Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 15 of 77
Found at i:2492510 original size:43 final size:42
Alignment explanation
Indices: 2492411--2492518 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 42
2492401 CGTCCCCCAA
* * * * *
2492411 AAAATAATAAAATAAAATAATAATAATAATAATATTACAAAAT
1 AAAA-AATAAAAAAAAATAATAAGAATAATAAAAATACAAAAC
** *
2492454 ACGAAATACAAAAAAAATATTAAGAATAATATAAAATACAAAAC
1 AAAAAATA-AAAAAAAATAATAAGAATAATA-AAAATACAAAAC
*
2492498 AAAAAATAAAAAAAAAGAATA
1 AAAAAATAAAAAAAAATAATA
2492519 GAAAACAGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 4 0.08
43 32 0.63
44 15 0.29
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (42 bp):
AAAAAATAAAAAAAAATAATAAGAATAATAAAAATACAAAAC
Found at i:2493634 original size:21 final size:21
Alignment explanation
Indices: 2493592--2493638 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2493582 TTTTAATAAT
2493592 AATAA-AATGAAAATAAAGTAA
1 AATAATAATGAAAATAAAGT-A
* *
2493613 AATAATAATTAAAA-AAATTA
1 AATAATAATGAAAATAAAGTA
2493633 AATAAT
1 AATAAT
2493639 GCTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 9 0.39
22 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
AATAATAATGAAAATAAAGTA
Found at i:2494016 original size:29 final size:31
Alignment explanation
Indices: 2493961--2494033 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
2493951 TTATAATCTG
* *
2493961 AAATCCTTTAAATCCAAACCCCAAAATC-TCC
1 AAATCC-TAAAATCCAAAACCCAAAATCTTCC
* *
2493992 AAATTCTAAAAT-CAAAACCCTAAATCTTCC
1 AAATCCTAAAATCCAAAACCCAAAATCTTCC
*
2494022 ATATCCTAAAAT
1 AAATCCTAAAAT
2494034 TCAAGCCTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 12 0.34
30 18 0.51
31 5 0.14
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (31 bp):
AAATCCTAAAATCCAAAACCCAAAATCTTCC
Found at i:2494097 original size:12 final size:12
Alignment explanation
Indices: 2494072--2494106 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2494062 AACCAAACCT
2494072 TCAAAACCTCTAC
1 TCAAAACCT-TAC
*
2494085 TCAAACCCTTAC
1 TCAAAACCTTAC
2494097 TCAAAACCTT
1 TCAAAACCTT
2494107 CAAAAACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (12 bp):
TCAAAACCTTAC
Found at i:2497021 original size:27 final size:25
Alignment explanation
Indices: 2496983--2497045 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
2496973 ATAGAATGGC
2496983 ATTATTTAATCTAATCCTATTCATAAT
1 ATTATTT-ATCTAATCCTA-TCATAAT
* *
2497010 ATTATCTTATCTTATTCTATCATAAT
1 ATTAT-TTATCTAATCCTATCATAAT
*
2497036 CTTATTTATC
1 ATTATTTATC
2497046 AAATATGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 5 0.16
26 11 0.34
27 14 0.44
28 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTATTTATCTAATCCTATCATAAT
Found at i:2505849 original size:8 final size:8
Alignment explanation
Indices: 2505833--2505874 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2505823 TTAACAATTT
2505833 TAAATATAA
1 TAAA-ATAA
*
2505842 TACAATAA
1 TAAAATAA
*
2505850 TGAAAT-A
1 TAAAATAA
2505857 TAAAATAA
1 TAAAATAA
2505865 TAAAATAA
1 TAAAATAA
2505873 TA
1 TA
2505875 TAATTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
7 6 0.21
8 19 0.68
9 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (8 bp):
TAAAATAA
Found at i:2505883 original size:23 final size:23
Alignment explanation
Indices: 2505831--2505885 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
2505821 ATTTAACAAT
*
2505831 TTTAAATATAATACAATAATGAAA
1 TTTAAA-ATAATAAAATAATGAAA
*
2505855 TATAAAATAATAAAATAAT-ATAA
1 TTTAAAATAATAAAATAATGA-AA
2505878 TTTAAAAT
1 TTTAAAAT
2505886 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 21 0.78
24 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TTTAAAATAATAAAATAATGAAA
Found at i:2509331 original size:158 final size:158
Alignment explanation
Indices: 2508899--2509619 Score: 718
Period size: 158 Copynumber: 4.6 Consensus size: 158
2508889 CAACAACACT
* * * * *** * * *
2508899 GTTCAATACCATTTGTCCTACAATGTTTAGGAGTTCAATTATTACATTATCTATTTCATCAATAA
1 GTTCAATATCAATTATCCTGCAATGTTTAGTCTTTCAATTACTACACTATCTATTTCATCAACAA
* * * * * *
2508964 TCACAGTACAC-AACTAGAATCACAAAGCATA-ATAAGCAATTGTTTTTACCTTCACAAAATGAT
66 TCACAATACACAAAC-AAAATCACAAAGCA-AGATACGCAATAGTTTTCACCTTCACAAAATCAT
*
2509027 TTCATCTTAATAAGCACAAAATACTATATA
129 TTCATCTCAATAAGCACAAAATACTATATA
** * * ** *
2509057 GTTCAATATCAATCGTCTTGCAATATTTAGT-TTTCAATTACTGTACTATCTACTTCATCAACAA
1 GTTCAATATCAATTATCCTGCAATGTTTAGTCTTTCAATTACTACACTATCTATTTCATCAACAA
* * * * * * * *
2509121 TCATAATACACAATCAAAATTACAAAACAAAATACGTAATAGTTTTCGCCTTCACAAAGTCATTT
66 TCACAATACACAAACAAAATCACAAAGCAAGATACGCAATAGTTTTCACCTTCACAAAATCATTT
2509186 CATCTCAATAAGCACAAAATACTATATA
131 CATCTCAATAAGCACAAAATACTATATA
* * * *
2509214 GTTCAATATCAATTACCCTACAATGTTTAGTCCTTCAATTACTACACTATCTATTTCATCAACAT
1 GTTCAATATCAATTATCCTGCAATGTTTAGTCTTTCAATTACTACACTATCTATTTCATCAACAA
* * * * * * * * *
2509279 TTAGAATACATAAACAAAATCACAAAGCAAGTTATGTAATAGTTTTCACCTTCATAAAGTCATTG
66 TCACAATACACAAACAAAATCACAAAGCAAGATACGCAATAGTTTTCACCTTCACAAAATCATTT
* * *
2509344 CATCTTAATAAACATAAAATACTATATA
131 CATCTCAATAAGCACAAAATACTATATA
* * * * *
2509372 GTTCAATACCATTTGTCCTGCAATGTTTAGTCTTTCAATTAATACACTATCTAATTT-ATCAATA
1 GTTCAATATCAATTATCCTGCAATGTTTAGTCTTTCAATTACTACACTATCT-ATTTCATCAACA
* * * * * * * * *
2509436 ATTACAATATACAACCAGAATCAGAAAGTAAGTTACACAATAG--TTCACCTTCATAAAATCATT
65 ATCACAATACACAAACAAAATCACAAAGCAAGATACGCAATAGTTTTCACCTTCACAAAATCATT
*
2509499 TCATCTCAATAAGCACAAAATACTATTTA
130 TCATCTCAATAAGCACAAAATACTATATA
* * * * *
2509528 GTTTAATAT-AATTTATCCTGTAATGTTTAGTCTTTTAATTACTACACCATCTACTTCATCAACA
1 GTTCAATATCAA-TTATCCTGCAATGTTTAGTCTTTCAATTACTACACTATCTATTTCATCAACA
* * *
2509592 ATCACAATATACAACCAGAATCACAAAG
65 ATCACAATACACAAACAAAATCACAAAG
2509620 TAAGTTACAC
Statistics
Matches: 466, Mismatches: 91, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
155 4 0.01
156 118 0.25
157 125 0.27
158 215 0.46
159 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (158 bp):
GTTCAATATCAATTATCCTGCAATGTTTAGTCTTTCAATTACTACACTATCTATTTCATCAACAA
TCACAATACACAAACAAAATCACAAAGCAAGATACGCAATAGTTTTCACCTTCACAAAATCATTT
CATCTCAATAAGCACAAAATACTATATA
Found at i:2509590 original size:314 final size:314
Alignment explanation
Indices: 2509005--2509591 Score: 746
Period size: 314 Copynumber: 1.9 Consensus size: 314
2508995 ATAAGCAATT
* * * * *
2509005 GTTTTTACCTTCACAAAATGATTTCATCTTAATAAGCACAAAATACTATATAGTTCAATATCAAT
1 GTTTTCACCTTCACAAAATCATTGCATCTTAATAAACACAAAATACTATATAGTTCAATACCAAT
* * ** * * *
2509070 CGTCTTGCAATATTTAGTTTTCAATTACTGTACTATCTACTTCATCAACAATCATAATACACAAT
66 CGTCCTGCAATATTTAGTTTTCAATTAATACACTATCTAATTCATCAACAATCACAATACACAAC
* ** * *
2509135 CAAAATTACAAAACAAAATACGTAATAGTTTTCGCCTTCACAAAGTCATTTCATCTCAATAAGCA
131 CAAAATCACAAAACAAAATACACAATAG-TTTCACCTTCACAAAATCATTTCATCTCAATAAGCA
*
2509200 CAAAATACTATATAGTTCAATATCAATTACCCTACAATGTTTAGTCCTTCAATTACTACACTATC
195 CAAAATACTATATAGTTCAATATCAATTACCCTACAATGTTTAGTCCTTCAATTACTACACCATC
*
2509265 TATTTCATCAACATTTAGAATACATAAACAAAATCACAAAGCAAGTTATGTAATA
260 TACTTCATCAACATTTAGAATACATAAACAAAATCACAAAGCAAGTTATGTAATA
* * * *
2509320 GTTTTCACCTTCATAAAGTCATTGCATCTTAATAAACATAAAATACTATATAGTTCAATACCATT
1 GTTTTCACCTTCACAAAATCATTGCATCTTAATAAACACAAAATACTATATAGTTCAATACCAAT
* * * * * *
2509385 TGTCCTGCAATGTTTAGTCTTTCAATTAATACACTATCTAATTTATCAATAATTACAATATACAA
66 CGTCCTGCAATATTTAGT-TTTCAATTAATACACTATCTAATTCATCAACAATCACAATACACAA
* * ** ** *
2509450 CCAGAATCAGAAAGTAAGTTACACAATAG-TTCACCTTCATAAAATCATTTCATCTCAATAAGCA
130 CCAAAATCACAAAACAAAATACACAATAGTTTCACCTTCACAAAATCATTTCATCTCAATAAGCA
* * * ** * *
2509514 CAAAATACTATTTAGTTTAATAT-AATTTATCCTGTAATGTTTAGTCTTTTAATTACTACACCAT
195 CAAAATACTATATAGTTCAATATCAA-TTACCCTACAATGTTTAGTCCTTCAATTACTACACCAT
2509578 CTACTTCATCAACA
259 CTACTTCATCAACA
2509592 ATCACAATAT
Statistics
Matches: 227, Mismatches: 43, Indels: 5
0.83 0.16 0.02
Matches are distributed among these distances:
313 2 0.01
314 98 0.43
315 71 0.31
316 56 0.25
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (314 bp):
GTTTTCACCTTCACAAAATCATTGCATCTTAATAAACACAAAATACTATATAGTTCAATACCAAT
CGTCCTGCAATATTTAGTTTTCAATTAATACACTATCTAATTCATCAACAATCACAATACACAAC
CAAAATCACAAAACAAAATACACAATAGTTTCACCTTCACAAAATCATTTCATCTCAATAAGCAC
AAAATACTATATAGTTCAATATCAATTACCCTACAATGTTTAGTCCTTCAATTACTACACCATCT
ACTTCATCAACATTTAGAATACATAAACAAAATCACAAAGCAAGTTATGTAATA
Found at i:2509616 original size:314 final size:314
Alignment explanation
Indices: 2508915--2509626 Score: 791
Period size: 315 Copynumber: 2.3 Consensus size: 314
2508905 TACCATTTGT
*** * ** * * *
2508915 CCTACAATGTTTAGGAGTTCAATTATTACATTATCTATTTCATCAATAATCACAGTACACAACTA
1 CCTACAATGTTTAGTCCTTCAATTACTACACCATCTATTTCATCAACAATCACAATACACAACCA
* * * * * *
2508980 GAATCACAAAGCATA-ATAAGCAATTGTTTTTACCTTCACAAAATGATTTCATCTTAATAAGCAC
