Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 62 of 290
Found at i:20318425 original size:19 final size:19
Alignment explanation
Indices: 20318401--20318440 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20318391 TTAAAACCAC
*
20318401 TGCCCACCATAATCAAATT
1 TGCCCACCACAATCAAATT
*
20318420 TGCCCACCGCAATCAAATT
1 TGCCCACCACAATCAAATT
20318439 TG
1 TG
20318441 TTATTAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.25
Consensus pattern (19 bp):
TGCCCACCACAATCAAATT
Found at i:20320440 original size:7 final size:7
Alignment explanation
Indices: 20320428--20320462 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
20320418 TCAAACCGCC
20320428 AAACCCT
1 AAACCCT
20320435 AAACCCT
1 AAACCCT
20320442 AAACCCT
1 AAACCCT
*
20320449 AAAACCAT
1 -AAACCCT
20320457 AAACCC
1 AAACCC
20320463 CCAAACCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.11
Consensus pattern (7 bp):
AAACCCT
Found at i:20320447 original size:14 final size:15
Alignment explanation
Indices: 20320428--20320462 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20320418 TCAAACCGCC
*
20320428 AAACCCT-AAACCCT
1 AAACCCTAAAACCAT
20320442 AAACCCTAAAACCAT
1 AAACCCTAAAACCAT
20320457 AAACCC
1 AAACCC
20320463 CCAAACCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.11
Consensus pattern (15 bp):
AAACCCTAAAACCAT
Found at i:20320948 original size:18 final size:19
Alignment explanation
Indices: 20320927--20320962 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20320917 GATGAAAGTT
20320927 AATA-ACAAATTTGATTAC
1 AATAGACAAATTTGATTAC
*
20320945 AATAGGCAAATTTGATTA
1 AATAGACAAATTTGATTA
20320963 TTGTGGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (19 bp):
AATAGACAAATTTGATTAC
Found at i:20325673 original size:25 final size:26
Alignment explanation
Indices: 20325645--20325696 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
20325635 AAGTTGTAAA
20325645 TAAAAAAATATC-TCTAGA-AATTTTC
1 TAAAAAAATATCTTC-AGAGAATTTTC
* *
20325670 TAAAATAATCTCTTCAGAGAATTTTC
1 TAAAAAAATATCTTCAGAGAATTTTC
20325696 T
1 T
20325697 CTCTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (26 bp):
TAAAAAAATATCTTCAGAGAATTTTC
Found at i:20325830 original size:15 final size:16
Alignment explanation
Indices: 20325812--20325841 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20325802 TTAATATTAA
20325812 ATTAAGAT-AATATTT
1 ATTAAGATAAATATTT
20325827 ATTAAGATAAATATT
1 ATTAAGATAAATATT
20325842 AAATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTAAGATAAATATTT
Found at i:20325916 original size:62 final size:59
Alignment explanation
Indices: 20325806--20325922 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
20325796 ATCACTTTAA
* * * *
20325806 TATTAAATTAAGATAATATTTATTAAGATAAATATTAAATTAAATTTAATATTAAATCT
1 TATTAAAATAAGAGAATATTTATTAAGAAAAACATTAAATTAAATTTAATATTAAATCT
*
20325865 TATTAAAATAATAGAATATTTATCTACAAGAAAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAAGAGAATATTTAT-T--AAGAAAAACATTAAATTAAATTTAATATTAA
20325923 GATGATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 1 0.02
62 29 0.58
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (59 bp):
TATTAAAATAAGAGAATATTTATTAAGAAAAACATTAAATTAAATTTAATATTAAATCT
Found at i:20326957 original size:23 final size:23
Alignment explanation
Indices: 20326927--20326992 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
20326917 CAATGAGACA
20326927 ATACAAAATTTGCCACAAAGGCC
1 ATACAAAATTTGCCACAAAGGCC
* *
20326950 ATACAAAATATGCCACAAAGGCT
1 ATACAAAATTTGCCACAAAGGCC
* * *
20326973 ATATAGAATTCGCCACAAAG
1 ATACAAAATTTGCCACAAAG
20326993 ACTTTGCAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (23 bp):
ATACAAAATTTGCCACAAAGGCC
Found at i:20328728 original size:25 final size:25
Alignment explanation
Indices: 20328675--20328785 Score: 68
Period size: 25 Copynumber: 4.5 Consensus size: 25
20328665 ATCAATTCCA
* * *
20328675 GCTCTTATGAGCTTACCGA-TACTCA
1 GCTCGTATGAGCTTACC-ATTATTCT
20328700 GCTCGTATGAGCTTACCATTATTCT
1 GCTCGTATGAGCTTACCATTATTCT
* * * **
20328725 GCTCGGAGGAGTTTACTGTTATT-T
1 GCTCGTATGAGCTTACCATTATTCT
* *
20328749 AGCTCGGAGGAGCTTACCATT-TATC-
1 -GCTCGTATGAGCTTACCATTAT-TCT
*
20328774 ACTCGTATGAGC
1 GCTCGTATGAGC
20328786 ATACATGTAC
Statistics
Matches: 68, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
24 12 0.18
25 56 0.82
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (25 bp):
GCTCGTATGAGCTTACCATTATTCT
Found at i:20329174 original size:25 final size:25
Alignment explanation
Indices: 20329140--20329192 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
20329130 TTCTGTGTTA
20329140 TACGAACTTACTAAGCTTAATTGCT
1 TACGAACTTACTAAGCTTAATTGCT
20329165 TACGAACTTACTAAGCTTAATTGCT
1 TACGAACTTACTAAGCTTAATTGCT
20329190 TAC
1 TAC
20329193 TCTGTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (25 bp):
TACGAACTTACTAAGCTTAATTGCT
Found at i:20338815 original size:16 final size:17
Alignment explanation
Indices: 20338779--20338817 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20338769 CAATTAGTCG
* *
20338779 AAAAAGTTTTTTCTATT
1 AAAAAGTATTTTCTATA
20338796 AAAAAGTATTTT-TATA
1 AAAAAGTATTTTCTATA
20338812 AAAAAG
1 AAAAAG
20338818 CCAATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (17 bp):
AAAAAGTATTTTCTATA
Found at i:20338924 original size:16 final size:17
Alignment explanation
Indices: 20338903--20338940 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
20338893 TAATTTTTTT
*
20338903 AAAAATAATTT-TACAA
1 AAAAATAATTTGAACAA
*
20338919 AAAAATTATTTGAACAA
1 AAAAATAATTTGAACAA
20338936 AAAAA
1 AAAAA
20338941 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATAATTTGAACAA
Found at i:20340628 original size:21 final size:21
Alignment explanation
Indices: 20340584--20340654 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
20340574 ATAACAGATT
* * *
20340584 CAGATCATGCTTAACA-AATA
1 CAGATCATACTTATCATATTA
20340604 CAGATCATACTTATCATATTA
1 CAGATCATACTTATCATATTA
** * *
20340625 CAGATTGTACTTATCTTATCA
1 CAGATCATACTTATCATATTA
20340646 CAGATCATA
1 CAGATCATA
20340655 TTGGGCATGT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (21 bp):
CAGATCATACTTATCATATTA
Found at i:20341421 original size:41 final size:41
Alignment explanation
Indices: 20341367--20341449 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
20341357 AGTCTAGCAT
* *
20341367 ATGGCTTGGCACACG-TTCATATGTCACACACGACTTACCAC
1 ATGGCATGGCACACGCCT-ATATGTCACACACGACTTACCAC
* *
20341408 ATGGCATGTCACACGCCTATGTGTCACACACGACTTACCAC
1 ATGGCATGGCACACGCCTATATGTCACACACGACTTACCAC
20341449 A
1 A
20341450 CAGCCATGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (41 bp):
ATGGCATGGCACACGCCTATATGTCACACACGACTTACCAC
Found at i:20352639 original size:43 final size:42
Alignment explanation
Indices: 20352497--20352649 Score: 155
Period size: 43 Copynumber: 3.6 Consensus size: 42
20352487 TGTACAACGC
* *
20352497 CAACGTCCCAGACGTGGTCTTACATGTAAACAC-AGATCGATG
1 CAACATCCCAGACGTGGTCTTACATGAAAACACAAG-TCGATG
* ** * * *
20352539 CCACTATCCCAGACAAGGTCTCACACGAAAATACAAGTCGATG
1 CAAC-ATCCCAGACGTGGTCTTACATGAAAACACAAGTCGATG
*
20352582 CCAACATTCCAGACGTGGTCTTACATGAAAACACAAGTCGATG
1 -CAACATCCCAGACGTGGTCTTACATGAAAACACAAGTCGATG
* * *
20352625 TTAACGTCCCAGACGTTGTCTTACA
1 -CAACATCCCAGACGTGGTCTTACA
20352650 CAAAAAAATT
Statistics
Matches: 88, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
42 3 0.03
43 80 0.91
44 5 0.06
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (42 bp):
CAACATCCCAGACGTGGTCTTACATGAAAACACAAGTCGATG
Found at i:20360933 original size:28 final size:29
Alignment explanation
Indices: 20360879--20360938 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
20360869 AAAAGAACAA
*
20360879 AAAAAAGAAGAAAAGAAAAGATAAAAATAGG
1 AAAAAAGAAAAAAAGAAAAG--AAAAATAGG
*
20360910 AAAAAAGAAAAAAAGAACAG-AAAATAGG
1 AAAAAAGAAAAAAAGAAAAGAAAAATAGG
20360938 A
1 A
20360939 CGATGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 9 0.33
31 18 0.67
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (29 bp):
AAAAAAGAAAAAAAGAAAAGAAAAATAGG
Found at i:20366415 original size:22 final size:21
Alignment explanation
Indices: 20366386--20366440 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
20366376 CAGATTCAAT
20366386 AAAAAAAAGAGAAGGAAAAAA-
1 AAAAAAAAG-GAAGGAAAAAAG
* *
20366407 ATAAAAAAAGTAATGAAAAAAG
1 A-AAAAAAAGGAAGGAAAAAAG
20366429 AAAAAAAAGGAA
1 AAAAAAAAGGAA
20366441 AAAGTCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGGAAGGAAAAAAG
Found at i:20366546 original size:14 final size:15
Alignment explanation
Indices: 20366524--20366560 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20366514 AAAGTCATCC
*
20366524 AAATCAAAAAT-AAA
1 AAATGAAAAATGAAA
20366538 AAATGAAAAATGAAA
1 AAATGAAAAATGAAA
20366553 AAA-GAAAA
1 AAATGAAAA
20366561 GAAAGAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (15 bp):
AAATGAAAAATGAAA
Found at i:20368952 original size:44 final size:45
Alignment explanation
Indices: 20368852--20369223 Score: 152
Period size: 44 Copynumber: 8.0 Consensus size: 45
20368842 GATTGAAGCC
* * * **
20368852 AGAAATCTTATCTCCCT-AGGATTACAGCGGAGCAGGTGGAAGCT--
1 AGAAATCTTATCTCCCTGA-GATTACAGTGGAGCAGAT-TAAAATAA
* *
20368896 AGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
1 AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * * * * * *
20368941 AG-GATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCATCAGATTGAA
1 AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGAT----T-AAAAT-AA
** **
20368991 GCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCT--
1 ---AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAA
* * *
20369038 AGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAA
