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 64 of 125
Found at i:19634321 original size:48 final size:48
Alignment explanation
Indices: 19634256--19634379 Score: 212
Period size: 48 Copynumber: 2.5 Consensus size: 48
19634246 GTGATTACAG
*
19634256 AACGTTTGAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAGAC
1 AACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAGAC
*
19634304 AACGTTTAAGCTTGTCAGCTATTTAGAATAAGGATGATCATGACAGAC
1 AACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAGAC
19634352 AGAACGTTTAAGCTCGTCAGCTATTTAG
1 --AACGTTTAAGCTCGTCAGCTATTTAG
19634380 GATCAGAATA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 46 0.65
50 25 0.35
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (48 bp):
AACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAGAC
Found at i:19634379 original size:50 final size:50
Alignment explanation
Indices: 19634252--19634422 Score: 238
Period size: 50 Copynumber: 3.5 Consensus size: 50
19634242 AGATGTGATT
*
19634252 ACAGAACGTTTGAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAG
1 ACAGAACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAG
*
19634302 AC--AACGTTTAAGCTTGTCAGCTATTTAGAATAAGGATGATCATGACAG
1 ACAGAACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAG
* * * * **
19634350 ACAGAACGTTTAAGCTCGTCAGCTATTTAGGATCAGAATAATCATGTTAG
1 ACAGAACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAG
* *
19634400 ATAGAACGTTTAAGCTTGTCAGC
1 ACAGAACGTTTAAGCTCGTCAGC
19634423 AATACAGAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
48 46 0.43
50 62 0.57
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (50 bp):
ACAGAACGTTTAAGCTCGTCAGCTATTTAGAATAAGGATGATCATGACAG
Found at i:19636917 original size:22 final size:22
Alignment explanation
Indices: 19636892--19636940 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
19636882 GATCAAAGGG
*
19636892 AAAAAAAAAAG-AAACAGAATT
1 AAAAAAAAAAGAAAACAAAATT
*
19636913 AAAAATAAAAGAAAACAAAATT
1 AAAAAAAAAAGAAAACAAAATT
19636935 AAAAAA
1 AAAAAA
19636941 TAGAAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAAGAAAACAAAATT
Found at i:19637772 original size:19 final size:19
Alignment explanation
Indices: 19637748--19637790 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19637738 AAACATAAAT
19637748 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
19637767 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
19637786 TAAAT
1 TAAAT
19637791 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:19638676 original size:9 final size:9
Alignment explanation
Indices: 19638581--19638677 Score: 52
Period size: 10 Copynumber: 10.2 Consensus size: 9
19638571 AATATTTTAA
19638581 AAAATTA-T
1 AAAATTATT
19638589 AAAATTATCT
1 AAAATTAT-T
**
19638599 AAAGCCTATT
1 AAA-ATTATT
*
19638609 AAGAATTATA
1 AA-AATTATT
*
19638619 AGAAATTATA
1 A-AAATTATT
*
19638629 AAAAGTTTTT
1 AAAA-TTATT
* *
19638639 AAAGTTTTT
1 AAAATTATT
* *
19638648 AAAATAATA
1 AAAATTATT
19638657 AAAATTAATT
1 AAAATT-ATT
19638667 AAAATTATT
1 AAAATTATT
19638676 AA
1 AA
19638678 GAATCATGCT
Statistics
Matches: 68, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
8 7 0.10
9 23 0.34
10 33 0.49
11 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (9 bp):
AAAATTATT
Found at i:19638677 original size:28 final size:28
Alignment explanation
Indices: 19638605--19638677 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
19638595 ATCTAAAGCC
* *
19638605 TATTAAGAATTATAAGAAATTATAAAAAGT
1 TATTAA-AATTATTA-AAATAATAAAAAGT
* * *
19638635 TTTTAAAGTTTTTAAAATAATAAAAA-T
1 TATTAAAATTATTAAAATAATAAAAAGT
19638662 TAATTAAAATTATTAA
1 T-ATTAAAATTATTAA
19638678 GAATCATGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
27 2 0.06
28 22 0.65
29 5 0.15
30 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (28 bp):
TATTAAAATTATTAAAATAATAAAAAGT
Found at i:19644058 original size:17 final size:17
Alignment explanation
Indices: 19644036--19644071 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
19644026 AATATTATTC
19644036 ATTAAATTAATTTT-TCA
1 ATTAAA-TAATTTTCTCA
19644053 ATTAAATAATTTTCTCA
1 ATTAAATAATTTTCTCA
19644070 AT
1 AT
19644072 CCAATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAAATAATTTTCTCA
Found at i:19644062 original size:16 final size:16
Alignment explanation
Indices: 19644024--19644071 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
19644014 TGTCCTAAAA
*
19644024 TAAAT-ATTATTC-AT
1 TAAATAATTTTTCAAT
19644038 TAAATTAATTTTTCAAT
1 TAAA-TAATTTTTCAAT
19644055 TAAATAATTTTCTCAAT
1 TAAATAATTTT-TCAAT
19644072 CCAATTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.14
15 1 0.03
16 13 0.45
17 11 0.38
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATAATTTTTCAAT
Found at i:19644114 original size:23 final size:23
Alignment explanation
Indices: 19644087--19644131 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19644077 TCTAATTTCG
*
19644087 TTAAAATCATGACAATTTTACCA
1 TTAAAATCATGACAACTTTACCA
19644110 TTAAAATCATGACAACTTTACC
1 TTAAAATCATGACAACTTTACC
19644132 GTAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (23 bp):
TTAAAATCATGACAACTTTACCA
Found at i:19650124 original size:20 final size:20
Alignment explanation
Indices: 19650077--19650125 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
19650067 ATATAGGGGT
19650077 ACCAAAGTGCAAGTAGGGCC
1 ACCAAAGTGCAAGTAGGGCC
* * *
19650097 ATCGAAGTGCAATTAGGGCC
1 ACCAAAGTGCAAGTAGGGCC
19650117 ACCAAAGTG
1 ACCAAAGTG
19650126 TAAACAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.29, T:0.14
Consensus pattern (20 bp):
ACCAAAGTGCAAGTAGGGCC
Found at i:19653348 original size:264 final size:265
Alignment explanation
Indices: 19652878--19653417 Score: 861
Period size: 264 Copynumber: 2.0 Consensus size: 265
19652868 GCAAGGAAAT
19652878 TCAAAAGATTCATGAAATTCAACAAAGCCAAAAGATTTCCAAGAAAAGACATCATCAAGGGTGAA
1 TCAAAAGATTCATGAAATTCAACAAAGCCAAAAGATTTCCAAGAAAAGACATCATCAAGGGTGAA
* *
19652943 CAAGCATAAAGGAAAAGGACCCAATCATTTGCTATGAGTACAAAAAGCCGAGTCTCATTAAATTT
66 CAAGCATAAAGAAAAAGGACCCAATCATTTGCTATGAGTACAAAAAGCCGAGTCTCATCAAATTT
* * * *
19653008 GACTTCCCATAATAAAAGAGGAAAGAGGTATCAAAACAAAAGAAGAAAGCTATGATAGCAGCTTG
131 GACTTCCAAAAATAAAAGAAGAAAGAGGCATCAAAACAAAAGAAGAAAGCTATGATAGCAGCTTG
* * *
19653073 GATCGATAGTGATTCATC-T-TGATGAGGATAATGAAATTGCCCAACTATGTCTTATGACTATTG
196 GACCAATAGTGATTCATCATGTGATGAGGACAATGAAATTGCCCAACTATGTCTTATGACTATTG
19653136 AAGAA
261 AAGAA
*
19653141 TCAAAAGATTCATGAAATTCAATAAAGCCAAAAGATTTCCAAGAAAAGACATCATCAAGGGTGAA
1 TCAAAAGATTCATGAAATTCAACAAAGCCAAAAGATTTCCAAGAAAAGACATCATCAAGGGTGAA
* * *
19653206 CCAAGCATAAAGAAAAAGGACCCAATCATTTGCTATGAGTGCAAAAAGTCGGGTCTCATCAAATT
66 -CAAGCATAAAGAAAAAGGACCCAATCATTTGCTATGAGTACAAAAAGCCGAGTCTCATCAAATT
** * *
19653271 TGACTTCCAAAAATTGAAGAAGAAAGAGGCATCAAAACAAAAGAAGAAAGCTATGATGGTAGCTT
130 TGACTTCCAAAAATAAAAGAAGAAAGAGGCATCAAAACAAAAGAAGAAAGCTATGATAGCAGCTT
*
19653336 GGACCAATAGTGATTCATCTGATGGTGATGAGGACAATGAAATTGCCCAACTATGTCTTATGGCT
195 GGACCAATAGTGATTCATC--AT-GTGATGAGGACAATGAAATTGCCCAACTATGTCTTATGACT
19653401 ATTGAAGAA
257 ATTGAAGAA
19653410 -CAAAAGAT
1 TCAAAAGAT
19653418 AAATCTAAAC
Statistics
Matches: 253, Mismatches: 18, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
263 64 0.25
264 133 0.53
267 1 0.00
268 8 0.03
269 47 0.19
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (265 bp):
TCAAAAGATTCATGAAATTCAACAAAGCCAAAAGATTTCCAAGAAAAGACATCATCAAGGGTGAA
CAAGCATAAAGAAAAAGGACCCAATCATTTGCTATGAGTACAAAAAGCCGAGTCTCATCAAATTT
GACTTCCAAAAATAAAAGAAGAAAGAGGCATCAAAACAAAAGAAGAAAGCTATGATAGCAGCTTG
GACCAATAGTGATTCATCATGTGATGAGGACAATGAAATTGCCCAACTATGTCTTATGACTATTG
AAGAA
Found at i:19659256 original size:21 final size:21
Alignment explanation
Indices: 19659217--19659256 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19659207 TACCTTGCAC
**
19659217 TTCTACCGAAACATTTATGGG
1 TTCTACCGAAACAAGTATGGG
*
19659238 TTCTACCGAAATAAGTATG
1 TTCTACCGAAACAAGTATG
19659257 CAGAATCTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Found at i:19659846 original size:27 final size:27
Alignment explanation
Indices: 19659796--19659980 Score: 237
Period size: 27 Copynumber: 6.8 Consensus size: 27
19659786 AAAATGGTTA
* *
19659796 GCTCTTACGAGCCTAGAATCAGAATAAT
1 GCTCTTTCGAGCC-AGAATCAGAATAAC
*
19659824 GCTCTTTCAAGCCAGAATCAGAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
19659851 ACTCTTTCGAGCCAGAATCA-AATTAAC
1 GCTCTTTCGAGCCAGAATCAGAA-TAAC
* * *
19659878 ACTCTTTCAAGCCAGAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
19659905 GCTCTTTCGAGCCAGAATCAGACTAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
* * *
19659932 GCTCTTTCAAGCTAGAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
19659959 GCTCTTTCGAGCCAAAATCAGA
1 GCTCTTTCGAGCCAGAATCAGA
19659981 TTACTCCTCA
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.01
27 122 0.89
28 13 0.09
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAATCAGAATAAC
Found at i:19659883 original size:54 final size:54
Alignment explanation
Indices: 19659796--19659983 Score: 261
Period size: 54 Copynumber: 3.5 Consensus size: 54
19659786 AAAATGGTTA
* * *
19659796 GCTCTTACGAGCCTAGAATCAGAA-TAATGCTCTTTCAAGCCAGAATCAGAATAAC
1 GCTCTTTCGAGCC-AGAATCA-AATTAACGCTCTTTCAAGCCAGAATCAAAATAAC
* *
19659851 ACTCTTTCGAGCCAGAATCAAATTAACACTCTTTCAAGCCAGAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAAATTAACGCTCTTTCAAGCCAGAATCAAAATAAC
* * *
19659905 GCTCTTTCGAGCCAGAATCAGACTAACGCTCTTTCAAGCTAGAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAAATTAACGCTCTTTCAAGCCAGAATCAAAATAAC
* *
19659959 GCTCTTTCGAGCCAAAATCAGATTA
1 GCTCTTTCGAGCCAGAATCAAATTA
19659984 CTCCTCAAGC
Statistics
Matches: 120, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
53 2 0.02
54 107 0.89
55 11 0.09
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (54 bp):
GCTCTTTCGAGCCAGAATCAAATTAACGCTCTTTCAAGCCAGAATCAAAATAAC
Found at i:19662179 original size:51 final size:51
Alignment explanation
Indices: 19661941--19662172 Score: 365
Period size: 51 Copynumber: 4.5 Consensus size: 51
19661931 TAAACGAAAT
*
19661941 GTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
*
19661992 GTCCGATGGCTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
*
19662043 GTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