66 GAATCACAAAGCA-AGTTAAGCAATAGTTTTCACCTTCACAAAATCATTGCATCTTAATAAACAC
* * * **
2509044 AAAATACTATATAGTTCAATATCAATCGTCTTGCAATATTTAGTTTTCAATTACTGTACTATCTA
130 AAAATACTATATAGTTCAATACCAATCGTCCTGCAATATTTAGTTTTCAATTAATACACTATCTA
* * * * ** *
2509109 CTTCATCAACAATCATAATACACAATCAAAATTACAAAACAAAATACGTAATAGTTTTCGCCTTC
195 ATTCATCAACAATCACAATACACAACCAAAATCACAAAACAAAATACACAATAG-TTTCACCTTC
*
2509174 ACAAAGTCATTTCATCTCAATAAGCACAAAATACTATATAGTTCAATATCAATTAC
259 ACAAAATCATTTCATCTCAATAAGCACAAAATACTATATAGTTCAATATCAATTAC
* * * * * *
2509230 CCTACAATGTTTAGTCCTTCAATTACTACACTATCTATTTCATCAACATTTAGAATACATAAACA
1 CCTACAATGTTTAGTCCTTCAATTACTACACCATCTATTTCATCAACAATCACAATACACAACCA
* * * * * *
2509295 AAATCACAAAGCAAGTTATGTAATAGTTTTCACCTTCATAAAGTCATTGCATCTTAATAAACATA
66 GAATCACAAAGCAAGTTAAGCAATAGTTTTCACCTTCACAAAATCATTGCATCTTAATAAACACA
* * *
2509360 AAATACTATATAGTTCAATACCATTTGTCCTGCAATGTTTAGTCTTTCAATTAATACACTATCTA
131 AAATACTATATAGTTCAATACCAATCGTCCTGCAATATTTAGT-TTTCAATTAATACACTATCTA
* * * * * * ** **
2509425 ATTTATCAATAATTACAATATACAACCAGAATCAGAAAGTAAGTTACACAATAG-TTCACCTTCA
195 ATTCATCAACAATCACAATACACAACCAAAATCACAAAACAAAATACACAATAGTTTCACCTTCA
* * * *
2509489 TAAAATCATTTCATCTCAATAAGCACAAAATACTATTTAGTTTAATAT-AATTTAT
260 CAAAATCATTTCATCTCAATAAGCACAAAATACTATATAGTTCAATATCAA-TTAC
** * * * *
2509544 CCTGTAATGTTTAGTCTTTTAATTACTACACCATCTACTTCATCAACAATCACAATATACAACCA
1 CCTACAATGTTTAGTCCTTCAATTACTACACCATCTATTTCATCAACAATCACAATACACAACCA
*
2509609 GAATCACAAAGTAAGTTA
66 GAATCACAAAGCAAGTTA
2509627 CACATCAGTT
Statistics
Matches: 325, Mismatches: 69, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
313 2 0.01
314 126 0.39
315 141 0.43
316 56 0.17
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (314 bp):
CCTACAATGTTTAGTCCTTCAATTACTACACCATCTATTTCATCAACAATCACAATACACAACCA
GAATCACAAAGCAAGTTAAGCAATAGTTTTCACCTTCACAAAATCATTGCATCTTAATAAACACA
AAATACTATATAGTTCAATACCAATCGTCCTGCAATATTTAGTTTTCAATTAATACACTATCTAA
TTCATCAACAATCACAATACACAACCAAAATCACAAAACAAAATACACAATAGTTTCACCTTCAC
AAAATCATTTCATCTCAATAAGCACAAAATACTATATAGTTCAATATCAATTAC
Found at i:2509917 original size:33 final size:34
Alignment explanation
Indices: 2509880--2510043 Score: 187
Period size: 33 Copynumber: 4.9 Consensus size: 34
2509870 AATAAATAAT
* *
2509880 AAGTAAT-TTTTTGTCTCAACATT-AAAAAATAGC
1 AAGTAATATTTTT-TCTCAATATTGCAAAAATAGC
*
2509913 AAGTAATATTTTTTCTTAATATTGCAAAAATAGC
1 AAGTAATATTTTTTCTCAATATTGCAAAAATAGC
* *
2509947 AAGTAATCTCTTTTT-T-AATATTGTAAAAATAGC
1 AAGTAATAT-TTTTTCTCAATATTGCAAAAATAGC
*
2509980 AAGTAAT-TTTTTTCTCAATATTGCAAAAATACC
1 AAGTAATATTTTTTCTCAATATTGCAAAAATAGC
* * *
2510013 AAGTAAT-CTCTTTCTTAATATTGCAAAAATA
1 AAGTAATATTTTTTCTCAATATTGCAAAAATA
2510044 CTTTGTCTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
31 5 0.04
32 2 0.02
33 81 0.70
34 23 0.20
35 5 0.04
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (34 bp):
AAGTAATATTTTTTCTCAATATTGCAAAAATAGC
Found at i:2510016 original size:66 final size:67
Alignment explanation
Indices: 2509904--2510043 Score: 237
Period size: 66 Copynumber: 2.1 Consensus size: 67
2509894 CTCAACATTA
* * *
2509904 AAAAATAGCAAGTAATATTTTTTCTTAATATTGCAAAAATAGCAAGTAATCTCTTTTTTAATATT
1 AAAAATAGCAAGTAATATTTTTTCTCAATATTGCAAAAATACCAAGTAATCTCTTTCTTAATATT
*
2509969 GT
66 GC
2509971 AAAAATAGCAAGTAAT-TTTTTTCTCAATATTGCAAAAATACCAAGTAATCTCTTTCTTAATATT
1 AAAAATAGCAAGTAATATTTTTTCTCAATATTGCAAAAATACCAAGTAATCTCTTTCTTAATATT
2510035 GC
66 GC
2510037 AAAAATA
1 AAAAATA
2510044 CTTTGTCTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
66 53 0.77
67 16 0.23
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (67 bp):
AAAAATAGCAAGTAATATTTTTTCTCAATATTGCAAAAATACCAAGTAATCTCTTTCTTAATATT
GC
Found at i:2510044 original size:33 final size:33
Alignment explanation
Indices: 2509904--2510043 Score: 199
Period size: 33 Copynumber: 4.2 Consensus size: 33
2509894 CTCAACATTA
* *
2509904 AAAAATAGCAAGTAATATTTTTTCTTAATATTGC
1 AAAAATAGCAAGTAAT-CTCTTTCTTAATATTGC
* *
2509938 AAAAATAGCAAGTAATCTCTTTTTTAATATTGT
1 AAAAATAGCAAGTAATCTCTTTCTTAATATTGC
* * *
2509971 AAAAATAGCAAGTAATTTTTTTCTCAATATTGC
1 AAAAATAGCAAGTAATCTCTTTCTTAATATTGC
*
2510004 AAAAATACCAAGTAATCTCTTTCTTAATATTGC
1 AAAAATAGCAAGTAATCTCTTTCTTAATATTGC
2510037 AAAAATA
1 AAAAATA
2510044 CTTTGTCTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 77 0.83
34 16 0.17
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (33 bp):
AAAAATAGCAAGTAATCTCTTTCTTAATATTGC
Found at i:2510385 original size:23 final size:24
Alignment explanation
Indices: 2510350--2510394 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2510340 ATTGCAAATA
2510350 TAATAGACCTTCATCAATGAATGT
1 TAATAGACCTTCATCAATGAATGT
* *
2510374 TAAT-GACTTTCATCGATGAAT
1 TAATAGACCTTCATCAATGAAT
2510395 TTTCCATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (24 bp):
TAATAGACCTTCATCAATGAATGT
Found at i:2511096 original size:31 final size:31
Alignment explanation
Indices: 2511061--2511121 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2511051 AAATTCAAAT
2511061 TTAAATCATTTCGA-ATTTAAATAATTTTAAG
1 TTAAATCATTTC-ATATTTAAATAATTTTAAG
* *
2511092 TTAAATTATTTCATATTTACATAATTTTAA
1 TTAAATCATTTCATATTTAAATAATTTTAA
2511122 ATTTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (31 bp):
TTAAATCATTTCATATTTAAATAATTTTAAG
Found at i:2511125 original size:16 final size:16
Alignment explanation
Indices: 2511038--2511135 Score: 63
Period size: 16 Copynumber: 6.2 Consensus size: 16
2511028 TTATATTTAA
* * *
2511038 TTTAAGTTTGAATAAA
1 TTTAAATTTAAATAAT
* *
2511054 TTCAAATTTAAATCAT
1 TTTAAATTTAAATAAT
**
2511070 TTCGAATTTAAATAAT
1 TTTAAATTTAAATAAT
* *
2511086 TTT-AAGTTAAATTAT
1 TTTAAATTTAAATAAT
* * *
2511101 TTCATATTTACATAAT
1 TTTAAATTTAAATAAT
* *
2511117 TTTAAATTTGAATTAT
1 TTTAAATTTAAATAAT
2511133 TTT
1 TTT
2511136 TGAATTTGAC
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
15 12 0.20
16 49 0.80
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATAAT
Found at i:2514091 original size:13 final size:12
Alignment explanation
Indices: 2514051--2514093 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
2514041 CTATTTATTA
2514051 TTTTTTTTTCAT
1 TTTTTTTTTCAT
2514063 TCATTTTTTTTC-T
1 T--TTTTTTTTCAT
2514076 TTTCTTTTTTCAT
1 TTT-TTTTTTCAT
2514089 TTTTT
1 TTTTT
2514094 GTTCCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 2 0.07
12 10 0.37
13 6 0.22
14 9 0.33
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTCAT
Found at i:2514092 original size:14 final size:13
Alignment explanation
Indices: 2514051--2514093 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
2514041 CTATTTATTA
2514051 TTTTTTTTTCATT
1 TTTTTTTTTCATT
*
2514064 CATTTTTTTTC-TT
1 -TTTTTTTTTCATT
*
2514077 TTCTTTTTTCATT
1 TTTTTTTTTCATT
2514090 TTTT
1 TTTT
2514094 GTTCCAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.33
13 7 0.29
14 9 0.38
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTCATT
Found at i:2515036 original size:20 final size:19
Alignment explanation
Indices: 2514994--2515052 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2514984 TTTGAAAGTG
* *
2514994 AAAAATATATTTTTATAA-A
1 AAAAATATCTTTTCA-AATA
*
2515013 AAAACTATCTTTTCAAATA
1 AAAAATATCTTTTCAAATA
*
2515032 AAAAATATCTTTTGAAATA
1 AAAAATATCTTTTCAAATA
2515051 AA
1 AA
2515053 GTTTTCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 2 0.06
19 32 0.94
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATATCTTTTCAAATA
Found at i:2515813 original size:20 final size:19
Alignment explanation
Indices: 2515784--2515843 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
2515774 GATATTTATT
2515784 TTTATTCATTTATTAATAA
1 TTTATTCATTTATTAATAA
2515803 TTTATTTCA-TTA-TAA-AA
1 TTTA-TTCATTTATTAATAA
*
2515820 TTTATT-ATTTATTTATATA
1 TTTATTCATTTATTAATA-A
2515839 TTTAT
1 TTTAT
2515844 CCAATTTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 8 0.23
18 4 0.11
19 13 0.37
20 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTCATTTATTAATAA
Found at i:2517814 original size:35 final size:35
Alignment explanation
Indices: 2517775--2517842 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
2517765 TTATAATAGG
2517775 ATTTTTT-GGATTTTACAAATAAAATTAATATCTGA
1 ATTTTTTAGG-TTTTACAAATAAAATTAATATCTGA
* *
2517810 ATTTTTTAGGTTTTACAGATAAAATTTATATCT
1 ATTTTTTAGGTTTTACAAATAAAATTAATATCT
2517843 TAAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.93
36 2 0.07
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (35 bp):
ATTTTTTAGGTTTTACAAATAAAATTAATATCTGA
Found at i:2519963 original size:20 final size:18
Alignment explanation
Indices: 2519924--2519970 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2519914 ATTTTTATTT
2519924 TATA-AAAATTTAAAATA
