Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 179 of 221
Found at i:53466035 original size:21 final size:21
Alignment explanation
Indices: 53466011--53466066 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
53466001 TTAAACCTCT
*
53466011 GCTTCTCTCGCTGCAGCCTTC
1 GCTTCCCTCGCTGCAGCCTTC
*
53466032 GCTTCCCTCGCTGCAGCCTTT
1 GCTTCCCTCGCTGCAGCCTTC
53466053 GCTTCCCTCGCTGC
1 GCTTCCCTCGCTGC
53466067 CGTATCTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.04, C:0.45, G:0.20, T:0.32
Consensus pattern (21 bp):
GCTTCCCTCGCTGCAGCCTTC
Found at i:53471508 original size:9 final size:9
Alignment explanation
Indices: 53471485--53471651 Score: 190
Period size: 9 Copynumber: 18.4 Consensus size: 9
53471475 TGCACGGGTC
*
53471485 AGTTATTTA
1 AGTTATGTA
*
53471494 ATTTATGTA
1 AGTTATGTA
53471503 AGTTATGTA
1 AGTTATGTA
53471512 AGTTATGTA
1 AGTTATGTA
*
53471521 AGTTATTTA
1 AGTTATGTA
*
53471530 ATTTATGTA
1 AGTTATGTA
*
53471539 GGTTATGTA
1 AGTTATGTA
* * *
53471548 AGTCCACGGA
1 AGT-TATGTA
*
53471558 ATTTATGTA
1 AGTTATGTA
53471567 AGTTATGTA
1 AGTTATGTA
*
53471576 AGTTATTTA
1 AGTTATGTA
*
53471585 ATTTATGTA
1 AGTTATGTA
53471594 AGTTATGTA
1 AGTTATGTA
*
53471603 AGTTATTTA
1 AGTTATGTA
*
53471612 ATTTATGTA
1 AGTTATGTA
53471621 AGTTATGTA
1 AGTTATGTA
*
53471630 AGTTATTTA
1 AGTTATGTA
*
53471639 ATTTATGTA
1 AGTTATGTA
53471648 AGTT
1 AGTT
53471652 TCTATATATG
Statistics
Matches: 128, Mismatches: 29, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
9 123 0.96
10 5 0.04
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (9 bp):
AGTTATGTA
Found at i:53471526 original size:27 final size:27
Alignment explanation
Indices: 53471485--53471812 Score: 264
Period size: 27 Copynumber: 11.6 Consensus size: 27
53471475 TGCACGGGTC
* * * *
53471485 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
53471512 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
* * ***
53471539 GGTTATGTAAGTCCACGGAATTTATGTA
1 AGTTATGTAAGT-TATTTAATTTATGTA
53471567 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
53471594 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
53471621 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
* * * *
53471648 AGTTTCTATATATGTT-TATATATTGTATGTT
1 AG--T-TATGTAAGTTATTTA-ATT-TATGTA
* ** *
53471679 AGTTAT-TATGTTATTATGTTATTATATA
1 AGTTATGTAAGTTATT-TAAT-TTATGTA
* ** *
53471707 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATT-TAAT-TTATGT-A
* *
53471737 AGTATTATGTAATTTATTATGTTATTATATGTA
1 AG--TTATGTAAGTTA-T-T-TAATT-TATGTA
53471770 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
*
53471797 AGTTATGCAAGCTTAT
1 AGTTATGTAAG-TTAT
53471813 ATACAAGTTA
Statistics
Matches: 251, Mismatches: 33, Indels: 33
0.79 0.10 0.10
Matches are distributed among these distances:
27 123 0.49
28 45 0.18
29 28 0.11
30 15 0.06
31 18 0.07
32 10 0.04
33 5 0.02
34 7 0.03
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (27 bp):
AGTTATGTAAGTTATTTAATTTATGTA
Found at i:53471693 original size:8 final size:8
Alignment explanation
Indices: 53471680--53471732 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
53471670 TTGTATGTTA
53471680 GTTATTAT
1 GTTATTAT
53471688 GTTATTAT
1 GTTATTAT
53471696 GTTATTATAT
