Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 9 of 125
Found at i:2959326 original size:144 final size:144
Alignment explanation
Indices: 2959126--2959412 Score: 565
Period size: 144 Copynumber: 2.0 Consensus size: 144
2959116 CTTGCAGCAT
2959126 TAATAGTTCCTACTGTCCGATGTCACATTAGCTTTTGGCTTTGTTCATTAGAGCTGGTTAGTTCA
1 TAATAGTTCCTACTGTCCGATGTCACATTAGCTTTTGGCTTTGTTCATTAGAGCTGGTTAGTTCA
2959191 ACTAGGTTTGATAGAAATGCAAACACAAATTTGATTGATGTCAGCTTATATATCTACCATCTATC
66 ACTAGGTTTGATAGAAATGCAAACACAAATTTGATTGATGTCAGCTTATATATCTACCATCTATC
2959256 TATGGATGAGAACG
131 TATGGATGAGAACG
*
2959270 TAATAGTTGCTACTGTCCGATGTCACATTAGCTTTTGGCTTTGTTCATTAGAGCTGGTTAGTTCA
1 TAATAGTTCCTACTGTCCGATGTCACATTAGCTTTTGGCTTTGTTCATTAGAGCTGGTTAGTTCA
2959335 ACTAGGTTTGATAGAAATGCAAACACAAATTTGATTGATGTCAGCTTATATATCTACCATCTATC
66 ACTAGGTTTGATAGAAATGCAAACACAAATTTGATTGATGTCAGCTTATATATCTACCATCTATC
2959400 TATGGATGAGAAC
131 TATGGATGAGAAC
2959413 CTAGGTTGGC
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (144 bp):
TAATAGTTCCTACTGTCCGATGTCACATTAGCTTTTGGCTTTGTTCATTAGAGCTGGTTAGTTCA
ACTAGGTTTGATAGAAATGCAAACACAAATTTGATTGATGTCAGCTTATATATCTACCATCTATC
TATGGATGAGAACG
Found at i:2963034 original size:6 final size:6
Alignment explanation
Indices: 2963014--2963079 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
2963004 TAATTAAAAG
* * *
2963014 TTTAAA -TTAAT TTTAAA TTT-AT TTTAAA TTTAAA TTTACCTA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA
*
2963062 TTT-AC TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
2963080 CTAATCAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
5 12 0.26
6 30 0.64
8 5 0.11
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:2963034 original size:17 final size:17
Alignment explanation
Indices: 2963014--2963123 Score: 59
Period size: 17 Copynumber: 6.6 Consensus size: 17
2963004 TAATTAAAAG
*
2963014 TTTAAATTAATTTTAAA
1 TTTAAATTAAATTTAAA
**
2963031 TTTATTTTAAATTTAAA
1 TTTAAATTAAATTTAAA
**
2963048 TTT-ACCT--ATTTAAA
1 TTTAAATTAAATTTAAA
**
2963062 TTTACTTTAAATTTAAA
1 TTTAAATTAAATTTAAA
* *
2963079 TCT-AATCAAATTTAAA
1 TTTAAATTAAATTTAAA
* *
2963095 -CTAATATTAAACTTAAA
1 TTTAA-ATTAAATTTAAA
*
2963112 ATTAAAGTTAAA
1 TTTAAA-TTAAA
2963124 AGTTCAATTA
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
14 10 0.14
15 3 0.04
16 12 0.17
17 37 0.53
18 8 0.11
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTAAATTAAATTTAAA
Found at i:2963044 original size:11 final size:11
Alignment explanation
Indices: 2963014--2963045 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2963004 TAATTAAAAG
*
2963014 TTTAAATTAAT
1 TTTAAATTTAT
2963025 TTTAAATTTAT
1 TTTAAATTTAT
2963036 TTTAAATTTA
1 TTTAAATTTA
2963046 AATTTACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:2963091 original size:16 final size:15
Alignment explanation
Indices: 2963070--2963099 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2963060 AATTTACTTT
2963070 AAATTTAAATCTAATC
1 AAATTTAAA-CTAATC
2963086 AAATTTAAACTAAT
1 AAATTTAAACTAAT
2963100 ATTAAACTTA
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTTAAACTAATC
Found at i:2963967 original size:18 final size:18
Alignment explanation
Indices: 2963932--2963976 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2963922 TTAATAATAT
2963932 TATTAATAACATTAATGA
1 TATTAATAACATTAATGA
*
2963950 TATTAATGACAGTT-ATGA
1 TATTAATAACA-TTAATGA
*
2963968 TAATAATAA
1 TATTAATAA
2963977 TAGATGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (18 bp):
TATTAATAACATTAATGA
Found at i:2964021 original size:15 final size:18
Alignment explanation
Indices: 2963986--2964028 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 18
2963976 ATAGATGAGT
2963986 TTAATAATAAGTATAATA
1 TTAATAATAAGTATAATA
2964004 TTAATAATAA-TAT-A-A
1 TTAATAATAAGTATAATA
2964019 TTAATAATAA
1 TTAATAATAA
2964029 AAAAGGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.44
16 1 0.04
17 3 0.12
18 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TTAATAATAAGTATAATA
Found at i:2965290 original size:59 final size:59
Alignment explanation
Indices: 2965154--2965514 Score: 514
Period size: 58 Copynumber: 6.2 Consensus size: 59
2965144 AAAATTATAT
* * *
2965154 TTTTACCCTCAAACTTTCCAAAATCCCA-TTTTAACCCTGATTTTACC-AAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
*
2965211 TTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * * **
2965270 TTTTACCCCCGAACTTTCCAAAATTCCAATTTTAACCTTGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
*
2965329 -TTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * * * **
2965387 -TTTACCCCCGAACTTTCCAAAATACCATTTTTAACCTCAATTTCACCAAAAGCTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * *
2965445 TTTTACCCCCAAACTTTCCAAAATCTCATTTTTTAACCTCGATTCCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCA-TTTTTAACCCCGATTTCACCAAAAATTACCA
2965505 TTTTACCCCC
1 TTTTACCCCC
2965515 GAAAGTCAAA
Statistics
Matches: 270, Mismatches: 30, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
57 26 0.10
58 120 0.44
59 87 0.32
60 37 0.14
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.32
Consensus pattern (59 bp):
TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:2965348 original size:117 final size:118
Alignment explanation
Indices: 2965154--2965517 Score: 547
Period size: 117 Copynumber: 3.1 Consensus size: 118
2965144 AAAATTATAT
* * * * *
2965154 TTTTACCCTCAAACTTTCCAAAA-TCCCATTTTAACCCTGATTTTACC-AAAATTACCATTTTAC
1 TTTTACCCCCGAACTTTCCAAAATTCCAATTTTAACCTTGATTTCACCAAAAATTACCATTTTAC
*
2965217 CCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
66 CCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
2965270 TTTTACCCCCGAACTTTCCAAAATTCCAATTTTAACCTTGATTTCACCAAAAATTACCA-TTTAC
1 TTTTACCCCCGAACTTTCCAAAATTCCAATTTTAACCTTGATTTCACCAAAAATTACCATTTTAC
*
2965334 CCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
66 CCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * ** **
2965387 -TTTACCCCCGAACTTTCCAAAATACCATTTTTAACCTCAATTTCACCAAAAGCTACCATTTTAC
1 TTTTACCCCCGAACTTTCCAAAATTCCAATTTTAACCTTGATTTCACCAAAAATTACCATTTTAC
* * *
2965451 CCCCAAACTTTCCAAAATCTCATTTTTTAACCTCGATTCCACCAAAAATTACCA
66 CCCCAAACTTTCCAAAATCCCA-TTTTTAACCCCGATTTCACCAAAAATTACCA
2965505 TTTTACCCCCGAA
1 TTTTACCCCCGAA
2965518 AGTCAAAAAT
Statistics
Matches: 226, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
116 73 0.32
117 102 0.45
118 39 0.17
119 12 0.05
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (118 bp):
TTTTACCCCCGAACTTTCCAAAATTCCAATTTTAACCTTGATTTCACCAAAAATTACCATTTTAC
CCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:2979438 original size:30 final size:29
Alignment explanation
Indices: 2979402--2979482 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
2979392 GTTTCTATTT
2979402 ATATTGCTTGTGATGAAAGTAATTCTGATA
1 ATATTGCTTGTGATGAAAG-AATTCTGATA
* * *
2979432 ATATTGCTTAT-AGTGAACCGAATTTTGATA
1 ATATTGCTTGTGA-TGAA-AGAATTCTGATA
* *
2979462 ATATTACTTGTGATAAAAGAA
1 ATATTGCTTGTGATGAAAGAA
2979483 ATGAGAAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
29 4 0.10
30 35 0.85
31 2 0.05
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (29 bp):
ATATTGCTTGTGATGAAAGAATTCTGATA
Found at i:2979951 original size:17 final size:17
Alignment explanation
Indices: 2979915--2979974 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
2979905 GTTTAAATAG
*
2979915 ATTTAAATTTATTGTTAA
1 ATTTAAATTTAAT-TTAA
**
2979933 ATTTAAATTTGCTTTAA
1 ATTTAAATTTAATTTAA
* *
2979950 ATCTAAATTTAATTAAA
1 ATTTAAATTTAATTTAA
2979967 ATTTAAAT
1 ATTTAAAT
2979975 CAATATTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
17 24 0.69
18 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:2982020 original size:29 final size:29
Alignment explanation
Indices: 2981952--2982292 Score: 200
Period size: 29 Copynumber: 11.8 Consensus size: 29
2981942 GGTGGTCCCT
* *
2981952 AAACTTCCAAAAATTAAATTTT--CCCCC
1 AAACTTCCAAAAATTACATTTTAACCCCA
* * *
2981979 TAACTTTCAAAAATTTCATTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTAACCCCA
* * *
2982008 AAAATTCCCAAAATTCCATTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTAACCCCA
*
2982037 AAACTTCCAAAAATTACACTTTT-GCCCTC-
1 AAACTTCCAAAAATTACA-TTTTAACCC-CA
* * * *
2982066 GAACTTTCAAAAATTCCATTTTAACCCTA
1 AAACTTCCAAAAATTACATTTTAACCCCA
* * * * ***
2982095 AAAATTCCCAAAATTACGTTTTTATCCTTG
1 AAACTTCCAAAAATTAC-ATTTTAACCCCA
*
2982125 AAACTTCCAAAAATTACATTTTTA-CCCA
1 AAACTTCCAAAAATTACATTTTAACCCCA
* * *
2982153 CGAACTTCCAAAAATTCCATTTTTGAA-CTCA
1 -AAACTTCCAAAAATTACA-TTTT-AACCCCA
* *
2982184 AAATTTTCC-AAAATTACATTTTTACCCTCA
1 AAA-CTTCCAAAAATTACATTTTAACCC-CA
* * *
2982214 AAA-TTCCAAAAATTTCATTTTTGACCCCG
1 AAACTTCCAAAAATTACA-TTTTAACCCCA
* * *
2982243 ACACTTTC-AAAATTACCATTTT-ACCCCT
1 AAACTTCCAAAAATTA-CATTTTAACCCCA
* *
2982271 AAA-TATCCGAAAATTCCATTTT
1 AAACT-TCCAAAAATTACATTTT
2982293 TGATCCTGAT
Statistics
Matches: 240, Mismatches: 55, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
27 19 0.08
28 25 0.10
29 128 0.53
30 60 0.25
31 8 0.03
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAACCCCA
Found at i:2982236 original size:59 final size:58
Alignment explanation
Indices: 2981952--2982295 Score: 236
Period size: 59 Copynumber: 5.9 Consensus size: 58
2981942 GGTGGTCCCT