1 TATATAAAATTTAAAATA
2519941 TATATAAAATTTAAAATA
1 TATATAAAATTTAAAATA
*
2519959 TATATATAATTT
1 TATATAAAATTT
2519971 GATTCGATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATAAAATTTAAAATA
Found at i:2525369 original size:25 final size:25
Alignment explanation
Indices: 2525322--2525369 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2525312 AGAGTTTTAT
* **
2525322 TATAAATGTATTATTTTTTATATAA
1 TATAAATATATTATTTTAAATATAA
2525347 TATAAATATATTATTTTAAATAT
1 TATAAATATATTATTTTAAATAT
2525370 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATAAATATATTATTTTAAATATAA
Found at i:2531185 original size:3 final size:3
Alignment explanation
Indices: 2531177--2531203 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2531167 TTAACAGCAA
2531177 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2531204 TCGCTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2532788 original size:138 final size:136
Alignment explanation
Indices: 2532541--2532790 Score: 351
Period size: 138 Copynumber: 1.8 Consensus size: 136
2532531 TGAGAGAGGT
** * *
2532541 GAAATTTTATTGGCGGGAGGGAAATACCGATCATCTTGCTTGAATGAAAAAAAAAAATTTTTTGT
1 GAAATTTTATTGGCGAAAAGGAAATACCGATCATCTTGCTTGAATGAAAAAAAAAAATTTTTTAT
* **
2532606 AAGAAAAAATTCAAAGATAGATAGACTGCTCAATCTTTCAAGTCATAGCAAGATATGCTGTACTT
66 AAGAAAAAATTCAAAGATAAATAGACTGCTCAATCTCCCAAGTCATAGCAAGATATGCTGTACTT
2532671 AACAGC
131 AACAGC
*
2532677 GAAATTTTATTGGC-AAAAGGAAATATCGATCATCTTGCTTGAATGAAAAAAAAAAATTTTTTTT
1 GAAATTTTATTGGCGAAAAGGAAATACCGATCATCTTGCTTGAATGAAAAAAAAAAA---TTTTT
* * *
2532741 TATAAGAAAAAATTCAAAGGTAAATA-AGCTGCTTAGTCTCCCAAGTCATA
63 TATAAGAAAAAATTCAAAGATAAATAGA-CTGCTCAATCTCCCAAGTCATA
2532791 ACTATCGTAC
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
135 38 0.38
136 14 0.14
137 1 0.01
138 46 0.46
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (136 bp):
GAAATTTTATTGGCGAAAAGGAAATACCGATCATCTTGCTTGAATGAAAAAAAAAAATTTTTTAT
AAGAAAAAATTCAAAGATAAATAGACTGCTCAATCTCCCAAGTCATAGCAAGATATGCTGTACTT
AACAGC
Found at i:2533230 original size:29 final size:31
Alignment explanation
Indices: 2533179--2533247 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
2533169 AATATTACGA
*
2533179 ATAATTTTTAAATTATAATAAATTATTTAAT
1 ATAATATTTAAATTATAATAAATTATTTAAT
* *
2533210 ATGATATTTAAATT-TAA-AAATTTTTTAAT
1 ATAATATTTAAATTATAATAAATTATTTAAT
2533239 ATAATATTT
1 ATAATATTT
2533248 GAATAACGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
30 3 0.09
31 12 0.35
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
ATAATATTTAAATTATAATAAATTATTTAAT
Found at i:2533924 original size:28 final size:29
Alignment explanation
Indices: 2533883--2533951 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2533873 TAAATATCAA
* * *
2533883 ATTA-ATTAATAAA-TTTATAATTTAAAT
1 ATTATATTAAAAAATTTTAAAATTTAAAC
2533910 ATTATATTAAAAAATTTTAAAATTTAAAC
1 ATTATATTAAAAAATTTTAAAATTTAAAC
**
2533939 ACCATATTAAAAA
1 ATTATATTAAAAA
2533952 TTTCATTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 4 0.11
28 8 0.23
29 23 0.66
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (29 bp):
ATTATATTAAAAAATTTTAAAATTTAAAC
Found at i:2540807 original size:19 final size:21
Alignment explanation
Indices: 2540783--2540825 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2540773 AATTCACGAA
2540783 TTTAAT-TAAATTTTT-TTAT
1 TTTAATATAAATTTTTATTAT
*
2540802 TTTAATATATATTTTTATTAT
1 TTTAATATAAATTTTTATTAT
2540823 TTT
1 TTT
2540826 GTTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTAATATAAATTTTTATTAT
Found at i:2542164 original size:43 final size:42
Alignment explanation
Indices: 2542112--2542198 Score: 95
Period size: 43 Copynumber: 2.0 Consensus size: 42
2542102 AATTTGGATA
* *
2542112 TAAAATATT-AGTAATATTATATTTACTTCATAATAAATATAAT
1 TAAAATATTAAGTAAAAATATATTTA-TTCATAATAAAT-TAAT
* * *
2542155 TAAATTATTAAATTAAAAATATATTTATTGATAATAAATTAAT
1 TAAAATATT-AAGTAAAAATATATTTATTCATAATAAATTAAT
2542198 T
1 T
2542199 TTTGTAGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
43 13 0.35
44 11 0.30
45 13 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (42 bp):
TAAAATATTAAGTAAAAATATATTTATTCATAATAAATTAAT
Found at i:2556454 original size:7 final size:7
Alignment explanation
Indices: 2556442--2556483 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
2556432 CAAAAGTATT
2556442 TTATTTA
1 TTATTTA
2556449 TTATTTA
1 TTATTTA
*
2556456 TTATTTT
1 TTATTTA
2556463 TTAATTTA
1 TT-ATTTA
2556471 TT-TTTA
1 TTATTTA
2556477 TTATTTA
1 TTATTTA
2556484 GTTGGTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 19 0.61
8 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:2556476 original size:21 final size:21
Alignment explanation
Indices: 2556440--2556482 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2556430 CCCAAAAGTA
2556440 TTTTATTTATTATTTATTATT
1 TTTTATTTATTATTTATTATT
2556461 TTTTAATTTATT-TTTATTATT
1 TTTT-ATTTATTATTTATTATT
2556482 T
1 T
2556483 AGTTGGTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTATTTATTATTTATTATT
Found at i:2557657 original size:12 final size:12
Alignment explanation
Indices: 2557640--2557664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2557630 TACTAACAAC
2557640 TTGGAAAATTAA
1 TTGGAAAATTAA
2557652 TTGGAAAATTAA
1 TTGGAAAATTAA
2557664 T
1 T
2557665 GATAAATTCA
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TTGGAAAATTAA
Found at i:2559362 original size:44 final size:45
Alignment explanation
Indices: 2559284--2559374 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 45
2559274 AAAAAGCATA
* * *
2559284 ATACCTTATCATCTAAGTCATCTTCTTCTGTTTTAGATCTATTTC
1 ATACCTCATCATCTAAGTCATCATCTTCTATTTTAGATCTATTTC
*
2559329 ATACCTCATCATC-AAGTCATCATCTTTTATTTTAGATCTATTTC
1 ATACCTCATCATCTAAGTCATCATCTTCTATTTTAGATCTATTTC
2559373 AT
1 AT
2559375 TTAGATTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 30 0.71
45 12 0.29
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.47
Consensus pattern (45 bp):
ATACCTCATCATCTAAGTCATCATCTTCTATTTTAGATCTATTTC
Found at i:2566784 original size:13 final size:13
Alignment explanation
Indices: 2566749--2566796 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
2566739 AATAAGGTAA
*
2566749 TTAAAAAATAATTT
1 TTAAAAAA-AAATT
* *
2566763 TTTATAAAAAATT
1 TTAAAAAAAAATT
2566776 TTAAAAAAAAATT
1 TTAAAAAAAAATT
2566789 TTAAAAAA
1 TTAAAAAA
2566797 TATATGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAAAAAATT
Found at i:2567447 original size:26 final size:25
Alignment explanation
Indices: 2567411--2567459 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2567401 AATAAAGTAC
2567411 TTTTAGATTTTAAATTTTTTAAAAGT
1 TTTTAGATTTT-AATTTTTTAAAAGT
* *
2567437 TTTTATATTTTTATTTTTTAAAA
1 TTTTAGATTTTAATTTTTTAAAA
2567460 AACCCACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTAGATTTTAATTTTTTAAAAGT
Found at i:2567829 original size:20 final size:21
Alignment explanation
Indices: 2567775--2567828 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2567765 TAAATGTCTC
2567775 AAAATTATTTTTTAAACATTT
1 AAAATTATTTTTTAAACATTT
*
2567796 AAAATTATTTTTTAATA-TTTT
1 AAAATTATTTTTTAA-ACATTT
2567817 AAAATTATTTTT
1 AAAATTATTTTT
2567829 ATGACTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AAAATTATTTTTTAAACATTT
Found at i:2567837 original size:21 final size:20
Alignment explanation
Indices: 2567775--2567837 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
2567765 TAAATGTCTC
* *
2567775 AAAATTATTTTTTAAACATTT
1 AAAATTA-TTTTTATACTTTT
2567796 AAAATTATTTTTTAATA-TTTT
1 AAAATTA-TTTTT-ATACTTTT
2567817 AAAATTATTTTTATGACTTTT
1 AAAATTATTTTTAT-ACTTTT
2567838 TTATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 27 0.73
22 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (20 bp):
AAAATTATTTTTATACTTTT
Found at i:2570414 original size:28 final size:28
Alignment explanation
Indices: 2570356--2570414 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2570346 GATTTGCTTT
* *
2570356 GATTGTTTTCACTTATGGAGTCTGCTCG
1 GATTGTTTTCACTTATGGAATCTGATCG
**
2570384 GATTGTTTTCGTTTATGGAATCTAGAT-G
1 GATTGTTTTCACTTATGGAATCT-GATCG
2570412 GAT
1 GAT
2570415 AGAAATAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (28 bp):
GATTGTTTTCACTTATGGAATCTGATCG
Found at i:2570555 original size:19 final size:19
Alignment explanation
Indices: 2570531--2570569 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2570521 ATCTTTTTGT
*
2570531 AATAATTGCAATCTTGATG
1 AATAATTACAATCTTGATG
2570550 AATAATTACAATCTTGATG
1 AATAATTACAATCTTGATG
2570569 A
1 A
2570570 GTCAATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
AATAATTACAATCTTGATG
Found at i:2570602 original size:3 final size:3
Alignment explanation
Indices: 2570594--2570630 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2570584 AACTTATCTC