* * * * * **
19662094 GTCCGATGACTAATTATCATCGTGAGTAAATAAATCCATGACAAATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
*
19662145 GTCCGATGACTTAGTGTCATCGTGAGTA
1 GTCCGATGACTAAGTGTCATCGTGAGTA
19662173 TATAAATTCC
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 166 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (51 bp):
GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
Found at i:19669359 original size:51 final size:51
Alignment explanation
Indices: 19669278--19669515 Score: 264
Period size: 51 Copynumber: 4.6 Consensus size: 51
19669268 GCTATAAACG
* *
19669278 AAAGGTACGATGACTAAGTGTCATCGTGAGTAAATGAATGCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
19669329 AAAGGTCCGATGAGTAAGTGTCATCATGAGTAAATGAATCCTTAACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
19669380 AAAGGTTCGAT-AGGTAAGTGTCATCGTGAGTAAATGAATCCTTTCCGGATT
1 AAAGGTCCGATGA-CTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * * * * **
19669431 AAATATCCGATGACTCAGTGTCATCGTGAGTATATAAATTCCTATACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
19669483 AAAGGGGTCCGATGACTATA-TGTCTTCGTGAGT
1 AAA--GGTCCGATGACTA-AGTGTCATCGTGAGT
19669516 GTTAAATGAA
Statistics
Matches: 157, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
50 1 0.01
51 120 0.76
52 13 0.08
54 22 0.14
55 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:19676612 original size:51 final size:51
Alignment explanation
Indices: 19676536--19676720 Score: 273
Period size: 51 Copynumber: 3.6 Consensus size: 51
19676526 GCTATAAACG
*
19676536 AAAGGTCCGATGAGTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
19676587 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTCCGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * *
19676638 AATGGTTCGATGACTAAGTATCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
19676689 AAAGGTCCGATGACTCAA-TGTCATCGTGAGTA
1 AAAGGTCCGATGACT-AAGTGTCATCGTGAGTA
19676721 TATAAATTCC
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
51 119 0.98
52 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:19679507 original size:20 final size:20
Alignment explanation
Indices: 19679461--19679563 Score: 66
Period size: 20 Copynumber: 5.0 Consensus size: 20
19679451 AGTTTGAAAC
*
19679461 AATTTTAAAATCAAGTTAAAAT
1 AATTTT-AAA-CAAGTCAAAAT
* *
19679483 GATTTTAAACATGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* *
19679503 AA-TTTGAACTAAGTTAAAAT
1 AATTTTAAAC-AAGTCAAAAT
* ** *
19679523 CATTTT-AACACTTAAAAAT
1 AATTTTAAACAAGTCAAAAT
*
19679542 ATTTTTCAAACAAGTCAAAAT
1 AATTTT-AAACAAGTCAAAAT
19679563 A
1 A
19679564 GCTTTAGGCC
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
19 17 0.28
20 22 0.36
21 17 0.28
22 5 0.08
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:19681340 original size:34 final size:34
Alignment explanation
Indices: 19681290--19681360 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
19681280 TAGTTAAACA
* *
19681290 TTAGATAACTATTGAGCTAATATTTGCTTCCATT
1 TTAGATAACTAGTGAGCTAACATTTGCTTCCATT
*
19681324 TTAGATAATTAGTGAGCTAACATTTGCTTCCATT
1 TTAGATAACTAGTGAGCTAACATTTGCTTCCATT
19681358 TTA
1 TTA
19681361 CTTTGCATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (34 bp):
TTAGATAACTAGTGAGCTAACATTTGCTTCCATT
Found at i:19681888 original size:22 final size:22
Alignment explanation
Indices: 19681855--19681910 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
19681845 TATGCCAACC
*
19681855 TAACAATATACCATTTTCATA-
1 TAACAATATACCATTTTAATAG
*
19681876 TAACTAATGTACCATTTTAATAG
1 TAAC-AATATACCATTTTAATAG
19681899 TAACAATATACC
1 TAACAATATACC
19681911 TACACCTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 22 0.73
23 4 0.13
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
TAACAATATACCATTTTAATAG
Found at i:19687717 original size:16 final size:16
Alignment explanation
Indices: 19687698--19687746 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
19687688 ATATTGTTTT
19687698 TTATTTAATTTCTCAA
1 TTATTTAATTTCTCAA
*
19687714 TTATTT--TTT-TGAA
1 TTATTTAATTTCTCAA
*
19687727 GT-TTTAATTTCTCAA
1 TTATTTAATTTCTCAA
19687742 TTATT
1 TTATT
19687747 AATACAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 3 0.12
13 4 0.16
14 6 0.24
15 4 0.16
16 8 0.32
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (16 bp):
TTATTTAATTTCTCAA
Found at i:19698947 original size:17 final size:18
Alignment explanation
Indices: 19698905--19698949 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
19698895 AAATCAATTT
*
19698905 TAATATAAATATTTAATA
1 TAATATAAATAATTAATA
*
19698923 CAAT-TAAATAATTAA-A
1 TAATATAAATAATTAATA
19698939 TAATATAAATA
1 TAATATAAATA
19698950 GTACAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATATAAATAATTAATA
Found at i:19700802 original size:32 final size:32
Alignment explanation
Indices: 19700758--19700832 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
19700748 AATGTGAGGT
* * *
19700758 TTTCGGGTTTTAGATTTCAAAATTTTTGGGAA
1 TTTCGGGATTTAGATTTCAAAAATTTAGGGAA
* * * *
19700790 TTTGGGGATTTAGGTTTTAAAAATTTAGGGAT
1 TTTCGGGATTTAGATTTCAAAAATTTAGGGAA
19700822 TTTCGGGATTT
1 TTTCGGGATTT
19700833 TTAGGGTTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.47
Consensus pattern (32 bp):
TTTCGGGATTTAGATTTCAAAAATTTAGGGAA
Found at i:19700895 original size:45 final size:45
Alignment explanation
Indices: 19700844--19700935 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
19700834 TAGGGTTGTT
*
19700844 GGGTTTGGAGAATTTGGTTTATGTTTAAGAAATTTAGGGA-TTTCG
1 GGGTTTGGAGAATTTGGTTTAAGTTTAA-AAATTTAGGGATTTTCG
* * *
19700889 GGGTTTGGAGATTTTGGTTTAAGTTTAAAATTTTGGGGATTTTCG
1 GGGTTTGGAGAATTTGGTTTAAGTTTAAAAATTTAGGGATTTTCG
19700934 GG
1 GG
19700936 ACTTAGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 9 0.21
45 33 0.79
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (45 bp):
GGGTTTGGAGAATTTGGTTTAAGTTTAAAAATTTAGGGATTTTCG
Found at i:19704999 original size:29 final size:29
Alignment explanation
Indices: 19704967--19705235 Score: 108
Period size: 30 Copynumber: 9.2 Consensus size: 29
19704957 ACCCGAGGGC
19704967 AAAATGGTAATTTTGGTAAAATCGAGGTT
1 AAAATGGTAATTTTGGTAAAATCGAGGTT
* * ** *
19704996 AAAAATAG-AATTTT-TTAGAGTTCGAGGGT
1 -AAAATGGTAATTTTGGTA-AAATCGAGGTT
19705025 -AAATGGTAATTTATGGTAAAATCGAGGTT
1 AAAATGGTAATTT-TGGTAAAATCGAGGTT
* ** * * *
19705054 AAAAATAG-AA-TTTGG-AACGTTTGGGGGT
1 -AAAATGGTAATTTTGGTAA-AATCGAGGTT
* * *
19705082 AAAATGATAATTTTTGGTGAAACCGAGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGTT
* * ** * *
19705112 AAAAATGG-GATTTTAG-AAGGTTCGGGGCT
1 -AAAATGGTAATTTTGGTAA-AATCGAGGTT
* *
19705141 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGTT
* ** *
19705171 AAAAATGG-AATTTTAG-AAGGTTCGAGGGT
1 -AAAATGGTAATTTTGGTAA-AATCGAGGTT
* *
19705200 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGTT
19705230 AAAATG
1 AAAATG
19705236 AAATTTTAGA
Statistics
Matches: 166, Mismatches: 52, Indels: 42
0.64 0.20 0.16
Matches are distributed among these distances:
27 12 0.07
28 33 0.20
29 49 0.30
30 51 0.31
31 21 0.13
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTAAAATCGAGGTT
Found at i:19705153 original size:59 final size:60
Alignment explanation
Indices: 19704960--19705272 Score: 380
Period size: 58 Copynumber: 5.4 Consensus size: 60
19704950 TTTAGATACC
* *
19704960 CGAGGGC-AAAATGGTAA-TTTTGGTAAAATCGAGGTTAAAAATAGAATTTTTTAG-A-GTT
1 CGAGGGCTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAA--TTTTAGAAGGTT
* * * * *
19705018 CGAGGG-T-AAATGGTAATTTATGGTAAAATCGAGGTTAAAAATAGAA-TTTGGAACGTT
1 CGAGGGCTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTT
* * * * *
19705075 TG-GGGGTAAAATGATAATTTTTGGTGAAACCGAGGTTAAAAATGGGATTTTAGAAGGTT
1 CGAGGGCTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTT
*
19705134 CG-GGGCTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
1 CGAGGGCTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTT
* *
19705193 CGAGGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGAAATTTTAGAAGGTT
1 CGAGGGCTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTT
*
19705251 TGAGGGC-AAAATGGTAATTTTT
1 CGAGGGCTAAAATGGTAATTTTT
19705273 TGAAGTTTCG
Statistics
Matches: 227, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
55 4 0.02
56 4 0.02
57 14 0.06
58 107 0.47
59 95 0.42
60 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (60 bp):
CGAGGGCTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTT
Found at i:19705182 original size:117 final size:119
Alignment explanation
Indices: 19704960--19705272 Score: 392
Period size: 117 Copynumber: 2.7 Consensus size: 119
19704950 TTTAGATACC
* * *
19704960 CGAGGGCAAAATGGTAA-TTTTGGTAAAATCGAGGTTAAAAATAGAATTTTTTAG-A-GTTCGAG
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAA--TTTTAGAAGGTTCGAG
* *
19705022 GG-T-AAATGGTAATTTATGGTAAAATCGAGGTTAAAAATAGAA-TTTGGAACGTT
64 GGCTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAATTTTAGAACGTT
* * * * *
19705075 TGGGGGTAAAATGATAATTTTTGGTGAAACCGAGGTTAAAAATGGGATTTTAGAAGGTTCG-GGG
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCGAGGG
* * * *
19705139 CTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTT
66 CTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAATTTTAGAACGTT
* * *
19705193 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGAAATTTTAGAAGGTTTGAGGG
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCGAGGG
19705257 C-AAAATGGTAATTTTT
66 CTAAAATGGTAATTTTT
19705273 TGAAGTTTCG
Statistics
Matches: 169, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
114 6 0.04
115 17 0.10
116 31 0.18
117 70 0.41
118 45 0.27
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (119 bp):
CGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCGAGGG
CTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAATTTTAGAACGTT
Found at i:19705242 original size:29 final size:30
Alignment explanation
Indices: 19705076--19705235 Score: 114
Period size: 30 Copynumber: 5.4 Consensus size: 30
19705066 TGGAACGTTT
* * *
19705076 GGGGGTAAAATGATAATTTTTGGTGAAACC
1 GGGGTTAAAATGGTAATTTTTGGTGAAATC
* * * ** **
19705106 GAGGTTAAAAATGG-GATTTTAGAAG-GTTC
1 GGGGTT-AAAATGGTAATTTTTGGTGAAATC
*
19705135 GGGGCTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTTAAAATGGTAATTTTTGGTGAAATC
* ** **
19705165 GGGGTTAAAAATGG-AATTTTAGAAG-GTTC