1 AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * * * *
20369083 AG-GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTATCAGATTGAAA
1 AGAAATCTTATCTCCCTGAGA-TTACAGTGGAGCAGAT--TA--A-AAT--AA
* * **
20369134 CCAGAAATCTTATCTCCCTGAGATTACGGCGGAGCAGATTGAAGCT--
1 --AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAA
* * * * *
20369180 AGTAATCCTATTTCCCTGATATTACAGTGGAGCGGATTAAAATA
1 AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATA
20369224 GAGGATCTTA
Statistics
Matches: 244, Mismatches: 55, Indels: 58
0.68 0.15 0.16
Matches are distributed among these distances:
43 10 0.04
44 149 0.61
45 5 0.02
46 2 0.01
48 2 0.01
49 5 0.02
50 6 0.02
51 3 0.01
52 1 0.00
53 5 0.02
54 55 0.23
55 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
AGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
Found at i:20369018 original size:142 final size:142
Alignment explanation
Indices: 20368762--20369268 Score: 863
Period size: 142 Copynumber: 3.6 Consensus size: 142
20368752 CCACAGGTCT
*
20368762 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
* *
20368827 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCT-AGGATTACAGCGGAGCAGGTGG
66 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGA-GATTACAGCGGAGCAGATTG
20368891 AAGCTAGTAATCC
130 AAGCTAGTAATCC
* *
20368904 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
*
20368969 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
66 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
20369034 AGCTAGTAATCC
131 AGCTAGTAATCC
20369046 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
* * *
20369111 GAGTAGATCGTATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTACGGCGGAGCAGATTGA
66 GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
20369176 AGCTAGTAATCC
131 AGCTAGTAATCC
* * * *
20369188 TATTTCCCTGATATTACAGTGGAGCGGATTAAAATAGAGGATCTTATATCTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
* *
20369253 GGGTAGATCACATCAG
66 GAGTAGATCGCATCAG
20369269 GTCTTATCTC
Statistics
Matches: 345, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
142 344 1.00
143 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (142 bp):
TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
GAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA
AGCTAGTAATCC
Found at i:20369418 original size:50 final size:50
Alignment explanation
Indices: 20369363--20369519 Score: 152
Period size: 50 Copynumber: 3.1 Consensus size: 50
20369353 CCACATCGGT
* * *
20369363 GAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAAAGGTACAGCAGC
1 GAATCTTGCCTCCCAGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGC
* * * * * ** * * * * *
20369413 AAATCTTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGT
1 GAATCTTGCCTCCCAGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGC
* * *
20369463 GAATCTGGCCTCCCTGACATTGCGGTTAAAAAGGTTAAAGCTACAGCAGC
1 GAATCTTGCCTCCCAGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGC
20369513 GAATCTT
1 GAATCTT
20369520 ACATTCCTAG
Statistics
Matches: 76, Mismatches: 31, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (50 bp):
GAATCTTGCCTCCCAGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGC
Found at i:20369485 original size:100 final size:100
Alignment explanation
Indices: 20369336--20369604 Score: 335
Period size: 100 Copynumber: 2.7 Consensus size: 100
20369326 CAAACGATGT
* * *
20369336 AGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATC-TGCTTCCCTGACATTGCGGTTAAAAAGATTAA
* *
20369401 AGGTACAGCAGCAAATCTTAC-CTCCCAGGCAGTGC
65 AGCTACAGCAGCAAATCTTACACTCCCAGGAAGTGC
* *
20369436 AGTGGAACAGATTAAAGCCACAACGGTGAATCTGGCCTCCCTGACATTGCGGTTAAAAAGGTTAA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCT-GCTTCCCTGACATTGCGGTTAAAAAGATTAA
* * * *
20369501 AGCTACAGCAGCGAATCTTACATTCCTAGGAAGTGT
65 AGCTACAGCAGCAAATCTTACACTCCCAGGAAGTGC
* ** * * *
20369537 AGT-GAAGCAGATTAAAGCCATAACAATGAATCATGCTTCCCTGACCTTGCAGTTGAAAAGATTA
1 AGTGGAA-CAGATTAAAGCCACAACGGTGAATC-TGCTTCCCTGACATTGCGGTTAAAAAGATTA
20369601 AAGC
64 AAGC
20369605 CACGATGGAA
Statistics
Matches: 146, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 80 0.55
101 64 0.44
102 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (100 bp):
AGTGGAACAGATTAAAGCCACAACGGTGAATCTGCTTCCCTGACATTGCGGTTAAAAAGATTAAA
GCTACAGCAGCAAATCTTACACTCCCAGGAAGTGC
Found at i:20370223 original size:17 final size:19
Alignment explanation
Indices: 20370195--20370233 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
20370185 GGAAGAAAAG
*
20370195 AAAAGAGAAAAATAACA-A
1 AAAAGAGAAAAAGAACAGA
20370213 AAAAGA-AAAAAGAACAGA
1 AAAAGAGAAAAAGAACAGA
20370231 AAA
1 AAA
20370234 TAAGACGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAGAGAAAAAGAACAGA
Found at i:20373461 original size:21 final size:21
Alignment explanation
Indices: 20373437--20373476 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20373427 GAACAAAATT
20373437 TTAATGTTTTATGTGAACATA
1 TTAATGTTTTATGTGAACATA
* *
20373458 TTAATTTTTTGTGTGAACA
1 TTAATGTTTTATGTGAACA
20373477 CATCTAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (21 bp):
TTAATGTTTTATGTGAACATA
Found at i:20375155 original size:40 final size:40
Alignment explanation
Indices: 20375111--20375211 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
20375101 ACATTGTCGG
*
20375111 TTTATCTGACTAGTGCTGGGCACACATTTGACATTATCAA
1 TTTATCTGACTAGTGCTGGGCACACATTTGACATCATCAA
* * **
20375151 TTTATCCGACTAGTGTTGGGCACACATTTGACATCATCGG
1 TTTATCTGACTAGTGCTGGGCACACATTTGACATCATCAA
*
20375191 TTTAT-TCGACTACTGCTGGGC
1 TTTATCT-GACTAGTGCTGGGC
20375212 GCAAGATGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (40 bp):
TTTATCTGACTAGTGCTGGGCACACATTTGACATCATCAA
Found at i:20375400 original size:40 final size:40
Alignment explanation
Indices: 20375329--20375414 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 40
20375319 TGCCAATAAC
** *
20375329 AGGTTGAAAAGGATGATATCCAAAAAGGATATCAAATG-AA
1 AGGTTGAAAAGGACAATATACAAAAAGGATATC-AATGAAA
20375369 AGGTTGAAAAGGACAATATACAAAGAA-GATATCAATGAAA
1 AGGTTGAAAAGGACAATATACAAA-AAGGATATCAATGAAA
20375409 AGGTTG
1 AGGTTG
20375415 GTATTTCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
39 4 0.10
40 35 0.85
41 2 0.05
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (40 bp):
AGGTTGAAAAGGACAATATACAAAAAGGATATCAATGAAA
Found at i:20378897 original size:34 final size:34
Alignment explanation
Indices: 20378833--20378897 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
20378823 ATAAGTCCAA
*
20378833 TATTGTAATTATTAAGATTTATTTATTATTTATT
1 TATTGTAATTATTAAGATTTATTTAGTATTTATT
*
20378867 TATTTTAATT-TTAAGATATT-TTTAAGTATTT
1 TATTGTAATTATTAAGAT-TTATTT-AGTATTT
20378898 TAAGTTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (34 bp):
TATTGTAATTATTAAGATTTATTTAGTATTTATT
Found at i:20379254 original size:33 final size:33
Alignment explanation
Indices: 20379216--20379281 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
20379206 TTATTTATCG
20379216 GTGGGTTTATTAGAGTCTTTAATTGAATTTATT
1 GTGGGTTTATTAGAGTCTTTAATTGAATTTATT
*
20379249 GTGGGTTTATTAGAGTCTTTACTTGAATTTATT
1 GTGGGTTTATTAGAGTCTTTAATTGAATTTATT
20379282 AGGATTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.52
Consensus pattern (33 bp):
GTGGGTTTATTAGAGTCTTTAATTGAATTTATT
Found at i:20382812 original size:21 final size:21
Alignment explanation
Indices: 20382786--20382840 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
20382776 GAATCCGAGC
*
20382786 TAGCTTTATAACACTCGGACG
1 TAGCTTTATAACACTCAGACG
20382807 TAGCTTTATAACACTCAGACG
1 TAGCTTTATAACACTCAGACG
20382828 TAGCTTTATAACA
1 TAGCTTTATAACA
20382841 TCTTCGGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (21 bp):
TAGCTTTATAACACTCAGACG
Found at i:20392745 original size:19 final size:20
Alignment explanation
Indices: 20392721--20392763 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
20392711 TAGATTTATT
20392721 CTTAATTAATC-TGAATTAA
1 CTTAATTAATCATGAATTAA
*
20392740 CTTAATTAATCATTAATTAA
1 CTTAATTAATCATGAATTAA
20392760 -TTAA
1 CTTAA
20392764 ACTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (20 bp):
CTTAATTAATCATGAATTAA
Found at i:20393052 original size:120 final size:120
Alignment explanation
Indices: 20392834--20393073 Score: 399
Period size: 120 Copynumber: 2.0 Consensus size: 120
20392824 ACTAAGATGG
* * * *
20392834 TTTAGTTACTATTTTGAACCCTTGGCAATATAAAAATCTATAGCTATTAGACTTTTATGATGTAG
1 TTTAATTACTATTTTGAACCCTTAGCAATATAAAAATCTATAGCTATTAGACTTTTATAATGTAC
*
20392899 TCTTTATACCTTAATTAACTATCACATCGACAAAATTACTGGACCAAACTTTCAT
66 TCTTTATACCTTAATTAACTATCACATCAACAAAATTACTGGACCAAACTTTCAT
* *
20392954 TTTAATTACTATTTTGAACCCTTAGCAATGTAAAAATCTATAGCTATTAGACTTTTATAATTTAC
1 TTTAATTACTATTTTGAACCCTTAGCAATATAAAAATCTATAGCTATTAGACTTTTATAATGTAC
* *
20393019 TCTTTGTACCTTAATTAACTATCATATCAACAAAATTACTGGACCAAACTTTCAT
66 TCTTTATACCTTAATTAACTATCACATCAACAAAATTACTGGACCAAACTTTCAT
20393074 AAACTTTCAT
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
120 111 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.39
Consensus pattern (120 bp):
TTTAATTACTATTTTGAACCCTTAGCAATATAAAAATCTATAGCTATTAGACTTTTATAATGTAC
TCTTTATACCTTAATTAACTATCACATCAACAAAATTACTGGACCAAACTTTCAT
Found at i:20394650 original size:27 final size:27
Alignment explanation
Indices: 20394611--20394679 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
20394601 GTCGGGTGGC
* *
20394611 GCCTCACAGGGAGGCACCATTAAATGT
1 GCCTCATAGGGAGGCACCATTAAAAGT
*
20394638 GCCTCATAAGGAGGCACCATTAAAAGT
1 GCCTCATAGGGAGGCACCATTAAAAGT
20394665 GCCTCATAGGGAGGC
1 GCCTCATAGGGAGGC
20394680 GCCAATGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (27 bp):
GCCTCATAGGGAGGCACCATTAAAAGT