2570594 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2570631 CTGTATAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2574550 original size:19 final size:19
Alignment explanation
Indices: 2574514--2574551 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2574504 TTTAATAAAA
*
2574514 TTAATTTAATTTTTATTAT
1 TTAATTTAATTTTAATTAT
2574533 TTAATTTTAA-TTTAATTAT
1 TTAA-TTTAATTTTAATTAT
2574552 ATATTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAATTTAATTTTAATTAT
Found at i:2574611 original size:18 final size:18
Alignment explanation
Indices: 2574581--2574629 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2574571 ACCTAAAATT
*
2574581 AATATA-TATAAATAATAT
1 AATATATTA-AAATAATAA
2574599 AATA-ATTTAAAATAATAA
1 AATATA-TTAAAATAATAA
2574617 AATATATTAAAAT
1 AATATATTAAAAT
2574630 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 23 0.85
19 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATATTAAAATAATAA
Found at i:2574616 original size:25 final size:26
Alignment explanation
Indices: 2574581--2574636 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 26
2574571 ACCTAAAATT
2574581 AATATATATAAATA-ATATAATAATTTAA
1 AATATATA-AAATATAT-TAA-AATTTAA
2574609 AATA-ATAAAATATATTAAAATTTAA
1 AATATATAAAATATATTAAAATTTAA
2574634 AAT
1 AAT
2574637 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 10 0.37
26 8 0.30
27 5 0.19
28 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATATAAAATATATTAAAATTTAA
Found at i:2586919 original size:17 final size:16
Alignment explanation
Indices: 2586884--2586934 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
2586874 ATGAGTTTCT
*
2586884 AAAAATAAATTTTCA-
1 AAAAATAAATTTTTAG
2586899 AAAAATCAAACTTTTT-G
1 AAAAAT-AAA-TTTTTAG
2586916 AAAAATAAATTTTTAG
1 AAAAATAAATTTTTAG
2586932 AAA
1 AAA
2586935 GTCACCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 11 0.35
16 10 0.32
17 10 0.32
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (16 bp):
AAAAATAAATTTTTAG
Found at i:2586929 original size:16 final size:15
Alignment explanation
Indices: 2586884--2586934 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
2586874 ATGAGTTTCT
2586884 AAAAATAAATTTTCA-
1 AAAAATAAATTTT-AG
*
2586899 AAAAATCAAACTTTTTG
1 AAAAAT-AAA-TTTTAG
2586916 AAAAATAAATTTTTAG
1 AAAAATAAA-TTTTAG
2586932 AAA
1 AAA
2586935 GTCACCCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 6 0.20
16 14 0.47
17 10 0.33
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (15 bp):
AAAAATAAATTTTAG
Found at i:2587599 original size:33 final size:34
Alignment explanation
Indices: 2587543--2587629 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
2587533 ATATAACTTG
* * *
2587543 TCAAAAATCTATTTTCAATAAAATT-TATG-ATTT
1 TCAAAAATTTATTTCCAA-AAAATTACATGAATTT
*
2587576 TCTAGAAATTTATTTCCAAAAAATTACATGAATTT
1 TC-AAAAATTTATTTCCAAAAAATTACATGAATTT
*
2587611 TCAAAAATTCATTTCCAAA
1 TCAAAAATTTATTTCCAAA
2587630 GTTATAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
33 8 0.18
34 31 0.69
35 6 0.13
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (34 bp):
TCAAAAATTTATTTCCAAAAAATTACATGAATTT
Found at i:2587807 original size:29 final size:29
Alignment explanation
Indices: 2587742--2587812 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2587732 TTAGTCCCTC
2587742 TCTAAACTTTTAATATTTTATTACAATCAA
1 TCTAAA-TTTTAATATTTTATTACAATCAA
* * * *
2587772 TCAAAATTTTAATTTTTTATTTCGATTCAA
1 TCTAAATTTTAATATTTTATTAC-AATCAA
2587802 T-TAAATTTTAA
1 TCTAAATTTTAA
2587813 ATGGATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (29 bp):
TCTAAATTTTAATATTTTATTACAATCAA
Found at i:2593202 original size:30 final size:30
Alignment explanation
Indices: 2593166--2593226 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2593156 AGAATGAATC
*
2593166 TGCTGTATCAAGACCAAGCAAACATATAAG
1 TGCTGTATAAAGACCAAGCAAACATATAAG
*
2593196 TGCTGTATAAAGACCAAGCAAACTTATAAG
1 TGCTGTATAAAGACCAAGCAAACATATAAG
2593226 T
1 T
2593227 ACAAAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (30 bp):
TGCTGTATAAAGACCAAGCAAACATATAAG
Found at i:2595009 original size:34 final size:34
Alignment explanation
Indices: 2594775--2595017 Score: 95
Period size: 34 Copynumber: 7.2 Consensus size: 34
2594765 TTTAAAATAG
* * * * **
2594775 ATTTTTGAGAATAGACTGTAATTCTTGGAAATGG
1 ATTTTTGAGAATACATTGTAATTCTCGAAAATTC
* * * *
2594809 ACTTTTGAGAATACAATGTAATTTTTGAAAA-T-
1 ATTTTTGAGAATACATTGTAATTCTCGAAAATTC
* * * * * ***
2594841 ATGTTTTCAAGAAAACATTATACTTCTCGATAACAA
1 AT-TTTT-GAGAATACATTGTAATTCTCGAAAATTC
* * * *
2594877 ATTTTCGAGTATACAATGTAATTGTCGAAAATTC
1 ATTTTTGAGAATACATTGTAATTCTCGAAAATTC
* * * *
2594911 ATTTTCGAGAAT-TATTTTGCATTCT--AAAATTTC
1 ATTTTTGAGAATACATTGT-AATTCTCGAAAA-TTC
* ** * **
2594944 ATTTCT-AGAAATACATCATAATTTTTAAAAATTC
1 ATTTTTGAG-AATACATTGTAATTCTCGAAAATTC
2594978 ATTTTTGAGAATACATTGTAATTCTCGAAAA-TC
1 ATTTTTGAGAATACATTGTAATTCTCGAAAATTC
2595011 TATTTTT
1 -ATTTTT
2595018 AAGATTTATG
Statistics
Matches: 150, Mismatches: 47, Indels: 24
0.68 0.21 0.11
Matches are distributed among these distances:
32 7 0.05
33 23 0.15
34 109 0.73
35 9 0.06
36 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (34 bp):
ATTTTTGAGAATACATTGTAATTCTCGAAAATTC
Found at i:2601982 original size:21 final size:21
Alignment explanation
Indices: 2601954--2602012 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
2601944 TTTTCTTTCC
*
2601954 TTTTT-TTTAATTTTTTA-TA
1 TTTTTATTTTATTTTTTATTA
**
2601973 TTTTTATTTTCCTTTTTATTA
1 TTTTTATTTTATTTTTTATTA
2601994 TTTTTATTATTTATTTTTT
1 TTTTTA-T-TTTATTTTTT
2602013 TACTTACCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 8 0.26
22 1 0.03
23 8 0.26
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTATTTTATTTTTTATTA
Found at i:2601984 original size:31 final size:28
Alignment explanation
Indices: 2601949--2602010 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
2601939 ATAGGTTTTC
* *
2601949 TTTCCTTTTTTTTAATTTTTTATATTTTTAT
1 TTTCCTTTTTATT-A-TTTTTAT-TATTTAT
2601980 TTTCCTTTTTATTATTTTTATTATTTAT
1 TTTCCTTTTTATTATTTTTATTATTTAT
2602008 TTT
1 TTT
2602011 TTTACTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.31
29 7 0.24
30 1 0.03
31 12 0.41
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTCCTTTTTATTATTTTTATTATTTAT
Found at i:2601997 original size:28 final size:28
Alignment explanation
Indices: 2601957--2602010 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
2601947 TCTTTCCTTT
2601957 TTTTTAATTTTTTATATT-TTTATTTTCC
1 TTTTTAATTTTTT-TATTATTTATTTTCC
2601985 TTTTT-ATTATTTTTATTATTTATTTT
1 TTTTTAATT-TTTTTATTATTTATTTT
2602011 TTTACTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTAATTTTTTTATTATTTATTTTCC
Found at i:2602185 original size:11 final size:10
Alignment explanation
Indices: 2602169--2602221 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
2602159 CAATTTTTTC
2602169 TTAAAATAAAT
1 TTAAAA-AAAT
*
2602180 TTAAAAATAT
1 TTAAAAAAAT
*
2602190 TTAGAAAAAT
1 TTAAAAAAAT
*
2602200 GTTATAAAAAT
1 -TTAAAAAAAT
2602211 TTAATAAAAAT
1 TTAA-AAAAAT
2602222 ATAATTGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 14 0.40
11 21 0.60
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:2602196 original size:49 final size:48
Alignment explanation
Indices: 2602072--2602198 Score: 155
Period size: 49 Copynumber: 2.6 Consensus size: 48
2602062 ATGAAAATTG
* *
2602072 AAAATAATTTTGAAAATGTTTAGGAAAAAATAAAATATCAATTTTTTCT
1 AAAATAAATTTGAAAATATTTA-GAAAAAATAAAATATCAATTTTTTCT
* ** * *
2602121 AAAAAAAATTTGAAAACCTTTAAGAAAAACTTAAATATCAATTTTTTCTT
1 AAAATAAATTTGAAAATATTT-AGAAAAAATAAAATATCAATTTTTTC-T
*
2602171 AAAATAAATTTAAAAATATTTAGAAAAA
1 AAAATAAATTTGAAAATATTTAGAAAAA
2602199 TGTTATAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
49 47 0.71
50 19 0.29
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (48 bp):
AAAATAAATTTGAAAATATTTAGAAAAAATAAAATATCAATTTTTTCT
Found at i:2602271 original size:14 final size:14
Alignment explanation
Indices: 2602261--2602287 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2602251 CCATAAAATT
2602261 AATATTTTAAAAAC
1 AATATTTTAAAAAC
2602275 AATATTTTAAAAA
1 AATATTTTAAAAA
2602288 AAAATTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATTTTAAAAAC
Found at i:2602715 original size:14 final size:14
Alignment explanation
Indices: 2602693--2602728 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2602683 CAGTCATAGG
2602693 AAGAAACTTAGTAA
1 AAGAAACTTAGTAA
*
2602707 AAGAGACTTAGTAA
1 AAGAAACTTAGTAA
2602721 AAGAAACT
1 AAGAAACT
2602729 ATGAANNNNN
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (14 bp):
AAGAAACTTAGTAA
Found at i:2614003 original size:23 final size:25
Alignment explanation
Indices: 2613975--2614022 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2613965 ATTAAAATAA