1 GGGGTT-AAAATGGTAATTTTTGGTGAAATC
19705194 GAGGG-TAAAATGGTAATTTTTGGTGAAATC
1 G-GGGTTAAAATGGTAATTTTTGGTGAAATC
19705224 GGGGTTAAAATG
1 GGGGTTAAAATG
19705236 AAATTTTAGA
Statistics
Matches: 93, Mismatches: 29, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
28 14 0.15
29 27 0.29
30 39 0.42
31 13 0.14
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (30 bp):
GGGGTTAAAATGGTAATTTTTGGTGAAATC
Found at i:19705269 original size:29 final size:29
Alignment explanation
Indices: 19705113--19705285 Score: 97
Period size: 30 Copynumber: 5.9 Consensus size: 29
19705103 ACCGAGGTTA
*
19705113 AAAATGG-GATTTTAGAAGGTTCG-GGGCT
1 AAAATGGTAATTTTAGAAGGTTCGAGGG-T
* ** **
19705141 AAAATGGTAATTTTTGGTGAAATCG-GGGTT
1 AAAATGGTAATTTTAGAAG-GTTCGAGGG-T
19705171 AAAAATGG-AATTTTAGAAGGTTCGAGGGT
1 -AAAATGGTAATTTTAGAAGGTTCGAGGGT
* ** **
19705200 AAAATGGTAATTTTTGGTGAAATCG-GGGTT
1 AAAATGGTAATTTTAGAAG-GTTCGAGGG-T
* * *
19705230 AAAAT-GAAATTTTAGAAGGTTTGAGGGC
1 AAAATGGTAATTTTAGAAGGTTCGAGGGT
* *
19705258 AAAATGGTAATTTTTTGAAGTTTCGAGG
1 AAAATGGTAA-TTTTAGAAGGTTCGAGG
19705286 TCAGAATGTA
Statistics
Matches: 106, Mismatches: 29, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
28 21 0.20
29 37 0.35
30 41 0.39
31 7 0.07
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTAGAAGGTTCGAGGGT
Found at i:19705794 original size:14 final size:14
Alignment explanation
Indices: 19705775--19705803 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19705765 TTTTTTAGTA
19705775 TTTTTTCATTTCAT
1 TTTTTTCATTTCAT
19705789 TTTTTTCATTTCAT
1 TTTTTTCATTTCAT
19705803 T
1 T
19705804 AAAAATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTCATTTCAT
Found at i:19707137 original size:36 final size:37
Alignment explanation
Indices: 19707096--19707165 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
19707086 GTTTGGGGTG
*
19707096 TTTGGG-CCAATTGGGCCTTGTATGTTGGA-TTTGAGT
1 TTTGGGCCCAATTGGGCCATGTAT-TTGGACTTTGAGT
19707132 TTTGGGCCCAATTGGGCCATGTATTTGGACTTTG
1 TTTGGGCCCAATTGGGCCATGTATTTGGACTTTG
19707166 GACATTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (37 bp):
TTTGGGCCCAATTGGGCCATGTATTTGGACTTTGAGT
Found at i:19707224 original size:11 final size:11
Alignment explanation
Indices: 19707209--19707287 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
19707199 TATAATAATA
19707209 TTAAATTTAAA-
1 TTAAA-TTAAAT
19707220 TTAAATTCAAAT
1 TTAAATT-AAAT
* *
19707232 TAAAATTGAAT
1 TTAAATTAAAT
*
19707243 TTAAAATAAAT
1 TTAAATTAAAT
19707254 TTAAAATTAAA-
1 TT-AAATTAAAT
* *
19707265 ATAAATCAAAT
1 TTAAATTAAAT
*
19707276 TTCAAAGTAAAT
1 TT-AAATTAAAT
19707288 GGTTTGGGCC
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
10 9 0.17
11 23 0.44
12 20 0.38
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:19707226 original size:28 final size:28
Alignment explanation
Indices: 19707192--19707270 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
19707182 TTTCTTTTAT
*
19707192 TTAAATTTATAA-TAATATTAAATTTAAA
1 TTAAATTTA-AATTAAAATTAAATTTAAA
* *
19707220 TTAAATTCAAATTAAAATTGAATTTAAA
1 TTAAATTTAAATTAAAATTAAATTTAAA
*
19707248 ATAAATTTAAAATTAAAA-TAAAT
1 TTAAATTT-AAATTAAAATTAAAT
19707271 CAAATTTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.05
28 32 0.74
29 9 0.21
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TTAAATTTAAATTAAAATTAAATTTAAA
Found at i:19707231 original size:17 final size:16
Alignment explanation
Indices: 19707209--19707287 Score: 59
Period size: 17 Copynumber: 4.7 Consensus size: 16
19707199 TATAATAATA
19707209 TTAAATTTAAATTAAAT
1 TTAAA-TTAAATTAAAT
* *
19707226 TCAAATTAAAATTGAAT
1 TTAAATT-AAATTAAAT
* *
19707243 TTAAAATAAATTTAAAA
1 TTAAATTAAA-TTAAAT
* *
19707260 TTAAAATAAATCAAAT
1 TTAAATTAAATTAAAT
*
19707276 TTCAAAGTAAAT
1 TT-AAATTAAAT
19707288 GGTTTGGGCC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.22
17 39 0.78
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (16 bp):
TTAAATTAAATTAAAT
Found at i:19707246 original size:12 final size:12
Alignment explanation
Indices: 19707209--19707264 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
19707199 TATAATAATA
*
19707209 TTAAATTTAAA-
1 TTAAAATTAAAT
19707220 TT-AAATTCAAA-
1 TTAAAATT-AAAT
*
19707231 TTAAAATTGAAT
1 TTAAAATTAAAT
19707243 TTAAAA-TAAAT
1 TTAAAATTAAAT
19707254 TTAAAATTAAA
1 TTAAAATTAAA
19707265 ATAAATCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.11
11 19 0.50
12 15 0.39
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
TTAAAATTAAAT
Found at i:19707265 original size:6 final size:6
Alignment explanation
Indices: 19707211--19707266 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
19707201 TAATAATATT
* * * * *
19707211 AAATTT AAATT- AAATTC AAATTA AAATTG AATTTA AAA-TA AATTTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
19707257 AAATTA AAAT
1 AAATTA AAAT
19707267 AAATCAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 9 0.22
6 32 0.78
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (6 bp):
AAATTA
Found at i:19707277 original size:22 final size:22
Alignment explanation
Indices: 19707209--19707287 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
19707199 TATAATAATA
*
19707209 TTAAATTTAAATTAAATTCAAA-
1 TTAAAATTAAATTAAA-TCAAAT
*
19707231 TTAAAATTGAATTTAAAAT-AAAT
1 TTAAAATT-AAATT-AAATCAAAT
*
19707254 TTAAAATTAAAATAAATCAAAT
1 TTAAAATTAAATTAAATCAAAT
* *
19707276 TTCAAAGTAAAT
1 TTAAAATTAAAT
19707288 GGTTTGGGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
21 4 0.09
22 26 0.57
23 13 0.28
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (22 bp):
TTAAAATTAAATTAAATCAAAT
Found at i:19707729 original size:38 final size:37
Alignment explanation
Indices: 19707679--19708040 Score: 144
Period size: 38 Copynumber: 9.5 Consensus size: 37
19707669 TATCCAACTC
19707679 TACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCT
1 TACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTCT
* * * *
19707717 TACTTCAATTTC-AGA-GAT-AAAGACTTGAT-ATCCAACT
1 TACTTCAATTTCAAGAGGATGGAA-AC--GATCTTGC-TCT
*
19707754 CTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 -TACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTCT
* * * *
19707793 TACTTCAATTTC-AGA-GAT-AAAGACG-TGTTATCCACTT
1 TACTTCAATTTCAAGAGGATGGAA-ACGAT-CT-TGCTC-T
*
19707830 TACTTCAATTTCAAGAGGATAGGAAATGA-CGTTGCTCT
1 TACTTCAATTTCAAGAGGAT-GGAAACGATC-TTGCTCT
* * * *
19707868 TACTTCAATTTC-AGAGAGAT-AAAGACG-TGTTATCCACT
1 TACTTCAATTTCAAGAG-GATGGAA-ACGAT-CT-TGCTCT
* *
19707906 CTACTTTAATTTCAAGAGGATAGGAAATGA-CGTTGCTCT
1 -TACTTCAATTTCAAGAGGAT-GGAAACGATC-TTGCTCT
* * * *
19707945 TACTTCAATTTC-AGAGAGAT-AAAGACGTGAT-ATCCAACT
1 TACTTCAATTTCAAGAG-GATGGAA-AC--GATCTTGC-TCT
* * * *
19707984 CTACTTCAACTTCAAGAGGATAGGAGATGATGTTGCTCT
1 -TACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTCT
19708023 TACTTCAATTTCAGAGAG
1 TACTTCAATTTCA-AGAG
19708041 ATAAAGACTT
Statistics
Matches: 237, Mismatches: 44, Indels: 85
0.65 0.12 0.23
Matches are distributed among these distances:
34 5 0.02
35 5 0.02
36 15 0.06
37 36 0.15
38 87 0.37
39 45 0.19
40 31 0.13
41 10 0.04
42 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (37 bp):
TACTTCAATTTCAAGAGGATGGAAACGATCTTGCTCT
Found at i:19708032 original size:78 final size:78
Alignment explanation
Indices: 19707634--19708098 Score: 748
Period size: 78 Copynumber: 6.0 Consensus size: 78
19707624 GCTTCGTCTA
*
19707634 GCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
* *
19707699 GGGAAACGATCTT
66 AGGAAATGATCTT
*
19707712 GCTCTTACTTCAATTTC--AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
19707775 AGGAAATGATCTT
66 AGGAAATGATCTT
* *
19707788 GCTCTTACTTCAATTTC--AGAGATAAAGACGTGTTATCC-ACTTTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
19707850 AGGAAATGA-CGTT
66 AGGAAATGATC-TT
* *
19707863 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGTTATCC-ACTCTACTTTAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
19707927 AGGAAATGA-CGTT
66 AGGAAATGATC-TT
*
19707940 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAACTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
* *
19708005 AGGAGATGATGTT
66 AGGAAATGATCTT
*
19708018 GCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
19708083 AGGAAATGATCTT
66 AGGAAATGATCTT
19708096 GCT
1 GCT
19708099 GCGGTCTAAC
Statistics
Matches: 366, Mismatches: 16, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
74 1 0.00
75 51 0.14
76 93 0.25
77 95 0.26
78 126 0.34
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (78 bp):
GCTCTTACTTCAATTTCAGAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
AGGAAATGATCTT
Found at i:19718840 original size:14 final size:15
Alignment explanation
Indices: 19718818--19718859 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
19718808 GCATATGGAT
*
19718818 GCAAAATCACAC-TA
1 GCAATATCACACATA
19718832 GCAATATCACACAGTA
1 GCAATATCACACA-TA
19718848 G-AATATCACACA
1 GCAATATCACACA
19718860 AAGATGTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 11 0.44
15 11 0.44
16 3 0.12
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.17
Consensus pattern (15 bp):
GCAATATCACACATA
Found at i:19720216 original size:29 final size:28
Alignment explanation
Indices: 19720182--19720339 Score: 99
Period size: 29 Copynumber: 5.5 Consensus size: 28
19720172 ACTCGGGGGC
19720182 AAAATGGTAATTTTGGTGAAATTGAGGTT
1 AAAATGG-AATTTTGGTGAAATTGAGGTT
* * *
19720211 AAAATGGAATTTT--TGAGAGTTTAGGGGT
1 AAAATGGAATTTTGGTGA-AATTGA-GGTT
*
19720239 AAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAATGG-AA-TTTTGGTGAAATTGAGGTT
* * * * *
19720269 AAAAATGGGATTTT--AGAAGGTTTGGGGGT
1 -AAAATGGAATTTTGGTGAA--ATTGAGGTT
* * *
19720298 AAAATGGTATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATTGAGGTT
19720327 AAAATGGAATTTT
1 AAAATGGAATTTT
19720340 AGAAGGTTCG
Statistics
Matches: 97, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
26 3 0.03
27 7 0.07
28 28 0.29
29 35 0.36
30 8 0.08
31 13 0.13
32 3 0.03
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATTGAGGTT
Found at i:19720310 original size:58 final size:58
Alignment explanation
Indices: 19720176--19720369 Score: 277
Period size: 57 Copynumber: 3.4 Consensus size: 58
19720166 TTGGATACTC
* *
19720176 GGGGGCAAAATGGTAA-TTTTGGTGAAATTGAGGTTAAAATGGAATTTTTG-AGAGTTT