Found at i:20394737 original size:19 final size:19
Alignment explanation
Indices: 20394688--20394882 Score: 110
Period size: 19 Copynumber: 9.3 Consensus size: 19
20394678 GCGCCAATGA
*
20394688 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
20394707 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
20394728 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
20394747 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
20394770 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
20394790 GT-ATTTTGTATGAATATTGTAATTTT
1 GTAATTTTGTATG-A-A---T-A--TT
20394816 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
20394835 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
20394858 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
20394877 GTAATT
1 GTAATT
20394883 ATTTTATAAT
Statistics
Matches: 140, Mismatches: 11, Indels: 50
0.70 0.05 0.25
Matches are distributed among these distances:
17 3 0.02
18 1 0.01
19 52 0.37
20 15 0.11
21 22 0.16
22 8 0.06
23 20 0.14
24 3 0.02
25 2 0.01
26 4 0.03
27 10 0.07
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:20394822 original size:27 final size:27
Alignment explanation
Indices: 20394792--20394868 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
20394782 TTGGATTAGT
20394792 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
20394819 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
20394844 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
20394869 TGAATATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 22 0.48
27 24 0.52
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:20394945 original size:60 final size:60
Alignment explanation
Indices: 20394875--20394996 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
20394865 TGTATGAATA
* * * * *
20394875 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
20394935 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
20394995 TT
1 TT
20394997 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 50 0.89
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:20395150 original size:15 final size:16
Alignment explanation
Indices: 20395114--20395150 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
20395104 CTCATTTAAT
20395114 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
20395130 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
20395145 TTTTAT
1 TTTTAT
20395151 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:20400275 original size:21 final size:19
Alignment explanation
Indices: 20400245--20400293 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
20400235 TTCCAAAAAG
*
20400245 TATCGGTACCCATATGATTTT
1 TATCGATACCCATAT--TTTT
20400266 TATCGATA-CCATATTTTT
1 TATCGATACCCATATTTTT
*
20400284 TATTGATACC
1 TATCGATACC
20400294 AAAATTGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 6 0.24
21 7 0.28
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (19 bp):
TATCGATACCCATATTTTT
Found at i:20401921 original size:16 final size:17
Alignment explanation
Indices: 20401900--20401935 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
20401890 AGGGGTTGAA
20401900 AAACCAAAATTAGAA-T
1 AAACCAAAATTAGAAGT
20401916 AAACCAAAATTAGAAGT
1 AAACCAAAATTAGAAGT
20401933 AAA
1 AAA
20401936 AGGTTGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (17 bp):
AAACCAAAATTAGAAGT
Found at i:20403401 original size:19 final size:20
Alignment explanation
Indices: 20403377--20403416 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20403367 AACTTGAAAC
*
20403377 AAAACA-GAAAATTTTGGAA
1 AAAACATGAAAATTTGGGAA
20403396 AAAACATGAAAATTTGGGAA
1 AAAACATGAAAATTTGGGAA
20403416 A
1 A
20403417 CAGGGGTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (20 bp):
AAAACATGAAAATTTGGGAA
Found at i:20411829 original size:13 final size:13
Alignment explanation
Indices: 20411811--20411838 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20411801 GATCTAAACG
20411811 AAATAAATAATTC
1 AAATAAATAATTC
20411824 AAATAAATAATTC
1 AAATAAATAATTC
20411837 AA
1 AA
20411839 CACCACTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAATAATTC
Found at i:20420691 original size:15 final size:16
Alignment explanation
Indices: 20420653--20420692 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
20420643 GGCTTATGTG
20420653 ATATATGTGATGATTT
1 ATATATGTGATGATTT
* *
20420669 AAACATGTGA-GATTT
1 ATATATGTGATGATTT
20420684 ATATATGTG
1 ATATATGTG
20420693 GTTTTTAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (16 bp):
ATATATGTGATGATTT
Found at i:20420933 original size:49 final size:51
Alignment explanation
Indices: 20420880--20421022 Score: 164
Period size: 51 Copynumber: 2.8 Consensus size: 51
20420870 AAGGTGGAAG
* * * * *
20420880 CAGTGGCAATATATCTATAGATCAGTGGTGGCTTGTCCATAAAA-T-TTAT
1 CAGTGGCAGTATATCTGTAAATCAGTGGTGGCTTGTCCACAAAAGTGCTAT
* * * * *
20420929 CAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGCTAT
1 CAGTGGCAGTATATCTGTAAATCAGTGGTGGCTTGTCCACAAAAGTGCTAT
* *
20420980 CAGTGGCAGTTTATCTGTAAATCAGTGGTGGTTTGTCCACAAA
1 CAGTGGCAGTATATCTGTAAATCAGTGGTGGCTTGTCCACAAA
20421023 TGGTGTTTCA
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 36 0.47
50 1 0.01
51 39 0.51
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (51 bp):
CAGTGGCAGTATATCTGTAAATCAGTGGTGGCTTGTCCACAAAAGTGCTAT
Found at i:20421274 original size:51 final size:51
Alignment explanation
Indices: 20421194--20421290 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
20421184 ATTGTGATTG
* *
20421194 TATCAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGC
1 TATCAGTGACAGTATATCTGCAAACCAGTGGTGGCTTGTCCACAAAAGTGC
* * * * *
20421245 TATCAGTGGCAGTTTATCTGTAAATCAGTGGTGGTTTGTCCACAAA
1 TATCAGTGACAGTATATCTGCAAACCAGTGGTGGCTTGTCCACAAA
20421291 TGGTGTTTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (51 bp):
TATCAGTGACAGTATATCTGCAAACCAGTGGTGGCTTGTCCACAAAAGTGC
Found at i:20421403 original size:268 final size:268
Alignment explanation
Indices: 20420926--20421464 Score: 1069
Period size: 268 Copynumber: 2.0 Consensus size: 268
20420916 CCATAAAATT
20420926 TATCAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGCTATCAGTGGCAGTT
1 TATCAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGCTATCAGTGGCAGTT
20420991 TATCTGTAAATCAGTGGTGGTTTGTCCACAAATGGTGTTTCAGATAAATGAGTTTTGGGAACTTG
66 TATCTGTAAATCAGTGGTGGTTTGTCCACAAATGGTGTTTCAGATAAATGAGTTTTGGGAACTTG
20421056 ATATTGGTGTGTAGCAGAGAAGGGTAGGACTGTTTTCAGAAAATCTGTATTGTTTTGCAAAATGT
131 ATATTGGTGTGTAGCAGAGAAGGGTAGGACTGTTTTCAGAAAATCTGTATTGTTTTGCAAAATGT
*
20421121 GCATTGACATGATCATACATATTATAAGTGTGAAATATTGAGTTATATGAAACTGGTATGATTAT
196 GCATTGACATGATCATACATATTATAAGTGTGAAATATTGAGTTATATGAAACTGATATGATTAT
20421186 TGTGATTG
261 TGTGATTG
20421194 TATCAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGCTATCAGTGGCAGTT
1 TATCAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGCTATCAGTGGCAGTT
20421259 TATCTGTAAATCAGTGGTGGTTTGTCCACAAATGGTGTTTCAGATAAATGAGTTTTGGGAACTTG
66 TATCTGTAAATCAGTGGTGGTTTGTCCACAAATGGTGTTTCAGATAAATGAGTTTTGGGAACTTG
20421324 ATATTGGTGTGTAGCAGAGAAGGGTAGGACTGTTTTCAGAAAATCTGTATTGTTTTGCAAAATGT
131 ATATTGGTGTGTAGCAGAGAAGGGTAGGACTGTTTTCAGAAAATCTGTATTGTTTTGCAAAATGT
20421389 GCATTGACATGATCATACATATTATAAGTGTGAAATATTGAGTTATATGAAACTGATATGATTAT
196 GCATTGACATGATCATACATATTATAAGTGTGAAATATTGAGTTATATGAAACTGATATGATTAT
20421454 TGTGATTG
261 TGTGATTG
20421462 TAT
1 TAT
20421465 AATGTATATG
Statistics
Matches: 270, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
268 270 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (268 bp):
TATCAGTGACAGTATATCTGCATACCAGTGGTGGCTTGTCTACAAAAGTGCTATCAGTGGCAGTT
TATCTGTAAATCAGTGGTGGTTTGTCCACAAATGGTGTTTCAGATAAATGAGTTTTGGGAACTTG
ATATTGGTGTGTAGCAGAGAAGGGTAGGACTGTTTTCAGAAAATCTGTATTGTTTTGCAAAATGT
GCATTGACATGATCATACATATTATAAGTGTGAAATATTGAGTTATATGAAACTGATATGATTAT
TGTGATTG
Found at i:20426374 original size:12 final size:12
Alignment explanation
Indices: 20426357--20426381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20426347 ATGTAGGGTT
20426357 TGCACATGTAAG
1 TGCACATGTAAG
20426369 TGCACATGTAAG
1 TGCACATGTAAG
20426381 T
1 T
20426382 CATATGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (12 bp):
TGCACATGTAAG
Found at i:20427722 original size:18 final size:18
Alignment explanation
Indices: 20427696--20427743 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
20427686 CATAAAACTT
20427696 AAAAAAATAAAAACT-AA
1 AAAAAAATAAAAACTGAA
20427713 AAATAAAAT-AAAACTGAA
1 AAA-AAAATAAAAACTGAA
*
20427731 AAAAAAAGAAAAA
1 AAAAAAATAAAAA
20427744 AAATAGAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.10
Consensus pattern (18 bp):
AAAAAAATAAAAACTGAA
Found at i:20427727 original size:17 final size:16
Alignment explanation
Indices: 20427687--20427742 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
20427677 GAACATTTTC
*
20427687 ATAAAACT-TAAAAAA
1 ATAAAACTAAAAAAAA
20427702 ATAAAAACTAAAAATAAA
1 AT-AAAACTAAAAA-AAA
20427720 ATAAAACTGAAAAAAAA
1 ATAAAACT-AAAAAAAA
*
20427737 AGAAAA
1 ATAAAA
20427743 AAAATAGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.06
16 6 0.17
17 17 0.49
18 10 0.29
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (16 bp):
ATAAAACTAAAAAAAA
Found at i:20430654 original size:26 final size:24
Alignment explanation
Indices: 20430625--20430691 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 24
20430615 AAGTACATAT
20430625 ATATATATTATAAAGA-ATGTATAAAC
1 ATATATATTATAAA-ATATG-A-AAAC
*
20430651 ATATATAGATTATAAAATATGAAAAT
1 ATATAT--ATTATAAAATATGAAAAC
*
20430677 ATAAATATTATAAAA
1 ATATATATTATAAAA
20430692 ATATAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 9 0.25
26 14 0.39
27 2 0.06
28 11 0.31