* * * * * * * *
2981952 AAAC-TTCCAAAAATTA-AATTTTCCCCCTAACTTTCAAAAATTTCA-TTTTAACCCCA
1 AAACTTTCC-AAAATTACATTTTTACCCCAAAATTCCAAAAATTACATTTTTGACCTCA
* * * * * *
2982008 AAAATTCCCAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTACACTTTTGCCCTC-
1 AAACTTTCCAAAATTACATTTTTACCCCAAAA-TTCCAAAAATTACATTTTTGACCTCA
* * * * * * * **
2982066 GAACTTTCAAAAATTCCATTTTAACCCTAAAAATTCCCAAAATTACGTTTTT-ATCCTTG
1 AAACTTTCCAAAATTACATTTTTACCC-CAAAATTCCAAAAATTACATTTTTGA-CCTCA
* * * *
2982125 AAAC-TTCCAAAAATTACATTTTTACCCACGAACTTCCAAAAATTCCATTTTTGAACTCA
1 AAACTTTCC-AAAATTACATTTTTACCC-CAAAATTCCAAAAATTACATTTTTGACCTCA
* * * *
2982184 AAATTTTCCAAAATTACATTTTTACCCTCAAAATTCCAAAAATTTCATTTTTGACCCCG
1 AAACTTTCCAAAATTACATTTTTACCC-CAAAATTCCAAAAATTACATTTTTGACCTCA
* * * *
2982243 ACACTTT-CAAAATTACCA-TTTTACCCCTAAATATCCGAAAATTCCATTTTTGA
1 AAACTTTCCAAAATTA-CATTTTTACCCCAAAAT-TCCAAAAATTACATTTTTGA
2982296 TCCTGATTTT
Statistics
Matches: 226, Mismatches: 50, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
56 9 0.04
57 18 0.08
58 91 0.40
59 103 0.46
60 5 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTTCCAAAATTACATTTTTACCCCAAAATTCCAAAAATTACATTTTTGACCTCA
Found at i:2982364 original size:59 final size:59
Alignment explanation
Indices: 2982251--2982387 Score: 152
Period size: 58 Copynumber: 2.3 Consensus size: 59
2982241 CGACACTTTC
* * *
2982251 AAAATTACCATTTTACCCCTAAATATCCGAAAATTCCATTTTTGATCCTGATTTTTTTA
1 AAAATTACCATTTTACCCCTAAATATCCGAAAATTCCATTTTTAACCCTAATTTTTTTA
* * * * * **
2982310 AAAATTACCGTTTTACCCTTGAATAT-CTAAAATGT-CATTTTTAACCCTAAATTTTTCC
1 AAAATTACCATTTTACCCCTAAATATCCGAAAAT-TCCATTTTTAACCCTAATTTTTTTA
2982368 AAAATTACCATTTTTACCCC
1 AAAATTACCA-TTTTACCCC
2982388 CTAGAGTCCA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
58 32 0.50
59 32 0.50
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAATATCCGAAAATTCCATTTTTAACCCTAATTTTTTTA
Found at i:2982372 original size:58 final size:59
Alignment explanation
Indices: 2982129--2982387 Score: 176
Period size: 59 Copynumber: 4.4 Consensus size: 59
2982119 TCCTTGAAAC
* * * * *
2982129 TTCCAAAAATTA-CATTTTTACCCACGAACT-TCCAAAAATTCCATTTTTGAACTC-AAAATT
1 TTCC-AAAATTACCA-TTTTACCC-CTAAATATCCGAAAATTCCATTTTT-AACCCTAAATTT
* * * * * * *
2982189 TTCCAAAATTA-CATTTTTACCCTCAAAAT-TCCAAAAATTTCATTTTTGACCCCGACA-CT
1 TTCCAAAATTACCA-TTTTACCC-CTAAATATCCGAAAATTCCATTTTT-AACCCTAAATTT
* * * *
2982248 TT-CAAAATTACCATTTTACCCCTAAATATCCGAAAATTCCATTTTTGATCCTGATTTT
1 TTCCAAAATTACCATTTTACCCCTAAATATCCGAAAATTCCATTTTTAACCCTAAATTT
** * * * *
2982306 TTTAAAAATTACCGTTTTACCCTTGAATAT-CTAAAATGT-CATTTTTAACCCTAAATTT
1 TTCCAAAATTACCATTTTACCCCTAAATATCCGAAAAT-TCCATTTTTAACCCTAAATTT
2982364 TTCCAAAATTACCATTTTTACCCC
1 TTCCAAAATTACCA-TTTTACCCC
2982388 CTAGAGTCCA
Statistics
Matches: 160, Mismatches: 32, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
57 7 0.04
58 67 0.42
59 80 0.50
60 6 0.04
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
TTCCAAAATTACCATTTTACCCCTAAATATCCGAAAATTCCATTTTTAACCCTAAATTT
Found at i:2984401 original size:90 final size:88
Alignment explanation
Indices: 2984181--2984901 Score: 451
Period size: 90 Copynumber: 8.2 Consensus size: 88
2984171 AGTATGTTGT
* * * * * *
2984181 TGCAATAA-ATTTTTTATATTCTGGAATAATTATAATAATTGCTATTTAATTT-ACTTCATTTTC
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTT-ATTTCATTTTATTTTA
* * * *
2984244 GAGTACTTGGCCTTGAGTTTAGCCTAC
65 GGGCACTTGG-CTTGAGTCTAG--TGC
* * * * * *
2984271 TACAATAACATTTTTTTATTTTCCAAAATAGTTATAATAATTGCAACTTATTTCATTTTATTTTA
1 TGCAATAATA-TTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTTATTTTA
*
2984336 GGGGCACTTAGGCTTGAGTCTAGTGT
65 -GGGCACTT-GGCTTGAGTCTAGTGC
* * *
2984362 TGCAATAATATTTTTTATTTTCCGGAATAATTATAATAATTGCTATTTATTTCATTTAATTTATG
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTTATTT-TA
* * *
2984427 GGGCACTTGAGCTTGATTTTGGTGC
65 GGGCACTTG-GCTTGAGTCTAGTGC
** * * ** **
2984452 TATAATAATATTTTTTATTTTCTGAAATAATTATAATAATTGTTATCCATTTCATTTTATTCCCA
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTTATT-TTA
** *
2984517 GAACACTTGGACTTGAGTCTGGTGC
65 GGGCACTTGG-CTTGAGTCTAGTGC
* * * * *
2984542 TGCAATAAT-TTTTTTATTTTTCGAAATAATTATAATAGTTGCAAATTTATTTCATTTCATTCTC
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGC-TATTTATTTCATTTTATT-TT
* * *
2984606 AAGGAACTTAGACTTGAG--TAGTGC
64 AGGGCACTT-GGCTTGAGTCTAGTGC
* * * * * * *
2984630 TGCGACAATATTTTTTTATTTT-CAAAATAATTATAATAGTTACGATTTATTTTATTTTATTTTC
1 TGCAATAATA-TTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTTATTTT-
* * *
2984694 AGGGTATTTGGGCTTGAGTCT-GATGT
64 AGGGCACTT-GGCTTGAGTCTAG-TGC
* * * * * *
2984720 TGTAATAATATTTTGT-TTTT--GGAATAATTGTAATAA----T-TTCATTCCA---T-TTTT-G
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTTATTTTAG
* * *
2984772 GGCTCTTTGGCTTAAGTCTCGTGC
66 GGCAC-TTGGCTTGAGTCTAGTGC
* * * *
2984796 TGCAATAATATTTTTTTATTTT-CTAGAATAATTATAAGAATTGCTATTTATTTCATTTCATTCC
1 TGCAATAATA-TTTTTTATTTTCCGA-AATAATTATAATAATTGCTATTTATTTCATTTTATT-T
* ** * *
2984860 CAAAGAACTTGGGTTTGAGTCTAGTGC
63 TAGGGCACTT-GGCTTGAGTCTAGTGC
2984887 TGCAATAAT-TTTTTT
1 TGCAATAATATTTTTT
2984902 GGAATATTTA
Statistics
Matches: 486, Mismatches: 110, Indels: 71
0.73 0.16 0.11
Matches are distributed among these distances:
76 24 0.05
77 8 0.02
78 8 0.02
79 1 0.00
80 12 0.02
82 6 0.01
84 1 0.00
85 7 0.01
87 13 0.03
88 44 0.09
89 64 0.13
90 201 0.41
91 40 0.08
92 39 0.08
93 16 0.03
94 2 0.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (88 bp):
TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTTATTTTAG
GGCACTTGGCTTGAGTCTAGTGC
Found at i:2985334 original size:27 final size:27
Alignment explanation
Indices: 2985296--2985358 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
2985286 GTATAAATGG
2985296 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
2985323 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
2985350 ATGGTGCCT
1 GTGGTGCCT
2985359 TTCTATCAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:2985367 original size:27 final size:27
Alignment explanation
Indices: 2985297--2985373 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
2985287 TATAAATGGG
*
2985297 TGGTGCCTACCTGA-CAGGCGGCACCAG
1 TGGTGCCTACCT-ATCAGGCGGCACCAA
*
2985324 TGGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
** *
2985351 TGGTGCCTTTCTATCAGGTGGCA
1 TGGTGCCTACCTATCAGGCGGCA
2985374 TCAACTCGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.17, C:0.30, G:0.31, T:0.22
Consensus pattern (27 bp):
TGGTGCCTACCTATCAGGCGGCACCAA
Found at i:2985644 original size:57 final size:55
Alignment explanation
Indices: 2985530--2985660 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
2985520 AAAAATTAAA
* * *
2985530 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
2985585 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
2985642 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
2985661 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:2985766 original size:27 final size:27
Alignment explanation
Indices: 2985725--2985785 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
2985715 TTTGACAAGA
2985725 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
**
2985752 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
2985779 GGTGCCT
1 GGTGCCT
2985786 TTGTCAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.21
Consensus pattern (27 bp):
GGTGCCTACCAGGTAGGCGGCACTAGT
Found at i:2985855 original size:25 final size:25
Alignment explanation
Indices: 2985820--2985869 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2985810 CAGATCTGTT
2985820 TAACAGCAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
*
2985845 TAACAGTAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
2985870 AGGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (25 bp):
TAACAGCAAATTTTTGAAGAAGGAA
Found at i:2985917 original size:26 final size:26
Alignment explanation
Indices: 2985860--2985917 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2985850 GTAAATTTTT
* * *
2985860 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
2985886 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
2985912 GCAGAA
1 GAAGAA
2985918 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:2988717 original size:28 final size:28
Alignment explanation
Indices: 2988664--2988721 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
2988654 CATTTTTCTG
*
2988664 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
2988692 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
2988720 TT
1 TT
2988722 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:2988762 original size:26 final size:26
Alignment explanation
Indices: 2988713--2988762 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2988703 TCTATTTAAA
* **
2988713 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTAATTTAATAAGGTTTATG
*
2988739 TTTGAATTAATTTAATTAGGTTTA
1 TTTGAATTAATTTAATAAGGTTTA
2988763 GCAAATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAAGGTTTATG
Found at i:2988839 original size:6 final size:6
Alignment explanation
Indices: 2988828--2988880 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
2988818 ATATTTGCAT
* *
2988828 ACATAA ACATAA ATA-AGA ATATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