1 GTTA-T-TAT
*
53471706 AAGTTATTTAA
1 --GTTA-TTAT
53471717 GTTATTAT
1 GTTATTAT
53471725 GTTATTAT
1 GTTATTAT
53471733 ATAAAGTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 23 0.59
9 5 0.13
10 3 0.08
11 2 0.05
12 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.58
Consensus pattern (8 bp):
GTTATTAT
Found at i:53471720 original size:29 final size:29
Alignment explanation
Indices: 53471679--53471785 Score: 135
Period size: 32 Copynumber: 3.6 Consensus size: 29
53471669 ATTGTATGTT
*
53471679 AGTTAT-TATGTTATTATGTTATTATATA
1 AGTTATGTAAGTTATTATGTTATTATATA
*
53471707 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATTATGTTATTATAT-A
*
53471737 AGTATTATGTAATTTATTATGTTATTATATGTA
1 AG--TTATGTAAGTTATTATGTTATTATA--TA
53471770 AGTTATGTAAGTTATT
1 AGTTATGTAAGTTATT
53471786 TAATTTATGT
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.09
29 20 0.29
30 3 0.04
31 13 0.19
32 23 0.33
33 3 0.04
34 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (29 bp):
AGTTATGTAAGTTATTATGTTATTATATA
Found at i:53471752 original size:37 final size:37
Alignment explanation
Indices: 53471679--53471752 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
53471669 ATTGTATGTT
* * * *
53471679 AGTTATTATGTTATTATGTTATTATATAAGTTATTTA
1 AGTTATTATGTTATTATATAAGTATATAAGTAATTTA
*
53471716 AGTTATTATGTTATTATATAAAGTAT-TATGTAATTTA
1 AGTTATTATGTTATTATAT-AAGTATATAAGTAATTTA
53471753 TTATGTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 27 0.87
38 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (37 bp):
AGTTATTATGTTATTATATAAGTATATAAGTAATTTA
Found at i:53471770 original size:22 final size:23
Alignment explanation
Indices: 53471688--53471812 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 23
53471678 TAGTTATTAT
*
53471688 GTTAT-TATGTTATTATA--TAA
1 GTTATGTAAGTTATTATATGTAA
* *
53471708 GTTATTTAAGTTA-T-TATGTTA
1 GTTATGTAAGTTATTATATGTAA
*
53471729 -TTATATAAAG-TA-T-TATGTAA
1 GTTATGT-AAGTTATTATATGTAA
* *
53471749 TTTAT-TATGTTATTATATGTAA
1 GTTATGTAAGTTATTATATGTAA
53471771 GTTATGTAAGTTATTTAATTTATGTAA
1 GTTATGTAAGTTA-TT-A--TATGTAA
*
53471798 GTTATGCAAGCTTAT
1 GTTATGTAAG-TTAT
53471813 ATACAAGTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
19 4 0.05
20 23 0.28
21 16 0.19
22 11 0.13
23 6 0.07
24 2 0.02
25 1 0.01
27 17 0.20
28 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (23 bp):
GTTATGTAAGTTATTATATGTAA
Found at i:53471778 original size:9 final size:9
Alignment explanation
Indices: 53471764--53471826 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
53471754 TATGTTATTA
53471764 TATGTAAGT
1 TATGTAAGT
53471773 TATGTAAGT
1 TATGTAAGT
* *
53471782 TATTTAATT
1 TATGTAAGT
53471791 TATGTAAGT
1 TATGTAAGT
*
53471800 TATGCAAGCT
1 TATGTAAG-T
*
53471810 TATATACAAGT
1 TATGT--AAGT
53471821 TATGTA
1 TATGTA
53471827 TTATAACATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 31 0.72
10 4 0.09
11 5 0.12
12 3 0.07
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:53472068 original size:16 final size:16
Alignment explanation
Indices: 53472043--53472080 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
53472033 GAAAATGAAG
*
53472043 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