1 GGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTAGAAG-GTTT
* * *
19720233 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTAGAAGGTTT
1 GGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTAGAAGGTTT
* * *
19720292 GGGGGTAAAATGGT-ATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGGTTC
1 GGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTAGAAGGTTT
19720349 GGGGGCAAAATGGTAATTTTT
1 GGGGGCAAAATGGTAATTTTT
19720370 TGAAGTTTCG
Statistics
Matches: 123, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
57 47 0.38
58 44 0.36
59 30 0.24
60 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (58 bp):
GGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTAGAAGGTTT
Found at i:19720353 original size:29 final size:28
Alignment explanation
Indices: 19720270--19720382 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 28
19720260 ATCGAGGTTA
* *
19720270 AAAATGGGATTTTAGAAGGTTTGGGGGT
1 AAAATGGAATTTTAGAAGGTTCGGGGGT
* * ** ** *
19720298 AAAATGGTATTTTTGGTGAAATCGGGGTT
1 AAAATGGAATTTTAGAAG-GTTCGGGGGT
*
19720327 AAAATGGAATTTTAGAAGGTTCGGGGGC
1 AAAATGGAATTTTAGAAGGTTCGGGGGT
* *
19720355 AAAATGGTAATTTTTTGAAGTTTCGGGG
1 AAAATGG-AA-TTTTAGAAGGTTCGGGG
19720383 TCAGAATGTA
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
28 27 0.42
29 22 0.34
30 15 0.23
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTAGAAGGTTCGGGGGT
Found at i:19720382 original size:30 final size:30
Alignment explanation
Indices: 19720279--19720396 Score: 86
Period size: 29 Copynumber: 4.1 Consensus size: 30
19720269 AAAAATGGGA
* *
19720279 TTTTAGAAGGTTTGGGGGTAAAATGGT-AT
1 TTTTAGAAGGTTCGGGGGCAAAATGGTAAT
* * **
19720308 TTTTGGTGAA--ATCGGGGTTAAAATGG-AA-
1 TTTT--AGAAGGTTCGGGGGCAAAATGGTAAT
19720336 TTTTAGAAGGTTCGGGGGCAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGGCAAAATGGTAAT
* * * *
19720366 TTTTTGAAGTTTCGGGGTCAGAAT-GTAAT
1 TTTTAGAAGGTTCGGGGGCAAAATGGTAAT
19720395 TT
1 TT
19720397 CCTAAAATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
26 3 0.04
28 17 0.24
29 27 0.39
30 20 0.29
31 3 0.04
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.36
Consensus pattern (30 bp):
TTTTAGAAGGTTCGGGGGCAAAATGGTAAT
Found at i:19720393 original size:29 final size:29
Alignment explanation
Indices: 19720319--19720396 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
19720309 TTTGGTGAAA
* *
19720319 TCGGGGTTAAAATGGAA-TTTTAGAAGGT
1 TCGGGGTCAAAATGTAATTTTTAGAAGGT
* * *
19720347 TCGGGGGCAAAATGGTAATTTTTTGAAGTT
1 TCGGGGTCAAAAT-GTAATTTTTAGAAGGT
*
19720377 TCGGGGTCAGAATGTAATTT
1 TCGGGGTCAAAATGTAATTT
19720397 CCTAAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.27
29 10 0.24
30 20 0.49
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.35
Consensus pattern (29 bp):
TCGGGGTCAAAATGTAATTTTTAGAAGGT
Found at i:19722235 original size:36 final size:37
Alignment explanation
Indices: 19722194--19722263 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
19722184 GTTTGGGGTG
*
19722194 TTTGGG-CCAATTGGGCCTTGTATGTTGGA-TTTGAGT
1 TTTGGGCCCAATTGGGCCATGTAT-TTGGACTTTGAGT
19722230 TTTGGGCCCAATTGGGCCATGTATTTGGACTTTG
1 TTTGGGCCCAATTGGGCCATGTATTTGGACTTTG
19722264 GACATTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (37 bp):
TTTGGGCCCAATTGGGCCATGTATTTGGACTTTGAGT
Found at i:19722332 original size:22 final size:21
Alignment explanation
Indices: 19722288--19722367 Score: 70
Period size: 23 Copynumber: 3.6 Consensus size: 21
19722278 TCTTTCTTTT
*
19722288 ATTTAAATTTATAATAATATTAA
1 ATTTAAA-TTAAAATAA-ATTAA
* *
19722311 ATTTAGATTAAATTCAAATTAAA
1 ATTTAAATTAAAAT-AAATT-AA
*
19722334 ATTGAAATTAAAATAAATTAA
1 ATTTAAATTAAAATAAATTAA
*
19722355 ATTTCAAAGTAAA
1 ATTT-AAATTAAA
19722368 TGGTTTGGGC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
21 5 0.11
22 20 0.43
23 21 0.46
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTTAAATTAAAATAAATTAA
Found at i:19722341 original size:12 final size:11
Alignment explanation
Indices: 19722306--19722355 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
19722296 TTATAATAAT
* *
19722306 ATTAAATTTAG
1 ATTAAAATTAA
19722317 ATT-AAATTCAA
1 ATTAAAATT-AA
19722328 ATTAAAATTGAA
1 ATTAAAATT-AA
19722340 ATTAAAA-TAA
1 ATTAAAATTAA
19722350 ATTAAA
1 ATTAAA
19722356 TTTCAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 12 0.35
11 8 0.24
12 14 0.41
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (11 bp):
ATTAAAATTAA
Found at i:19722355 original size:5 final size:5
Alignment explanation
Indices: 19722306--19722357 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
19722296 TTATAATAAT
* *
19722306 ATTAA ATTTAG ATTAA ATTCAA ATTAAA ATTGAA ATTAA AATAA ATTAA
1 ATTAA A-TTAA ATTAA ATT-AA ATT-AA ATT-AA ATTAA ATTAA ATTAA
19722355 ATT
1 ATT
19722358 TCAAAGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 20 0.51
6 19 0.49
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:19725577 original size:44 final size:44
Alignment explanation
Indices: 19725488--19725587 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
19725478 CTAAGTCCCG
* * * *
19725488 AAAATCCCCAGATTTTTAAACTTAAACCAAAATCTCCAAACCCC
1 AAAATCCCTAAATTTTTAAACCTAAACCAAAATCCCCAAACCCC
*
19725532 AAAATCCCTAAATTTCTTAAACCTAAACCAAATTCCCCAAA-CCC
1 AAAATCCCTAAATTT-TTAAACCTAAACCAAAATCCCCAAACCCC
19725576 AACAA-CCCTAAA
1 AA-AATCCCTAAA
19725588 AATCTCGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 25 0.51
45 24 0.49
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (44 bp):
AAAATCCCTAAATTTTTAAACCTAAACCAAAATCCCCAAACCCC
Found at i:19728917 original size:15 final size:15
Alignment explanation
Indices: 19728897--19728928 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19728887 ATTATTATCT
19728897 TTAGATACCAAAATA
1 TTAGATACCAAAATA
19728912 TTAGATACCAAAATA
1 TTAGATACCAAAATA
19728927 TT
1 TT
19728929 GCATGCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (15 bp):
TTAGATACCAAAATA
Found at i:19730121 original size:22 final size:22
Alignment explanation
Indices: 19730096--19730139 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19730086 GTCTCAAATA
19730096 TCTCAATCATCATTTTGTCTGC
1 TCTCAATCATCATTTTGTCTGC
*
19730118 TCTCAATCATCGTTTTGTCTGC
1 TCTCAATCATCATTTTGTCTGC
19730140 AGACTATGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.45
Consensus pattern (22 bp):
TCTCAATCATCATTTTGTCTGC
Found at i:19733123 original size:20 final size:20
Alignment explanation
Indices: 19733084--19733123 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19733074 ATGTTCATTT
*
19733084 AATTAAAAAAATATTCAAAA
1 AATTAAAAAAATAATCAAAA
19733104 AATTAAATAAAATAAT-AAAA
1 AATTAAA-AAAATAATCAAAA
19733124 TTAAAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AATTAAAAAAATAATCAAAA
Found at i:19733525 original size:13 final size:13
Alignment explanation
Indices: 19733503--19733539 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
19733493 AACCGCTACA
*
19733503 CAAGCACTCCTGG
1 CAAGCCCTCCTGG
19733516 CAAGCCCTCCTGG
1 CAAGCCCTCCTGG
19733529 CAAGCCCTCCT
1 CAAGCCCTCCT
19733540 TTTTTCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.16
Consensus pattern (13 bp):
CAAGCCCTCCTGG
Found at i:19735366 original size:26 final size:26
Alignment explanation
Indices: 19735337--19735387 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19735327 CATATCTTTA
**
19735337 ACCAAACTTTTTAAAAGTACTTTTCC
1 ACCAAACTTTTTAAAAACACTTTTCC
19735363 ACCAAACTTTTTAAAAACACTTTTC
1 ACCAAACTTTTTAAAAACACTTTTC
19735388 AAAAGCAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (26 bp):
ACCAAACTTTTTAAAAACACTTTTCC
Found at i:19736443 original size:35 final size:35
Alignment explanation
Indices: 19736404--19736471 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
19736394 AATTCATTTC
19736404 CACGTCAGATTCAATTTCTAAAAGTTTTTTTTTTT
1 CACGTCAGATTCAATTTCTAAAAGTTTTTTTTTTT
* ***
19736439 CACGTCAGTTTCAATTTCTCCTAGTTTTTTTTT
1 CACGTCAGATTCAATTTCTAAAAGTTTTTTTTT
19736472 CAAATTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (35 bp):
CACGTCAGATTCAATTTCTAAAAGTTTTTTTTTTT
Found at i:19739190 original size:5 final size:5
Alignment explanation
Indices: 19739180--19739240 Score: 88
Period size: 5 Copynumber: 12.2 Consensus size: 5
19739170 GGTTCGAACC
*
19739180 AGAAA AGAAA AGAGAA A-AAA AGAAA AGAAA GGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGA-AA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
*
19739230 AGAAA ACAAA A
1 AGAAA AGAAA A
19739241 AATATCCTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
4 3 0.06
5 45 0.88
6 3 0.06
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:19748108 original size:9 final size:9
Alignment explanation
Indices: 19748094--19748119 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19748084 TTTTATATTT
19748094 TCAAGAAAA
1 TCAAGAAAA
19748103 TCAAGAAAA
1 TCAAGAAAA
19748112 TCAAGAAA
1 TCAAGAAA
19748120 CAAAATCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
TCAAGAAAA
Found at i:19749553 original size:50 final size:50
Alignment explanation
Indices: 19749453--19749555 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
19749443 CAAATGCAAA
* * *
19749453 AAAATTATGAACAAGTATAATTCATTAATAAAAGAATAAATGGTACTATG
1 AAAATTATGAACAAATATAATTCATTAATAAAAGAATAAACGCTACTATG
* * *
19749503 AAAATTAT-ATACAAATATAATTCATTGATAAAAGAATAAGCGCTAGTATG
1 AAAATTATGA-ACAAATATAATTCATTAATAAAAGAATAAACGCTACTATG
19749553 AAA
1 AAA
19749556 TAAATTTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 1 0.02
50 45 0.98
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (50 bp):
AAAATTATGAACAAATATAATTCATTAATAAAAGAATAAACGCTACTATG
Found at i:19753221 original size:45 final size:45
Alignment explanation
Indices: 19753157--19753246 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
19753147 GATGCTTAGT
19753157 TGAATGAATTGTTGGATTCACATTTTAATTAATTTGTATAATTTG
1 TGAATGAATTGTTGGATTCACATTTTAATTAATTTGTATAATTTG
19753202 TGAATGAATTGTTGGATTCACATTTTAATTAATTTGTATAATTTG
1 TGAATGAATTGTTGGATTCACATTTTAATTAATTTGTATAATTTG
19753247 GGTTGTTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (45 bp):
TGAATGAATTGTTGGATTCACATTTTAATTAATTTGTATAATTTG
Found at i:19753238 original size:25 final size:25
Alignment explanation
Indices: 19753165--19753238 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
19753155 GTTGAATGAA