*
2613975 TAAAA-TTA-ATTTTTTATTAATTT
1 TAAAATTTAGATTTTTTAATAATTT
2613998 TAAAATTTATGATTTTTTAATAATT
1 TAAAATTTA-GATTTTTTAATAATT
2614023 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
26 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TAAAATTTAGATTTTTTAATAATTT
Found at i:2614135 original size:34 final size:33
Alignment explanation
Indices: 2614097--2614178 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 33
2614087 TTTAAAATGG
2614097 ATTTTCAGAAAATCTTATAACTTTCCGA-AAATCT
1 ATTTTCAGAAAAT-TTATAA-TTTCCGAGAAATCT
* * * * *
2614131 ATTTTCAATAAAATTTATGATTTTCTAGAAATTT
1 ATTTTC-AGAAAATTTATAATTTCCGAGAAATCT
2614165 ATTTTCAGAAAATT
1 ATTTTCAGAAAATT
2614179 ACATGAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
33 12 0.30
34 22 0.55
35 6 0.15
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (33 bp):
ATTTTCAGAAAATTTATAATTTCCGAGAAATCT
Found at i:2614197 original size:34 final size:34
Alignment explanation
Indices: 2614124--2614202 Score: 81
Period size: 34 Copynumber: 2.3 Consensus size: 34
2614114 TAACTTTCCG
* * *
2614124 AAAATCTATTTTCAATAAAATTTATGATTTTCTA
1 AAAATTTATTTTCAAGAAAATTCATGATTTTCTA
*
2614158 GAAATTTATTTTC-AGAAAATTACATGAATTTTC-A
1 AAAATTTATTTTCAAGAAAATT-CATG-ATTTTCTA
*
2614192 AAAATTCATTT
1 AAAATTTATTT
2614203 CCAAAGTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
33 7 0.19
34 24 0.65
35 6 0.16
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (34 bp):
AAAATTTATTTTCAAGAAAATTCATGATTTTCTA
Found at i:2614385 original size:29 final size:29
Alignment explanation
Indices: 2614320--2614390 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2614310 TTAATCCCTC
2614320 TCTAAACTTTTAATATTTTATTACAATCAA
1 TCTAAA-TTTTAATATTTTATTACAATCAA
* * * *
2614350 TCAAAATTTTAATTTTTTATTTCGATTCAA
1 TCTAAATTTTAATATTTTATTAC-AATCAA
2614380 T-TAAATTTTAA
1 TCTAAATTTTAA
2614391 ATGGATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (29 bp):
TCTAAATTTTAATATTTTATTACAATCAA
Found at i:2615430 original size:1 final size:1
Alignment explanation
Indices: 2615424--2615451 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2615414 AATTTCAGGG
2615424 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2615452 AATAATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2619782 original size:30 final size:30
Alignment explanation
Indices: 2619746--2619806 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2619736 AGAATGAATC
*
2619746 TGCTGTATCAAGACCAAGCAAACATATAAG
1 TGCTGTATAAAGACCAAGCAAACATATAAG
*
2619776 TGCTGTATAAAGACCAAGCAAACTTATAAG
1 TGCTGTATAAAGACCAAGCAAACATATAAG
2619806 T
1 T
2619807 ACAAAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (30 bp):
TGCTGTATAAAGACCAAGCAAACATATAAG
Found at i:2621496 original size:34 final size:34
Alignment explanation
Indices: 2621458--2621534 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
2621448 TCGATAACAA
2621458 ATTTTCAAGTATACAATGTAATTGTCGAAAATCC
1 ATTTTCAAGTATACAATGTAATTGTCGAAAATCC
* *
2621492 ATTTTCGAGTATACAATGTAATTGTCGAAAATTC
1 ATTTTCAAGTATACAATGTAATTGTCGAAAATCC
2621526 ATTTTCAAG
1 ATTTTCAAG
2621535 AATTATTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (34 bp):
ATTTTCAAGTATACAATGTAATTGTCGAAAATCC
Found at i:2628545 original size:21 final size:22
Alignment explanation
Indices: 2628521--2628581 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
2628511 TTTTCTTTCC
2628521 TTTTTTTTTAATTTTTTA-TAT
1 TTTTTTTTTAATTTTTTATTAT
* **
2628542 TTTTGTTTT-CCTTTTTATTAT
1 TTTTTTTTTAATTTTTTATTAT
*
2628563 TTTTATTATTTATTTTTTT
1 TTTT-TT-TTTAATTTTTT
2628582 TACTTACCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 6 0.20
21 15 0.50
22 1 0.03
23 3 0.10
24 5 0.17
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTAATTTTTTATTAT
Found at i:2628579 original size:29 final size:28
Alignment explanation
Indices: 2628525--2628580 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
2628515 CTTTCCTTTT
*
2628525 TTTTTAATTTTTTATATTTTTGTTTTCC
1 TTTTTAATTTTTTATATTTATGTTTTCC
* *
2628553 TTTTTATTATTTTTATTATTTATTTTTT
1 TTTTTAAT-TTTTTA-TATTTATGTTTT
2628581 TTACTTACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 6 0.26
30 10 0.43
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (28 bp):
TTTTTAATTTTTTATATTTATGTTTTCC
Found at i:2628715 original size:26 final size:25
Alignment explanation
Indices: 2628640--2628721 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
2628630 AATGAAATTG
*
2628640 AAAATAATTTTGAAAATGTTTAGGAA
1 AAAATAAATTTGAAAAT-TTTAGGAA
* *
2628666 AAAATAAA-AT-ATCAATTTTA--AA
1 AAAATAAATTTGA-AAATTTTAGGAA
2628688 AAAATAAATTTGAAAATATTTAGGAA
1 AAAATAAATTTGAAAAT-TTTAGGAA
2628714 AAAATAAA
1 AAAATAAA
2628722 ATATCAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 10 0.22
23 4 0.09
24 10 0.22
25 4 0.09
26 17 0.38
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (25 bp):
AAAATAAATTTGAAAATTTTAGGAA
Found at i:2628764 original size:49 final size:50
Alignment explanation
Indices: 2628640--2628814 Score: 214
Period size: 49 Copynumber: 3.6 Consensus size: 50
2628630 AATGAAATTG
* * **
2628640 AAAATAATTTTGAAAATGTTTAGGAAAAAATAAAATATCAA--TTTTAAA
1 AAAATAAATTTGAAAATATTTAGGAAAAAATAAAATATCAATTTTTTCTA
2628688 AAAATAAATTTGAAAATATTTAGGAAAAAATAAAATATCAATTTTTTCTA
1 AAAATAAATTTGAAAATATTTAGGAAAAAATAAAATATCAATTTTTTCTA
* ** * * * *
2628738 AAAA-AACTTTGAAAACCTTTAAGAAAAACTTAAATATCAATTTTTTCTT
1 AAAATAAATTTGAAAATATTTAGGAAAAAATAAAATATCAATTTTTTCTA
*
2628787 AAAATAAATTTAAAAATATTTA-GAAAAA
1 AAAATAAATTTGAAAATATTTAGGAAAAA
2628815 TGTTATAAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
48 39 0.36
49 48 0.44
50 22 0.20
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (50 bp):
AAAATAAATTTGAAAATATTTAGGAAAAAATAAAATATCAATTTTTTCTA
Found at i:2629330 original size:14 final size:14
Alignment explanation
Indices: 2629311--2629339 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2629301 TCATAGGAAA
2629311 AGACTTAGTAAAAG
1 AGACTTAGTAAAAG
2629325 AGACTTAGTAAAAG
1 AGACTTAGTAAAAG
2629339 A
1 A
2629340 AACTATGAAA
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:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AGACTTAGTAAAAG
Found at i:2639234 original size:575 final size:574
Alignment explanation
Indices: 2638144--2639285 Score: 2034
Period size: 575 Copynumber: 2.0 Consensus size: 574
2638134 TGTAAATGAC
*
2638144 ACATTAGTACTCGTAAATTACTCAGGTTCAATTCGAATAAAATTCGAATTCGACTCAATTATTAT
1 ACATTAGTACTCGCAAATTACTCAGGTTCAATTCGAATAAAATTCGAATTCGACTCAATTATTAT
* *
2638209 TGAGTCGAGCTTGAGCTCAAGTAGTTGACTCATCGATTGAGCTGAGTTCAAACACTCTTATATCC
66 TGAGTCGAGCTTGAGCTCAAATAGTCGACTCATCGATTGAGCTGAGTTCAAACACTCTTATATCC
*
2638274 GGCTCGAGTAGCTCACGAGCCTAATCAAGTTTTTATATTTAAATATATTTTTATTATTTTAATTA
131 GGCTCGAGTAGCTCACGAGCCTAATCAAGTTTTTATATTTAAATATACTTTTATTATTTTAATTA
*
2638339 ATAAAATATCTCGAGCTCAAGCTCGAGCACAAATAATTAAACTTTTATCAAATATAAGAATCGAG
196 ATAAAATATCTCGAGCTCAAGCTCGAGCACAAATAATCAAACTTTTATCAAATATAAGAATCGAG
* * *
2638404 CTTATTTTTACATATTAATTGAGCCTAATCGAGTGATCTCGAGTAACTTAATTGCTAAGTTATCC
261 CTTATTTTTACATATTAATTGAGCCTAATCGAGTGAGCACGAGTAACTTAATTACTAAGTTATCC
*
2638469 CCTAAATACAAAACGAGAAAACTTTTATATTAAGTTATAGATATGTATATAATATAATATTCATT
326 CCTAAATACAAAACGAGAAAACTTTAATATTAAGTTATAGATATGTATATAATATAATATTCATT
* *
2638534 AAATATAATGTAATCTATAATTTAGTCTTTGTTACATTTGTGGTCAAGCAACTAGAAACTATCAT
391 AAATATAACGTAATCTATAATTTAGTCTTTGCTACATTTGTGGTCAAGCAACTAGAAACTATCAT
* *
2638599 AATTTGAATTCATACAATCATTCGAGTAGTGATTTATTTAAAGTTAAAATCTTAATATCTGTAAT
456 AATCTGAATTCATACAATCATTCAAGTAGTGATTTATTTAAAGTTAAAATCTTAATATCTGTAAT
*
2638664 TTTTTTATCCTAAAGCTCACAACCTCCTTTGTTAAAAAAAAAAAAAACTAAGAT
521 TTTTTTATCCCAAAGCTCACAACCTCCTTTGTTAAAAAAAAAAAAAACTAAGAT
*
2638718 ACATTAGTACTCGCAAATTACTC-GGATTCAATTCGAATAAAATTCGAATTCGACTTAATTATTA
1 ACATTAGTACTCGCAAATTACTCAGG-TTCAATTCGAATAAAATTCGAATTCGACTCAATTATTA
*
2638782 TTGAGTCGAGCTTGAGCTCAAATAGCTCGACTCATCTATTGAGCTGAGTTCAAACACTCTTATAT
65 TTGAGTCGAGCTTGAGCTCAAATAG-TCGACTCATCGATTGAGCTGAGTTCAAACACTCTTATAT
* *
2638847 CCGGTTCGAGTAGCTCGCGAGCCTAATCAAGTTTTTATATTTAAATATACTTTTATTATTTTAAT
129 CCGGCTCGAGTAGCTCACGAGCCTAATCAAGTTTTTATATTTAAATATACTTTTATTATTTTAAT
* * *
2638912 TAATAAAATATCTCGAGCTCAAGCTCGAGCATAAATAATCAAACTTTTGTCAAATATAATAATCG
194 TAATAAAATATCTCGAGCTCAAGCTCGAGCACAAATAATCAAACTTTTATCAAATATAAGAATCG
*
2638977 AGCTTATTTTTACATATTAATTGAGCCTAATCGAGTGAGCACGAGTAATTTAATTACTAAGTTAT
259 AGCTTATTTTTACATATTAATTGAGCCTAATCGAGTGAGCACGAGTAACTTAATTACTAAGTTAT
* *
2639042 CCCCTAAATACAAAATGAGATAACTTTAATATTAAGTTATAGATATGTATATAATATAATATTCA
324 CCCCTAAATACAAAACGAGAAAACTTTAATATTAAGTTATAGATATGTATATAATATAATATTCA
2639107 TTAAATATAACGTAATCTATAATTTAGTCTTTGCTACATTTGTGGTCAAGCAACTAGAAACTATC