53472058 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
53472074 TAAATTT
1 TAAATTT
53472081 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:53472095 original size:13 final size:13
Alignment explanation
Indices: 53472077--53472104 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53472067 ATACAAATAA
53472077 ATTTAGAAAACTT
1 ATTTAGAAAACTT
53472090 ATTTAGAAAACTT
1 ATTTAGAAAACTT
53472103 AT
1 AT
53472105 AAATTTAAAA
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:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:53472116 original size:17 final size:17
Alignment explanation
Indices: 53472090--53472122 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53472080 TAGAAAACTT
*
53472090 ATTTAGAAAACTTATAA
1 ATTTAAAAAACTTATAA
53472107 ATTTAAAAAACTTATA
1 ATTTAAAAAACTTATA
53472123 GAGATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTAAAAAACTTATAA
Found at i:53472969 original size:37 final size:37
Alignment explanation
Indices: 53472928--53473003 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
53472918 GGAAAGAAGT
53472928 AAACAGAAGATTATTTAAGTACATTTAGATTCAAATC
1 AAACAGAAGATTATTTAAGTACATTTAGATTCAAATC
*
53472965 AAACAGAAGATTATTTAAGTACATTTATATTCAAATC
1 AAACAGAAGATTATTTAAGTACATTTAGATTCAAATC
53473002 AA
1 AA
53473004 CTTAATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (37 bp):
AAACAGAAGATTATTTAAGTACATTTAGATTCAAATC
Found at i:53473196 original size:27 final size:29
Alignment explanation
Indices: 53473142--53473196 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
53473132 TAATTATCAC
*
53473142 AACAATAAACTTAATAATAATTGATAAAGT
1 AACAATAAACTTAATAATAAAT-ATAAAGT
*
53473172 AACAATCAACTTAAT-ATAAAT-TAAA
1 AACAATAAACTTAATAATAAATATAAA
53473197 TCAGAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
29 5 0.22
30 14 0.61
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (29 bp):
AACAATAAACTTAATAATAAATATAAAGT
Found at i:53473613 original size:17 final size:17
Alignment explanation
Indices: 53473567--53473613 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
53473557 TGAAAAGCCA
53473567 AAAACCCGAAAATAACTC
1 AAAACCCG-AAATAACTC
* * *
53473585 AAAACTCAAAATAACTT
1 AAAACCCGAAATAACTC
53473602 AAAACCCGAAAT
1 AAAACCCGAAAT
53473614 GAGCTAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.57, C:0.23, G:0.04, T:0.15
Consensus pattern (17 bp):
AAAACCCGAAATAACTC
Found at i:53475909 original size:116 final size:114
Alignment explanation
Indices: 53475702--53475909 Score: 242
Period size: 116 Copynumber: 1.8 Consensus size: 114
53475692 AAGATAAATG
*
53475702 AAAAACGGCAACGTTTTCTTAACAGTCTTGTGGCGCTTATGATAAAGCGCCGCTAATTCTTGACT
1 AAAAACGGCAACGTTTTCTTAACAGTCTTGTGGCGCTTATGACAAAGCGCCGCTAATTCTTGACT
* * **
53475767 ATAGCAGCGTTTTTCATTAAGCGCCACTAAAGTCCCCAAAATCTAAACT
66 ATAGCAGCGTTTCTAAGAAAGCGCCACTAAAGTCCCCAAAATCTAAACT
* * *
53475816 AAAAACGGCAGCGTTTTTCTTAACAGTTTTTGTGGCGTTTATGACCAAA-CGCCAG-TAATTCTT
1 AAAAACGGCAACG-TTTTCTTAACAG-TCTTGTGGCGCTTATGA-CAAAGCGCC-GCTAATTCTT
* * * *
53475879 G-CATATTGCGGTGTTTCTAAGAAAGGGCCAC
62 GAC-TATAGCAGCGTTTCTAAGAAAGCGCCAC
53475910 AAATGTTTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
114 12 0.16
115 13 0.17
116 48 0.62
117 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (114 bp):