19753165 TTGTTGGATTCACATTTTAATTAAT
1 TTGTTGGATTCACATTTTAATTAAT
*
19753190 TTG-T--A-T-A-ATTTGTGAATGAA-
1 TTGTTGGATTCACATTT-T-AATTAAT
19753210 TTGTTGGATTCACATTTTAATTAAT
1 TTGTTGGATTCACATTTTAATTAAT
19753235 TTGT
1 TTGT
19753239 ATAATTTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 4 0.11
20 5 0.13
21 7 0.18
22 1 0.03
23 1 0.03
24 7 0.18
25 9 0.24
26 4 0.11
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.51
Consensus pattern (25 bp):
TTGTTGGATTCACATTTTAATTAAT
Found at i:19755767 original size:266 final size:266
Alignment explanation
Indices: 19755293--19756067 Score: 1407
Period size: 266 Copynumber: 2.9 Consensus size: 266
19755283 TTTTACATAA
* * * * *
19755293 TTTATGGTCAATATTTGATTGCTACAACAAGAGTATCGCTTACTATAAATATCACTGTCCAAAGC
1 TTTATGGTCAATGTTTGATTGCTACAACAAGAGTATCGCTTACTGTTAATATCAATGTCCAAAGA
*
19755358 CTTAATATTAATGTTGTGTTTGGTATCTTGAGATGAGATTAGCTATTATTCTGAATTTATTGTTT
66 CTTGATATTAATGTTGTGTTTGGTATCTTGAGATGAGATTAGCTATTATTCTGAATTTATTGTTT
19755423 ACTTCTGAATATTCATGTGAGCTTGTTTCTATCTATTTTGTTCTATATTCAGCTATAATCTTTTG
131 ACTTCTGAATATTCATGTGAGCTTGTTTCTATCTATTTTGTTCTATATTCAGCTATAATCTTTTG
19755488 CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAATATAAATTATATA
196 CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAATATAAATTATATA
19755553 CTCATT
261 CTCATT
*
19755559 TTTATGGTCAATGTTTGATTGCTACAACAAGAGTATCGCTTACTGTTAATATCAATGTTCAAAGA
1 TTTATGGTCAATGTTTGATTGCTACAACAAGAGTATCGCTTACTGTTAATATCAATGTCCAAAGA
* *
19755624 CTTGATATTAATGTTGTGTTTGGTATCTTGAGATGGGATTAGCTATTATTCTTAATTTATTGTTT
66 CTTGATATTAATGTTGTGTTTGGTATCTTGAGATGAGATTAGCTATTATTCTGAATTTATTGTTT
*
19755689 ACTTCTAAATATTCATGTGAGCTTGTTTCTATCTATTTTGTTCTATATTCAGCTATAATCTTTTG
131 ACTTCTGAATATTCATGTGAGCTTGTTTCTATCTATTTTGTTCTATATTCAGCTATAATCTTTTG
*
19755754 CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAATATCAATTATATA
196 CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAATATAAATTATATA
19755819 CTCATT
261 CTCATT
19755825 TTTATGGTCAATGTTTGATTGCTACAACAAGAGTATCGCTTACTGTTAATATCAATGTCCAAAGA
1 TTTATGGTCAATGTTTGATTGCTACAACAAGAGTATCGCTTACTGTTAATATCAATGTCCAAAGA
19755890 CTTGATATTAATGTTGTGTTTGGTATCTTGAGATGAGATTAGCTATTATTCTGAATTTATTGTTT
66 CTTGATATTAATGTTGTGTTTGGTATCTTGAGATGAGATTAGCTATTATTCTGAATTTATTGTTT
*
19755955 ACTTCTGAATATTCATGTGAGCTTGTTTCTGTCTA---T-TT-TATATTCAGCTATAATCTTTTG
131 ACTTCTGAATATTCATGTGAGCTTGTTTCTATCTATTTTGTTCTATATTCAGCTATAATCTTTTG
19756015 CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAAT
196 CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAAT
19756068 TTTAAGGAAT
Statistics
Matches: 493, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
261 75 0.15
262 2 0.00
263 1 0.00
266 415 0.84
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (266 bp):
TTTATGGTCAATGTTTGATTGCTACAACAAGAGTATCGCTTACTGTTAATATCAATGTCCAAAGA
CTTGATATTAATGTTGTGTTTGGTATCTTGAGATGAGATTAGCTATTATTCTGAATTTATTGTTT
ACTTCTGAATATTCATGTGAGCTTGTTTCTATCTATTTTGTTCTATATTCAGCTATAATCTTTTG
CTGCCACAATATCTGCTAATATAAATTCTATACTCATTTTTAATGGGACTAATATAAATTATATA
CTCATT
Found at i:19758700 original size:220 final size:220
Alignment explanation
Indices: 19758318--19758754 Score: 707
Period size: 220 Copynumber: 2.0 Consensus size: 220
19758308 TCCCCAAATT
* *
19758318 ACACATGAGTAACTTTTCTAATATCTCATCTTTGGAAAACAGAGAGCCACCCTCTCAAAATTGCT
1 ACACATGAATAACTTTTCTAATATCTCATCTTTGGAAAACAGAGAGCCACCATCTCAAAATTGCT
* * *
19758383 TATGTGCTAATTTGAAAGATCAAAACCCCAAGATCCATAGATTTCAAGAAATCGATGAATTAAGG
66 TATGTGCTAATTTGAAAGATCAAAACCCCAAAATCCATAGATTTCAAAAAAACGATGAATTAAGG
19758448 TACGCTTCCACATCTAGTTTTGTTTCTGATTTATTCTTGATGACTTGACATGATAGATCATAG-T
131 TACGCTTCCACATCTAGTTTTGTTTCTGATTTATTCTTGATGACTTGACATGATAGATCAT-GTT
*
19758512 TTATGGTTTATTAAGTTTTATTTCAG
195 TTATGGTTTATTAAGTTTAATTTCAG
*
19758538 ACACATGAATAACTTTTCTAATATCTCATCTTTGGAAAAGAGAGAGCCACCATCTCAAAATTGCT
1 ACACATGAATAACTTTTCTAATATCTCATCTTTGGAAAACAGAGAGCCACCATCTCAAAATTGCT
* * * **
19758603 TGTGTGCTAATTT-AGAAGATCAAAACCCCAAAATCCGTATATTTCAAAAAAACGATGAATTTTG
66 TATGTGCTAATTTGA-AAGATCAAAACCCCAAAATCCATAGATTTCAAAAAAACGATGAATTAAG
* * *
19758667 GTACGCTTCCGCATCTAGTTTTGTTTTTGATTTATTCTTGATGATTTGACATGATAGATCATGTT
130 GTACGCTTCCACATCTAGTTTTGTTTCTGATTTATTCTTGATGACTTGACATGATAGATCATGTT
19758732 TTATGGTTTATTAAGTTTAATTT
195 TTATGGTTTATTAAGTTTAATTT
19758755 TAGATTTATT
Statistics
Matches: 200, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
219 2 0.01
220 198 0.99
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (220 bp):
ACACATGAATAACTTTTCTAATATCTCATCTTTGGAAAACAGAGAGCCACCATCTCAAAATTGCT
TATGTGCTAATTTGAAAGATCAAAACCCCAAAATCCATAGATTTCAAAAAAACGATGAATTAAGG
TACGCTTCCACATCTAGTTTTGTTTCTGATTTATTCTTGATGACTTGACATGATAGATCATGTTT
TATGGTTTATTAAGTTTAATTTCAG
Found at i:19761248 original size:59 final size:61
Alignment explanation
Indices: 19761170--19761322 Score: 211
Period size: 60 Copynumber: 2.5 Consensus size: 61
19761160 AAAAAATAAG
* * * *
19761170 GAAAAAGAATCTTCAAGAAATTGAATTTGAC-AAAAAACTAGGAGAAATTGAAACTGATGT
1 GAAAAAGAACCTTCAAGAAATTGAATATGACAAAAAAAATAGGAGAAATTGAAACTGACGT
*
19761230 GAAAAA-AACCTTCAAGAAATTGAATATGACAAAAAAAATAGGAGAAATTGAAATTGACGT
1 GAAAAAGAACCTTCAAGAAATTGAATATGACAAAAAAAATAGGAGAAATTGAAACTGACGT
* *
19761290 GAAAAAAGAACCTTTTAAGAAATTGAATCTGAC
1 G-AAAAAGAACC-TTCAAGAAATTGAATATGAC
19761323 GTGGAAATGA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
59 22 0.27
60 33 0.40
61 5 0.06
62 4 0.05
63 18 0.22
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (61 bp):
GAAAAAGAACCTTCAAGAAATTGAATATGACAAAAAAAATAGGAGAAATTGAAACTGACGT
Found at i:19761296 original size:32 final size:30
Alignment explanation
Indices: 19761201--19761296 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 30
19761191 TGAATTTGAC
19761201 AAAAAACTAGGAGAAATTGAAACTGATGTGAA
1 AAAAAACTAGGAGAAATTGAAA-TGA-GTGAA
* ***
19761233 AAAAACCTTCAAGAAATTG-AAT-A-TGACA
1 AAAAAACTAGGAGAAATTGAAATGAGTGA-A
*
19761261 AAAAAAATAGGAGAAATTGAAATTGACGTGAA
1 AAAAAACTAGGAGAAATTGAAA-TGA-GTGAA
19761293 AAAA
1 AAAA
19761297 GAACCTTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.06
28 15 0.31
29 3 0.06
30 2 0.04
31 3 0.06
32 20 0.41
33 3 0.06
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.19
Consensus pattern (30 bp):
AAAAAACTAGGAGAAATTGAAATGAGTGAA
Found at i:19764865 original size:40 final size:41
Alignment explanation
Indices: 19764821--19764900 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
19764811 AATTTTCACA
*
19764821 ATTTTAATTATTTTT-AAATGATTCTTTTAC-ATTTTTAATG
1 ATTTTAATAATTTTTAAAAT-ATTCTTTTACAATTTTTAATG
* *
19764861 ATTTTCATAATTTTTAAAATATTTTTTTACAATTTTTAAT
1 ATTTTAATAATTTTTAAAATATTCTTTTACAATTTTTAAT
19764901 ACTTTTTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 22 0.63
41 13 0.37
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (41 bp):
ATTTTAATAATTTTTAAAATATTCTTTTACAATTTTTAATG
Found at i:19764901 original size:20 final size:22
Alignment explanation
Indices: 19764830--19764899 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
19764820 AATTTTAATT
*
19764830 ATTTTTAAATGATTCTTTTAC-
1 ATTTTTAAATGATTTTTTTACA
* *
19764851 ATTTTT-AATGA--TTTTCATA
1 ATTTTTAAATGATTTTTTTACA
19764870 ATTTTTAAAAT-ATTTTTTTACA
1 ATTTTT-AAATGATTTTTTTACA
19764892 ATTTTTAA
1 ATTTTTAA
19764900 TACTTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 4 0.10
19 6 0.15
20 6 0.15
21 11 0.28
22 12 0.31
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (22 bp):
ATTTTTAAATGATTTTTTTACA
Found at i:19764939 original size:11 final size:11
Alignment explanation
Indices: 19764918--19764954 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
19764908 AACTATTTAC
19764918 AATTTTT-AAT
1 AATTTTTAAAT
19764928 AATTTTTAAAT
1 AATTTTTAAAT
*
19764939 ACTTTTTAAA-
1 AATTTTTAAAT
19764949 AATTTT
1 AATTTT
19764955 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 12 0.50
11 12 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
AATTTTTAAAT
Found at i:19765056 original size:29 final size:30
Alignment explanation
Indices: 19765023--19765100 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
19765013 TTTTGTAATT
*
19765023 TTTATTTTTATAATTTTTTCTAGA-TTATA
1 TTTATTTTTATAATTTTTTATAGACTTATA
* * * * *
19765052 TTTATATTTCTAAATTTTTATATACTTATT
1 TTTATTTTTATAATTTTTTATAGACTTATA
*
19765082 TTTATTTTTTATAGTTTTT
1 TTTA-TTTTTATAATTTTT
19765101 AATATTTATA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 19 0.51
30 8 0.22
31 10 0.27
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (30 bp):
TTTATTTTTATAATTTTTTATAGACTTATA
Found at i:19768395 original size:15 final size:17
Alignment explanation
Indices: 19768365--19768401 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
19768355 TCTCCCTCTC
19768365 TTCTCTCTTCTCTCTAA
1 TTCTCTCTTCTCTCTAA
*
19768382 TTCTCTC-TCT-TCTAC
1 TTCTCTCTTCTCTCTAA
19768397 TTCTC
1 TTCTC
19768402 GGAAACTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (17 bp):
TTCTCTCTTCTCTCTAA
Found at i:19769426 original size:31 final size:32
Alignment explanation
Indices: 19769391--19769456 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
19769381 TTTAACCATT
*
19769391 TTTAATTTTTAT-TT-TAATATTTTTGTTTTTA
1 TTTAATTTTTATATTCTAAT-TTTTTCTTTTTA
19769422 TTTAATTTTTATATTCTAATTTTTTCTTTTTA
1 TTTAATTTTTATATTCTAATTTTTTCTTTTTA
19769454 TTT
1 TTT
19769457 GCTTTTGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 12 0.38
32 16 0.50
33 4 0.12
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (32 bp):
TTTAATTTTTATATTCTAATTTTTTCTTTTTA
Found at i:19780287 original size:17 final size:15
Alignment explanation
Indices: 19780265--19780335 Score: 61
Period size: 17 Copynumber: 4.3 Consensus size: 15
19780255 AAAAATAGTA
19780265 TATTTAGTTTTATATTT
1 TATTTA-TTTT-TATTT
19780282 TATTTATTTTTATTT
1 TATTTATTTTTATTT
* *
19780297 TCATTTACATTTCATTT
1 T-ATTTA-TTTTTATTT
19780314 TCATTTTTATTTTTATTT
1 T-A--TTTATTTTTATTT
19780332 TATT
1 TATT
19780336 ATGCACTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
15 8 0.17
16 9 0.20
17 17 0.37
18 8 0.17
19 4 0.09
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (15 bp):
TATTTATTTTTATTT
Found at i:19780326 original size:12 final size:12
Alignment explanation
Indices: 19780279--19780332 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
19780269 TAGTTTTATA
19780279 TTTTA-TTT-AT
1 TTTTATTTTCAT