389 TTAAATATAACGTAATCTATAATTTAGTCTTTGCTACATTTGTGGTCAAGCAACTAGAAACTATC
*
2639172 ATAATCTGAATTCGTACAATCATTCAAGTAGTGATTTATTTAAAGTTAAAATCTTAATATCTGTA
454 ATAATCTGAATTCATACAATCATTCAAGTAGTGATTTATTTAAAGTTAAAATCTTAATATCTGTA
2639237 ATTTTTTTATCCCAAAGCTCACAACCTCCTTTGTTAAAAAAAAAAAAAA
519 ATTTTTTTATCCCAAAGCTCACAACCTCCTTTGTTAAAAAAAAAAAAAA
2639286 AAACTAAAAA
Statistics
Matches: 541, Mismatches: 25, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
573 2 0.00
574 83 0.15
575 456 0.84
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (574 bp):
ACATTAGTACTCGCAAATTACTCAGGTTCAATTCGAATAAAATTCGAATTCGACTCAATTATTAT
TGAGTCGAGCTTGAGCTCAAATAGTCGACTCATCGATTGAGCTGAGTTCAAACACTCTTATATCC
GGCTCGAGTAGCTCACGAGCCTAATCAAGTTTTTATATTTAAATATACTTTTATTATTTTAATTA
ATAAAATATCTCGAGCTCAAGCTCGAGCACAAATAATCAAACTTTTATCAAATATAAGAATCGAG
CTTATTTTTACATATTAATTGAGCCTAATCGAGTGAGCACGAGTAACTTAATTACTAAGTTATCC
CCTAAATACAAAACGAGAAAACTTTAATATTAAGTTATAGATATGTATATAATATAATATTCATT
AAATATAACGTAATCTATAATTTAGTCTTTGCTACATTTGTGGTCAAGCAACTAGAAACTATCAT
AATCTGAATTCATACAATCATTCAAGTAGTGATTTATTTAAAGTTAAAATCTTAATATCTGTAAT
TTTTTTATCCCAAAGCTCACAACCTCCTTTGTTAAAAAAAAAAAAAACTAAGAT
Found at i:2654925 original size:16 final size:16
Alignment explanation
Indices: 2654906--2654966 Score: 74
Period size: 15 Copynumber: 3.9 Consensus size: 16
2654896 GATTACGATA
2654906 ATTTTGAATTCAAATT
1 ATTTTGAATTCAAATT
* *
2654922 ATTTTAAATT-TAATT
1 ATTTTGAATTCAAATT
2654937 ATTTTG-ATTC-AATT
1 ATTTTGAATTCAAATT
2654951 AATTTTGAATTCAAAT
1 -ATTTTGAATTCAAAT
2654967 AATTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.18
15 15 0.39
16 13 0.34
17 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (16 bp):
ATTTTGAATTCAAATT
Found at i:2654969 original size:16 final size:16
Alignment explanation
Indices: 2654903--2654970 Score: 77
Period size: 16 Copynumber: 4.4 Consensus size: 16
2654893 TATGATTACG
2654903 ATAATTTTGAATTCAA
1 ATAATTTTGAATTCAA
* * *
2654919 ATTATTTTAAATT-TA
1 ATAATTTTGAATTCAA
*
2654934 ATTATTTTG-ATTCAA
1 ATAATTTTGAATTCAA
*
2654949 TTAATTTTGAATTCAA
1 ATAATTTTGAATTCAA
2654965 ATAATT
1 ATAATT
2654971 AAAATTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 3 0.07
15 17 0.40
16 22 0.52
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (16 bp):
ATAATTTTGAATTCAA
Found at i:2658671 original size:29 final size:29
Alignment explanation
Indices: 2658638--2658696 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2658628 GAAAGAGCAA
*
2658638 AAAAATGG-AAAAAGAAAAGAGAGAAAGAG
1 AAAAATGGTAAAAA-AAAACAGAGAAAGAG
*
2658667 AAAAATGGTAAAAAAGAACAGAGAAAGAG
1 AAAAATGGTAAAAAAAAACAGAGAAAGAG
2658696 A
1 A
2658697 TAACGAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (29 bp):
AAAAATGGTAAAAAAAAACAGAGAAAGAG
Found at i:2658671 original size:31 final size:30
Alignment explanation
Indices: 2658628--2658696 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2658618 AAATAAATTT
*
2658628 GAAAGAGCAAAAAAATGG-AAAAAGAAAAGAGA
1 GAAAGAG--AAAAAATGGTAAAAA-AAAACAGA
*
2658660 GAAAGAG-AAAAATGGTAAAAAAGAACAGA
1 GAAAGAGAAAAAATGGTAAAAAAAAACAGA
2658689 GAAAGAGA
1 GAAAGAGA
2658697 TAACGAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 21 0.64
30 5 0.15
32 7 0.21
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.04
Consensus pattern (30 bp):
GAAAGAGAAAAAATGGTAAAAAAAAACAGA
Found at i:2660925 original size:14 final size:14
Alignment explanation
Indices: 2660893--2660936 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2660883 GATCCTGAGG
*
2660893 TTTT-ATTTTTGTT
1 TTTTAATTTTTGCT
2660906 TGTTTAATTTTTGCT
1 T-TTTAATTTTTGCT
*
2660921 TTTTAATCTTTGCT
1 TTTTAATTTTTGCT
2660935 TT
1 TT
2660937 CACTATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 1 0.04
14 17 0.63
15 9 0.33
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (14 bp):
TTTTAATTTTTGCT
Found at i:2661010 original size:15 final size:16
Alignment explanation
Indices: 2660990--2661019 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2660980 GTTATAAAGC
2660990 TTTTA-TATATTTAGG
1 TTTTATTATATTTAGG
2661005 TTTTATTATATTTAG
1 TTTTATTATATTTAG
2661020 TGGTAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
TTTTATTATATTTAGG
Found at i:2664625 original size:31 final size:32
Alignment explanation
Indices: 2664582--2664644 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
2664572 ATTATTTAAA
2664582 GCCTATTTTTTTTCCATTAAGAAGGCTTTCTT
1 GCCTATTTTTTTTCCATTAAGAAGGCTTTCTT
* *
2664614 GCCT-TTTTTTTTCCTTTAAGAAGGTTTTCTT
1 GCCTATTTTTTTTCCATTAAGAAGGCTTTCTT
2664645 TTGATGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.16, C:0.17, G:0.13, T:0.54
Consensus pattern (32 bp):
GCCTATTTTTTTTCCATTAAGAAGGCTTTCTT
Found at i:2664979 original size:68 final size:68
Alignment explanation
Indices: 2664832--2664958 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 68
2664822 GCAATACACT
* *
2664832 AATGAATAGGATGTTTATAAAATTATTTTGGCTGGTATATAAGTGAATGATTACCTTTTGTATAT
1 AATGAATAAGATGTTTATAAAATTATTTTGGCTGGTATATAAGTGAATGATTACCTTCTGTATAT
2664897 ATG
66 ATG
2664900 AATGAATAAGATGTTTATAAAATTATTTCT-GCTAGG-ATATGAA-TGAATGATTACCTTCT
1 AATGAATAAGATGTTTATAAAATTATTT-TGGCT-GGTATAT-AAGTGAATGATTACCTTCT
2664959 TACTTTTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
68 49 0.91
69 5 0.09
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.41
Consensus pattern (68 bp):
AATGAATAAGATGTTTATAAAATTATTTTGGCTGGTATATAAGTGAATGATTACCTTCTGTATAT
ATG
Found at i:2665145 original size:15 final size:15
Alignment explanation
Indices: 2665122--2665151 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2665112 AGATATTCAA
2665122 TGATATTTGTTTTAT
1 TGATATTTGTTTTAT
*
2665137 TGATGTTTGTTTTAT
1 TGATATTTGTTTTAT
2665152 CATACTTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (15 bp):
TGATATTTGTTTTAT
Found at i:2665324 original size:24 final size:24
Alignment explanation
Indices: 2665284--2665330 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2665274 AAAATATATC
* *
2665284 ATATTATGATTATAAATA-AATTA
1 ATATTATAATTAAAAATATAATTA
2665307 ATATTAATAATTAAAAATATAATT
1 ATATT-ATAATTAAAAATATAATT
2665331 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATTATAATTAAAAATATAATTA
Found at i:2665558 original size:49 final size:49
Alignment explanation
Indices: 2665495--2665604 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 49
2665485 GTAAAAAAAT
* * *
2665495 TAAAAAATAAAAGTCTAAACTGACAAATGTTAAACATTGGTATAGGTAA
1 TAAAAATTAAAAGTCTAAACTGACAAACGTTAAACATTGATATAGGTAA
* * *** *
2665544 TAAAAATTACAAGTCTATACTGATGGACGTTAATCATTGATATAGGTAA
1 TAAAAATTAAAAGTCTAAACTGACAAACGTTAAACATTGATATAGGTAA
*
2665593 AAAAAATTAAAA
1 TAAAAATTAAAA
2665605 CATATAAGTC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (49 bp):
TAAAAATTAAAAGTCTAAACTGACAAACGTTAAACATTGATATAGGTAA
Found at i:2665604 original size:56 final size:56
Alignment explanation
Indices: 2665544--2665709 Score: 168
Period size: 56 Copynumber: 3.1 Consensus size: 56
2665534 GTATAGGTAA
*
2665544 TAAAAATTACAAGTCTATACTGATGGACGTTAATCATTGATATAGGTAAAAAAAAT
1 TAAAAATTACAAGTCTATACTGATGGACGTTAATCATTGGTATAGGTAAAAAAAAT
* ** * *
2665600 TAAAACA-TATAAGTCTATACTGATGGGTGCTAATCATTGGTATAAGT------AA-
1 TAAAA-ATTACAAGTCTATACTGATGGACGTTAATCATTGGTATAGGTAAAAAAAAT
* * * * *
2665649 GAAAAATTACAAGTTTATACTGACGGACGTTAACCGTTGGTATAGGTAAAAAAAAT
1 TAAAAATTACAAGTCTATACTGATGGACGTTAATCATTGGTATAGGTAAAAAAAAT
2665705 TAAAA
1 TAAAA
2665710 CATATAAATT
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
48 1 0.01
49 35 0.42
50 2 0.02
55 2 0.02
56 43 0.51
57 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.30
Consensus pattern (56 bp):
TAAAAATTACAAGTCTATACTGATGGACGTTAATCATTGGTATAGGTAAAAAAAAT
Found at i:2665739 original size:105 final size:105
Alignment explanation
Indices: 2665472--2665739 Score: 333
Period size: 105 Copynumber: 2.6 Consensus size: 105
2665462 AATAGTCTTT
* * * * *
2665472 ACCATCGATATAGGT-AAAAAAATTAAAAAATA-AAAGTCTAAACTGACAAATGTTAAACATTGG
1 ACCATTGATATAGGTAAAAAAAATTAAAACATATAAA-TCTATACTGACAAGTGTTAATCATTGG
* * *
2665535 TATAGGTAATAAAAATTACAAGTCTATACTGATGGACGTTA
65 TATAAGTAAGAAAAATTACAAGTCTATACTGACGGACGTTA
* * *** *
2665576 ATCATTGATATAGGTAAAAAAAATTAAAACATATAAGTCTATACTGATGGGTGCTAATCATTGGT
1 ACCATTGATATAGGTAAAAAAAATTAAAACATATAAATCTATACTGACAAGTGTTAATCATTGGT
*
2665641 ATAAGTAAGAAAAATTACAAGTTTATACTGACGGACGTTA
66 ATAAGTAAGAAAAATTACAAGTCTATACTGACGGACGTTA
* * * **
2665681 ACCGTTGGTATAGGTAAAAAAAATTAAAACATATAAATTTATACCAACAAGTGTTAATC
1 ACCATTGATATAGGTAAAAAAAATTAAAACATATAAATCTATACTGACAAGTGTTAATC
2665740 GTCGACAAAA
Statistics
Matches: 136, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
104 13 0.10
105 121 0.89
106 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (105 bp):
ACCATTGATATAGGTAAAAAAAATTAAAACATATAAATCTATACTGACAAGTGTTAATCATTGGT