2988876 ACATA
1 ACATA
2988881 TTTAATGGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.66, C:0.13, G:0.02, T:0.19
Consensus pattern (6 bp):
ACATAA
Found at i:2989322 original size:6 final size:6
Alignment explanation
Indices: 2989313--2989349 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2989303 CTGCGACTGC
2989313 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
2989350 CCGGCTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:2991244 original size:16 final size:15
Alignment explanation
Indices: 2991210--2991254 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
2991200 TTCGTTTTAA
*
2991210 AAAATATTTTAA-A-
1 AAAATATTTAAATAT
2991223 AAAATATTTAATATAT
1 AAAATATTTAA-ATAT
2991239 AAAATATTTAAATAT
1 AAAATATTTAAATAT
2991254 A
1 A
2991255 TCAATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
15 6 0.21
16 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATTTAAATAT
Found at i:2992258 original size:27 final size:27
Alignment explanation
Indices: 2992220--2992272 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2992210 GAGTGAATCA
*
2992220 GGTGCCGCCTACCAGATAGGCACCACT
1 GGTGCCGCCTACCAGACAGGCACCACT
2992247 GGTGCCGCCTACCAGACAGGCACCAC
1 GGTGCCGCCTACCAGACAGGCACCAC
2992273 CCAAAAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.40, G:0.26, T:0.11
Consensus pattern (27 bp):
GGTGCCGCCTACCAGACAGGCACCACT
Found at i:2992755 original size:93 final size:93
Alignment explanation
Indices: 2992584--2992812 Score: 231
Period size: 93 Copynumber: 2.5 Consensus size: 93
2992574 TAATAATATT
* ***
2992584 TTTTATTTTTGGAATAATTATAATAATTTATATTTATTTTATTTCATTCTCAAGGCACTTGGCCT
1 TTTTATTTTTGGAATAATTATAATAATTGATATTTATTTTATTTCATTCTCAAGGCACTTCAACT
* *
2992649 TGAGTATAATGCTGTAAT-ATTTTTTTA
66 TGAGTAGAATGCTGTAATAATATTTTTA
* * * **
2992676 TTTTATTTTTTGGAATAGTTATAATTATTGATATTTATTTTATTTTATT-TTTAGGACACTTCAA
1 TTTTA-TTTTTGGAATAATTATAATAATTGATATTTATTTTATTTCATTCTCAAGG-CACTTCAA
** *
2992740 CTTTTGTAGAGTGCTGTAATAATATTTTTA
64 CTTGAGTAGAATGCTGTAATAATATTTTTA
* *
2992770 TTTTCA------AAATAATTATAATAATTGTTATTTATTTTATTTCATT
1 TTTT-ATTTTTGGAATAATTATAATAATTGATATTTATTTTATTTCATT
2992813 TTCAGGGTAA
Statistics
Matches: 114, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
88 32 0.28
92 9 0.08
93 60 0.53
94 12 0.11
95 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.55
Consensus pattern (93 bp):
TTTTATTTTTGGAATAATTATAATAATTGATATTTATTTTATTTCATTCTCAAGGCACTTCAACT
TGAGTAGAATGCTGTAATAATATTTTTA
Found at i:2993102 original size:90 final size:89
Alignment explanation
Indices: 2992582--2993755 Score: 633
Period size: 90 Copynumber: 13.1 Consensus size: 89
2992572 ACTAATAATA
*** * *
2992582 TTTTTTATTTTTGGAATAATTATAATAATT-TATATTTATTTTATTTCATTCTCAAGGCACTTGG
1 TTTTTTATTTTCAAAATAATTATAATAATTGT-TATTTATTTTATTTCATTTTCAGGGCACTTGG
* ** * **
2992646 CCTTGAGTATAATGCTGTAATATTTTT
65 GCTTGAGTATGGTGCTGCAATA--AAT
*** * * * * * * *
2992673 TTATTTTATTTTTTGGAATAGTTATAATTATTGATATTTATTTTATTTTATTTTTAGGACACTTC
1 TT-TTTTA-TTTTCAAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTG
** ** *
2992738 AACTTTTGTA-GAGTGCTGTAAT-AAT
64 GGCTTGAGTATG-GTGCTGCAATAAAT
* * * *
2992763 ATTTTTATTTTCAAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGTAATTGAG
1 TTTTTTATTTTCAAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTGGG
* * * * * *
2992828 CATGAGTTTAGCGCTACAATAGTAAA
66 CTTGAGTATGGTGCTGCAATA--AAT
* ** * * * *
2992854 TTTTTTATTTTCAAGAATAATTATAATTATAATTATTTATTTTATTTCATTTTTAAGGTATTTGG
1 TTTTTTATTTTCAA-AATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTGG
* * *
2992919 ACTTGAGTTTGGTGCTGCAGTAAAAT
65 GCTTGAGTATGGTGCTGCAAT-AAAT
* * * * *
2992945 TTTTTTATTTTCTCATAGAATTATAATAATT-TCTATTTATTTCATTTCA--TTCATTGGACACT
1 TTTTTTATTTTC-AAAATAATTATAATAATTGT-TATTTATTTTATTTCATTTTCA--GGGCACT
*
2993007 GGGGCTTGAGTATGGTGCTGCAATAAAT
62 TGGGCTTGAGTATGGTGCTGCAATAAAT
* * *
2993035 TTTTTTATTTTCCAAAAT-ATGTTTAATAATTGTTATTTATTTTATTTTATTTTCAGGGTACTTG
1 TTTTTTATTTT-CAAAATAAT-TATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTG
* ** * *
2993099 GGCTTG-GTTCTAATGCTACTA-AAAT
64 GGCTTGAG-TATGGTGCTGCAATAAAT
* * ** * ** * *
2993124 ATTTTTTATTTT-TAAATTATTATAATAATTACTATTTATTTCATTTCATTCCCTGGGGACTTGG
1 -TTTTTTATTTTCAAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTGG
* *
2993188 GCTTGAGTTTGGTGTTGCAATAATAT
65 GCTTGAGTATGGTGCTGCAATAA-AT
* ** * * * *
2993214 TTTATTATTTTCGGAATAATTATAATAATTGTTATTAATTTTATTTCATTATC-GAGCACTTGGA
1 TTTTTTATTTTCAAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTGGG
* * ** *
2993278 CTTGAGTCTGATGCCACAATAATT
66 CTTGAGTATGGTGCTGCAATAAAT
** *
2993302 TCTTTTTATTTTTTGAAATAATTATAATAATAGTTATTTATTTTCATTTCA-TTTC-GAGGCACT
1 T-TTTTTA-TTTTCAAAATAATTATAATAATTGTTATTTATTTT-ATTTCATTTTCAG-GGCACT
* * * *
2993365 TGGGCTTGAGTGTAGTACTACAAT--AT
62 TGGGCTTGAGTATGGTGCTGCAATAAAT
* * * * ** * * * *
2993391 ATATATATATT-GGAATAATTATAATAATT-TATATGTATTTCA-TTCATTTT--GGGGATTTGG
1 TTTTTTATTTTCAAAATAATTATAATAATTGT-TATTTATTTTATTTCATTTTCAGGGCACTTGG
* * * *
2993451 CCTTGA-TATGGTGTTGTAATAACAA
65 GCTTGAGTATGGTGCTGCAATAA-AT
* * * *
2993476 TTTTTTATTTT-ATCGAATAATTATAATAATCT-TTATTTATTTTCTTTCATTTTCGGGGCATTT
1 TTTTTTATTTTCA--AAATAATTATAATAAT-TGTTATTTATTTTATTTCATTTTCAGGGCACTT
* * * *
2993539 GAGCGTGAGT-TGGTGCTGCAACATAT
63 GGGCTTGAGTATGGTGCTGCAATAAAT
* ** * * *
2993565 TTTTAT-TTTTCGGAATAATTATAATAATT-TCTATTTATTTTATTTCA-TTTCTATGCCATTTG
1 TTTTTTATTTTCAAAATAATTATAATAATTGT-TATTTATTTTATTTCATTTTC-AGGGCACTTG
* * **
2993627 GGTTTGAGTTTGGTGCTGTTATAATAAT
64 GGCTTGAGTATGGTGCTGCAAT-A-AAT
* ** * * * * *
2993655 TTTTATATTTTCTGGAATAATTATAATAATTTTTATTTATTTCATTTTATTTT-TGGAGCATTTG
1 TTTTTTATTTTC-AAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGG-GCACTTG
* * *
2993719 GGCTTGAATTTGGTACTGCAAT-AAT
64 GGCTTGAGTATGGTGCTGCAATAAAT
2993744 ATTTTTTATTTT
1 -TTTTTTATTTT
2993756 TTGGAATAAC
Statistics
Matches: 837, Mismatches: 192, Indels: 109
0.74 0.17 0.10
Matches are distributed among these distances:
82 8 0.01
83 12 0.01
84 5 0.01
85 13 0.02
86 30 0.04
87 71 0.08
88 136 0.16
89 71 0.08
90 183 0.22
91 119 0.14
92 123 0.15
93 66 0.08
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (89 bp):
TTTTTTATTTTCAAAATAATTATAATAATTGTTATTTATTTTATTTCATTTTCAGGGCACTTGGG
CTTGAGTATGGTGCTGCAATAAAT
Found at i:2993164 original size:178 final size:180
Alignment explanation
Indices: 2992853--2993354 Score: 464
Period size: 178 Copynumber: 2.8 Consensus size: 180
2992843 ACAATAGTAA
* ** * * ** * *
2992853 ATTTT-TTATTTTCAAGAATAATTATAATTATAATTATTTATTTTATTTCATTTTTAAGGTATTT
1 ATTTTATTATTTTCAA-AATAATTATAATAATTGTTATTAATTTTATTTCATTATCGA-GCACTT
* ** ** * * * * * * * *
2992917 GGACTTGAGTTTGGTGCTGCAGTAAAATTTTTTTATTTTCTCATAGAATTATAATAATTTCTATT
64 GGACTTGAGTCTAATGCCACAATAATATCTTTTTATTTTTTGAAATAATTATAATAATTACTATT
*
2992982 TATTTCATTTCATTCATTGGACACTGGGGCTTGAGTATGGTGCTGCAATAA-
129 TATTTCATTTCATTCACTGGACACTGGGGCTTGAGTATGGTGCTGCAATAAT
* * * * * * *
2993033 ATTTTTTTATTTTCCAAAAT-ATGTTTAATAATTGTTATTTATTTTATTTTATTTTCAGGGTACT
1 ATTTTATTATTTT-CAAAATAAT-TATAATAATTGTTATTAATTTTATTTCATTATC-GAGCACT
* * *
2993097 TGGGCTTG-GTTCTAATGCTACTAA-AATAT-TTTTTA-TTTTT-AAATTATTATAATAATTACT
63 TGGACTTGAG-TCTAATGCCAC-AATAATATCTTTTTATTTTTTGAAATAATTATAATAATTACT
* ** * * *
2993157 ATTTATTTCATTTCATTCCCTGGGGACTTGGGCTTGAGTTTGGTGTTGCAATAAT
126 ATTTATTTCATTTCATTCACTGGACACTGGGGCTTGAGTATGGTGCTGCAATAAT
**
2993212 ATTTTATTATTTTCGGAATAATTATAATAATTGTTATTAATTTTATTTCATTATCGAGCACTTGG
1 ATTTTATTATTTTCAAAATAATTATAATAATTGTTATTAATTTTATTTCATTATCGAGCACTTGG
* * *
2993277 ACTTGAGTCTGATGCCACAATAATTTCTTTTTATTTTTTGAAATAATTATAATAA-TAGTTATTT
66 ACTTGAGTCTAATGCCACAATAATATCTTTTTATTTTTTGAAATAATTATAATAATTA-CTATTT
2993341 ATTTTCATTTCATT
130 A-TTTCATTTCATT
2993355 TCGAGGCACT
Statistics
Matches: 264, Mismatches: 43, Indels: 29
0.79 0.13 0.09
Matches are distributed among these distances:
176 2 0.01
177 25 0.09
178 103 0.39
179 25 0.09
180 34 0.13
181 71 0.27
182 4 0.02
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.50
Consensus pattern (180 bp):
ATTTTATTATTTTCAAAATAATTATAATAATTGTTATTAATTTTATTTCATTATCGAGCACTTGG
ACTTGAGTCTAATGCCACAATAATATCTTTTTATTTTTTGAAATAATTATAATAATTACTATTTA
TTTCATTTCATTCACTGGACACTGGGGCTTGAGTATGGTGCTGCAATAAT
Found at i:2997577 original size:22 final size:21
Alignment explanation
Indices: 2997552--2997597 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
2997542 AACATAGAAA
2997552 AAATAAAGAAAAAAATTAAAAG
1 AAATAAAGAAAAAAA-TAAAAG
* *
2997574 AAATGAAGAAAAAAATAAAGG
1 AAATAAAGAAAAAAATAAAAG
2997595 AAA
1 AAA
2997598 AAGCAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (21 bp):
AAATAAAGAAAAAAATAAAAG
Found at i:3015092 original size:3 final size:3
Alignment explanation
Indices: 3015079--3015114 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
3015069 ATTCCCCTAA
3015079 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3015115 ACCTCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3015267 original size:26 final size:25
Alignment explanation
Indices: 3015221--3015269 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
3015211 TTTAATTAAC
*
3015221 AAATAAAATTTATTTTCAATAATGA
1 AAATAAAATATATTTTCAATAATGA
3015246 AAATATAAATATATGTTT-AATAAT