AAAAACGGCAACGTTTTCTTAACAGTCTTGTGGCGCTTATGACAAAGCGCCGCTAATTCTTGACT
ATAGCAGCGTTTCTAAGAAAGCGCCACTAAAGTCCCCAAAATCTAAACT
Found at i:53488021 original size:20 final size:20
Alignment explanation
Indices: 53487996--53488057 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
53487986 AATAGACCCG
53487996 ACTATAATGTTGGTGTCATC
1 ACTATAATGTTGGTGTCATC
*** * *
53488016 ACTATAAT-AACGT-AC-CC
1 ACTATAATGTTGGTGTCATC
53488033 ACTATAATGTTGGTGTCATC
1 ACTATAATGTTGGTGTCATC
53488053 ACTAT
1 ACTAT
53488058 CCTTACGATG
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
17 9 0.31
18 3 0.10
19 3 0.10
20 14 0.48
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (20 bp):
ACTATAATGTTGGTGTCATC
Found at i:53490566 original size:16 final size:16
Alignment explanation
Indices: 53490545--53490579 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53490535 ACTTGCGATC
53490545 CAAGTCAATGTAGGAA
1 CAAGTCAATGTAGGAA
*
53490561 CAAGTCAATGTATGAA
1 CAAGTCAATGTAGGAA
53490577 CAA
1 CAA
53490580 TAAAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (16 bp):
CAAGTCAATGTAGGAA
Found at i:53494206 original size:46 final size:46
Alignment explanation
Indices: 53494135--53494320 Score: 153
Period size: 46 Copynumber: 4.1 Consensus size: 46
53494125 TTTAATTATG
* * **
53494135 TTATTTGAATTAATTATGTTTGATCTGCATATTCGTATTGATTCTA
1 TTATTCGAAATAATTATGTCCGATCTGCATATTCGTATTGATTCTA
* * * * * *
53494181 TTATTCGAAATAATAATGTCCGATCTGTATATCCATTTTGATTCTG
1 TTATTCGAAATAATTATGTCCGATCTGCATATTCGTATTGATTCTA
* * * * *
53494227 TTATTCAAAATAATTACGTCCGATCT--ATCTATCTGTATTGATTTTG
1 TTATTCGAAATAATTATGTCCGATCTGCATAT-TC-GTATTGATTCTA
* * * * *
53494273 TCATTCGAAATCATTATGTCCAATCTACATA-TCGTATTGATTTTA
1 TTATTCGAAATAATTATGTCCGATCTGCATATTCGTATTGATTCTA
53494318 TTA
1 TTA
53494321 CTGGCATTTG
Statistics
Matches: 110, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
44 3 0.03
45 14 0.13
46 91 0.83
48 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.46
Consensus pattern (46 bp):
TTATTCGAAATAATTATGTCCGATCTGCATATTCGTATTGATTCTA
Found at i:53502239 original size:17 final size:17
Alignment explanation
Indices: 53502217--53502249 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53502207 ATTTTTTTTA
53502217 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
53502234 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
53502250 TATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:53502699 original size:21 final size:21
Alignment explanation
Indices: 53502674--53502730 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
53502664 CCTTTGTTTC
53502674 TAATCTCATTGCTACAAT-AT
1 TAATCTCATTGCTACAATAAT
**
53502694 TCAATCTCATCACTACAATAAT
1 T-AATCTCATTGCTACAATAAT
*
53502716 TAATTTCATTGCTAC
1 TAATCTCATTGCTAC
53502731 CGCTATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.87
22 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (21 bp):
TAATCTCATTGCTACAATAAT
Found at i:53503265 original size:16 final size:15
Alignment explanation
Indices: 53503244--53503302 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
53503234 ATTTGAAAAC
53503244 AAATTAAAAATTTTAA
1 AAATTAAAAATTTT-A
*
53503260 AAATT-ATAATTGTTA
1 AAATTAAAAATT-TTA