19780289 TTTTATTTTCAT
1 TTTTATTTTCAT
**
19780301 TTACA-TTTCAT
1 TTTTATTTTCAT
* *
19780312 TTTCATTTTTAT
1 TTTTATTTTCAT
19780324 TTTTATTTT
1 TTTTATTTT
19780333 ATTATGCACT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 5 0.14
11 13 0.36
12 18 0.50
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTTCAT
Found at i:19780332 original size:11 final size:11
Alignment explanation
Indices: 19780267--19780335 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
19780257 AAATAGTATA
19780267 TTTAGTTTTATAT
1 TTTA-TTTTAT-T
19780280 TTTA-TTTATT
1 TTTATTTTATT
19780290 TTTATTTTCATT
1 TTTATTTT-ATT
** *
19780302 TACATTTCATT
1 TTTATTTTATT
*
19780313 TTCATTTTTATT
1 TTTA-TTTTATT
19780325 TTTATTTTATT
1 TTTATTTTATT
19780336 ATGCACTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 5 0.11
11 21 0.45
12 17 0.36
13 4 0.09
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:19781286 original size:15 final size:15
Alignment explanation
Indices: 19781266--19781305 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
19781256 ATAGAAAAAA
19781266 AAGAAAAAAAATGTG
1 AAGAAAAAAAATGTG
19781281 AAG--AAAAAA-GTG
1 AAGAAAAAAAATGTG
19781293 AAGAGAAAAAAAT
1 AAGA-AAAAAAAT
19781306 TTGATTGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
15 9 0.43
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (15 bp):
AAGAAAAAAAATGTG
Found at i:19790480 original size:44 final size:44
Alignment explanation
Indices: 19790417--19790527 Score: 186
Period size: 44 Copynumber: 2.5 Consensus size: 44
19790407 TTATATCCCG
*
19790417 ACTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAGCAA
1 ACTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAACAA
* *
19790461 ACTTGGAACAAAAATAGTAATTTAAATTAGATGTATTAAAATAA
1 ACTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAACAA
*
19790505 ACTTGGAACAAACATAGAAATTT
1 ACTTGGAACAAACATAGTAATTT
19790528 CATCATCGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.30
Consensus pattern (44 bp):
ACTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAACAA
Found at i:19793253 original size:12 final size:12
Alignment explanation
Indices: 19793234--19793266 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19793224 GATTTTTATA
19793234 TAAATAAAATTCT
1 TAAATAAAATT-T
19793247 T-AATAAAATTT
1 TAAATAAAATTT
19793258 TAAATAAAA
1 TAAATAAAA
19793267 CAACAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.84
13 1 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATAAAATTT
Found at i:19793384 original size:27 final size:27
Alignment explanation
Indices: 19793353--19793408 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
19793343 CGTAAACATT
*
19793353 AAAATAAACTTTATACT-AATTAAAAAC
1 AAAATAAACTTTA-AATAAATTAAAAAC
**
19793380 AAAATAATTTTTAAATAAATTAAAAAC
1 AAAATAAACTTTAAATAAATTAAAAAC
19793407 AA
1 AA
19793409 CAACAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAATAAACTTTAAATAAATTAAAAAC
Found at i:19798781 original size:14 final size:14
Alignment explanation
Indices: 19798731--19798783 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
19798721 ATCCTTTCTC
19798731 AAACCTCTAAACCTT
1 AAACC-CTAAACCTT
*
19798746 AAA-CCTAAACCAT
1 AAACCCTAAACCTT
* **
19798759 ATATACTAAACCTT
1 AAACCCTAAACCTT
19798773 AAACCCTAAAC
1 AAACCCTAAAC
19798784 ATAATTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 10 0.33
14 17 0.57
15 3 0.10
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:19798811 original size:26 final size:26
Alignment explanation
Indices: 19798779--19798884 Score: 158
Period size: 26 Copynumber: 4.1 Consensus size: 26
19798769 CCTTAAACCC
* * *
19798779 TAAACATAATTAATTAAACACAAGCA
1 TAAACATAATTAATGAAATACAAACA
19798805 TAAACATAATTAATGAAATACAAACA
1 TAAACATAATTAATGAAATACAAACA
* *
19798831 TAAACATAATTAATGAAATGCAAAAA
1 TAAACATAATTAATGAAATACAAACA
*
19798857 TAAACATAATTAATTAAATACAAACA
1 TAAACATAATTAATGAAATACAAACA
19798883 TA
1 TA
19798885 TACTGAGTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.60, C:0.11, G:0.04, T:0.25
Consensus pattern (26 bp):
TAAACATAATTAATGAAATACAAACA
Found at i:19799936 original size:26 final size:26
Alignment explanation
Indices: 19799907--19800037 Score: 190
Period size: 26 Copynumber: 5.0 Consensus size: 26
19799897 GACAAACTCA
*
19799907 GTTTATGTTTGTATTTAATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
**
19799933 GTTTATGTTTACATTTCATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
*
19799959 GTTTATGTTTTTATTTCATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
* *
19799985 GTTTATGTTTGTTTTTCAGTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
* *
19800011 GTTTATGTTTGTATATAATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
19800037 G
1 G
19800038 GTTAGGGTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 93 1.00
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.60
Consensus pattern (26 bp):
GTTTATGTTTGTATTTCATTAATTAT
Found at i:19800068 original size:21 final size:21
Alignment explanation
Indices: 19800039--19800098 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
19800029 TTAATTATGG
19800039 TTAGGGTTTAGGGTTTAATTT
1 TTAGGGTTTAGGGTTTAATTT
* *
19800060 TTAGTGTTTAGGGTTTAA-TG
1 TTAGGGTTTAGGGTTTAATTT
*
19800080 TTAGAGGTTAAGGGTTTAA
1 TTAG-GGTTTAGGGTTTAA
19800099 GGTTTAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTTAATTT
Found at i:19800754 original size:14 final size:14
Alignment explanation
Indices: 19800731--19800826 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 14
19800721 TATTAAGTAA
*
19800731 TAAACACTAAACCT
1 TAAACCCTAAACCT
19800745 TAAACCCTAAA--T
1 TAAACCCTAAACCT
* *
19800757 TGAGTACCTTAAACCT
1 T-A-AACCCTAAACCT
*
19800773 TAAACCTTAAACCT
1 TAAACCCTAAACCT
* * * *
19800787 TATACACTAAGCCC
1 TAAACCCTAAACCT
* *
19800801 TAGACCTTAAACCT
1 TAAACCCTAAACCT
19800815 TAAACCCTAAAC
1 TAAACCCTAAAC
19800827 ATAATTAATT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
12 2 0.03
13 1 0.02
14 56 0.90
15 1 0.02
16 2 0.03
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:19800772 original size:7 final size:7
Alignment explanation
Indices: 19800762--19800826 Score: 69
Period size: 7 Copynumber: 9.3 Consensus size: 7
19800752 TAAATTGAGT
19800762 ACCTTAA
1 ACCTTAA
19800769 ACCTTAA
1 ACCTTAA
19800776 ACCTTAA
1 ACCTTAA
*
19800783 ACCTTAT
1 ACCTTAA
19800790 ACAC-TAA
1 AC-CTTAA
* * *
19800797 GCCCTAG
1 ACCTTAA
19800804 ACCTTAA
1 ACCTTAA
19800811 ACCTTAA
1 ACCTTAA
*
19800818 ACCCTAA
1 ACCTTAA
19800825 AC
1 AC
19800827 ATAATTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 1 0.02
7 46 0.96
8 1 0.02
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.25
Consensus pattern (7 bp):
ACCTTAA
Found at i:19800854 original size:26 final size:26
Alignment explanation
Indices: 19800822--19800955 Score: 214
Period size: 26 Copynumber: 5.2 Consensus size: 26
19800812 CCTTAAACCC
19800822 TAAACATAATTAATTAAATACAAACA
1 TAAACATAATTAATTAAATACAAACA
*
19800848 TGAACATAATTAATTAAATACAAACA
1 TAAACATAATTAATTAAATACAAACA
* *
19800874 TAAACATAATTAGTGAAATACAAACA
1 TAAACATAATTAATTAAATACAAACA
* * *
19800900 TAAGCATAATTAATGAAATATAAACA
1 TAAACATAATTAATTAAATACAAACA
19800926 TAAACATAATTAATTAAATACAAACA
1 TAAACATAATTAATTAAATACAAACA
19800952 TAAA
1 TAAA
19800956 TTGATTTTGT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 98 1.00
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.26
Consensus pattern (26 bp):
TAAACATAATTAATTAAATACAAACA
Found at i:19801348 original size:24 final size:24
Alignment explanation
Indices: 19801321--19801389 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
19801311 GCTCCGAATG
*
19801321 ATATTTATGGCCTAACCAACCCGT
1 ATATTCATGGCCTAACCAACCCGT
* * *
19801345 ATATCCATGGCCTGACCACCCCGT
1 ATATTCATGGCCTAACCAACCCGT
19801369 ATGATATCCATGGCCTAACCA
1 AT-AT-T-CATGGCCTAACCA
19801390 CCTTGGATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 22 0.61
25 2 0.06
27 12 0.33
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (24 bp):
ATATTCATGGCCTAACCAACCCGT
Found at i:19801399 original size:27 final size:27
Alignment explanation
Indices: 19801318--19801401 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
19801308 GAAGCTCCGA
** *
19801318 ATGATATTTATGGCCTAACCAACCC-G
1 ATGATATCCATGGCCTAACCACCCCGG
* *
19801344 -T-ATATCCATGGCCTGACCACCCCGT
1 ATGATATCCATGGCCTAACCACCCCGG
**
19801369 ATGATATCCATGGCCTAACCACCTTGG
1 ATGATATCCATGGCCTAACCACCCCGG
19801396 ATGATA
1 ATGATA
19801402 AGAGTCGGGC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 18 0.39
25 1 0.02
26 1 0.02
27 26 0.57
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (27 bp):
ATGATATCCATGGCCTAACCACCCCGG
Found at i:19801438 original size:6 final size:6
Alignment explanation
Indices: 19801423--19801452 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
19801413 TCGGATCGGT
*
19801423 CTCAAA CTCAAG CTCAAG CTCAAG CTCAAG
1 CTCAAG CTCAAG CTCAAG CTCAAG CTCAAG
19801453 TGGATGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (6 bp):
CTCAAG
Found at i:19809333 original size:36 final size:36
Alignment explanation
Indices: 19809293--19809440 Score: 233
Period size: 36 Copynumber: 4.1 Consensus size: 36
19809283 TGATAGTTGT
*
19809293 GACAGTAAATATGTGGATATGTTATTCATGCCATGA
1 GACAGTAAATATGTGGGTATGTTATTCATGCCATGA
*
19809329 GACAGTAAATATTTGGGTATGTTATTCATGCCATGA
1 GACAGTAAATATGTGGGTATGTTATTCATGCCATGA
* *
19809365 GATAGTAAATATGTGGGTATTTTATTCATGCCATGA
1 GACAGTAAATATGTGGGTATGTTATTCATGCCATGA
* * *
19809401 GACAGTAAATATGTGGGTATGTTATTTATGTCATGT
1 GACAGTAAATATGTGGGTATGTTATTCATGCCATGA
19809437 GACA
1 GACA
19809441 ATGAATAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 102 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.36
Consensus pattern (36 bp):
GACAGTAAATATGTGGGTATGTTATTCATGCCATGA
Found at i:19811048 original size:57 final size:59
Alignment explanation
Indices: 19810982--19811111 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 59
19810972 TTTCAATAGC
* * * * *
19810982 AAAATGGTAATTTTTGGAAAAGTTAAGGTTAAAAAT-GACATTTTAGACATCCGGGGGT
1 AAAATGGTAATTTTTAGAAAAATCAAGATCAAAAATGGACATTTTAGACATCCGGGGGT
* * ** * *
19811040 AAAA-GGTAATCTTTAGAAAAATCGAGATCAAAAATGGAGTTTTTGGACATCTGGGGGT
1 AAAATGGTAATTTTTAGAAAAATCAAGATCAAAAATGGACATTTTAGACATCCGGGGGT
19811098 AAAATGGTAATTTT
1 AAAATGGTAATTTT