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.34
Consensus pattern (24 bp):
ATATATATTATAAAATATGAAAAC
Found at i:20430694 original size:17 final size:17
Alignment explanation
Indices: 20430667--20430715 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
20430657 AGATTATAAA
*
20430667 ATATGAAAATATAAATAT
1 ATAT-AAAATATAAATGT
20430685 -TATAAAAATATAAATGT
1 ATAT-AAAATATAAATGT
20430702 ATATAAAATATAAA
1 ATATAAAATATAAA
20430716 AACTATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 25 0.89
18 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAAATGT
Found at i:20430704 original size:25 final size:25
Alignment explanation
Indices: 20430623--20430726 Score: 81
Period size: 25 Copynumber: 4.0 Consensus size: 25
20430613 AAAAGTACAT
*
20430623 ATATATATATTATAAAGAATGTAT-AAA
1 ATATATAAATTATAAA-AA--TATGAAA
*
20430650 CATATATAGATTAT-AAAATATGAAA
1 -ATATATAAATTATAAAAATATGAAA
20430675 ATATA-AATATTATAAAAATAT-AAA
1 ATATATAA-ATTATAAAAATATGAAA
* *
20430699 TGTATATAAAATATAAAAACTATGAAA
1 -ATATATAAATTATAAAAA-TATGAAA
20430726 A
1 A
20430727 GAAAAGAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
23 1 0.02
24 16 0.25
25 23 0.36
26 7 0.11
27 5 0.08
28 12 0.19
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (25 bp):
ATATATAAATTATAAAAATATGAAA
Found at i:20430717 original size:8 final size:8
Alignment explanation
Indices: 20430664--20430717 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
20430654 TATAGATTAT
*
20430664 AAAATATG
1 AAAATATA
20430672 AAAATATA
1 AAAATATA
*
20430680 AATATTATA
1 AA-AATATA
20430689 AAAATATA
1 AAAATATA
**
20430697 AATGTATA
1 AAAATATA
20430705 TAAAATATA
1 -AAAATATA
20430714 AAAA
1 AAAA
20430718 CTATGAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 24 0.65
9 13 0.35
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (8 bp):
AAAATATA
Found at i:20430726 original size:17 final size:16
Alignment explanation
Indices: 20430664--20430726 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
20430654 TATAGATTAT
20430664 AAAATATGAAAATATA
1 AAAATATGAAAATATA
* *
20430680 AATATTATAAAAATATA
1 AA-AATATGAAAATATA
*
20430697 AATGTATAT-AAAATATA
1 AA--AATATGAAAATATA
20430714 AAAACTATGAAAA
1 AAAA-TATGAAAA
20430727 GAAAAGAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 28 0.76
18 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATATGAAAATATA
Found at i:20430842 original size:3 final size:3
Alignment explanation
Indices: 20430823--20430890 Score: 68
Period size: 3 Copynumber: 22.0 Consensus size: 3
20430813 GCATGTATAT
* *
20430823 ATA AGA ATA AGA ATA ATA AT- ATA CGAT- ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA AT-A ATA ATA ATA ATA
20430869 ATA ATA ATA ACTA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA
20430891 TAGTGATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 4 0.07
3 43 0.78
4 6 0.11
5 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20430845 original size:22 final size:22
Alignment explanation
Indices: 20430819--20430892 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
20430809 ATGCGCATGT
* *
20430819 ATATATAAGAATAAGAATAATA
1 ATATATAATAATAATAATAATA
*
20430841 ATATACGATATAATAAATAATAATA
1 ATATA-TA-ATAAT-AATAATAATA
20430866 ATA-ATAATAATAACTAATAATA
1 ATATATAATAATAA-TAATAATA
20430888 ATATA
1 ATATA
20430893 GTGATAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.05
22 21 0.49
23 3 0.07
24 5 0.12
25 12 0.28
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (22 bp):
ATATATAATAATAATAATAATA
Found at i:20431438 original size:5 final size:5
Alignment explanation
Indices: 20431428--20431456 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
20431418 TTTAAGAAAC
20431428 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
20431457 AACAGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20433601 original size:16 final size:17
Alignment explanation
Indices: 20433580--20433613 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20433570 AAATTATTTT
20433580 AAATAATT-AAATTTAA
1 AAATAATTAAAATTTAA
20433596 AAATAATTAAAATTTAA
1 AAATAATTAAAATTTAA
20433613 A
1 A
20433614 TTCAACCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAATTAAAATTTAA
Found at i:20436019 original size:7 final size:7
Alignment explanation
Indices: 20436007--20436047 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
20435997 TTAGCCTCTC
20436007 CATTTTT
1 CATTTTT
20436014 CA-TTTT
1 CATTTTT
20436020 C-TATTTT
1 CAT-TTTT
*
20436027 CAGTTTT
1 CATTTTT
20436034 CATTTTT
1 CATTTTT
20436041 CATTTTT
1 CATTTTT
20436048 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:20436047 original size:14 final size:13
Alignment explanation
Indices: 20436007--20436046 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
20435997 TTAGCCTCTC
20436007 CATTTTTCATTTT
1 CATTTTTCATTTT
20436020 C-TATTTTCAGTTTT
1 CAT-TTTTCA-TTTT
20436034 CATTTTTCATTTT
1 CATTTTTCATTTT
20436047 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 11 0.46
14 11 0.46
15 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.68
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:20436055 original size:17 final size:17
Alignment explanation
Indices: 20436030--20436066 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20436020 CTATTTTCAG
*
20436030 TTTTCATTTTTCATTTT
1 TTTTAATTTTTCATTTT
*
20436047 TTTTAATTTTTTATTTT
1 TTTTAATTTTTCATTTT
20436064 TTT
1 TTT
20436067 GACTCAGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTAATTTTTCATTTT
Found at i:20437049 original size:21 final size:21
Alignment explanation
Indices: 20436999--20437049 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20436989 TTTGACCTTG
*
20436999 ATTTTTATTTTGATTTTTCTT
1 ATTTTTTTTTTGATTTTTCTT
* * *
20437020 CTTTGTTTTTTGATTTTTTTT
1 ATTTTTTTTTTGATTTTTCTT
20437041 ATTTTTTTT
1 ATTTTTTTT
20437050 GAGCTCATAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (21 bp):
ATTTTTTTTTTGATTTTTCTT
Found at i:20450706 original size:25 final size:25
Alignment explanation
Indices: 20450672--20450726 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
20450662 ATTACTATCT
*
20450672 TCTTCATCGTCTTTATCACCGTTTG
1 TCTTCATCGTCTTCATCACCGTTTG
20450697 TCTTCATCGTCTTCATCACCGTTTG
1 TCTTCATCGTCTTCATCACCGTTTG
20450722 TCTTC
1 TCTTC
20450727 CTTGTTAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.11, C:0.31, G:0.11, T:0.47
Consensus pattern (25 bp):
TCTTCATCGTCTTCATCACCGTTTG
Found at i:20453355 original size:108 final size:108
Alignment explanation
Indices: 20453166--20453381 Score: 387
Period size: 108 Copynumber: 2.0 Consensus size: 108
20453156 CCCCGATTTC
* * *
20453166 TATTCCCTGTCCAAAGTTCAGAATAGCTTCCGTTTAGCATTTTTGAAATTTCTATGCCCTGTTTT
1 TATTCCCTGCCCAAAGATCAGAATAGCTTCCGTTTAGCATTCTTGAAATTTCTATGCCCTGTTTT
20453231 GCCCTCATCTTCCAAGCCGAAATCCACCTCCAGAACTCTCCCT
66 GCCCTCATCTTCCAAGCCGAAATCCACCTCCAGAACTCTCCCT
* *
20453274 TATTCCCTGCCCAACGATCAGAATAGCTTCCGTTTAGCATTCTTGAAATTTTTATGCCCTGTTTT
1 TATTCCCTGCCCAAAGATCAGAATAGCTTCCGTTTAGCATTCTTGAAATTTCTATGCCCTGTTTT
20453339 GCCCTCATCTTCCAAGCCGAAATCCACCTCCAGAACTCTCCCT
66 GCCCTCATCTTCCAAGCCGAAATCCACCTCCAGAACTCTCCCT
20453382 CCCAACATCA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.33
Consensus pattern (108 bp):
TATTCCCTGCCCAAAGATCAGAATAGCTTCCGTTTAGCATTCTTGAAATTTCTATGCCCTGTTTT
GCCCTCATCTTCCAAGCCGAAATCCACCTCCAGAACTCTCCCT
Found at i:20454773 original size:24 final size:25
Alignment explanation
Indices: 20454721--20454781 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
20454711 GCTGAAGCTT
*
20454721 TAGTTGCAATTTAAGAGGTATTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
20454746 TAGTTGCAATTCAAGAGGT-TTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
20454770 TAGTTGCAATTC
1 TAGTTGCAATTC
20454782 TGGTTTGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 17 0.49
25 18 0.51
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (25 bp):
TAGTTGCAATTCAAGAGGTATTTTA
Found at i:20455017 original size:22 final size:22
Alignment explanation
Indices: 20454989--20455030 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
20454979 ATGGCTTGCG
20454989 TTTGAATGTGTTCTTATTTAAA
1 TTTGAATGTGTTCTTATTTAAA
20455011 TTTGAATGTGTTCTTATTTA
1 TTTGAATGTGTTCTTATTTA
20455031 GTGCAGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (22 bp):
TTTGAATGTGTTCTTATTTAAA
Found at i:20457725 original size:110 final size:116
Alignment explanation
Indices: 20457606--20457871 Score: 350
Period size: 122 Copynumber: 2.3 Consensus size: 116
20457596 AATAAAGTAG
*
20457606 ATTA-TAAATTATAATTTAATAATAATTA-GTTAAATTATATTTTATATTATTATATATTATGA-
1 ATTATTAAATTAT-ATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGAT
*
20457668 TT-TTAGTAAATTCATA-TAAGAATA-A-GA-ATTTTATTAAATTATATATT
65 TTATTAGTAAATTCATATTAAGAATATATAACATTTTATTAAATTATATATT
* *
20457715 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTGTTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGA-T
20457780 TTATTAGTAAATTCATATTTAAGAATATTTATTAATCATTTTATTAAATTATATATT
65 TTATTAGTAAATTCATA-TTAAGAATA--TA-TAA-CATTTTATTAAATTATATATT
* * *
20457837 TTTATTAAATTATATTTTATAACAATTATGTTAAA
1 ATTATTAAATTATATTTAATAATAATTATGTTAAA
20457872 ATATGATTAA
Statistics
Matches: 135, Mismatches: 8, Indels: 15
0.85 0.05 0.09
Matches are distributed among these distances:
109 19 0.14
110 39 0.29
112 2 0.01
113 14 0.10
115 8 0.06
118 1 0.01
120 1 0.01
122 51 0.38
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (116 bp):
ATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGATT
TATTAGTAAATTCATATTAAGAATATATAACATTTTATTAAATTATATATT
Found at i:20457748 original size:26 final size:28
Alignment explanation
Indices: 20457694--20457757 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