1 AAATA-AAATATAT-TTTCAATAAT
3015270 TGTTTTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 13 0.62
27 3 0.14
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (25 bp):
AAATAAAATATATTTTCAATAATGA
Found at i:3021163 original size:15 final size:16
Alignment explanation
Indices: 3021122--3021164 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
3021112 TTACAATTTG
*
3021122 AATTTAATTCTTATAT
1 AATTTAATTTTTATAT
* *
3021138 AAATTACTTTTTA-AT
1 AATTTAATTTTTATAT
3021153 AATTTAATTTTT
1 AATTTAATTTTT
3021165 GAATTTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTAATTTTTATAT
Found at i:3029742 original size:7 final size:7
Alignment explanation
Indices: 3029725--3029754 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
3029715 AAGTTTATGC
3029725 ATAACATT
1 ATAA-ATT
3029733 ATAAATT
1 ATAAATT
3029740 ATAAATT
1 ATAAATT
3029747 ATAAATT
1 ATAAATT
3029754 A
1 A
3029755 AATCAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:3043352 original size:16 final size:16
Alignment explanation
Indices: 3043328--3043361 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3043318 TTATTCCAAC
*
3043328 AAATTTGAAAAATAAA
1 AAATATGAAAAATAAA
*
3043344 AAATATGAAATATAAA
1 AAATATGAAAAATAAA
3043360 AA
1 AA
3043362 CAAAATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AAATATGAAAAATAAA
Found at i:3046191 original size:3 final size:3
Alignment explanation
Indices: 3046177--3046211 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3046167 ATTTTTATTT
*
3046177 TAC TAC TTC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
3046212 ATAATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (3 bp):
TAC
Found at i:3056297 original size:8 final size:8
Alignment explanation
Indices: 3056284--3056313 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3056274 TAGAAATATC
3056284 AAAAATAA
1 AAAAATAA
*
3056292 AAAAATAT
1 AAAAATAA
3056300 AAAAATAA
1 AAAAATAA
3056308 AAAAAT
1 AAAAAT
3056314 GATTTAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:3056305 original size:16 final size:17
Alignment explanation
Indices: 3056277--3056313 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
3056267 CTCAAGATAG
3056277 AAATATCAAAAATAAAA
1 AAATATCAAAAATAAAA
3056294 AAATAT-AAAAATAAAA
1 AAATATCAAAAATAAAA
3056310 AAAT
1 AAAT
3056314 GATTTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATATCAAAAATAAAA
Found at i:3056541 original size:29 final size:29
Alignment explanation
Indices: 3056499--3056556 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3056489 GGGTAAATTT
3056499 TTAATTTTAATAATAATAATAATAA-TATA
1 TTAATTTTAATAATAATAAT-ATAAGTATA
** *
3056528 TTAATTTTTTTAATATTAATATAAGTATA
1 TTAATTTTAATAATAATAATATAAGTATA
3056557 AATATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAATTTTAATAATAATAATATAAGTATA
Found at i:3065726 original size:18 final size:18
Alignment explanation
Indices: 3065703--3065739 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3065693 TACCTGAACA
3065703 TAATTACCTAACAACTTC
1 TAATTACCTAACAACTTC
3065721 TAATTACCTAACAACTTC
1 TAATTACCTAACAACTTC
3065739 T
1 T
3065740 TTTCATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTACCTAACAACTTC
Found at i:3074586 original size:18 final size:18
Alignment explanation
Indices: 3074549--3074591 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3074539 GAATATGTTT
3074549 TTAATTAAATAAATTTAA
1 TTAATTAAATAAATTTAA
* *
3074567 TTGATTAAA-AATTTTAAA
1 TTAATTAAATAAATTT-AA
3074585 TTAATTA
1 TTAATTA
3074592 CACATTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAATAAATTTAA
Found at i:3077405 original size:20 final size:20
Alignment explanation
Indices: 3077358--3077413 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
3077348 AATAGTTAAA
**
3077358 TATTTAATATTATAATTTTTTG
1 TATTTAAT-TTA-AATTTAATG
*
3077380 TTTTTAATTTAAATTTAATG
1 TATTTAATTTAAATTTAATG
*
3077400 TATTTATTTTAAAT
1 TATTTAATTTAAAT
3077414 AACCATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 19 0.66
21 3 0.10
22 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TATTTAATTTAAATTTAATG
Found at i:3079051 original size:31 final size:30
Alignment explanation
Indices: 3078976--3079051 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
3078966 ATACATAAAT
* *
3078976 TTTAA-TTTGATTTAATTATATATTGAAAT
1 TTTAATTTTGATTTAAATATATATTGAAAC
* * *
3079005 TTTAATTGTGGTTTAAATGTATACTTGAAAC
1 TTTAATTTTGATTTAAATATATA-TTGAAAC
*
3079036 TTTATTTTTGATTTAA
1 TTTAATTTTGATTTAA
3079052 TCATGCATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 5 0.14
30 13 0.35
31 19 0.51
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.54
Consensus pattern (30 bp):
TTTAATTTTGATTTAAATATATATTGAAAC
Found at i:3079221 original size:29 final size:28
Alignment explanation
Indices: 3079189--3079248 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
3079179 AGAAATAAAG
**
3079189 CAAATCAAAATTTTGTGTATAAAAATACA
1 CAAATCAAAA-TTCATGTATAAAAATACA
*
3079218 CAAAATCAAAATTCATGTATAAAATTACA
1 C-AAATCAAAATTCATGTATAAAAATACA
3079247 CA
1 CA
3079249 TTAAATTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 17 0.63
30 9 0.33
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.28
Consensus pattern (28 bp):
CAAATCAAAATTCATGTATAAAAATACA
Found at i:3079699 original size:2 final size:2
Alignment explanation
Indices: 3079688--3079722 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3079678 AAAATTTAAT
3079688 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3079723 ACATTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3083137 original size:13 final size:13
Alignment explanation
Indices: 3083119--3083161 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3083109 AAATAAAATG
3083119 TTTATATTTTTTA
1 TTTATATTTTTTA
* *
3083132 TTTATAATTTTAA
1 TTTATATTTTTTA
*
3083145 TTTATAATTTATTA
1 TTTAT-ATTTTTTA
3083159 TTT
1 TTT
3083162 GATTTAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTTTTTA
Found at i:3085434 original size:17 final size:17
Alignment explanation
Indices: 3085412--3085453 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3085402 CTATGGTCAA
*
3085412 AAGAAGGACAAATGAGT
1 AAGAAGGACAAATGAGC
3085429 AAGAAGGACAAATGAGC
1 AAGAAGGACAAATGAGC
3085446 AAGAAGGA
1 AAGAAGGA
3085454 AACGAATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.07, G:0.31, T:0.07
Consensus pattern (17 bp):
AAGAAGGACAAATGAGC
Found at i:3088619 original size:8 final size:8
Alignment explanation
Indices: 3088608--3088690 Score: 71
Period size: 8 Copynumber: 10.0 Consensus size: 8
3088598 AAAAAACCAA
3088608 AAAAAAAG
1 AAAAAAAG
*
3088616 AAAAAAGG
1 AAAAAAAG
3088624 AAAAAAAG
1 AAAAAAAG
*
3088632 GAAAAAAG
1 AAAAAAAG
*
3088640 AGAAAAAG
1 AAAAAAAG
3088648 AAAAGGAAAAG
1 -AAA--AAAAG
3088659 AGAAGAAAAG
1 A-AA-AAAAG
*
3088669 AAGAAAAG
1 AAAAAAAG
3088677 --AAAAAG
1 AAAAAAAG
3088683 AAAAAAAG
1 AAAAAAAG
3088691 GGAGGTCGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
6 5 0.08
8 38 0.62
9 3 0.05
10 8 0.13
11 7 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3088620 original size:11 final size:11
Alignment explanation
Indices: 3088594--3088687 Score: 55
Period size: 11 Copynumber: 7.9 Consensus size: 11
3088584 AGAAATTTCA
*
3088594 AAAAAAAAAAC
1 AAAAAAAAAAG
*
3088605 CAAAAAAAAAG
1 AAAAAAAAAAG
3088616 AAAAAAGGAAAA-
1 AAAAAA--AAAAG
3088628 AAAGGAAAAAAGAG
1 AAA--AAAAAA-AG
*
3088642 AAAAAGAAAAG
1 AAAAAAAAAAG
* * *
3088653 GAAAAGAGAAG
1 AAAAAAAAAAG
3088664 AAAAGAAGAAAAG
1 AAAA-AA-AAAAG
3088677 AAAAAGAAAAA
1 AAAAA-AAAAA
3088688 AAGGGAGGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
11 28 0.43
12 17 0.26
13 14 0.22
14 6 0.09
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3088628 original size:19 final size:19
Alignment explanation
Indices: 3088606--3088689 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 19
3088596 AAAAAAAACC
3088606 AAAAAAAAAGAAAAAAGG-
1 AAAAAAAAAGAAAAAAGGA
*
3088624 -AAAAAAAGGAAAAAAGAGA
1 AAAAAAAAAGAAAAAAG-GA
* *
3088643 AAAAGAAAAGGAAAAGAGAAGA
1 AAAA-AAAAAGAAAA-A-AGGA
3088665 AAAGAAGAAAAG-AAAAA-GA
1 AAA-AA-AAAAGAAAAAAGGA
3088684 AAAAAA
1 AAAAAA
3088690 GGGAGGTCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
17 16 0.29
18 3 0.05
19 5 0.09
20 4 0.07
21 11 0.20
22 10 0.18
23 6 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAGGA
Found at i:3088652 original size:30 final size:31
Alignment explanation
Indices: 3088618--3088691 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
3088608 AAAAAAAGAA
3088618 AAAAGGAAAAAAAGGAA-AAAAG-AGAAAAAG
1 AAAAGGAAAAAAAGGAAGAAAAGAAG-AAAAG
*
3088648 AAAAGG-AAAAGA-GAAGAAAAGAAGAAAAG
1 AAAAGGAAAAAAAGGAAGAAAAGAAGAAAAG
*
3088677 AAAAAGAAAAAAAGG
1 AAAAGGAAAAAAAGG
3088692 GAGGTCGAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 3 0.08
29 20 0.54
30 13 0.35
31 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (31 bp):
AAAAGGAAAAAAAGGAAGAAAAGAAGAAAAG
Found at i:3089000 original size:80 final size:80
Alignment explanation
Indices: 3088867--3089410 Score: 627
Period size: 80 Copynumber: 6.8 Consensus size: 80
3088857 GTACTGCAAG
*
3088867 TTGAAGAAATCCAATCTTTTACCCT-ACCTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACC
1 TTGAAGAAATCCAATCTTTTACCCTAACC-AGAGGGCAAGATTGAAGACCATCCAATCTTTTACC