19811112 CACAAGTTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
57 24 0.41
58 26 0.45
59 8 0.14
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAAAATCAAGATCAAAAATGGACATTTTAGACATCCGGGGGT
Found at i:19811149 original size:30 final size:30
Alignment explanation
Indices: 19811067--19811465 Score: 284
Period size: 30 Copynumber: 13.5 Consensus size: 30
19811057 AAAATCGAGA
* * *
19811067 TCAAAAATGGAGTTTTTGGACA-TCTGGGGG
1 TCAAAAATGGAATTTTTGGA-AGTTTAGGGG
***
19811097 T--AAAATGGTAATTTTCACAAGTTTAGGGG
1 TCAAAAATGG-AATTTTTGGAAGTTTAGGGG
* *
19811126 TCAAAAATGGAATTTTTAGAAG-TTCGAGGG
1 TCAAAAATGGAATTTTTGGAAGTTTAG-GGG
*
19811156 T-AAAAATGTAATTTTTGGAAGTTTTA-GGG
1 TCAAAAATGGAATTTTTGGAAG-TTTAGGGG
* * ** *
19811185 TGAAAAAGGGAATTTTTAAAATTTTAGGGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
* * *
19811215 TAAAAACAT--AATTTTTTGAAGTTTTGGGG
1 TCAAAA-ATGGAATTTTTGGAAGTTTAGGGG
* *
19811244 TTAAAAATGGAATTGTTGGAA-TTCTAGGGG
1 TCAAAAATGGAATTTTTGGAAGTT-TAGGGG
* * * *
19811274 -GAAAAATGTAATTTTTGGAAGTTTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
* * * * * *
19811303 T-TAAAATGTAATTTTTAGATGTTTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
* * *
19811332 TCAAAAATGGAATTTTTGGATGTTTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
* * * *
19811362 TTAAAAATGGAATTTTTGGATGTTTTGGAG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
*
19811392 TCAAAAATGTAATTTTTGGAAGTTT-GGGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
* * *
19811421 T-AAAAATGTAATTTTTTGAAGTTTTGGGG
1 TCAAAAATGGAATTTTTGGAAGTTTAGGGG
*
19811450 TCAAAAATGTAATTTT
1 TCAAAAATGGAATTTT
19811466 GGAGGAGTTC
Statistics
Matches: 304, Mismatches: 47, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
28 32 0.11
29 121 0.40
30 141 0.46
31 10 0.03
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (30 bp):
TCAAAAATGGAATTTTTGGAAGTTTAGGGG
Found at i:19811161 original size:88 final size:87
Alignment explanation
Indices: 19811069--19811465 Score: 265
Period size: 88 Copynumber: 4.5 Consensus size: 87
19811059 AATCGAGATC
* * *
19811069 AAAAATGGAGTTTTTGGACA-TCTGGGGGTAAAATGGTAATTTTCACAAGTTTAGGGGTCAAAAA
1 AAAAATGGAATTTTTGGA-AGTCTGGGGGTAAAATGGTAATTTTTAAAAGTTTAGGGGT-AAAAA
19811133 TGGAATTTTTAGAAG-TTCGAGGGT
64 T-GAATTTTTAGAAGTTTCGAGGGT
* * ** * * *
19811157 AAAAATGTAATTTTTGGAAGTTTTAGGGTGAAAAAGGGAATTTTTAAAATTTTAGGGGTAAAAAC
1 AAAAATGGAATTTTTGGAAGTCTGGGGGT-AAAATGGTAATTTTTAAAAGTTTAGGGGT-AAAA-
* *
19811222 AT-AATTTTTTGAAGTTTTG-GGGTT
63 ATGAATTTTTAGAAGTTTCGAGGG-T
* * * ** * * *
19811246 AAAAATGGAATTGTTGGAATTCTAGGGGGAAAAAT-GTAATTTTTGGAAGTTTCGAGGTTAAAAT
1 AAAAATGGAATTTTTGGAAGTCT-GGGGGTAAAATGGTAATTTTTAAAAGTTTAGGGGTAAAAAT
*
19811310 GTAATTTTTAGATGTTTCGA-GGT
65 G-AATTTTTAGAAGTTTCGAGGGT
* * * * ** * * *
19811333 CAAAAATGGAATTTTTGGATGTTTCGAGGTTAAAAATGG-AATTTTTGGATGTTTTGGAGTCAAA
1 -AAAAATGGAATTTTTGGAAGTCT-GGGGGT-AAAATGGTAATTTTTAAAAGTTTAGGGGT-AAA
*
19811397 AATGTAATTTTTGGAAGTTT-G-GGGT
62 AATG-AATTTTTAGAAGTTTCGAGGGT
* * * *
19811422 AAAAATGTAATTTTTTGAAGTTTTGGGGTCAAAAAT-GTAATTTT
1 AAAAATGGAATTTTTGGAAGTCTGGGGGT--AAAATGGTAATTTT
19811466 GGAGGAGTTC
Statistics
Matches: 241, Mismatches: 52, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
86 2 0.01
87 9 0.04
88 123 0.51
89 81 0.34
90 26 0.11
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (87 bp):
AAAAATGGAATTTTTGGAAGTCTGGGGGTAAAATGGTAATTTTTAAAAGTTTAGGGGTAAAAATG
AATTTTTAGAAGTTTCGAGGGT
Found at i:19811216 original size:59 final size:56
Alignment explanation
Indices: 19811093--19811465 Score: 266
Period size: 59 Copynumber: 6.3 Consensus size: 56
19811083 TGGACATCTG
*** * *
19811093 GGGGT-AAAATGGTAATTTTCACAAGTTTAGGGGTCAAAAATGGAATTTTTAGAA-GTTC
1 GGGGTAAAAAT-GTAATTTTTGGAAGTTTA-GGGT-AAAAATGGAATTTTTA-AATTTTA
*
19811151 GAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTGAAAAAGGGAATTTTTAAAATTTTA
1 G-GGGTAAAAATGTAATTTTTGGAAG-TTTAGGGT-AAAAATGGAATTTTT-AAATTTTA
** * * ** *
19811211 GGGGTAAAAACATAATTTTTTGAAGTTTTGGGGTTAAAAATGGAATTGTTGGAATTCTA
1 GGGGTAAAAATGTAATTTTTGGAAG-TTTAGGG-TAAAAATGGAATT-TTTAAATTTTA
* * * * * *
19811270 GGGGGAAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAATGTAATTTTTAGATGTTTC
1 GGGGTAAAAATGTAATTTTTGGAAGTTTAG-GGTAAAAATGGAATTTTTAAAT-TTTA
* * * * ** *
19811328 GAGGTCAAAAATGGAATTTTTGGATGTTTCGAGGTTAAAAATGGAATTTTTGGATGTTTT
1 GGGGT-AAAAATGTAATTTTTGGAAGTTT--AGGGTAAAAATGGAATTTTTAAAT-TTTA
* * * *
19811388 GGAGTCAAAAATGTAATTTTTGGAAGTTTGGGGTAAAAATGTAATTTTTTGAAGTTTT-
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTAGGGTAAAAATGGAA-TTTTT-AAATTTTA
19811446 GGGGTCAAAAATGTAATTTT
1 GGGGT-AAAAATGTAATTTT
19811466 GGAGGAGTTC
Statistics
Matches: 253, Mismatches: 48, Indels: 28
0.77 0.15 0.09
Matches are distributed among these distances:
57 4 0.02
58 52 0.21
59 132 0.52
60 64 0.25
61 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (56 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTAAATTTTA
Found at i:19812796 original size:13 final size:13
Alignment explanation
Indices: 19812780--19812804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19812770 ATTACAACTA
19812780 TTATTATTATTAT
1 TTATTATTATTAT
19812793 TTATTATTATTA
1 TTATTATTATTA
19812805 ATAAAAAATC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:19813681 original size:17 final size:17
Alignment explanation
Indices: 19813655--19813748 Score: 91
Period size: 17 Copynumber: 5.4 Consensus size: 17
19813645 TTATATTTAT
* *
19813655 ATTTATATTTAAATTAA
1 ATTTAAATTTAAAATAA
*
19813672 ATTTAAATTTTAAAACAA
1 ATTTAAA-TTTAAAATAA
* *
19813690 ATTTAAACTTAAGATAA
1 ATTTAAATTTAAAATAA
*
19813707 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
*
19813724 ATTT-AATCTTAAAATCA
1 ATTTAAAT-TTAAAATAA
19813741 ATCTTAAA
1 AT-TTAAA
19813749 AGTGGGTTGA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 3 0.05
17 40 0.65
18 17 0.27
19 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:19813685 original size:7 final size:6
Alignment explanation
Indices: 19813639--19813729 Score: 57
Period size: 6 Copynumber: 15.7 Consensus size: 6
19813629 GTATTAAGTC
* * *
19813639 TTAAAT TTATAT TTATAT TTATAT TTAAA- TTAAAT TTAAATT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT
** * * *
19813686 ACAAAT TTAAAC TTAAGA- -TAAAT TTAAAT TCAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
19813730 TCTTAAAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
4 1 0.01
5 14 0.21
6 45 0.67
7 7 0.10
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:19814263 original size:17 final size:17
Alignment explanation
Indices: 19814241--19814280 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
19814231 AGTAGCTCTT
*
19814241 GCCTAAGTTACTTGTTA
1 GCCTAAGTTACTTATTA
19814258 GCCTAAGTTACTTATTA
1 GCCTAAGTTACTTATTA
*
19814275 ACCTAA
1 GCCTAA
19814281 CTTGTCACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (17 bp):
GCCTAAGTTACTTATTA
Found at i:19818428 original size:20 final size:21
Alignment explanation
Indices: 19818403--19818442 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
19818393 GCAAAAGAAT
*
19818403 TTAAAACAAC-ACAAGTAAAA
1 TTAAAACAACTAAAAGTAAAA
*
19818423 TTAAAATAACTAAAAGTAAA
1 TTAAAACAACTAAAAGTAAA
19818443 TAGAGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (21 bp):
TTAAAACAACTAAAAGTAAAA
Found at i:19828672 original size:17 final size:18
Alignment explanation
Indices: 19828650--19828689 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
19828640 AGATTGCATA
19828650 CATTTT-TATTGTCATCG
1 CATTTTATATTGTCATCG
* *
19828667 CATTTTATTTTGTCATTG
1 CATTTTATATTGTCATCG
19828685 CATTT
1 CATTT
19828690 CTTTTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (18 bp):
CATTTTATATTGTCATCG
Found at i:19829301 original size:9 final size:9
Alignment explanation
Indices: 19829289--19829322 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
19829279 GGAAAATGAG
19829289 AAAAAGAAA
1 AAAAAGAAA
19829298 AAAAAGAAA
1 AAAAAGAAA
19829307 AGAAAAGAAGA
1 A-AAAAGAA-A
19829318 AAAAA
1 AAAAA
19829323 AAGTTTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 10 0.43
10 11 0.48
11 2 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:19829317 original size:22 final size:23
Alignment explanation
Indices: 19829274--19829325 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
19829264 CAGTCACTTG
*
19829274 AAAAAGGAAAATGAGAAAAAGAA
1 AAAAAAGAAAATGAGAAAAAGAA
19829297 AAAAAAGAAAA-GA-AAAGAAGAA
1 AAAAAAGAAAATGAGAAA-AAGAA
19829319 AAAAAAG
1 AAAAAAG
19829326 TTTACTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.11
22 14 0.52
23 10 0.37
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAATGAGAAAAAGAA
Found at i:19831216 original size:18 final size:18
Alignment explanation
Indices: 19831193--19831237 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
19831183 ATTCATATAG
19831193 TTTGCATATTTA-GGATCA
1 TTTGCATA-TTAGGGATCA
19831211 TTTGC--ATTAGGGATCA
1 TTTGCATATTAGGGATCA
19831227 TTTGCAT-TTAG
1 TTTGCATATTAG
19831238 TTTAATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 4 0.17
18 5 0.21
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (18 bp):
TTTGCATATTAGGGATCA
Found at i:19834584 original size:15 final size:15
Alignment explanation
Indices: 19834560--19834607 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
19834550 TAGTTACGAT
* *
19834560 GATGACATCTATGAG
1 GATGATATCTATGAA
19834575 GATGATATCTATGAA
1 GATGATATCTATGAA
19834590 GATGGATA-CTATGAA
1 GAT-GATATCTATGAA
19834605 GAT
1 GAT
19834608 TGGGAGATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 26 0.87
16 4 0.13
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (15 bp):
GATGATATCTATGAA
Found at i:19839905 original size:36 final size:37
Alignment explanation
Indices: 19839847--19839953 Score: 157
Period size: 36 Copynumber: 3.0 Consensus size: 37
19839837 GCTTACTCCT
* *
19839847 TGCTCATTTCACTCTCTGTTGACCCAAAGGTT-ATGA
1 TGCTCATTTTACTCCCTGTTGACCCAAAGGTTCATGA
* *
19839883 TGCTCATTTTACTCCCTATTGACTCAAA-GTTCATGA
1 TGCTCATTTTACTCCCTGTTGACCCAAAGGTTCATGA
19839919 TGCTCATTTTACTCCCTGTTGACCCAAAGG-TCATG
1 TGCTCATTTTACTCCCTGTTGACCCAAAGGTTCATG
19839954 CCTCTTACCA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
35 3 0.05
36 59 0.94
37 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (37 bp):
TGCTCATTTTACTCCCTGTTGACCCAAAGGTTCATGA