53503275 AAA-TAAAAACTCTTTA
1 AAATTAAAAA-T-TTTA
53503291 AAATTCAAAAAT
1 AAATT-AAAAAT
53503303 AAAAATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 14 0.40
17 3 0.09
18 5 0.14
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
AAATTAAAAATTTTA
Found at i:53503325 original size:25 final size:24
Alignment explanation
Indices: 53503274--53503326 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
53503264 TATAATTGTT
* *
53503274 AAAATAAAAACTCTTTAAAATTCA
1 AAAATAAAAACTCTTTAAAACTAA
* *
53503298 AAAATAAAAATTATTTTAAAACTAA
1 AAAATAAAAACT-CTTTAAAACTAA
53503323 AAAA
1 AAAA
53503327 ATTCCAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAAAAACTCTTTAAAACTAA
Found at i:53507774 original size:90 final size:90
Alignment explanation
Indices: 53507616--53507779 Score: 229
Period size: 90 Copynumber: 1.8 Consensus size: 90
53507606 TAATGGTGGA
* ** * *
53507616 ATGTTAGAGGGATGATAAGAAAATGGCGATGGCGAAGGAGTCGAGAGGGATAAAAAAAAATGGTG
1 ATGTGAGAGGGACAATAAGAAAATGGCGATGGCGAAGGAGTCAAAAGGGATAAAAAAAAATGGTG
53507681 AAAAAGCCCCCTGTTTAGTAGTTGC
66 AAAAAGCCCCCTGTTTAGTAGTTGC
* * * * * *
53507706 ATGTGAGAGGGACAATAAGAAAATGGTGGTGGTGATGGAGTCAAAAGGGATGAAGAAAAATGGTG
1 ATGTGAGAGGGACAATAAGAAAATGGCGATGGCGAAGGAGTCAAAAGGGATAAAAAAAAATGGTG
53507771 AAAAAGCCC
66 AAAAAGCCC
53507780 TCCCTTTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.34, T:0.18
Consensus pattern (90 bp):
ATGTGAGAGGGACAATAAGAAAATGGCGATGGCGAAGGAGTCAAAAGGGATAAAAAAAAATGGTG
AAAAAGCCCCCTGTTTAGTAGTTGC
Found at i:53509834 original size:17 final size:16
Alignment explanation
Indices: 53509812--53509847 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
53509802 TTTTCAACGT
*
53509812 AAATTAAATTAAATTCA
1 AAATTAAAATAAATT-A
53509829 AAATTAAAATAAATTA
1 AAATTAAAATAAATTA
53509845 AAA
1 AAA
53509848 CAAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAATAAATTA
Found at i:53512495 original size:41 final size:41
Alignment explanation
Indices: 53512450--53512555 Score: 194
Period size: 41 Copynumber: 2.6 Consensus size: 41
53512440 ACTGGCAATT
* *
53512450 AGCCTGCTAGACGTAAAGTCTGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
53512491 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
53512532 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
53512556 TTATCTCATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:53519724 original size:17 final size:18
Alignment explanation
Indices: 53519693--53519731 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
53519683 AAACAATAAA
*
53519693 TTTTTTTGTTCAAATGAT
1 TTTTTTTGTTAAAATGAT
*
53519711 TTTTTTTG-TAAAATTAT
1 TTTTTTTGTTAAAATGAT
53519728 TTTT
1 TTTT
53519732 CGAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTTTTTGTTAAAATGAT
Found at i:53521738 original size:30 final size:26
Alignment explanation
Indices: 53521685--53521738 Score: 63
Period size: 30 Copynumber: 1.9 Consensus size: 26
53521675 TATAAATGCA
*
53521685 TAAAATAATAATGTTATTTTAAGTTT
1 TAAAATAATAATGTTATTGTAAGTTT
53521711 TAAAATAAGTAATTTGTATATTGTAAGT
1 TAAAATAA-TAA--TGT-TATTGTAAGT
53521739 GTTGAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 8 0.35
27 3 0.13
29 3 0.13
30 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (26 bp):