ATAAGTAAGAAAAATTACAAGTCTATACTGACGGACGTTA
Found at i:2665970 original size:20 final size:21
Alignment explanation
Indices: 2665935--2665974 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2665925 TTTATTGTGC
*
2665935 TATATTGATGAATTTTTTAGT
1 TATATCGATGAATTTTTTAGT
2665956 TATATCGAT-AATTTTTTAG
1 TATATCGATGAATTTTTTAG
2665975 CATCAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (21 bp):
TATATCGATGAATTTTTTAGT
Found at i:2668192 original size:11 final size:11
Alignment explanation
Indices: 2668176--2668216 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2668166 TCTATGCTAA
2668176 TAAAAAACAAT
1 TAAAAAACAAT
**
2668187 TAAAAAACCTT
1 TAAAAAACAAT
2668198 TAAAAAAACAAT
1 T-AAAAAACAAT
2668210 TAAAAAA
1 TAAAAAA
2668217 TTTAAATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAAAACAAT
Found at i:2668203 original size:12 final size:12
Alignment explanation
Indices: 2668177--2668216 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2668167 CTATGCTAAT
2668177 AAAAAACAATT-
1 AAAAAACAATTA
**
2668188 AAAAAACCTTTA
1 AAAAAACAATTA
2668200 AAAAAACAATTA
1 AAAAAACAATTA
2668212 AAAAA
1 AAAAA
2668217 TTTAAATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAACAATTA
Found at i:2668819 original size:3 final size:3
Alignment explanation
Indices: 2668811--2668841 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2668801 GACGAAGGTA
2668811 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2668842 GTATTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2677466 original size:35 final size:34
Alignment explanation
Indices: 2677402--2677468 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
2677392 ATTTATTAAA
*
2677402 TTTAATAAATAATTATAAATAATATTATAATATTC
1 TTTAATAAATAA-TATAAATAATAATATAATATTC
*
2677437 TTTAATAAAATAA-ATAGATAATAAATATAATA
1 TTTAAT-AAATAATATAAATAAT-AATATAATA
2677469 AAATTCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 8 0.29
35 14 0.50
36 6 0.21
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (34 bp):
TTTAATAAATAATATAAATAATAATATAATATTC
Found at i:2679141 original size:19 final size:20
Alignment explanation
Indices: 2679104--2679142 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2679094 ATTAAAAATT
* *
2679104 AAAATTAAAACAATATATAA
1 AAAATAAAAAAAATATATAA
2679124 AAAATAAAAAAAAT-TATAA
1 AAAATAAAAAAAATATATAA
2679143 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAAAAAAAATATATAA
Found at i:2681469 original size:29 final size:29
Alignment explanation
Indices: 2681422--2681492 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2681412 ATTATATTAG
* * * *
2681422 TTAACAAATTTATATAATTCAACTACCGCA
1 TTAA-AAATTTTTAAAATTCAAATACCACA
*
2681452 TTAAAAATTTTTAAAATTCAAATATCACA
1 TTAAAAATTTTTAAAATTCAAATACCACA
*
2681481 TTAAATATTTTT
1 TTAAAAATTTTT
2681493 TTAAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAAAAATTTTTAAAATTCAAATACCACA
Found at i:2693209 original size:25 final size:25
Alignment explanation
Indices: 2693167--2693215 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2693157 CACTTACACT
*
2693167 AATATAAATATAAAATAAATAAATA
1 AATATAAATATAAAATAAAGAAATA
* **
2693192 AATATATATATATTATAAAGAAAT
1 AATATAAATATAAAATAAAGAAAT
2693216 TCAACTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AATATAAATATAAAATAAAGAAATA
Found at i:2698378 original size:21 final size:22
Alignment explanation
Indices: 2698354--2698394 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2698344 ATAATTTATT
2698354 ATTATAATT-AAAAATTACATA
1 ATTATAATTAAAAAATTACATA
2698375 ATTATAATTAAAAAATTACA
1 ATTATAATTAAAAAATTACA
2698395 AGTATATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTATAATTAAAAAATTACATA
Found at i:2698620 original size:34 final size:34
Alignment explanation
Indices: 2698582--2698646 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2698572 ATTTATTAAA
* *
2698582 TTTAAT-AAATAATTATAAATAATATATAATATTC
1 TTTAATAAAATAAATAGAAATAA-ATATAATATTC
*
2698616 TTTAATAAAATAAATAGATATAAATATAATA
1 TTTAATAAAATAAATAGAAATAAATATAATA
2698647 AATTCATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 14 0.52
35 13 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (34 bp):
TTTAATAAAATAAATAGAAATAAATATAATATTC
Found at i:2699462 original size:33 final size:33
Alignment explanation
Indices: 2699380--2699463 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
2699370 AAAAAATATT
* * *
2699380 TTTATTT-TAATGAAATAAGGTCTATTTGTTTTA
1 TTTATTTATAATG-GATAAGGTCAATTTGCTTTA
*
2699413 TTTGTTTATAATGGATAAGGTCAATTTGCTTTA
1 TTTATTTATAATGGATAAGGTCAATTTGCTTTA
*
2699446 -TTATTTGTAATAGGATAA
1 TTTATTTATAAT-GGATAA
2699464 AGCCCAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 9 0.21
33 29 0.67
34 5 0.12
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (33 bp):
TTTATTTATAATGGATAAGGTCAATTTGCTTTA
Found at i:2702623 original size:29 final size:29
Alignment explanation
Indices: 2702576--2702646 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2702566 GTTATATTAG
* * * *
2702576 TTAACAAATTTATATAATTCAACTATCGCA
1 TTAA-AAATTTTTAAAATTCAAATATCACA
*
2702606 TTAAAAATTTTTAAAATTTAAATATCACA
1 TTAAAAATTTTTAAAATTCAAATATCACA
*
2702635 TTAAATATTTTT
1 TTAAAAATTTTT
2702647 TTAAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAAAAATTTTTAAAATTCAAATATCACA
Found at i:2706934 original size:1 final size:1
Alignment explanation
Indices: 2706930--2706954 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2706920 AAACCATTGG
2706930 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2706955 GTTATCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2711822 original size:27 final size:27
Alignment explanation
Indices: 2711804--2711861 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2711794 ACCTTTACTT
*
2711804 CCACTACCTTTGTTACCACCGCCACTC
1 CCACTACCTTTGCTACCACCGCCACTC
2711831 CCACTACCTTTGCTACCACCGCCACTC
1 CCACTACCTTTGCTACCACCGCCACTC
2711858 CCAC
1 CCAC
2711862 CTTTGCCACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.52, G:0.07, T:0.22
Consensus pattern (27 bp):
CCACTACCTTTGCTACCACCGCCACTC
Found at i:2716601 original size:22 final size:22
Alignment explanation
Indices: 2716575--2716618 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2716565 TGTATATTTA
*
2716575 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2716597 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2716619 GAAGATTTAG
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:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:2716818 original size:25 final size:24
Alignment explanation
Indices: 2716766--2716830 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 24
2716756 AAAAATTTCA
* *
2716766 GCCTTCATTGCCG-ACTTTTTTAG
1 GCCTTCATTGCCGAACCTGTTTAG
2716789 GCCTTCATTGCCGAATCCTGTTTAG
1 GCCTTCATTGCCGAA-CCTGTTTAG
2716814 GCCTTCATTGCCGAACC
1 GCCTTCATTGCCGAACC
2716831 CTTTCAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 13 0.34
24 3 0.08
25 22 0.58
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.35
Consensus pattern (24 bp):
GCCTTCATTGCCGAACCTGTTTAG
Found at i:2720496 original size:22 final size:22
Alignment explanation
Indices: 2720470--2720513 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2720460 TGTATATTTA
*
2720470 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2720492 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2720514 GAAGATTTAG
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:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:2723705 original size:19 final size:18
Alignment explanation
Indices: 2723672--2723707 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2723662 AACTAAAGTG
2723672 CTTATTTTGTCATTTTAT
1 CTTATTTTGTCATTTTAT
*
2723690 CTTATGTTTGTTATTTTA
1 CTTAT-TTTGTCATTTTA
2723708 ATTGCCTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (18 bp):
CTTATTTTGTCATTTTAT
Found at i:2725106 original size:103 final size:103
Alignment explanation
Indices: 2724927--2725134 Score: 389
Period size: 103 Copynumber: 2.0 Consensus size: 103
2724917 TTCTGATCTC
*
2724927 CTACAGCAGCCACAGCATATTTTAATATCATTGCTATTGATTCTACAATCATGAATCCTGTTCTT
1 CTACAGCAGCCACAGCATATTTTAATATCATTGCAATTGATTCTACAATCATGAATCCTGTTCTT
2724992 GTTTGAACTTCAATTCTTGATCGATTTTAGCCAGTGTT
66 GTTTGAACTTCAATTCTTGATCGATTTTAGCCAGTGTT
*
2725030 CTACAGCAGCCACAGCATATTTTAATATCATTGCAATTGATTCTACGATCATGAATCCTGTTCTT
1 CTACAGCAGCCACAGCATATTTTAATATCATTGCAATTGATTCTACAATCATGAATCCTGTTCTT
*
2725095 GTTTGAACTTCAATTCTTTATCGATTTTAGCCAGTGTT
66 GTTTGAACTTCAATTCTTGATCGATTTTAGCCAGTGTT
2725133 CT
1 CT
2725135 GTTTTCTTTT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (103 bp):
CTACAGCAGCCACAGCATATTTTAATATCATTGCAATTGATTCTACAATCATGAATCCTGTTCTT
GTTTGAACTTCAATTCTTGATCGATTTTAGCCAGTGTT