* *
3088931 TCGATCATGAGGCAGA
65 CCGATCATGGGGCAGA
* *
3088947 TTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGTAAGATTGAAGACCATCCGATCTTTTACCC
1 TTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCC
*
3089012 CGATCATGGGACAGA
66 CGATCATGGGGCAGA
* * * * *
3089027 GTGAAGAAATCCAATCTTTTACCCTAACTAAAGGACAAGATTGAAGACCATCCAATCTTTTACCT
1 TTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCC
*
3089092 CGATCATGGGGTAGA
66 CGATCATGGGGCAGA
* * *
3089107 TTGAAGAAATCCAATCTTTTACCCTAACTAAAGGGTAAGATTGAAGACCATCCAATCTTTTACCC
1 TTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCC
*
3089172 CGATCATGGGGTAGA
66 CGATCATGGGGCAGA
* * * * * *
3089187 TTGAAGAAATCCAATCTCTTACCCCAACCAGAGGGCAAGATTGAAGACTATCCGATCTCTTACCT
1 TTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCC
*
3089252 CGATCATGGGGCAAA
66 CGATCATGGGGCAGA
* * * * * * *
3089267 TTGAA-AACTATCCAATCTTTTACCCTAATCATAGGG-TAGATTGAAAACAATCTAATCTCTTAC
1 TTGAAGAA--ATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTAC
* * **
3089330 CCCAACCATAAGGCAGA
64 CCCGATCATGGGGCAGA
* * * **
3089347 TTGAA-ACAAGCCAATCTTTTACACC-AACCATGA-GG-TAGATT-AAAAAAATCCAATCTTTTA
1 TTGAAGA-AATCCAATCTTTTAC-CCTAACCA-GAGGGCAAGATTGAAGACCATCCAATCTTTTA
3089407 CCCC
63 CCCC
3089411 TAAAGTTATA
Statistics
Matches: 409, Mismatches: 49, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
78 20 0.05
79 27 0.07
80 335 0.82
81 27 0.07
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (80 bp):
TTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCC
CGATCATGGGGCAGA
Found at i:3089464 original size:50 final size:50
Alignment explanation
Indices: 3089398--3089535 Score: 213
Period size: 50 Copynumber: 2.8 Consensus size: 50
3089388 AAAAAAATCC
* * *
3089398 AATCTTTTACCCCTAAAGTTATAGAGGGGTAGATTGAAGCTACAAAAACA
1 AATCTTATACCTCTAAAGTTATAGAGGGGTAGATTAAAGCTACAAAAACA
* *
3089448 AATCTTATACCTCTAAAGTTATAGAGGGGTAAATTAAAGCTACAAAAGCA
1 AATCTTATACCTCTAAAGTTATAGAGGGGTAGATTAAAGCTACAAAAACA
* *
3089498 AATCTTATACCTCTAAAGTAATAGAGGGATAGATTAAA
1 AATCTTATACCTCTAAAGTTATAGAGGGGTAGATTAAA
3089536 ACTCACAATA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (50 bp):
AATCTTATACCTCTAAAGTTATAGAGGGGTAGATTAAAGCTACAAAAACA
Found at i:3106262 original size:6 final size:6
Alignment explanation
Indices: 3106251--3106296 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
3106241 TTCCCTTTGA
3106251 TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC TCTG
1 TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC TCTG
3106297 GGTTTGTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.17, T:0.35
Consensus pattern (6 bp):
TCTGCC
Found at i:3107402 original size:18 final size:17
Alignment explanation
Indices: 3107348--3107402 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
3107338 AGCATAACTC
3107348 ATTTTTTA-AGTT-TGTA
1 ATTTTTTATA-TTATGTA
* * *
3107364 ATATTTTATATTATATT
1 ATTTTTTATATTATGTA
3107381 ATTTTTATATATTATGTA
1 ATTTTT-TATATTATGTA
3107399 ATTT
1 ATTT
3107403 AGAATACATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 9 0.30
17 8 0.27
18 13 0.43
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTTTTTATATTATGTA
Found at i:3120292 original size:29 final size:27
Alignment explanation
Indices: 3120260--3120313 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
3120250 TTCAAATCTG
3120260 AAGTAAAAAAATTAAATTCTTGAAAATAA
1 AAGTAAAAAAATTAAATT-TT-AAAATAA
* *
3120289 AAGTATAAGAATTAAATTTTAAAAT
1 AAGTAAAAAAATTAAATTTTAAAAT
3120314 TGTGGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 2 0.09
29 16 0.70
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (27 bp):
AAGTAAAAAAATTAAATTTTAAAATAA
Found at i:3121678 original size:28 final size:29
Alignment explanation
Indices: 3121618--3121678 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
3121608 TTACATTGAT
* *
3121618 TGATTATTTAACTAGTAAATGAAGTATAA
1 TGATTATTTAACTAATAAATCAAGTATAA
3121647 -GATTATTTAACTACATAAA-CAA-TATAA
1 TGATTATTTAACTA-ATAAATCAAGTATAA
3121674 TGATT
1 TGATT
3121679 TTAACTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.38
Consensus pattern (29 bp):
TGATTATTTAACTAATAAATCAAGTATAA
Found at i:3137407 original size:23 final size:23
Alignment explanation
Indices: 3137363--3137408 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3137353 ATATTGTTCG
* *
3137363 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
3137386 TGAACATGTTC-ATGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
3137409 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:3137459 original size:28 final size:28
Alignment explanation
Indices: 3137404--3137465 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
3137394 TTCATGAACA
* * *
3137404 TTAAACAAACGAACATGAACACATAATT
1 TTAAATAAACGAACATGAACAAAAAATT
*
3137432 TTAAATAAATGAACATGAACAAAAAATT
1 TTAAATAAACGAACATGAACAAAAAATT
*
3137460 TAAAAT
1 TTAAAT
3137466 TCTTAACGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.24
Consensus pattern (28 bp):
TTAAATAAACGAACATGAACAAAAAATT
Found at i:3142638 original size:21 final size:23
Alignment explanation
Indices: 3142612--3142653 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
3142602 TATTATTGTA
3142612 TCCAAAATA-TAT-TTTTTTATT
1 TCCAAAATATTATATTTTTTATT
3142633 TCCAAAATATTATATTTTTTA
1 TCCAAAATATTATATTTTTTA
3142654 GAAATTCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (23 bp):
TCCAAAATATTATATTTTTTATT
Found at i:3156232 original size:15 final size:15
Alignment explanation
Indices: 3156184--3156232 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
3156174 AACCTTCTGA
*
3156184 TGATTCTCTACCAAT
1 TGATTCTCTACCAGT
* *
3156199 TGAATCTCTAACAGT
1 TGATTCTCTACCAGT
3156214 TGATTCTCTACCAGT
1 TGATTCTCTACCAGT
3156229 TGAT
1 TGAT
3156233 GCCATGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (15 bp):
TGATTCTCTACCAGT
Found at i:3158688 original size:214 final size:214
Alignment explanation
Indices: 3158319--3158747 Score: 849
Period size: 214 Copynumber: 2.0 Consensus size: 214
3158309 CCTGAAAAAA
3158319 AAAAAAAACTCAGAAACTATAATACAAAATCAGAAAAAGTAGTAATAAGGATAGTTAAGAGCATG
1 AAAAAAAACTCAGAAACTATAATACAAAATCAGAAAAAGTAGTAATAAGGATAGTTAAGAGCATG
3158384 AAAGTAAAATGCAATGGTATATAAGTGCAGTTGAATTCAGGAAAGGAAAAAGCTAGGCACAAAGA
66 AAAGTAAAATGCAATGGTATATAAGTGCAGTTGAATTCAGGAAAGGAAAAAGCTAGGCACAAAGA
3158449 GAAATTGGTGATGGTTGAAAACTGTGTTATGTTCTGATAAGCATATATTAGTTTAAAGCTTATTT
131 GAAATTGGTGATGGTTGAAAACTGTGTTATGTTCTGATAAGCATATATTAGTTTAAAGCTTATTT
3158514 TGTATTACTAACCGTAAAC
196 TGTATTACTAACCGTAAAC
*
3158533 AAAAAAAACTCAGAAACTATAATACAAATTCAGAAAAAGTAGTAATAAGGATAGTTAAGAGCATG
1 AAAAAAAACTCAGAAACTATAATACAAAATCAGAAAAAGTAGTAATAAGGATAGTTAAGAGCATG
3158598 AAAGTAAAATGCAATGGTATATAAGTGCAGTTGAATTCAGGAAAGGAAAAAGCTAGGCACAAAGA
66 AAAGTAAAATGCAATGGTATATAAGTGCAGTTGAATTCAGGAAAGGAAAAAGCTAGGCACAAAGA
3158663 GAAATTGGTGATGGTTGAAAACTGTGTTATGTTCTGATAAGCATATATTAGTTTAAAGCTTATTT
131 GAAATTGGTGATGGTTGAAAACTGTGTTATGTTCTGATAAGCATATATTAGTTTAAAGCTTATTT
3158728 TGTATTACTAACCGTAAAC
196 TGTATTACTAACCGTAAAC
3158747 A
1 A
3158748 CTAGAACGAA
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 214 1.00
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (214 bp):
AAAAAAAACTCAGAAACTATAATACAAAATCAGAAAAAGTAGTAATAAGGATAGTTAAGAGCATG
AAAGTAAAATGCAATGGTATATAAGTGCAGTTGAATTCAGGAAAGGAAAAAGCTAGGCACAAAGA
GAAATTGGTGATGGTTGAAAACTGTGTTATGTTCTGATAAGCATATATTAGTTTAAAGCTTATTT
TGTATTACTAACCGTAAAC
Found at i:3172083 original size:21 final size:21
Alignment explanation
Indices: 3172046--3172086 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3172036 ATAATTCTTG
3172046 TTTTAAATTATACTATTTATGT
1 TTTTAAATTATA-TATTTATGT
3172068 TTTTAAATGTAT-TATTTAT
1 TTTTAAAT-TATATATTTAT
3172087 ATTCATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTAAATTATATATTTATGT
Found at i:3172446 original size:9 final size:9
Alignment explanation
Indices: 3172434--3172581 Score: 81
Period size: 9 Copynumber: 15.9 Consensus size: 9
3172424 TTAGTTTTAC
3172434 ATTTTTATA
1 ATTTTTATA
3172443 ATTTATTAT-
1 ATTT-TTATA
3172452 ATTTTTATA
1 ATTTTTATA
*
3172461 ATATTTATA
1 ATTTTTATA
*
3172470 ATTTTTTTA
1 ATTTTTATA
*
3172479 ATTTTAATGA
1 ATTTTTAT-A
* *
3172489 GTTTATATTA
1 ATTTTTA-TA
*
3172499 ATTTTAAT-
1 ATTTTTATA
3172507 ATTTTTACT-
1 ATTTTTA-TA
*
3172516 ATTTTT-TT
1 ATTTTTATA
3172524 ATTTTTATA
1 ATTTTTATA
*
3172533 GTTCTATTCA-A
1 ATT-T-TT-ATA
3172544 ATTTTTATA
1 ATTTTTATA
*
3172553 ATTTTTTTATG
1 A--TTTTTATA
3172564 ATTTTTAATA
1 ATTTTT-ATA
*
3172574 AATTTTAT
1 ATTTTTAT
3172582 GGGAAAATTA
Statistics
Matches: 107, Mismatches: 18, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
7 1 0.01
8 17 0.16
9 51 0.48
10 23 0.21
11 14 0.13
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:3172468 original size:20 final size:18
Alignment explanation
Indices: 3172434--3172556 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 18
3172424 TTAGTTTTAC
*
3172434 ATTTTTATAATTTATTAT
1 ATTTTTATAATTTATAAT
3172452 ATTTTTATAATATTTATAAT
1 ATTTTTAT-A-ATTTATAAT
3172472 -TTTTT-TAATTT-TAAT
1 ATTTTTATAATTTATAAT
*
3172487 GAGTTTATATTAATTT-TAAT
1 -A-TTTTTA-TAATTTATAAT
**
3172507 ATTTTTACT-ATTT-TTTT
1 ATTTTTA-TAATTTATAAT
*
3172524 ATTTTTATAGTTCTATTCAA-
1 ATTTTTATAATT-TA-T-AAT
3172544 ATTTTTATAATTT
1 ATTTTTATAATTT