Found at i:19842112 original size:11 final size:11
Alignment explanation
Indices: 19842096--19842129 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
19842086 AATATATAAA
19842096 ATAACAATCTC
1 ATAACAATCTC
19842107 ATAACAATCTC
1 ATAACAATCTC
*
19842118 ATAATAATCTC
1 ATAACAATCTC
19842129 A
1 A
19842130 AATAACACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAACAATCTC
Found at i:19844931 original size:36 final size:35
Alignment explanation
Indices: 19844875--19844975 Score: 166
Period size: 36 Copynumber: 2.8 Consensus size: 35
19844865 TCGATATCAG
19844875 ATTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
1 ATTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
*
19844910 ATTTCACTCCCTGTTGCCCCAAAGGTCATGATGCTC
1 ATTT-ACTCCCTGTTGACCCAAAGGTCATGATGCTC
*
19844946 ATTTTACTCCCTATTGACCCAAAGGTCATG
1 A-TTTACTCCCTGTTGACCCAAAGGTCATG
19844976 CCTATTACCA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
35 4 0.07
36 54 0.89
37 3 0.05
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.32
Consensus pattern (35 bp):
ATTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
Found at i:19857181 original size:2 final size:2
Alignment explanation
Indices: 19857174--19857205 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19857164 CAGAATCTAC
*
19857174 GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19857206 ATGCAACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19864274 original size:17 final size:17
Alignment explanation
Indices: 19864252--19864286 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
19864242 GATCGAGCAA
19864252 GCTCGTGCTGATAATGT
1 GCTCGTGCTGATAATGT
19864269 GCTCGTGCTGATAATGT
1 GCTCGTGCTGATAATGT
19864286 G
1 G
19864287 TTATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (17 bp):
GCTCGTGCTGATAATGT
Found at i:19869475 original size:40 final size:40
Alignment explanation
Indices: 19869420--19869515 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
19869410 AAAACGCTGT
*
19869420 AAAAGGTAAAGCAATAGCGGGGTTTTTGCATAAACACCAC
1 AAAAGGTAAAGCAATAGCGAGGTTTTTGCATAAACACCAC
* * * *
19869460 AAAAGGTTAAGCAATAGCGATGTTTTTGCATAAACGCCGC
1 AAAAGGTAAAGCAATAGCGAGGTTTTTGCATAAACACCAC
* *
19869500 AAAAGCTAAACCAATA
1 AAAAGGTAAAGCAATA
19869516 TCGGCATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.21
Consensus pattern (40 bp):
AAAAGGTAAAGCAATAGCGAGGTTTTTGCATAAACACCAC
Found at i:19869580 original size:41 final size:41
Alignment explanation
Indices: 19869532--19869843 Score: 390
Period size: 41 Copynumber: 7.6 Consensus size: 41
19869522 TTTATAAAAC
*
19869532 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTATCATA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
* * * * *
19869573 AATGCCGCTAAAGGTTAGAACATTAGCGGCGCTTCCTCTTA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
* * * * * *
19869614 AGCACCACTAAAGGTCTGGGCATTGGCGGCGCTTTCTCATA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
* * * * *
19869655 AACGCCGCTAAAGGTTAGATCATTAGCAGCGCTATCTCAAA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
* *
19869696 AACGCCGCTAAAGGTCAGAGCATTAGCGACGCTTTCTTATA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
* ** *
19869737 AACGCCGCTAAAGGTCAAAGCATTAGTAGCGCTTTCACATA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
* *
19869778 AATGCCGCTAAATGTCAGAGCATTAGCGGCGCTTTCTCATA
1 AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
*
19869819 AACGCCGCTAAAGGTCAAAGCATTA
1 AACGCCGCTAAAGGTCAGAGCATTA
19869844 ACGGTGTTTA
Statistics
Matches: 221, Mismatches: 50, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 221 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
AACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCATA
Found at i:19871541 original size:43 final size:43
Alignment explanation
Indices: 19871488--19871631 Score: 216
Period size: 43 Copynumber: 3.3 Consensus size: 43
19871478 TAATAAAAAT
* * * *
19871488 ATGTTCTTTAGCGGCGTTTGTTGGTAAAGCGTCGCTAAAAACC
1 ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACC
*
19871531 ATGTTCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACC
1 ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACC
*
19871574 ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGACC
1 ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACC
* *
19871617 ATGGTCTATAGCGGC
1 ATGTTCTTTAGCGGC
19871632 ATTTTTCTCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 92 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACC
Found at i:19874154 original size:41 final size:41
Alignment explanation
Indices: 19874101--19874335 Score: 312
Period size: 41 Copynumber: 5.7 Consensus size: 41
19874091 AAACCTTACG
* *
19874101 CTCATTAT-GAGACATGAGTCTTCCTTTAATATAACCTCATT
1 CTCATT-TCGAGACATGAGTCTTCCTTTAATATGATCTCATT
** * *
19874142 CTCACCTCGAGACATGAGTCTTCCTTTAGTATG-GCATCATT
1 CTCATTTCGAGACATGAGTCTTCCTTTAATATGATC-TCATT
*
19874183 CTCATCTCGAGACATGAGTCTTCCTTTAATATGATCTCATT
1 CTCATTTCGAGACATGAGTCTTCCTTTAATATGATCTCATT
* *
19874224 CTCATTTCGAGACATGAGTCTTCCTTTAGTATGATATCATT
1 CTCATTTCGAGACATGAGTCTTCCTTTAATATGATCTCATT
* *
19874265 CTCATTTCGAGACATGAGTCTTCCTTTAGTATAATCTCATT
1 CTCATTTCGAGACATGAGTCTTCCTTTAATATGATCTCATT
* *
19874306 CTCATTCCGAGACATGAGTATTCCATTTAA
1 CTCATTTCGAGACATGAGTCTTCC-TTTAA
19874336 ATATCAAGTT
Statistics
Matches: 174, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.01
41 167 0.96
42 5 0.03
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (41 bp):
CTCATTTCGAGACATGAGTCTTCCTTTAATATGATCTCATT
Found at i:19874234 original size:82 final size:82
Alignment explanation
Indices: 19874109--19874334 Score: 353
Period size: 82 Copynumber: 2.7 Consensus size: 82
19874099 CGCTCATTAT
* **
19874109 GAGACATGAGTCTTCCTTTAATATAACCTCATTCTCACCTCGAGACATGAGTCTTCCTTTAGTAT
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATTTCGAGACATGAGTCTTCCTTTAGTAT
*
19874174 GGCATCATTCTCATCTC
66 GACATCATTCTCATCTC
*
19874191 GAGACATGAGTCTTCCTTTAATATGATCTCATTCTCATTTCGAGACATGAGTCTTCCTTTAGTAT
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATTTCGAGACATGAGTCTTCCTTTAGTAT
* *
19874256 GATATCATTCTCATTTC
66 GACATCATTCTCATCTC
* * *
19874273 GAGACATGAGTCTTCCTTTAGTATAATCTCATTCTCATTCCGAGACATGAGTATTCCATTTA
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATTTCGAGACATGAGTCTTCC-TTTA
19874335 AATATCAAGT
Statistics
Matches: 132, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
82 128 0.97
83 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (82 bp):
GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATTTCGAGACATGAGTCTTCCTTTAGTAT
GACATCATTCTCATCTC
Found at i:19886683 original size:19 final size:19
Alignment explanation
Indices: 19886659--19886699 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19886649 CACAGCCTAG
19886659 ACACACGACCATGTGGCTC
1 ACACACGACCATGTGGCTC
19886678 ACACACGACCATGTGGCTC
1 ACACACGACCATGTGGCTC
19886697 ACA
1 ACA
19886700 TACATGGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.37, G:0.20, T:0.15
Consensus pattern (19 bp):
ACACACGACCATGTGGCTC
Found at i:19886834 original size:6 final size:6
Alignment explanation
Indices: 19886808--19886868 Score: 90
Period size: 6 Copynumber: 10.3 Consensus size: 6
19886798 AGTGATTTCA
*
19886808 TTTAGT TTTATAT TTTA-- TTTATT TTTATT TTTATT TTTATT TTTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
19886855 TTTATT TTTATT TT
1 TTTATT TTTATT TT
19886869 CCTTTTCCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
4 4 0.08
6 42 0.82
7 5 0.10
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:19886874 original size:6 final size:6
Alignment explanation
Indices: 19886865--19886905 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
19886855 TTTATTTTTA
19886865 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
19886906 GTTCTCGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCC
Found at i:19886874 original size:12 final size:12
Alignment explanation
Indices: 19886825--19886998 Score: 80
Period size: 12 Copynumber: 14.5 Consensus size: 12
19886815 TTATATTTTA
*
19886825 TTTATTTTTATT
1 TTTATTTTCATT
*
19886837 TTTATTTTTATT
1 TTTATTTTCATT
*
19886849 TTTATTTTTATT
1 TTTATTTTCATT
*
19886861 TTTATTTTCCTT
1 TTTATTTTCATT
** *
19886873 TTCCTTTTCCTT
1 TTTATTTTCATT
** *
19886885 TTCCTTTTCCTT
1 TTTATTTTCATT
** *
19886897 TTCCTTTTCGTT
1 TTTATTTTCATT
* ** *
19886909 CTCGTTCT-AGTT
1 TTTATTTTCA-TT
* * **
19886921 CTTGTTTTTGTT
1 TTTATTTTCATT
** *
19886933 TTCGTTTTCGTT
1 TTTATTTTCATT
*
19886945 TTTGTTTTCATT
1 TTTATTTTCATT
*
19886957 TTTATTTTTATT
1 TTTATTTTCATT
*
19886969 TTTATTTTTATT
1 TTTATTTTCATT
*
19886981 TTTATTTTTATT
1 TTTATTTTCATT
19886993 TTTATT
1 TTTATT
19886999 ATGCATTGTT
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
12 141 1.00
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (12 bp):
TTTATTTTCATT
Found at i:19886880 original size:18 final size:18
Alignment explanation
Indices: 19886859--19886905 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
19886849 TTTATTTTTA
*
19886859 TTTTTATTTTCCTTTTCC
1 TTTTCATTTTCCTTTTCC
*
19886877 TTTTCCTTTTCCTTTTCC
1 TTTTCATTTTCCTTTTCC
*
19886895 TTTTCCTTTTC
1 TTTTCATTTTC
19886906 GTTCTCGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCATTTTCCTTTTCC
Found at i:19886939 original size:6 final size:6
Alignment explanation
Indices: 19886865--19886958 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
19886855 TTTATTTTTA
* * * * * * *
19886865 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCG TTCTCG
1 TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG
* * * * *
19886913 TTCTAG TTCTT-G TTTTTG TTTTCG TTTTCG TTTTTG TTTTCA TTTT
1 TTTTCG TT-TTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTT
19886959 TATTTTTATT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
5 2 0.03
6 75 0.96
7 1 0.01
ACGTcount: A:0.02, C:0.21, G:0.09, T:0.68
Consensus pattern (6 bp):
TTTTCG
Found at i:19886963 original size:6 final size:6
Alignment explanation
Indices: 19886943--19886998 Score: 94
Period size: 6 Copynumber: 9.3 Consensus size: 6
19886933 TTCGTTTTCG
* *
19886943 TTTTTG TTTTCA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
19886991 TTTTTA TT
1 TTTTTA TT
19886999 ATGCATTGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTA
Done.