Found at i:2725287 original size:40 final size:40
Alignment explanation
Indices: 2725232--2725313 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2725222 GTCTCTACAC
*
2725232 AAAGAAAAGTTTAAAGACCTCAGATTTATTTTTCATTCAA
1 AAAGAAAAGTTTAAAGACCTCAGATTTAGTTTTCATTCAA
*
2725272 AAAGAAAAGTTTAAAGGCCTCAGATTTAGTTTTCATTCAA
1 AAAGAAAAGTTTAAAGACCTCAGATTTAGTTTTCATTCAA
2725312 AA
1 AA
2725314 TAATTTTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (40 bp):
AAAGAAAAGTTTAAAGACCTCAGATTTAGTTTTCATTCAA
Found at i:2727459 original size:3 final size:3
Alignment explanation
Indices: 2727451--2727487 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2727441 TCTAAGTTTG
2727451 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2727488 AGAAAGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2739599 original size:24 final size:25
Alignment explanation
Indices: 2739554--2739601 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2739544 AAGAGTCATA
2739554 CATACATGTATGATATATATTTGTG
1 CATACATGTATGATATATATTTGTG
2739579 CATACATGTATG-TATATATTTGT
1 CATACATGTATGATATATATTTGT
2739602 AAATATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (25 bp):
CATACATGTATGATATATATTTGTG
Found at i:2742641 original size:31 final size:32
Alignment explanation
Indices: 2742603--2742675 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
2742593 TACAAATGAA
2742603 ATCAAATGAAATCCAA-GTGCATTAATATTTT
1 ATCAAATGAAATCCAAGGTGCATTAATATTTT
2742634 ATCAAATGAAATCCAAGGTGCATTAATATTTT
1 ATCAAATGAAATCCAAGGTGCATTAATATTTT
*
2742666 ACCAAATGAA
1 ATCAAATGAA
2742676 TTTAAATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 16 0.40
32 24 0.60
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (32 bp):
ATCAAATGAAATCCAAGGTGCATTAATATTTT
Found at i:2743453 original size:12 final size:12
Alignment explanation
Indices: 2743432--2743473 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
2743422 TTTATATATT
2743432 TACA-CATGAAA
1 TACATCATGAAA
2743443 TACATCATGAAA
1 TACATCATGAAA
2743455 TACATCATGAAA
1 TACATCATGAAA
2743467 TACATCA
1 TACATCA
2743474 ATTACTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 4 0.13
12 26 0.87
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (12 bp):
TACATCATGAAA
Found at i:2747983 original size:50 final size:50
Alignment explanation
Indices: 2747929--2748027 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
2747919 TGTACCAACC
2747929 TGTTTCCTAATTTTTTCTATCACTTC-TTCAAAGTTTATATTATAGTAACT
1 TGTTTCCTAATTTTTTCTATCACTTCATT-AAAGTTTATATTATAGTAACT
* * * *
2747979 TGTTTTCTTATTTTTTCTATCATTTCATTAAAGTTTATATTGTAGTAAC
1 TGTTTCCTAATTTTTTCTATCACTTCATTAAAGTTTATATTATAGTAAC
2748028 AATTTATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 42 0.95
51 2 0.05
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (50 bp):
TGTTTCCTAATTTTTTCTATCACTTCATTAAAGTTTATATTATAGTAACT
Found at i:2753265 original size:64 final size:64
Alignment explanation
Indices: 2753160--2753290 Score: 244
Period size: 64 Copynumber: 2.0 Consensus size: 64
2753150 TAATCTACCC
* *
2753160 GAAACAAAAGCACTCTGAGCCTTACTAATGCAATCAGAAAGAATATCTTTAAGTCTATTAACTA
1 GAAACAAAAGCACTATGAGCCTTACTAATGCAATCAAAAAGAATATCTTTAAGTCTATTAACTA
2753224 GAAACAAAAGCACTATGAGCCTTACTAATGCAATCAAAAAGAATATCTTTAAGTCTATTAACTA
1 GAAACAAAAGCACTATGAGCCTTACTAATGCAATCAAAAAGAATATCTTTAAGTCTATTAACTA
2753288 GAA
1 GAA
2753291 CTTTAGAGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (64 bp):
GAAACAAAAGCACTATGAGCCTTACTAATGCAATCAAAAAGAATATCTTTAAGTCTATTAACTA
Found at i:2755406 original size:39 final size:39
Alignment explanation
Indices: 2755351--2755428 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
2755341 TTATGCTAAA
2755351 ATTGTTCAAAGTTTCACCAAAA-CTCTCCAAATGCATTTG
1 ATTGTTCAAAGTTTCACCAAAACCT-TCCAAATGCATTTG
2755390 ATTGTTCATAAG-TTCACCAAAACCTTCCAAATGCATTTG
1 ATTGTTCA-AAGTTTCACCAAAACCTTCCAAATGCATTTG
2755429 TTTAGTTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
39 32 0.86
40 5 0.14
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (39 bp):
ATTGTTCAAAGTTTCACCAAAACCTTCCAAATGCATTTG
Found at i:2757288 original size:20 final size:23
Alignment explanation
Indices: 2757263--2757316 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 23
2757253 AATATAATAC
2757263 TTTTTTAAATAAA-AAT-TTTA-
1 TTTTTTAAATAAATAATCTTTAT
2757283 TTTTTT-AATAAATAATCCTTTAT
1 TTTTTTAAATAAATAAT-CTTTAT
2757306 TTTTTTAAATA
1 TTTTTTAAATA
2757317 GTAGTGTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.21
20 9 0.31
22 4 0.14
23 6 0.21
24 4 0.14
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTAAATAAATAATCTTTAT
Found at i:2757309 original size:23 final size:20
Alignment explanation
Indices: 2757263--2757313 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2757253 AATATAATAC
*
2757263 TTTTTTAAATAAAAATTTTA
1 TTTTTTTAATAAAAATTTTA
2757283 -TTTTTTAATAAATAATCCTTTA
1 TTTTTTTAATAAA-AAT--TTTA
2757305 TTTTTTTAA
1 TTTTTTTAA
2757314 ATAGTAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
22 4 0.15
23 8 0.31
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTTAATAAAAATTTTA
Found at i:2758844 original size:14 final size:15
Alignment explanation
Indices: 2758818--2758846 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2758808 TCAATTCATT
2758818 ATATATGATATAAAA
1 ATATATGATATAAAA
2758833 ATATAT-ATATAAAA
1 ATATATGATATAAAA
2758847 GCACAAATAT
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:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATATATGATATAAAA
Found at i:2760256 original size:21 final size:22
Alignment explanation
Indices: 2760232--2760279 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2760222 AATATTTATA
2760232 TTTATA-TTTAAAAAATAATAT
1 TTTATATTTTAAAAAATAATAT
2760253 TTTATATTTTAAAAAATAATAT
1 TTTATATTTTAAAAAATAATAT
2760275 TTTAT
1 TTTAT
2760280 TAATTTCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTTTAAAAAATAATAT
Found at i:2761019 original size:6 final size:6
Alignment explanation
Indices: 2761008--2761042 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2760998 CCTTAATTTG
2761008 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
2761043 CACATTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:2762950 original size:16 final size:16
Alignment explanation
Indices: 2762931--2762973 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2762921 GATCTTAATT
*
2762931 AAATTAATTTGAACCC
1 AAATTAATTTAAACCC
**
2762947 AAATTAATTTAAACTT
1 AAATTAATTTAAACCC
2762963 AAATTAATTTA
1 AAATTAATTTA
2762974 GATTCAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATTAATTTAAACCC
Found at i:2762982 original size:16 final size:17
Alignment explanation
Indices: 2762931--2762982 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
2762921 GATCTTAATT
* *
2762931 AAATTAATTTGAAC-CC
1 AAATTAATTTAAACTTC
2762947 AAATTAATTTAAACTT-
1 AAATTAATTTAAACTTC
*
2762963 AAATTAATTTAGA-TTC
1 AAATTAATTTAAACTTC
2762979 AAAT
1 AAAT
2762983 GATTTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 2 0.06
16 29 0.94
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (17 bp):
AAATTAATTTAAACTTC
Found at i:2762982 original size:32 final size:30
Alignment explanation
Indices: 2762927--2762995 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 30
2762917 ATTTGATCTT
2762927 AATTAAATTAATTTGAACCCAAATTAATTTA
1 AATTAAATTAATTTGAACCCAAA-TAATTTA
** *
2762958 AACTTAAATTAATTT-AGATTCAAATGATTTA
1 AA-TTAAATTAATTTGA-ACCCAAATAATTTA
2762989 AATTAAA
1 AATTAAA
2762996 ACTCAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 5 0.15
31 11 0.33
32 17 0.52
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (30 bp):
AATTAAATTAATTTGAACCCAAATAATTTA
Found at i:2765171 original size:2 final size:2
Alignment explanation
Indices: 2765154--2765191 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2765144 TAAATGTGAG
*
2765154 TA TA T- TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2765192 GAAACGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2771868 original size:17 final size:17
Alignment explanation
Indices: 2771843--2771877 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2771833 AGATTTTTTA
*
2771843 ATTTATTTTCAAAAATC
1 ATTTATTTTAAAAAATC
*
2771860 ATTTTTTTTAAAAAATC
1 ATTTATTTTAAAAAATC
2771877 A
1 A
2771878 CAAAACTTTC
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:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTATTTTAAAAAATC
Found at i:2773345 original size:2 final size:2
Alignment explanation
Indices: 2773333--2773366 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2773323 AAGTGTAGGA
*
2773333 AT AT A- AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2773367 AAACTCCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.