3172557 TTTTATGATT
Statistics
Matches: 83, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
15 4 0.05
16 5 0.06
17 16 0.19
18 20 0.24
19 8 0.10
20 30 0.36
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTTATAATTTATAAT
Found at i:3172494 original size:46 final size:45
Alignment explanation
Indices: 3172434--3172554 Score: 106
Period size: 45 Copynumber: 2.6 Consensus size: 45
3172424 TTAGTTTTAC
* *
3172434 ATTTTTATAATTTATTATATTTTTATAATATTTATA-ATTTTTTT
1 ATTTTAATAGTTTATTATATTTTTATAATATTTATACATTTTTTT
* *
3172478 AATTTTAATGAGTTTA-TAT-TAATTT-TAATATTTTTACTATTTTTTT
1 -ATTTTAAT-AGTTTATTATAT-TTTTATAATATTTATAC-ATTTTTTT
* *
3172524 ATTTTTATAGTTCTATTCAAATTTTTATAAT
1 ATTTTAATAGTT-TATT-ATATTTTTATAAT
3172555 TTTTTTATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
44 15 0.25
45 22 0.37
46 14 0.23
47 4 0.07
48 5 0.08
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (45 bp):
ATTTTAATAGTTTATTATATTTTTATAATATTTATACATTTTTTT
Found at i:3185302 original size:11 final size:11
Alignment explanation
Indices: 3185286--3185321 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3185276 TTATTTCACG
3185286 TTATAATATTA
1 TTATAATATTA
3185297 TTATAATATTA
1 TTATAATATTA
*
3185308 TT-TAATTTTA
1 TTATAATATTA
3185318 TTAT
1 TTAT
3185322 CATTACTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATAATATTA
Found at i:3187108 original size:29 final size:28
Alignment explanation
Indices: 3187076--3187145 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
3187066 GTAATTAAAT
* *
3187076 CTAAATTTTAAAATCTAAAAGTA-AAAGGA
1 CTAAATTTTAAAA-ATAAAAATATAAA-GA
**
3187105 CTAAACTCCTAAAAATAAAAATATAAAGA
1 CTAAA-TTTTAAAAATAAAAATATAAAGA
3187134 CTAAATTTTAAA
1 CTAAATTTTAAA
3187146 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.15
29 19 0.58
30 9 0.27
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (28 bp):
CTAAATTTTAAAAATAAAAATATAAAGA
Found at i:3203977 original size:31 final size:30
Alignment explanation
Indices: 3203920--3203978 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
3203910 TAATAAATAA
* *
3203920 AAAATATATAAATTTATTAAATATTAAATT
1 AAAATATATAAATTTATAAAAAATTAAATT
3203950 AAAATAATATAAATATT-TAAAAAATTAAA
1 AAAAT-ATATAAAT-TTATAAAAAATTAAA
3203979 AATAATATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 18 0.72
32 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAATATATAAATTTATAAAAAATTAAATT
Found at i:3206170 original size:23 final size:21
Alignment explanation
Indices: 3206119--3206171 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
3206109 AAGAGGCCGA
*
3206119 AATTAAATTGTAATTTTTACG
1 AATTAAATTGTAATTTTTAAG
*
3206140 ATAATAAATATGTAATTTTTAAAG
1 A-ATTAAAT-TGTAATTTTT-AAG
3206164 AATTAAAT
1 AATTAAAT
3206172 CAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 6 0.23
23 16 0.62
24 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (21 bp):
AATTAAATTGTAATTTTTAAG
Found at i:3206241 original size:8 final size:9
Alignment explanation
Indices: 3206222--3206246 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3206212 TTTTTACTAA
3206222 TTTAAAATT
1 TTTAAAATT
3206231 TTTAAAATT
1 TTTAAAATT
3206240 TTTAAAA
1 TTTAAAA
3206247 GCAAGGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:3218051 original size:13 final size:13
Alignment explanation
Indices: 3218027--3218051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3218017 TTAAGTTCGA
3218027 GATTTGAAGTTTG
1 GATTTGAAGTTTG
3218040 GATTTGAAGTTT
1 GATTTGAAGTTT
3218052 AGAATTTTAA
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:0.00, G:0.28, T:0.48
Consensus pattern (13 bp):
GATTTGAAGTTTG
Found at i:3218145 original size:24 final size:24
Alignment explanation
Indices: 3218117--3218166 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3218107 AAAAATTATC
* *
3218117 AAAATTATATATAATTATA-TAAAT
1 AAAATTAT-TAAAATAATATTAAAT
3218141 AAAATTATTAAAATAATATTAAAT
1 AAAATTATTAAAATAATATTAAAT
3218165 AA
1 AA
3218167 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATTATTAAAATAATATTAAAT
Found at i:3218173 original size:20 final size:19
Alignment explanation
Indices: 3218146--3218189 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3218136 TAAATAAAAT
3218146 TATT-AAAATAA-TATTAAA
1 TATTAAAAATAACTA-TAAA
3218164 TAATTAAAAATAACTATAAA
1 T-ATTAAAAATAACTATAAA
3218184 TATTAA
1 TATTAA
3218190 GTTGAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 8 0.35
20 12 0.52
21 2 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTAAAAATAACTATAAA
Found at i:3225015 original size:9 final size:9
Alignment explanation
Indices: 3224982--3225130 Score: 72
Period size: 9 Copynumber: 15.7 Consensus size: 9
3224972 TTAAAAAGTC
3224982 ATAAAAATT
1 ATAAAAATT
* *
3224991 ATTAAAATG
1 ATAAAAATT
*
3225000 AGGAAAAATT
1 A-TAAAAATT
**
3225010 ATAAAAAAC
1 ATAAAAATT
3225019 A-AAATAATT
1 ATAAA-AATT
*
3225028 AATATTAAAATA
1 -ATA--AAAATT
*
3225040 ATAGAAAA-A
1 ATA-AAAATT
3225049 ATA-AAATAT
1 ATAAAAAT-T
3225058 ATAAAAATT
1 ATAAAAATT
*
3225067 GATATAAATTT
1 -ATA-AAAATT
3225078 ATAAAAATT
1 ATAAAAATT
3225087 ATAAAAATGT
1 ATAAAAAT-T
3225097 ATAATAAATCT
1 ATAA-AAAT-T
*
3225108 AT-TAAATT
1 ATAAAAATT
*
3225116 ATAAAAAAT
1 ATAAAAATT
3225125 ATAAAA
1 ATAAAA
3225131 TTAATTGAAC
Statistics
Matches: 107, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
7 3 0.03
8 6 0.06
9 51 0.48
10 26 0.24
11 16 0.15
12 3 0.03
13 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3225089 original size:29 final size:29
Alignment explanation
Indices: 3225049--3225122 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
3225039 AATAGAAAAA
*
3225049 ATAAAATATATAAAAAT-TGAT-ATAAATTT
1 ATAAAAT-TATAAAAATGT-ATAATAAATCT
3225078 ATAAAAATTATAAAAATGTATAATAAATCT
1 AT-AAAATTATAAAAATGTATAATAAATCT
*
3225108 ATTAAATTATAAAAA
1 ATAAAATTATAAAAA
3225123 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (29 bp):
ATAAAATTATAAAAATGTATAATAAATCT
Found at i:3226286 original size:18 final size:18
Alignment explanation
Indices: 3226259--3226296 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3226249 ATATATATTT
*
3226259 TAAATATTAATCTCATTA
1 TAAATATTAATCTCAATA
*
3226277 TAAATTTTAATCTCAATA
1 TAAATATTAATCTCAATA
3226295 TA
1 TA
3226297 TTCAAACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATTAATCTCAATA
Found at i:3226450 original size:7 final size:7
Alignment explanation
Indices: 3226438--3226464 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3226428 TTTGTTTTAA
3226438 TTATATT
1 TTATATT
3226445 TTATATT
1 TTATATT
3226452 TTATATT
1 TTATATT
3226459 TTATAT
1 TTATAT
3226465 AATGCTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATATT
Found at i:3226621 original size:7 final size:7
Alignment explanation
Indices: 3226609--3226640 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3226599 TTCCATTATC
3226609 ACTTTTT
1 ACTTTTT
3226616 ACTTTTT
1 ACTTTTT
3226623 ACTTTTT
1 ACTTTTT
3226630 ACTTTTT
1 ACTTTTT
3226637 ACTT
1 ACTT
3226641 CCCGTCGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
ACTTTTT
Found at i:3226955 original size:30 final size:30
Alignment explanation
Indices: 3226856--3226955 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
3226846 TTACATATTA
*
3226856 AATAAATTTAATTTTAAATAT-AAAATATTC
1 AATAAATTTAATTTTAATTATAAAAAT-TTC
* * * *
3226886 AACAAATTTTACTCTTAATATTTATAAAATTT-
1 AATAAA-TTTAATTTTAAT-TATA-AAAATTTC
* *
3226918 -ATCAATTTAATTTTAATTCTAAAAATTTC
1 AATAAATTTAATTTTAATTATAAAAATTTC
3226947 AATAAATTT
1 AATAAATTT
3226956 TAAAAAACCC
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 7 0.13
29 3 0.06
30 22 0.42
31 12 0.23
32 2 0.04
33 2 0.04
34 5 0.09
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (30 bp):
AATAAATTTAATTTTAATTATAAAAATTTC
Found at i:3228141 original size:53 final size:53
Alignment explanation
Indices: 3228083--3228203 Score: 154
Period size: 53 Copynumber: 2.3 Consensus size: 53
3228073 TGTTTTGAGG
* * *
3228083 CACATGGGCGTGGGTCAGGGTGTGTGTATACTGTTCT-AGGACACACGGGTTGA
1 CACATGGGCGTGGGTCAGGGTGTGTATATACTGTTCTGAGGA-ACACGAGCTGA
* * * *
3228136 CACATGGGCGTGTGTTAGGGTGTGTATATACTGTTTTGAGGAACATGAGCTGA
1 CACATGGGCGTGGGTCAGGGTGTGTATATACTGTTCTGAGGAACACGAGCTGA
*
3228189 CACATGGGTGTGGGT
1 CACATGGGCGTGGGT
3228204 ACATGGTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 54 0.93
54 4 0.07
ACGTcount: A:0.20, C:0.14, G:0.37, T:0.29
Consensus pattern (53 bp):
CACATGGGCGTGGGTCAGGGTGTGTATATACTGTTCTGAGGAACACGAGCTGA
Found at i:3228692 original size:40 final size:40
Alignment explanation
Indices: 3228645--3228749 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
3228635 TACTGAGTTA
* * *
3228645 GCAGTGACGCTGTAAACACTGCAATATTATAACTAAACCG
1 GCAGTGACACTGTAAACACTACAATATTACAACTAAACCG
* * * * * * *
3228685 GTAGTGACATTGTAAACACCACAAGATTACCACTGAACTG
1 GCAGTGACACTGTAAACACTACAATATTACAACTAAACCG
3228725 GCAGTGACACTGTAAACACTACAAT
1 GCAGTGACACTGTAAACACTACAAT
3228750 GTATCATACC
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (40 bp):
GCAGTGACACTGTAAACACTACAATATTACAACTAAACCG
Found at i:3228843 original size:29 final size:29
Alignment explanation
Indices: 3228810--3228894 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
3228800 AACGGATAAG
*
3228810 GTATCACGTCTGCATCTGTAACTGTATTT
1 GTATCACGTCTGCATCTGTAACTGTATAT