20457684 TAAGAATAAG
* * *
20457694 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
20457722 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
20457748 AATTATATTT
1 AATTATATTT
20457758 TATAGTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:20458067 original size:44 final size:46
Alignment explanation
Indices: 20458017--20458105 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
20458007 CCTCTATTCC
*
20458017 ATTCAACCAAACACAAGAA-TA-CTACTACGCCTCTATTCCATTAT
1 ATTCAACCAAACAAAAGAATTACCTACTACGCCTCTATTCCATTAT
* * *
20458061 ATTCAACCAAACAAAAGAATTACCTATTATGCCTCTATTTCATTA
1 ATTCAACCAAACAAAAGAATTACCTACTACGCCTCTATTCCATTA
20458106 CGCCTCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 18 0.46
45 2 0.05
46 19 0.49
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.30
Consensus pattern (46 bp):
ATTCAACCAAACAAAAGAATTACCTACTACGCCTCTATTCCATTAT
Found at i:20458121 original size:16 final size:16
Alignment explanation
Indices: 20458084--20458122 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20458074 AAAGAATTAC
*
20458084 CTATTATGCCTCTATT
1 CTATTACGCCTCTATT
20458100 -TCATTACGCCTCTATT
1 CT-ATTACGCCTCTATT
20458116 CTATTAC
1 CTATTAC
20458123 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.46
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:20466971 original size:19 final size:20
Alignment explanation
Indices: 20466934--20466973 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
20466924 CGAGACTAAA
20466934 TCAGAAACATATAGAATTTT
1 TCAGAAACATATAGAATTTT
20466954 TCAGAAA-ATA-ATGAATTTT
1 TCAGAAACATATA-GAATTTT
20466973 T
1 T
20466974 AAAACTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.05
19 11 0.58
20 7 0.37
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
TCAGAAACATATAGAATTTT
Found at i:20473995 original size:39 final size:39
Alignment explanation
Indices: 20473933--20474023 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
20473923 AAATTAAGAC
* *
20473933 ACATAATTAAA-AAACATATTAATGATGTTTAAACTA-AG
1 ACATAATTAAAGACACATATTAATGATGTTCAAAC-AGAG
20473971 ACATAATTAAAGACACATATTAATGATGTTCAAACAGAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACAGAG
20474010 ACATAATTAAAGAC
1 ACATAATTAAAGAC
20474024 TCAAACTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
38 12 0.24
39 37 0.76
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (39 bp):
ACATAATTAAAGACACATATTAATGATGTTCAAACAGAG
Found at i:20475467 original size:24 final size:26
Alignment explanation
Indices: 20475421--20475480 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
20475411 GCATGAAATT
* **
20475421 ATATTAGGTTTATGAATTTTTG-A-G
1 ATATTAGGTTTATCAATGATTGAATG
*
20475445 ATATTAGGTTTATCCATGATTGAATG
1 ATATTAGGTTTATCAATGATTGAATG
20475471 ATATTAGGTT
1 ATATTAGGTT
20475481 GCTATTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 18 0.60
25 1 0.03
26 11 0.37
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (26 bp):
ATATTAGGTTTATCAATGATTGAATG
Found at i:20494401 original size:51 final size:51
Alignment explanation
Indices: 20494324--20494426 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
20494314 TTCTTGGTGC
20494324 AATCTGAAAATACTCATGTAGCGACATTGGTACCAAAACATGACAAAATTA
1 AATCTGAAAATACTCATGTAGCGACATTGGTACCAAAACATGACAAAATTA
*
20494375 AATCTGAAAATACTCATGTAGTGACATTGGTACCAAAACATGACAAAATTA
1 AATCTGAAAATACTCATGTAGCGACATTGGTACCAAAACATGACAAAATTA
20494426 A
1 A
20494427 GGATAAATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (51 bp):
AATCTGAAAATACTCATGTAGCGACATTGGTACCAAAACATGACAAAATTA
Found at i:20508656 original size:38 final size:38
Alignment explanation
Indices: 20508607--20508682 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
20508597 CAAGAATTCC
*
20508607 TTCCTCATTCCTTAGAATTTTCGGGCAAAAGAAATGAA
1 TTCCTCATTCCTTAGAATTTTCGGCCAAAAGAAATGAA
*
20508645 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCATTCCTTAGAATTTTCGGCCAAAAGAAATGAA
20508683 AAAGGATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (38 bp):
TTCCTCATTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:20515692 original size:39 final size:40
Alignment explanation
Indices: 20515647--20515814 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
20515637 CGGGGTTTAG
* * *
20515647 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
20515686 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
20515726 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
20515766 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
20515807 CCGGATAT
1 CCGGATAT
20515815 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:20515797 original size:41 final size:40
Alignment explanation
Indices: 20515670--20515814 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
20515660 CTCGCACAAG
* * * * *
20515670 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
20515710 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
20515750 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
20515791 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
20515815 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:20520697 original size:50 final size:50
Alignment explanation
Indices: 20520587--20520835 Score: 200
Period size: 50 Copynumber: 4.9 Consensus size: 50
20520577 GACATTAGGG
* * *
20520587 GATGAGA--TCCCATGTAAGACCATGTCTGAGACATGGTATTGGCATTATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACTGA
*
20520638 GGTTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGA
1 -G--ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA
* *
20520691 GATGAGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACTGA
* * ** * * * * * *
20520741 TATTAGAACTCCCATGTAAGACTATATCTGGGATATGGCATTTGTAGT-A
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA
* * * ** * *
20520790 CAGGAAACATCCCATGTAAGACCATGTATGGGACATGGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
20520836 TGTTATTATC
Statistics
Matches: 159, Mismatches: 32, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
49 35 0.22
50 78 0.49
51 1 0.01
52 2 0.01
53 4 0.03
54 6 0.04
56 33 0.21
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA
Found at i:20521071 original size:16 final size:16
Alignment explanation
Indices: 20521049--20521087 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
20521039 GTAAGCAAGT
*
20521049 AAGTAAATAAATAAGA
1 AAGTAAATAAAGAAGA
*
20521065 GAGTAAATAAAGAAGA
1 AAGTAAATAAAGAAGA
20521081 AAGTAAA
1 AAGTAAA
20521088 GATCATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
AAGTAAATAAAGAAGA
Found at i:20527287 original size:38 final size:37
Alignment explanation
Indices: 20527235--20527426 Score: 215
Period size: 38 Copynumber: 5.1 Consensus size: 37
20527225 TGAATTATAT
20527235 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
1 TGTTATTC-GGCTTTGTGCCTAGCAGGCTTTGTGCCGG
** *
20527273 TGTTATTCGTGCTTTGTGTTTAGCAGGCTTTATGCCGG
1 TGTTATTCG-GCTTTGTGCCTAGCAGGCTTTGTGCCGG
* *
20527311 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGTCGG
1 TGTTATTC-GGCTTTGTGCCTAGCAGGCTTTGTGCCGG
* * *
20527349 TGTTATTTAGGC-TTGTGCCAAGCAGGCTTTGTGCTGG
1 TGTTA-TTCGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
* * * * *
20527386 TGTTATTCAAGTTTTGTGCCTAGCAGTCTTAGTTCCGG
1 TGTTATTC-GGCTTTGTGCCTAGCAGGCTTTGTGCCGG
20527424 TGT
1 TGT
20527427 ATTAAAAGTT
Statistics
Matches: 128, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
36 2 0.02
37 29 0.23
38 95 0.74
39 2 0.02
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (37 bp):
TGTTATTCGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
Found at i:20527403 original size:75 final size:76
Alignment explanation
Indices: 20527235--20527430 Score: 254
Period size: 75 Copynumber: 2.6 Consensus size: 76
20527225 TGAATTATAT
* * ***
20527235 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATTCGTGCTTTGTGTTTAGCAGG
1 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATTAGTGCTTTGTGCCAAGCAGG
20527300 CTTTATGCCGG
66 CTTTATGCCGG
*
20527311 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGTTATTTAG-GC-TTGTGCCAAGCAG
1 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTA-TTAGTGCTTTGTGCCAAGCAG
* *
20527374 GCTTTGTGCTGG
65 GCTTTATGCCGG
* * * *
20527386 TGTTATTCAAGTTTTGTGCCTAGCAGTCTTAGTTCCGGTG-TATTA
1 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATTA
20527431 AAAGTTAACA
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
73 3 0.03
74 2 0.02
75 55 0.52
76 43 0.41
77 3 0.03
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.41
Consensus pattern (76 bp):
TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATTAGTGCTTTGTGCCAAGCAGG
CTTTATGCCGG
Found at i:20531202 original size:30 final size:29
Alignment explanation
Indices: 20531168--20531246 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
20531158 CGGCTAAATA
*
20531168 AGGCCTATAGGCCGATTTTAATTTTTAATT
1 AGGCCTATAGGCCGATTTTAA-CTTTAATT
* *
20531198 AGGCCTTTAGGCCAATTTTAACTTTAATT
1 AGGCCTATAGGCCGATTTTAACTTTAATT
***
20531227 AGGGAAATAGGCCGATTTTA
1 AGGCCTATAGGCCGATTTTA
20531247 GGAGAGAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (29 bp):
AGGCCTATAGGCCGATTTTAACTTTAATT
Found at i:20538644 original size:43 final size:43
Alignment explanation
Indices: 20538592--20538758 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
20538582 TTTCAAAAAT
** *
20538592 AAATGCCACTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAATGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCACAC
* * * *
20538635 AAATGCCACTATAGACCATGACCTTTAACGGTGCTTTTCAGAC
1 AAATGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCACAC
** * *
20538678 AAATGCTGCTATAGACCATGACCTTTAGCGGCGCTTTT-ATCAT
