCCAAAGATTCCATTTTTAA
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* * * *
36607003 CCCTAAAAATTCCAAAGATTACA-TTTTAA
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* *
36607032 ACCTGAAATTTCCAAAAATTCCATTTTTGA-
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* * *
36607062 CCCAAAATTTCCAAAAATTCTATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * *
36607092 CTCGAAACTTCCAAAAATTACA-TTTAAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * * *
36607120 CTCGAAA-TCTCTAAAAATTCCATTTTAAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* * * *
36607149 CTCAAAACTTCCAAAACTTCCATTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
36607177 CTCTAAAACTTCCAAAAATTACCA-TTTTAC
1 CCCT-AAACTTCCAAAAATT-CCATTTTTAC
36607207 CC
1 CC
36607209 TCAGATTTCT
Statistics
Matches: 270, Mismatches: 43, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
27 1 0.00
28 23 0.09
29 165 0.61
30 80 0.30
31 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:36606998 original size:59 final size:58
Alignment explanation
Indices: 36606860--36607210 Score: 343
Period size: 58 Copynumber: 6.0 Consensus size: 58
36606850 AAAGGTCCCT
* *
36606860 AAACTATCTAAAAATTCCATTTTTACCCCTAAAA-TTCCAAAAATTCCATTTTAACCTCG
1 AAACT-TCCAAAAATTCCATTTTAACCCC-AAAATTTCCAAAAATTCCATTTTAACCTCG
* * *
36606919 AAACTTCCAAAAATTACATTTTAACCCCAAAATTTCAAAAAATTCCATTTTTAACC-CTA
1 AAACTTCCAAAAATTCCATTTTAACCCCAAAATTTCCAAAAATTCCA-TTTTAACCTC-G
* * * * * *
36606978 AAAATTCCAAAGATTCCATTTTTAACCCTAAAAATTCCAAAGATTACATTTTAAACCT-G
1 AAACTTCCAAAAATTCCA-TTTTAACCCCAAAATTTCCAAAAATTCCATTTT-AACCTCG
* * * *
36607037 AAATTTCCAAAAATTCCATTTTTGA-CCCAAAATTTCCAAAAATTCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTAACCCCAAAATTTCCAAAAATTCCA-TTTTAACCTCG
* * * * * *
36607096 AAACTTCCAAAAATTACA-TTTAACCTCGAAATCTCTAAAAATTCCATTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTAACCCCAAAATTTCCAAAAATTCCATTTTAACCTCG
* * * * * *
36607153 AAACTTCCAAAACTTCCATTTTGACTCTAAAACTTCCAAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTAACCCCAAAATTTCCAAAAATT-CCATTTTAACCTC
36607211 AGATTTCTAA
Statistics
Matches: 237, Mismatches: 44, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
57 33 0.14
58 89 0.38
59 87 0.37
60 28 0.12
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTAACCCCAAAATTTCCAAAAATTCCATTTTAACCTCG
Found at i:36612850 original size:7 final size:7
Alignment explanation
Indices: 36612838--36612923 Score: 102
Period size: 7 Copynumber: 11.6 Consensus size: 7
36612828 TGAATAAAAG
36612838 AAAAGAA
1 AAAAGAA
36612845 AAAAGAAAA
1 AAAAG--AA
*
36612854 AAAAAACA
1 AAAAGA-A
36612862 AAAAGAA
1 AAAAGAA
36612869 AAATA-AA
1 AAA-AGAA
36612876 AAAAGAA
1 AAAAGAA
36612883 AAAAGAA
1 AAAAGAA
36612890 AAAAGAAA
1 AAAAG-AA
36612898 AAAAGAAA
1 AAAAG-AA
36612906 AAAAGAA
1 AAAAGAA
36612913 AAAAGAA
1 AAAAGAA
36612920 AAAA
1 AAAA
36612924 AAAGGAGAGG
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
6 1 0.01
7 42 0.59
8 22 0.31
9 6 0.08
ACGTcount: A:0.87, C:0.01, G:0.10, T:0.01
Consensus pattern (7 bp):
AAAAGAA
Found at i:36612854 original size:1 final size:1
Alignment explanation
Indices: 36612833--36612926 Score: 80
Period size: 1 Copynumber: 94.0 Consensus size: 1
36612823 TTCAATGAAT
* * * * * * * * *
36612833 AAAAGAAAAGAAAAAAGAAAAAAAAAACAAAAAGAAAAATAAAAAAAGAAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
36612898 AAAAGAAAAAAAGAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36612927 GGAGAGGTCG
Statistics
Matches: 69, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.87, C:0.01, G:0.11, T:0.01
Consensus pattern (1 bp):
A
Done.