* *
3228839 GTATCACGTTTGCATTTGTAACTGTATAT
1 GTATCACGTCTGCATCTGTAACTGTATAT
* * *
3228868 GTATCATGTCTGCATCCGTAATTGTAT
1 GTATCACGTCTGCATCTGTAACTGTAT
3228895 CTGTGACATG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (29 bp):
GTATCACGTCTGCATCTGTAACTGTATAT
Found at i:3228904 original size:29 final size:29
Alignment explanation
Indices: 3228885--3228985 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
3228875 GTCTGCATCC
*
3228885 GTAATTGTATCTGTGACATGACTGTATAT
1 GTAATTGTATCTGTGACATGACTGTATCT
* * *
3228914 GTAAATGTATCTTTGACATGACAGTATCT
1 GTAATTGTATCTGTGACATGACTGTATCT
* *
3228943 ATAATTGTATCTGTGGCATGACTGTATCT
1 GTAATTGTATCTGTGACATGACTGTATCT
* **
3228972 ATAACCGTATCTGT
1 GTAATTGTATCTGT
3228986 ATTATTTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (29 bp):
GTAATTGTATCTGTGACATGACTGTATCT
Found at i:3228917 original size:58 final size:58
Alignment explanation
Indices: 3228855--3228987 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
3228845 CGTTTGCATT
* * * *
3228855 TGTAACTGTATATGTATCATGTCTGCATCCGTAATTGTATCTGTGACATGACTGTATA
1 TGTAACTGTATCTGTATCATGACAGCATCCATAATTGTATCTGTGACATGACTGTATA
* * * * * *
3228913 TGTAAATGTATCTTTGA-CATGACAGTATCTATAATTGTATCTGTGGCATGACTGTATC
1 TGTAACTGTATCTGT-ATCATGACAGCATCCATAATTGTATCTGTGACATGACTGTATA
* *
3228971 TATAACCGTATCTGTAT
1 TGTAACTGTATCTGTAT
3228988 TATTTTTATA
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
57 1 0.02
58 57 0.97
59 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (58 bp):
TGTAACTGTATCTGTATCATGACAGCATCCATAATTGTATCTGTGACATGACTGTATA
Found at i:3230217 original size:15 final size:17
Alignment explanation
Indices: 3230197--3230228 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3230187 ACTTCACACC
3230197 AATGAAT-TTAA-AAAA
1 AATGAATCTTAATAAAA
3230212 AATGAATCTTAATAAAA
1 AATGAATCTTAATAAAA
3230229 TTGGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (17 bp):
AATGAATCTTAATAAAA
Found at i:3236277 original size:40 final size:40
Alignment explanation
Indices: 3236214--3236294 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
3236204 ATCATTAATG
3236214 TATTAAATAATAATTCATATAATAATTATTGTTAATATTTTA
1 TATTAAATAATAATTCATATAATAATTATT-TTAA-ATTTTA
*
3236256 TATTAAAATAA-AATT-AT-TAATATTTATTTTAAATTTTA
1 TATT-AAATAATAATTCATATAATAATTATTTTAAATTTTA
3236294 T
1 T
3236295 TATATATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
38 7 0.19
39 4 0.11
40 10 0.27
41 2 0.05
42 8 0.22
43 6 0.16
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (40 bp):
TATTAAATAATAATTCATATAATAATTATTTTAAATTTTA
Found at i:3236341 original size:26 final size:26
Alignment explanation
Indices: 3236248--3236341 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
3236238 ATTATTGTTA
***
3236248 ATATTTTATATTAAAATAAAATTAT-T
1 ATATTTTAT-TTAAAATTTTATTATAT
*
3236274 A-ATATTTATTTTAAATTTTATTATAT
1 ATAT-TTTATTTAAAATTTTATTATAT
**
3236300 AT-TTCTT-TGAATAAATTTTATTATAT
1 ATATT-TTATTTA-AAATTTTATTATAT
3236326 ATATTTTATTTAAAAT
1 ATATTTTATTTAAAAT
3236342 AATGATGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
25 15 0.29
26 33 0.63
27 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATTTTATTTAAAATTTTATTATAT
Found at i:3236343 original size:30 final size:26
Alignment explanation
Indices: 3236256--3236327 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
3236246 TAATATTTTA
* *
3236256 TATTAAAATAAA-ATTATTA-ATATT
1 TATTTAAATAAATTTTATTATATATT
3236280 TATTT---TAAATTTTATTATATATT
1 TATTTAAATAAATTTTATTATATATT
* *
3236303 TCTTTGAATAAATTTTATTATATAT
1 TATTTAAATAAATTTTATTATATAT
3236328 ATTTTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.10
22 6 0.15
23 9 0.22
24 4 0.10
26 17 0.43
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
TATTTAAATAAATTTTATTATATATT
Found at i:3240770 original size:23 final size:22
Alignment explanation
Indices: 3240726--3240779 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
3240716 AAATTCTTGT
* *
3240726 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGCT-AAA
3240749 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGCTAAA
*
3240771 TAAACTAAA
1 TAAAATAAA
3240780 CTTCTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.41
23 11 0.41
24 5 0.19
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCTAAA
Found at i:3254430 original size:30 final size:30
Alignment explanation
Indices: 3254396--3254460 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
3254386 ATCATTTTGT
3254396 AATTTTATAAAATTGAGTTCCTAAAACATA
1 AATTTTATAAAATTGAGTTCCTAAAACATA
3254426 AATTTTATAAAATTGAGTTCCTAAAACATA
1 AATTTTATAAAATTGAGTTCCTAAAACATA
3254456 AATTT
1 AATTT
3254461 AGTAATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (30 bp):
AATTTTATAAAATTGAGTTCCTAAAACATA
Found at i:3257533 original size:134 final size:135
Alignment explanation
Indices: 3257220--3257583 Score: 486
Period size: 134 Copynumber: 2.7 Consensus size: 135
3257210 ACATTCGTGC
* * * *
3257220 AGTCAAACCCGGGTCTATTGTTTGGAAGGCAGTTATCCTAACCGTTGGACTACAAACCCTTGTTG
1 AGTCGAACCCGGGTCTATTGCTTGGAAGGCAGTTATCCTAACCGTTGGACTACAAACGCTGGTTG
* *
3257285 TTTAGGAGTTTTATTTTACAAAATAAAATGTGTTTTCAAGTGATTTTAAAAATATTAATTGCGTT
66 TTTAGGAGTTTTATTTTA-AAAATAAAATGTATTTTCAAGTGATTTTAAAAATA-TAACTGCGTT
3257350 TGCCGGG
129 TGCCGGG
* *
3257357 AGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGC-GGTAT
1 AGTCGAACCCGGGTCTATTGCTTGGAAGGCAGTTATCCTAACCGTTGGACTACAAACGCTGGT-T
* *
3257421 GTTTATGAGTTTTATTTT-AAAATAAAATGTATTTTTAAGTGATTTTAAAAA-A-AACTGCCTGT
65 GTTTAGGAGTTTTATTTTAAAAATAAAATGTATTTTCAAGTGATTTTAAAAATATAACTG-C-GT
3257483 TTGCCGGG
128 TTGCCGGG
* * *
3257491 AGTCGGACCCGGGTCTATTGCTTGAAAGGCAGTTATCCTAACCGTTGGACTACAAACGCTTGATT
1 AGTCGAACCCGGGTCTATTGCTTGGAAGGCAGTTATCCTAACCGTTGGACTACAAACGC-TGGTT
** *
3257556 -TTTAAAATTTTTATTTTAAAATATAAAA
65 GTTTAGGAGTTTTATTTTAAAA-ATAAAA
3257584 CTGAAAAAAA
Statistics
Matches: 202, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
132 4 0.02
133 1 0.00
134 80 0.40
135 35 0.17
136 10 0.05
137 72 0.36
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (135 bp):
AGTCGAACCCGGGTCTATTGCTTGGAAGGCAGTTATCCTAACCGTTGGACTACAAACGCTGGTTG
TTTAGGAGTTTTATTTTAAAAATAAAATGTATTTTCAAGTGATTTTAAAAATATAACTGCGTTTG
CCGGG
Found at i:3258050 original size:18 final size:19
Alignment explanation
Indices: 3258019--3258061 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3258009 ATATTTATTT
*
3258019 TTTA-TGAATATTTTTAAA
1 TTTATTGAATATTTTAAAA
3258037 TTTATTGAAT-TTTTAAAA
1 TTTATTGAATATTTTAAAA
3258055 TATTATT
1 T-TTATT
3258062 TTTATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTATTGAATATTTTAAAA
Found at i:3259351 original size:6 final size:6
Alignment explanation
Indices: 3259340--3259370 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3259330 TGGATCCTCT
3259340 GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC G
1 GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC G
3259371 ATGGTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.35, T:0.16
Consensus pattern (6 bp):
GGCTCC
Found at i:3273741 original size:2 final size:2
Alignment explanation
Indices: 3273736--3273768 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3273726 GTGTGTGTGT
3273736 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3273769 CTCACAGTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3277521 original size:14 final size:14
Alignment explanation
Indices: 3277502--3277528 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3277492 TTATTTACCT
3277502 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
3277516 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
3277529 AATCTTTTCC
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:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:3279095 original size:30 final size:30
Alignment explanation
Indices: 3279059--3279125 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
3279049 CTTGCCTTCT
** *
3279059 TGTAAATGCAGTTCGTGCGACTGCAATCCG
1 TGTAAATGCAACTCGTACGACTGCAATCCG
* *
3279089 TGTAAATGCAACTCGTATGACTGTAATCCG
1 TGTAAATGCAACTCGTACGACTGCAATCCG
3279119 TGTAAAT
1 TGTAAAT
3279126 ATAGCTCGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (30 bp):
TGTAAATGCAACTCGTACGACTGCAATCCG
Found at i:3279142 original size:30 final size:30
Alignment explanation
Indices: 3279071--3279143 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
3279061 TAAATGCAGT
* *
3279071 TCGTGCGACTGCAATCCGTGTAAATGCAAC
1 TCGTGCGACTGTAATCCGTGTAAATACAAC
** * *
3279101 TCGTATGACTGTAATCCGTGTAAATATAGC
1 TCGTGCGACTGTAATCCGTGTAAATACAAC
*
3279131 TCGTGCAACTGTA
1 TCGTGCGACTGTA
3279144 GTTTGTGTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (30 bp):
TCGTGCGACTGTAATCCGTGTAAATACAAC
Found at i:3288491 original size:22 final size:22
Alignment explanation
Indices: 3288465--3288506 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3288455 CATATATAAG
*
3288465 GTTGTAAATGAATAGAAGTTTT
1 GTTGTAAACGAATAGAAGTTTT
3288487 GTTGTAAACGAATAGAAGTT
1 GTTGTAAACGAATAGAAGTT
3288507 GAAACAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (22 bp):
GTTGTAAACGAATAGAAGTTTT
Found at i:3298946 original size:18 final size:17
Alignment explanation
Indices: 3298917--3298950 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3298907 TATGTTTATA