1 AAATGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCA-CAC
* * * *
20538721 AAACGCCGCTAAAGAGCA-AACCTTTAGCGGCGCTTTTC
1 AAATGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTC
20538759 GTAAAAACGC
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 19 0.18
43 85 0.82
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
AAATGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCACAC
Found at i:20538788 original size:42 final size:42
Alignment explanation
Indices: 20538698--20538788 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
20538688 ATAGACCATG
* *
20538698 ACCTTTAGCGGCGCTTTTATCATAAACGCCGCTAAAGAGCAA
1 ACCTTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGAACAA
*
20538740 ACCTTTAGCGGCGCTTTTCGT-AAAAACGCCGCTAAA-AACATA
1 ACCTTTAGCGGCGCTTTT-ATCAAAAACGCCGCTAAAGAACA-A
*
20538782 ATCTTTA
1 ACCTTTA
20538789 AAAAAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 39 0.91
43 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGAACAA
Found at i:20539724 original size:14 final size:14
Alignment explanation
Indices: 20539707--20539737 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20539697 GAAGCTTTTG
20539707 ATATAAAGCATTTA
1 ATATAAAGCATTTA
*
20539721 ATATCAAGCATTTA
1 ATATAAAGCATTTA
20539735 ATA
1 ATA
20539738 AAAACCGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (14 bp):
ATATAAAGCATTTA
Found at i:20543561 original size:21 final size:20
Alignment explanation
Indices: 20543537--20543579 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
20543527 AATGACGCTG
20543537 TTTTGCTCTACTAAAAAATTTT
1 TTTTG-TCTA-TAAAAAATTTT
*
20543559 TTTTGTCTATTAAAAATTTT
1 TTTTGTCTATAAAAAATTTT
20543579 T
1 T
20543580 AGTTAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 4 0.20
22 5 0.25
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTGTCTATAAAAAATTTT
Found at i:20544343 original size:14 final size:15
Alignment explanation
Indices: 20544317--20544345 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20544307 TTTAACCCCT
20544317 AACCCCTAACCCTTA
1 AACCCCTAACCCTTA
20544332 AACCCC-AACCCTTA
1 AACCCCTAACCCTTA
20544346 TAACTGTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCCCTAACCCTTA
Found at i:20545158 original size:28 final size:28
Alignment explanation
Indices: 20545095--20545169 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
20545085 CAAAAATCTA
*
20545095 CAAAAACCTTAAAATAGTA-ACCCCTAAAC
1 CAAAAACCTTAAACTA-TATA-CCCTAAAC
**
20545124 CTTAAA-CTCTAAACTATATACCCTAAAC
1 CAAAAACCT-TAAACTATATACCCTAAAC
20545152 CAAAAACCTTAAACTATA
1 CAAAAACCTTAAACTATA
20545170 GTGATAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 25 0.66
29 13 0.34
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (28 bp):
CAAAAACCTTAAACTATATACCCTAAAC
Found at i:20545331 original size:41 final size:41
Alignment explanation
Indices: 20545286--20545406 Score: 143
Period size: 41 Copynumber: 3.0 Consensus size: 41
20545276 TATGATAAAT
* * *
20545286 CTGAGTATTAGCGGCGCTTTTTAAAAAACACCACTAAAACC
1 CTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAACC
* * * * *
20545327 CTGAGCATTAGCGGTGCTGTTTCATAAACGCCTCTAAAGCC
1 CTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAACC
* * *
20545368 CTGGGCATTAGCGGCGCTTCTTCAAAAACGCCATTAAAA
1 CTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAA
20545407 ACGCCGCTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.25
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAACC
Found at i:20552394 original size:81 final size:81
Alignment explanation
Indices: 20552298--20552458 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
20552288 ACACCTTTAT
20552298 TCAAAGGCACCAACTATCGCATCTAAACTATCCTTAAAA-CCGCCACCCTCTTCAACTCTAAACC
1 TCAAAGGCACCAACTATCGCATCTAAACTATCC-TAAAACCCGCCACCCTCTTCAACTCTAAACC
20552362 TTACCATCGGCTACTCC
65 TTACCATCGGCTACTCC
20552379 TCAAAGGCACCAACTATCGCATCTAAACTATCCTAAAACCCGCCACCCTCTTCAACTCTAAACCT
1 TCAAAGGCACCAACTATCGCATCTAAACTATCCTAAAACCCGCCACCCTCTTCAACTCTAAACCT
20552444 TACCATCGGCTACTC
66 TACCATCGGCTACTC
20552459 AACCACATGC
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
80 5 0.06
81 74 0.94
ACGTcount: A:0.31, C:0.39, G:0.07, T:0.23
Consensus pattern (81 bp):
TCAAAGGCACCAACTATCGCATCTAAACTATCCTAAAACCCGCCACCCTCTTCAACTCTAAACCT
TACCATCGGCTACTCC
Found at i:20558011 original size:100 final size:100
Alignment explanation
Indices: 20557831--20558030 Score: 364
Period size: 100 Copynumber: 2.0 Consensus size: 100
20557821 CTTGTAGAAA
20557831 GTAAAGGTGAAAGTATATGCAATAAGATATATTATTGTTATAATACAGAATATGATCCTATTACA
1 GTAAAGGTGAAAGTATATGCAATAAGATATATTATTGTTATAATACAGAATATGATCCTATTACA
* *
20557896 TTTGAAGAGGCAATGGAATCTCAAGACTCTTCTTT
66 TTTGAAAAGGCAATGGAATCTCAAGACTATTCTTT
*
20557931 GTAAAGGTGAAAGTATATGCAATAAGATATATTATTGTTATAATACGGAATATGATCCTATTACA
1 GTAAAGGTGAAAGTATATGCAATAAGATATATTATTGTTATAATACAGAATATGATCCTATTACA
*
20557996 TTTGAAAAGGTAATGGAATCTCAAGACTATTCTTT
66 TTTGAAAAGGCAATGGAATCTCAAGACTATTCTTT
20558031 TTGGAAAGAA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (100 bp):
GTAAAGGTGAAAGTATATGCAATAAGATATATTATTGTTATAATACAGAATATGATCCTATTACA
TTTGAAAAGGCAATGGAATCTCAAGACTATTCTTT
Found at i:20558699 original size:153 final size:153
Alignment explanation
Indices: 20558454--20558733 Score: 506
Period size: 153 Copynumber: 1.8 Consensus size: 153
20558444 TTATATAAAC
* *
20558454 ACCAAAGCATTGACTCCAAAAGTTTGACAAGGTTGTTCTAGCTAATGGCTATAAAATAAATGAAT
1 ACCAAAGCATTGACACCAAAAGTTTGACAAGGTTGTTCTAACTAATGGCTATAAAATAAATGAAT
* *
20558519 CTGATAAGTGCATATATAAAAAATTTGAAAATAGAAAAGGTGTCATAATTTTCTTATATGTAAGC
66 CTGATAAGTGCATAAATAAAAAATTTGAAAATAGAAAAGGTGTCATAATTTGCTTATATGTAAGC
20558584 TTGTTAAATCTTTATATGGGCTT
131 TTGTTAAATCTTTATATGGGCTT
20558607 ACCAAAGCATTGACACCAAAAGTTTGACAAGGTTGTTCTAACTAATGGCTATAAAATAAATGAAT
1 ACCAAAGCATTGACACCAAAAGTTTGACAAGGTTGTTCTAACTAATGGCTATAAAATAAATGAAT
* *
20558672 CTGATAAGTGCATAAATAACAAATTTGAAAATGGAAAAGGTGTCATAATTTGCTTATATGTA
66 CTGATAAGTGCATAAATAAAAAATTTGAAAATAGAAAAGGTGTCATAATTTGCTTATATGTA
20558734 GATGACATGC
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 121 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (153 bp):
ACCAAAGCATTGACACCAAAAGTTTGACAAGGTTGTTCTAACTAATGGCTATAAAATAAATGAAT
CTGATAAGTGCATAAATAAAAAATTTGAAAATAGAAAAGGTGTCATAATTTGCTTATATGTAAGC
TTGTTAAATCTTTATATGGGCTT
Found at i:20563841 original size:23 final size:22
Alignment explanation
Indices: 20563765--20563841 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 22
20563755 CCAAACAATT
*
20563765 TTAAAATATAA-ATTTGATATTTA
1 TTAAAATTTAATATTT-A-ATTTA
20563788 -TAAAATTTAATATTTAATTTA
1 TTAAAATTTAATATTTAATTTA
*
20563809 TTCAACATTTAATATTTCAATTTA
1 TT-AAAATTTAATATTT-AATTTA
20563833 TTAAAATTT
1 TTAAAATTT
20563842 GACATCTCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.11
22 11 0.23
23 23 0.49
24 8 0.17
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAAAATTTAATATTTAATTTA
Found at i:20571197 original size:45 final size:45
Alignment explanation
Indices: 20571148--20571321 Score: 240
Period size: 45 Copynumber: 3.9 Consensus size: 45
20571138 AATTATATTT
* * ** * * ***
20571148 GGTGGAATTAGCATATAGCAACCACCTTTATTTTCATTGATTTTC
1 GGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCC
*
20571193 GGTGGAGTCAGCACATAGCAACCACCTTTATAATCAATGGTACCC
1 GGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCC
*
20571238 AGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCC
1 GGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCC
*
20571283 GGTGGAATCAGCACATAACAACCACCTTTATAATCAATG
1 GGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
20571322 ATACTCAGTA
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 115 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCC
Found at i:20571286 original size:90 final size:90
Alignment explanation
Indices: 20571106--20571330 Score: 256
Period size: 90 Copynumber: 2.5 Consensus size: 90
20571096 TCGTTACACA
* * * **** * *
20571106 GTGG-ATCAGCATATAAC-ACCACCCTTATAATCAATTATATTTGGTGGAATTAGCATATAGCAA
1 GTGGAATCAGCACATAACAACCACCTTTATAATCAATGATACCCAGTGGAATCAGCACATAGCAA
** * ***
20571169 CCACCTTTATTTTCATTGATTTTCG
66 CCACCTTTATAATCAATGATACCCG
* * *
20571194 GTGGAGTCAGCACATAGCAACCACCTTTATAATCAATGGTACCCAGTGGAATCAGCACATAGCAA
1 GTGGAATCAGCACATAACAACCACCTTTATAATCAATGATACCCAGTGGAATCAGCACATAGCAA
*
20571259 CCACCTTTATAATCAATGGTACCCG
66 CCACCTTTATAATCAATGATACCCG
*
20571284 GTGGAATCAGCACATAACAACCACCTTTATAATCAATGATACTCAGT
1 GTGGAATCAGCACATAACAACCACCTTTATAATCAATGATACCCAGT
20571331 ACACGTAGTA
Statistics
Matches: 112, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
88 4 0.04
89 10 0.09
90 98 0.88
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (90 bp):
GTGGAATCAGCACATAACAACCACCTTTATAATCAATGATACCCAGTGGAATCAGCACATAGCAA
CCACCTTTATAATCAATGATACCCG
Found at i:20572542 original size:20 final size:20
Alignment explanation
Indices: 20572513--20572577 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
20572503 ATGCTGGCAA
20572513 AGGCACCGAAGTGCAAACAG
1 AGGCACCGAAGTGCAAACAG
* * *
20572533 AGGCATCGAAGTGCAATCAA
1 AGGCACCGAAGTGCAAACAG
20572553 AGGCACCGAAGTGCAAACAG
1 AGGCACCGAAGTGCAAACAG
20572573 AGGCA
1 AGGCA
20572578 ACAAAGTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.23, G:0.29, T:0.08
Consensus pattern (20 bp):
AGGCACCGAAGTGCAAACAG
Found at i:20572584 original size:20 final size:20
Alignment explanation
Indices: 20572521--20572608 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
20572511 AAAGGCACCG
* *
20572521 AAGTGCAAACAGAGGCATCG
1 AAGTGCAAACAGAGGCAACA
* * * *
20572541 AAGTGCAATCAAAGGCACCG
1 AAGTGCAAACAGAGGCAACA
20572561 AAGTGCAAACAGAGGCAACA
1 AAGTGCAAACAGAGGCAACA
* *
20572581 AAGTGAAAATAGAGG-AATCA