3298917 ATATTTTATATTATGTT
1 ATATTTTATATTATGTT
3298934 ATATTTATATATTATGT
1 ATATTT-TATATTATGT
3298951 AACTTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
ATATTTTATATTATGTT
Found at i:3308204 original size:25 final size:23
Alignment explanation
Indices: 3308147--3308283 Score: 161
Period size: 23 Copynumber: 6.0 Consensus size: 23
3308137 TTACCGTTCA
*
3308147 GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
3308170 GCACTTTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
*
3308193 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
* *
3308216 GCACTTCGTGTGCCTACTGATTT-
1 GCACTTTGTGTGCTTACTG-TTTC
* * * * *
3308239 GCGCTATGTGCGCCTACTGATT-
1 GCACTTTGTGTGCTTACTGTTTC
*
3308261 GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
3308284 CCCAGCACAT
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
22 19 0.19
23 77 0.78
24 3 0.03
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (23 bp):
GCACTTTGTGTGCTTACTGTTTC
Found at i:3308691 original size:81 final size:84
Alignment explanation
Indices: 3308552--3308712 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 84
3308542 ATTAATCAAA
* * * * *
3308552 TCATAACAAACAAAAAAATTATTATGATTATTTTGTTTAGTGCGGATACTTTTGTGATTTAATTT
1 TCATAACAAACAAAAAAATTA-TATAATTATTTGGTTTAGTGCGGATACTTCTCTGATTCAATTT
3308617 CAAATAAAAAGACAACCATC
65 CAAATAAAAAGACAACCATC
* *
3308637 TCATAACAAAC-AAAAAA-TA-ATAATTATTTGGTTTTGTG-GGCATAGTTCTCTGATTCAATTT
1 TCATAACAAACAAAAAAATTATATAATTATTTGGTTTAGTGCGG-ATACTTCTCTGATTCAATTT
*
3308698 CAAATAAAAGGACAA
65 CAAATAAAAAGACAA
3308713 ATGAGTGAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 2 0.03
81 46 0.69
83 2 0.03
84 6 0.09
85 11 0.16
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (84 bp):
TCATAACAAACAAAAAAATTATATAATTATTTGGTTTAGTGCGGATACTTCTCTGATTCAATTTC
AAATAAAAAGACAACCATC
Found at i:3314873 original size:27 final size:26
Alignment explanation
Indices: 3314825--3314879 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
3314815 TAATAAAACA
** * *
3314825 TTAAATATTTATTTTTACATTAATAT
1 TTAAATATTTATAGTTAAATTAAAAT
3314851 TTAAATATTTTATAGTTAAATTAAAAT
1 TTAAATA-TTTATAGTTAAATTAAAAT
3314878 TT
1 TT
3314880 TAAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTAAATATTTATAGTTAAATTAAAAT
Found at i:3317364 original size:13 final size:13
Alignment explanation
Indices: 3317346--3317370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3317336 GATTTAAGCA
3317346 GAAGAAGAAAAAG
1 GAAGAAGAAAAAG
3317359 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3317371 AAGACACTAC
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAG
Found at i:3317677 original size:19 final size:19
Alignment explanation
Indices: 3317635--3317679 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3317625 CAAATTCAAA
3317635 TATTAATTTTATATTTAAC
1 TATTAATTTTATATTTAAC
* *
3317654 CATTAATTTTA-ATGTTAAG
1 TATTAATTTTATAT-TTAAC
3317673 TATTAAT
1 TATTAAT
3317680 AGTTTCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTAATTTTATATTTAAC
Found at i:3326711 original size:28 final size:28
Alignment explanation
Indices: 3326671--3326732 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
3326661 TTGGTTCAAT
* *
3326671 TTGGGCTTCGAGATGCCTTTAAAATAAC
1 TTGGGCCTCGAGATGACTTTAAAATAAC
*
3326699 TTGGGCCTCGAGATGATTTTAAAATAAC
1 TTGGGCCTCGAGATGACTTTAAAATAAC
3326727 TTGGGC
1 TTGGGC
3326733 TTGACTGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (28 bp):
TTGGGCCTCGAGATGACTTTAAAATAAC
Found at i:3327528 original size:11 final size:12
Alignment explanation
Indices: 3327516--3327555 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
3327506 AATTTAAATT
3327516 AAATTAAGTTTA
1 AAATTAAGTTTA
3327528 AAA-TAA-TTTA
1 AAATTAAGTTTA
*
3327538 AAATT-AGTTTC
1 AAATTAAGTTTA
3327549 AAATTAA
1 AAATTAA
3327556 CTGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
10 8 0.33
11 12 0.50
12 4 0.17
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (12 bp):
AAATTAAGTTTA
Found at i:3328703 original size:14 final size:14
Alignment explanation
Indices: 3328684--3328711 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3328674 ATAATCGTTC
3328684 GTATCCTTATGTTA
1 GTATCCTTATGTTA
3328698 GTATCCTTATGTTA
1 GTATCCTTATGTTA
3328712 AGGATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
GTATCCTTATGTTA
Found at i:3330816 original size:39 final size:40
Alignment explanation
Indices: 3330763--3330842 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
3330753 AAAAGATATG
* *
3330763 TCCAATATGAAAAGGGTTGTGACTCTTCGAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTATTCAAAAGGTGTCCA
*
3330803 TCCAATTTG-AAAGGGTTGTGACTATTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTATTCAAAAGGTGTCCA
3330842 T
1 T
3330843 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTATTCAAAAGGTGTCCA
Found at i:3335712 original size:39 final size:38
Alignment explanation
Indices: 3335668--3335758 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 38
3335658 TGGGACAAGT
*
3335668 CTCTTCCAAAAGGTAT-GTCCAATATGAAAAGGGTTGTGA
1 CTCTT-CAAAAGGTATCATCCAATATG-AAAGGGTTGTGA
* * *
3335707 CTCTTCGAAAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCAAAAGGTAT-CATCCAATATGAAAGGGTTGTGA
3335746 CTCTTCAAAAGGT
1 CTCTTCAAAAGGT
3335759 GTCCATTGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 8 0.18
39 29 0.64
40 8 0.18
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (38 bp):
CTCTTCAAAAGGTATCATCCAATATGAAAGGGTTGTGA
Found at i:3335759 original size:39 final size:40
Alignment explanation
Indices: 3335685--3335764 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
3335675 AAAAGGTATG
*
3335685 TCCAATATGAAAAGGGTTGTGACTCTTCGAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
*
3335725 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
3335764 T
1 T
3335765 TGAGTGCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:3344995 original size:36 final size:36
Alignment explanation
Indices: 3344955--3345038 Score: 168
Period size: 36 Copynumber: 2.3 Consensus size: 36
3344945 CATTGATCAG
3344955 ACTTAGCCACCGACGACGATGAAACCCCATTCCCAC
1 ACTTAGCCACCGACGACGATGAAACCCCATTCCCAC
3344991 ACTTAGCCACCGACGACGATGAAACCCCATTCCCAC
1 ACTTAGCCACCGACGACGATGAAACCCCATTCCCAC
3345027 ACTTAGCCACCG
1 ACTTAGCCACCG
3345039 CCCTCACACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.30, C:0.42, G:0.14, T:0.14
Consensus pattern (36 bp):
ACTTAGCCACCGACGACGATGAAACCCCATTCCCAC
Found at i:3352187 original size:28 final size:30
Alignment explanation
Indices: 3352156--3352212 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
3352146 TATTTAATAT
3352156 GAAAT-TTAAATTTATTAT-TAT-ATTTTTG
1 GAAATATT-AATTTATTATATATAATTTTTG
*
3352184 GAAATATTTATTTATTATATATAATTTTT
1 GAAATATTAATTTATTATATATAATTTTT
3352213 TGAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 14 0.56
29 5 0.20
30 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (30 bp):
GAAATATTAATTTATTATATATAATTTTTG
Found at i:3353655 original size:16 final size:18
Alignment explanation
Indices: 3353633--3353678 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
3353623 GTCTTAGACA
3353633 TTATTATTTTTAGAT-TT
1 TTATTATTTTTAGATATT
3353650 TT-TTATTTTTTAGATATT
1 TTATTA-TTTTTAGATATT
3353668 TTATTATTTTT
1 TTATTATTTTT
3353679 TAATTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 9 0.35
19 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
TTATTATTTTTAGATATT
Found at i:3353684 original size:16 final size:17
Alignment explanation
Indices: 3353633--3353687 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 17
3353623 GTCTTAGACA
3353633 TTATTA-TTTTTAGATT
1 TTATTATTTTTTAGATT
*
3353649 TTTTTATTTTTTAGATATT
1 TTATTATTTTTTAG--ATT
3353668 TTATTATTTTTTA-ATT
1 TTATTATTTTTTAGATT
3353684 TTAT
1 TTAT
3353688 AAAATTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
19 15 0.44
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (17 bp):
TTATTATTTTTTAGATT
Found at i:3353703 original size:18 final size:16
Alignment explanation
Indices: 3353680--3353728 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
3353670 ATTATTTTTT
3353680 AATTTTATAAAATTTGG
1 AATTTTATAAAATTT-G
3353697 AAGTTTTATAAATATATTG
1 AA-TTTTATAAA-AT-TTG
3353716 AATTTTA-AAAATT
1 AATTTTATAAAATT
3353729 ATTTTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.03
16 2 0.07
17 5 0.17
18 14 0.48
19 5 0.17
20 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
AATTTTATAAAATTTG
Found at i:3356322 original size:17 final size:17
Alignment explanation
Indices: 3356288--3356329 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
3356278 ATATGGGACA
*
3356288 AAAATGAGAATGATGTG
1 AAAATGAGAATGAAGTG
3356305 AAAAT-AGAATTGAAGTG
1 AAAATGAGAA-TGAAGTG
3356322 AAATATGA
1 AAA-ATGA
3356330 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAATGAGAATGAAGTG
Found at i:3359642 original size:18 final size:18
Alignment explanation
Indices: 3359601--3359642 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3359591 TATATTATAC
* *
3359601 AATAAAATATTATTATTT
1 AATATAATATTATTAATT
*
3359619 ATTATAATATTATTAATT
1 AATATAATATTATTAATT
3359637 AATATA
1 AATATA
3359643 TCTTTTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATAATATTATTAATT
Done.