1 AAGTGCAAACAGAGGCAA-CA
20572601 AAGTGCAA
1 AAGTGCAA
20572609 TCCCATACAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 2 0.04
20 55 0.96
ACGTcount: A:0.47, C:0.17, G:0.26, T:0.10
Consensus pattern (20 bp):
AAGTGCAAACAGAGGCAACA
Found at i:20572585 original size:40 final size:40
Alignment explanation
Indices: 20572510--20572585 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
20572500 AAAATGCTGG
* *
20572510 CAAAGGCACCGAAGTGCAAACAGAGGCATCGAAGTGCAAT
1 CAAAGGCACCGAAGTGCAAACAGAGGCAACAAAGTGCAAT
20572550 CAAAGGCACCGAAGTGCAAACAGAGGCAACAAAGTG
1 CAAAGGCACCGAAGTGCAAACAGAGGCAACAAAGTG
20572586 AAAATAGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.28, T:0.08
Consensus pattern (40 bp):
CAAAGGCACCGAAGTGCAAACAGAGGCAACAAAGTGCAAT
Found at i:20572605 original size:40 final size:40
Alignment explanation
Indices: 20572510--20572608 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 40
20572500 AAAATGCTGG
* * * * *
20572510 CAAAGGCACCGAAGTGCAAACAGAGGCATCGAAGTGCAAT
1 CAAAGGAACCAAAGTGCAAACAGAGGCAACAAAGTGAAAT
* *
20572550 CAAAGGCACCGAAGTGCAAACAGAGGCAACAAAGTGAAAAT
1 CAAAGGAACCAAAGTGCAAACAGAGGCAACAAAGTG-AAAT
* *
20572591 -AGAGGAATCAAAGTGCAA
1 CAAAGGAACCAAAGTGCAA
20572609 TCCCATACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 48 0.94
41 3 0.06
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.09
Consensus pattern (40 bp):
CAAAGGAACCAAAGTGCAAACAGAGGCAACAAAGTGAAAT
Found at i:20580672 original size:19 final size:19
Alignment explanation
Indices: 20580644--20580689 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
20580634 ACATGAGATT
20580644 ATAAAATATTTATCA-ATC
1 ATAAAATATTTATCACATC
*
20580662 ATAACAATATTTGTCACATC
1 ATAA-AATATTTATCACATC
*
20580682 ATATAATA
1 ATAAAATA
20580690 AAAATCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 14 0.58
20 6 0.25
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAAATATTTATCACATC
Found at i:20581528 original size:33 final size:34
Alignment explanation
Indices: 20581486--20581553 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
20581476 TTGTATGCTT
*
20581486 TTGATATGGTGCTGGTATGGTGG-TGTATTGGTGG
1 TTGATATGGTGCTGGTATAGTGGTTGTA-TGGTGG
* *
20581520 TTGA-ATGGTGGTGGTGTAGTGGTTGTATGGTGG
1 TTGATATGGTGCTGGTATAGTGGTTGTATGGTGG
20581553 T
1 T
20581554 GATTCGGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.12, C:0.01, G:0.46, T:0.41
Consensus pattern (34 bp):
TTGATATGGTGCTGGTATAGTGGTTGTATGGTGG
Found at i:20581563 original size:22 final size:21
Alignment explanation
Indices: 20581500--20581564 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
20581490 TATGGTGCTG
20581500 GTATGGTGGTGTATTGGTGGTT
1 GTATGGTGGTG-ATTGGTGGTT
* * *
20581522 GAATGGTGGTGGTGTAGTGGTT
1 GTATGGTGGTGAT-TGGTGGTT
20581544 GTATGGTGGTGATTCGGTGGT
1 GTATGGTGGTGATT-GGTGGT
20581565 GATAGAGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 33 0.94
ACGTcount: A:0.11, C:0.02, G:0.48, T:0.40
Consensus pattern (21 bp):
GTATGGTGGTGATTGGTGGTT
Found at i:20583634 original size:68 final size:68
Alignment explanation
Indices: 20583535--20583942 Score: 469
Period size: 68 Copynumber: 6.0 Consensus size: 68
20583525 TTCTTGATTC
* * * * * *
20583535 ACTATTCTGGTGAACTTCATATGTTGTCATAGCCTAGCTATGGTCTTACACCATACTATGCCATG
1 ACTATCCTGGCGAACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCATG
20583600 TTT
66 TTT
** * * * * * *
20583603 ACTATCCTGGCGGGCTTTATATGTTACCATAGCCCAGCTATAGTCCTAAACCATACGATGCCATG
1 ACTATCCTGGCGAACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCATG
*
20583668 TCT
66 TTT
* * * * ** * *
20583671 ATTGTCCTAGC-AGATTTCATATGTTTTCATAACCCAATTATGGTCTTACACCATACGATGCCAT
1 ACTATCCTGGCGA-ACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCAT
20583735 GTTT
65 GTTT
* * * * *
20583739 ATTATCCTAGAGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACAATGCCATG
1 ACTATCCTGGCGAACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCATG
20583804 -TT
66 TTT
* * * *
20583806 ACTATCTTGGCGGACTTCATATGTTACCATAGCCCAACTATGGTTTTACACCATACGATGCCATG
1 ACTATCCTGGCGAACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCATG
20583871 TTT
66 TTT
* * * *
20583874 ACTGTCCAGGCGAACTTCATATGTTGTCATAGCCCAACTATGGTCTTACACCATATGATGCCATG
1 ACTATCCTGGCGAACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCATG
20583939 TTT
66 TTT
20583942 A
1 A
20583943 TTGTCCTAAT
Statistics
Matches: 282, Mismatches: 55, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
67 58 0.21
68 223 0.79
69 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (68 bp):
ACTATCCTGGCGAACTTCATATGTTGCCATAGCCCAACTATGGTCTTACACCATACGATGCCATG
TTT
Found at i:20583889 original size:135 final size:135
Alignment explanation
Indices: 20583548--20583940 Score: 491
Period size: 135 Copynumber: 2.9 Consensus size: 135
20583538 ATTCTGGTGA
* * * * *
20583548 ACTTCATATGTTGTCATAGCCTAGCTATGGTCTTACACCATACTATGCCATGTTTACTATCCTGG
1 ACTTCATATGTTATCATAGCCCAACTATGGTCTTACACCATACGATGCCATGTTTACTATCCAGG
** * * * * * * *
20583613 CGGGCTTTATATGTTACCATAGCCCAGCTATAGTCCTAAACCATACGATGCCATGTCTATTGTCC
66 CGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACGATGCCATGT-TACTATCC
20583678 TAGCAG
130 TAGCAG
* * * * *
20583684 ATTTCATATGTTTTCATAACCCAATTATGGTCTTACACCATACGATGCCATGTTTATTATCCTA-
1 ACTTCATATGTTATCATAGCCCAACTATGGTCTTACACCATACGATGCCATGTTTACTATCC-AG
* * *
20583748 GAGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACAATGCCATGTTACTATCT
65 GCGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACGATGCCATGTTACTATCC
* *
20583813 TGGCGG
130 TAGCAG
* * *
20583819 ACTTCATATGTTACCATAGCCCAACTATGGTTTTACACCATACGATGCCATGTTTACTGTCCAGG
1 ACTTCATATGTTATCATAGCCCAACTATGGTCTTACACCATACGATGCCATGTTTACTATCCAGG
* * *
20583884 CGAACTTCATATGTTGTCATAGCCCAACTATGGTCTTACACCATATGATGCCATGTT
66 CGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACGATGCCATGTT
20583941 TATTGTCCTA
Statistics
Matches: 219, Mismatches: 36, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
134 1 0.00
135 116 0.53
136 102 0.47
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (135 bp):
ACTTCATATGTTATCATAGCCCAACTATGGTCTTACACCATACGATGCCATGTTTACTATCCAGG
CGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACGATGCCATGTTACTATCCT
AGCAG
Found at i:20583898 original size:203 final size:204
Alignment explanation
Indices: 20583545--20583960 Score: 606
Period size: 203 Copynumber: 2.0 Consensus size: 204
20583535 ACTATTCTGG
* * *
20583545 TGAACTTCATATGTTGTCATAGCCTAGCTATGGTCTTACACCATACTATGCCATGTTTACTATCC
1 TGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACAATGCCATGTTTACTATCC
* * * *
20583610 TGGCGGGCTTTATATGTTACCATAGCCCAGCTATAGTCCTAAACCATACGATGCCATGTCTATTG
66 TGGCGGACTTCATATGTTACCATAGCCCAACTATAGTCCTAAACCATACGATGCCATGTCTACTG
* * *
20583675 TCCTAGCAGATTTCATATGTTTTCATAACCCAATTATGGTCTTACACCATACGATGCCATGTTTA
131 TCCTAGCAGACTTCATATGTTGTCATAACCCAACTATGGTCTTACACCATACGATGCCATGTTTA
20583740 TTATCCTAGA
196 TTATCCTA-A
*
20583750 -GAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACAATGCCATG-TTACTATCT
1 TGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACAATGCCATGTTTACTATCC
* ** * *
20583813 TGGCGGACTTCATATGTTACCATAGCCCAACTATGGTTTTACACCATACGATGCCATGTTTACTG
66 TGGCGGACTTCATATGTTACCATAGCCCAACTATAGTCCTAAACCATACGATGCCATGTCTACTG
* *
20583878 TCC-AGGC-GAACTTCATATGTTGTCATAGCCCAACTATGGTCTTACACCATATGATGCCATGTT
131 TCCTA-GCAG-ACTTCATATGTTGTCATAACCCAACTATGGTCTTACACCATACGATGCCATGTT
*
20583941 TATTGTCCTAA
194 TATTATCCTAA
20583952 TGAACTTCA
1 TGAACTTCA
20583961 GATTTGAGGA
Statistics
Matches: 189, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
202 3 0.02
203 135 0.71
204 51 0.27
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (204 bp):
TGAACTTCATATGTTGCCATAGCCCAGCTATGGTCTTACACCATACAATGCCATGTTTACTATCC
TGGCGGACTTCATATGTTACCATAGCCCAACTATAGTCCTAAACCATACGATGCCATGTCTACTG
TCCTAGCAGACTTCATATGTTGTCATAACCCAACTATGGTCTTACACCATACGATGCCATGTTTA
TTATCCTAA
Found at i:20585085 original size:22 final size:24
Alignment explanation
Indices: 20585060--20585106 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
20585050 CAACTACTCA
20585060 TTGTAACACCTTCAGC-T-GCTTG
1 TTGTAACACCTTCAGCATGGCTTG
*
20585082 TTGTAGCACCTTCAGCATGGCTTG
1 TTGTAACACCTTCAGCATGGCTTG
20585106 T
1 T
20585107 GGCGCAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 1 0.05
24 6 0.27
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (24 bp):
TTGTAACACCTTCAGCATGGCTTG
Found at i:20591021 original size:17 final size:17
Alignment explanation
Indices: 20590996--20591030 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20590986 CGGTCAAGGT
*
20590996 ATGGCAATAGGGAGAAA
1 ATGGAAATAGGGAGAAA
*
20591013 ATGGAAATAGGGGGAAA
1 ATGGAAATAGGGAGAAA
20591030 A
1 A
20591031 AAGAACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.37, T:0.11
Consensus pattern (17 bp):
ATGGAAATAGGGAGAAA
Found at i:20593560 original size:68 final size:68
Alignment explanation
Indices: 20593441--20593602 Score: 195
Period size: 68 Copynumber: 2.4 Consensus size: 68
20593431 CGTACAATGT
* * *
20593441 CATGTTTACTGT-TATGGCGGACTTTATATGTTGCTACAACCCAACTTTGGTCTTACACCATACT
1 CATGTTTACTGTCT-TGGCGGACTTCATATGTTGCTACAACCCAACTATGGTCTTACACCATACG
20593505 ATGC
65 ATGC
* * *
20593509 CATGTTTGCTGTCTTGGAGGACTTCATATGTTG-T-CATAGCCCAGCTATGGTCTTACACCATAC
1 CATGTTTACTGTCTTGGCGGACTTCATATGTTGCTACA-A-CCCAACTATGGTCTTACACCATAC
*
20593572 GATGT
64 GATGC
* *
20593577 CATGTTTACTATCTTGGCTGACTTCA
1 CATGTTTACTGTCTTGGCGGACTTCA
20593603 GATTTTGAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
66 2 0.03
67 2 0.03
68 75 0.94
69 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (68 bp):
CATGTTTACTGTCTTGGCGGACTTCATATGTTGCTACAACCCAACTATGGTCTTACACCATACGA
TGC
Found at i:20600203 original size:41 final size:41
Alignment explanation
Indices: 20600141--20600234 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
20600131 AATTTAACAT
* *
20600141 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGCTTATAACCTG
* * *
20600182 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGCTTATAACCTG
20600223 ATTCAGATCACC
1 ATTCAGATCACC
20600235 AATTCCAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTACTAGGCTTATAACCTG
Found at i:20619421 original size:15 final size:16
Alignment explanation
Indices: 20619397--20619440 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
20619387 TAGGCTCGGG
20619397 TTTAATTTTAAATTAT
1 TTTAATTTTAAATTAT
20619413 TTT-ATTTT-AATTAT
1 TTTAATTTTAAATTAT
20619427 TTTAATTTTAAATT
1 TTTAATTTTAAATT
20619441 GCTTTCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.35
15 10 0.38
16 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATTTTAAATTAT
Found at i:20620545 original size:7 final size:7
Alignment explanation
Indices: 20620533--20620557 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20620523 CAATAAATAA
20620533 AAATATT
1 AAATATT
20620540 AAATATT
1 AAATATT
20620547 AAATATT
1 AAATATT
20620554 AAAT
1 AAAT
20620558 TAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:20621219 original size:28 final size:28
Alignment explanation
Indices: 20621179--20621235 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20621169 CGAGAGATGG
20621179 TTTATCTATTGTATGGAAAGACAAGTGC
1 TTTATCTATTGTATGGAAAGACAAGTGC
20621207 TTTATCTATTGTATGGAAAGACAAGTGC
1 TTTATCTATTGTATGGAAAGACAAGTGC
20621235 T
1 T
20621236 CTATTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (28 bp):
TTTATCTATTGTATGGAAAGACAAGTGC
Found at i:20621249 original size:24 final size:27
Alignment explanation
Indices: 20621181--20621251 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
20621171 AGAGATGGTT
* *
20621181 TATCTATTGTATGGAAAGACAAGTGCTT
1 TATCTA-TATATGGAAAGACAAGTGCTC
*
20621209 TATCTATTGTATGGAAAGACAAGTGCTC
1 TATCTA-TATATGGAAAGACAAGTGCTC
*
20621237 TAT-TA-ATATGAAAAG
1 TATCTATATATGGAAAG
20621252 TTACTTGACA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 8 0.20
27 2 0.05
28 30 0.75
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (27 bp):
TATCTATATATGGAAAGACAAGTGCTC
Found at i:20624958 original size:138 final size:138
Alignment explanation
Indices: 20624710--20625271 Score: 867
Period size: 139 Copynumber: 4.1 Consensus size: 138
20624700 GAGAACATAG
* * * * *
20624710 ATATAATTAATATATGAATTTAATTCATACAAAATATTCATTGTATATGTTTCACAGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
*
20624775 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACAT-GAAAGTTACTATTCTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAA-TTAATATTCTT
20624839 TTGGAAAGA
130 TTGGAAAGA
* *
20624848 ATATAATTAATATATGAATTTGATTCCTACGAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
20624913 AATATAAACAATTATATTAATTAATTTCGGTCAAAATGTAAAAGACATGGAAATTAGTATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
20624978 TGGAAAGA
131 TGGAAAGA
* *
20624986 ATATAATTAATATATGAATTTGATTCATACGAAATATTAATTGCATATATTTTACCGAATTTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAA-TTTAT
* * *
20625051 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
65 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
* *
20625116 TCGAAAAGA
130 TTGGAAAGA
* * *
20625125 ATATAATTAATATATGAATTTGATTTATACAAAAATATTAATTGTATAGATTTTACCAAATTTAT
1 ATATAATTAATATATGAATTTGATTCATAC-AAAATATTAATTGTATATATTTTACCGAATTTAT
** *
20625190 TAATATAAA-AAGTTATATTAATTAATTTCAATCAAAATATAAAAGACATGGGAATTAATATTCT
65 TAATATAAACAA-TTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCT
20625254 TTTGGAAAGA
129 TTTGGAAAGA
20625264 ATATAATT
1 ATATAATT
20625272 CATTTTTCTA
Statistics
Matches: 390, Mismatches: 30, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
138 182 0.47
139 183 0.47
140 25 0.06
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:20625130 original size:139 final size:138
Alignment explanation
Indices: 20624710--20625271 Score: 865
Period size: 138 Copynumber: 4.1 Consensus size: 138
20624700 GAGAACATAG
* * * * *
20624710 ATATAATTAATATATGAATTTAATTCATACAAAATATTCATTGTATATGTTTCACAGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
20624775 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAGTTACTATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
20624840 TGGAAAGA
131 TGGAAAGA
* *
20624848 ATATAATTAATATATGAATTTGATTCCTACGAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
20624913 AATATAAACAATTATATTAATTAATTTCGGTCAAAATGTAAAAGACATGGAAATTAGTATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
20624978 TGGAAAGA
131 TGGAAAGA
* *
20624986 ATATAATTAATATATGAATTTGATTCATACGAAATATTAATTGCATATATTTTACCGAATTTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAA-TTTAT
* *
20625051 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
65 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
* *
20625116 TCGAAAAGA
130 TTGGAAAGA
* * *
20625125 ATATAATTAATATATGAATTTGATTTATACAAAAATATTAATTGTATAGATTTTACCAAATTTAT
1 ATATAATTAATATATGAATTTGATTCATAC-AAAATATTAATTGTATATATTTTACCGAATTTAT
** **
20625190 TAATATAAA-AAGTTATATTAATTAATTTCAATCAAAATATAAAAGACATGGGAATTAATATTCT
65 TAATATAAACAA-TTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCT
20625254 TTTGGAAAGA
129 TTTGGAAAGA
20625264 ATATAATT
1 ATATAATT
20625272 CATTTTTCTA
Statistics
Matches: 389, Mismatches: 32, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
138 185 0.48
139 179 0.46
140 25 0.06
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
TGGAAAGA
Found at i:20625332 original size:75 final size:75
Alignment explanation
Indices: 20625247--20625544 Score: 560
Period size: 75 Copynumber: 4.0 Consensus size: 75
20625237 ATGGGAATTA
* *
20625247 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
1 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
20625312 GAATAATCTT
66 GAATAATCTT
20625322 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
1 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
20625387 GAATAATCTT
66 GAATAATCTT
20625397 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
1 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
20625462 GAATAATCTT
66 GAATAATCTT
* *
20625472 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
1 ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
20625537 GAATAATC
66 GAATAATC
20625545 CTAGTTTTCT
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 219 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (75 bp):
ATATTTTTTTGGAAATAATATAATTCATTTTTCTAACTTTTCATTTGCCTTCTCTATTAGTAAGG
GAATAATCTT
Found at i:20626656 original size:28 final size:30
Alignment explanation
Indices: 20626611--20626714 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 30
20626601 ACTTGCCCCA
** * *
20626611 TGTTTACTGTTTCGACGGAC-TGTATC-TG
1 TGTTTACTGTCCCAACGGACATCTATCATG
20626639 TGTTTACTGTCCCAACGGACTATCTATCATG
1 TGTTTACTGTCCCAACGGAC-ATCTATCATG
** *
20626670 TGTTTACTGTCCCTGCGGGATATCTATCATG
1 TGTTTACTGTCCCAAC-GGACATCTATCATG
*
20626701 TGTTTATTGTCCCA
1 TGTTTACTGTCCCA
20626715 GCAGACTATC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 17 0.27
30 5 0.08
31 38 0.60
32 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.40
Consensus pattern (30 bp):
TGTTTACTGTCCCAACGGACATCTATCATG
Found at i:20626675 original size:31 final size:31
Alignment explanation
Indices: 20626633--20626725 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
20626623 CGACGGACTG
*
20626633 TATC-TGTGTTTACTGTCCCAACGGACTATC
1 TATCATGTGTTTACTGTCCCAGCGGACTATC
*
20626663 TATCATGTGTTTACTGTCCCTGCGGGA-TATC
1 TATCATGTGTTTACTGTCCCAGC-GGACTATC
* *
20626694 TATCATGTGTTTATTGTCCCAGCAGACTATC
1 TATCATGTGTTTACTGTCCCAGCGGACTATC
20626725 T
1 T
20626726 GTTCTATGGA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
30 6 0.11
31 46 0.84
32 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (31 bp):
TATCATGTGTTTACTGTCCCAGCGGACTATC
Found at i:20631035 original size:16 final size:18
Alignment explanation
Indices: 20631009--20631041 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20630999 TTAAATTAAC
20631009 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
20631026 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
20631042 CCTAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:20635091 original size:32 final size:32
Alignment explanation
Indices: 20635050--20635114 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20635040 TTTATGTAAA
20635050 AATAGACTCATTAAAATTTCATTTCATATCTT
1 AATAGACTCATTAAAATTTCATTTCATATCTT
20635082 AATAGACTCATTAAAATTTCATTTCATATCTT
1 AATAGACTCATTAAAATTTCATTTCATATCTT
20635114 A
1 A
20635115 TTCTCTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.43
Consensus pattern (32 bp):
AATAGACTCATTAAAATTTCATTTCATATCTT
Found at i:20637054 original size:19 final size:19
Alignment explanation
Indices: 20637032--20637074 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20637022 CTAATATATA
*
20637032 TATATTATATTTTATACC-T
1 TATATTAT-TTATATACCTT
20637051 TATATTATTTATATACCTT
1 TATATTATTTATATACCTT
20637070 TATAT
1 TATAT
20637075 ACATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATTTATATACCTT
Found at i:20638675 original size:16 final size:16
Alignment explanation
Indices: 20638654--20638690 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
20638644 TTGAGGGGTT
20638654 AAAGTGTAAATATGAA
1 AAAGTGTAAATATGAA
20638670 AAAGTGTAAATATGAA
1 AAAGTGTAAATATGAA
20638686 AAAGT
1 AAAGT
20638691 TGAAGGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (16 bp):
AAAGTGTAAATATGAA
Done.