TAAAATAATAATGTTATTGTAAGTTT
Found at i:53522760 original size:15 final size:17
Alignment explanation
Indices: 53522720--53522765 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
53522710 TTTATGTTAA
*
53522720 ATATATTTAATAATTTT
1 ATATAATTAATAATTTT
*
53522737 ATGTAATTAA-AATTTT
1 ATATAATTAATAATTTT
53522753 A-ATAATTAATAAT
1 ATATAATTAATAAT
53522766 ATATTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATATAATTAATAATTTT
Found at i:53525453 original size:13 final size:14
Alignment explanation
Indices: 53525435--53525467 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53525425 AAGCTCAATT
53525435 TTTTTTATTTTCA-
1 TTTTTTATTTTCAC
*
53525448 TTTTTTCTTTTCAC
1 TTTTTTATTTTCAC
53525462 TTTTTT
1 TTTTTT
53525468 TAGAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTATTTTCAC
Found at i:53526358 original size:21 final size:18
Alignment explanation
Indices: 53526316--53526363 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
53526306 CGTGCACACT
*
53526316 AATAAGAATAGAGAAAAA
1 AATAAGAAAAGAGAAAAA
53526334 AATAAGATAAAGAGATAACAA
1 AATAAGA-AAAGAGA-AA-AA
53526355 AAT-AGAAAA
1 AATAAGAAAA
53526364 ATAACCGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 9 0.35
20 5 0.19
21 5 0.19
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (18 bp):
AATAAGAAAAGAGAAAAA
Found at i:53534645 original size:19 final size:19
Alignment explanation
Indices: 53534623--53534671 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
53534613 TGGGAACCGT
53534623 TTGTTGATAAGGGAACATC
1 TTGTTGATAAGGGAACATC
* ** *
53534642 TTGTTTATATTGGAACATT
1 TTGTTGATAAGGGAACATC
53534661 TTGTTGATAAG
1 TTGTTGATAAG
53534672 ATGCATTTTG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGTTGATAAGGGAACATC
Found at i:53534919 original size:27 final size:27
Alignment explanation
Indices: 53534883--53534952 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
53534873 AATTCATTAC
*
53534883 AAAAATTATAATTAAATTTTATTGTAA
1 AAAAAGTATAATTAAATTTTATTGTAA
*
53534910 AAAAAGTATAATTAAATTTTATTGTAT
1 AAAAAGTATAATTAAATTTTATTGTAA
53534937 AAAAAG--TAATTAAATT
1 AAAAAGTATAATTAAATT
53534953 AATTTAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 10 0.24
27 31 0.76
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (27 bp):
AAAAAGTATAATTAAATTTTATTGTAA
Found at i:53535795 original size:14 final size:15
Alignment explanation
Indices: 53535753--53535795 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
53535743 AAATATTATT
*
53535753 AAAT-ATCAAATAATA
1 AAATAATCAAA-ATTA
53535768 AAATAATCAAAATTA
1 AAATAATCAAAATTA
53535783 AAATAAT-AAAATT
1 AAATAATCAAAATT
53535796 GGATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAATCAAAATTA
Found at i:53540230 original size:9 final size:9
Alignment explanation
Indices: 53540216--53540246 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53540206 GTTAAACGAA
53540216 TCGAGTTAT
1 TCGAGTTAT
*
53540225 TCGAGTTAA
1 TCGAGTTAT
53540234 TCGAGTTAT
1 TCGAGTTAT
53540243 TCGA
1 TCGA
53540247 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53540317 original size:9 final size:9
Alignment explanation
Indices: 53540300--53540336 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53540290 TGAGTTTTCG
53540300 AATTCGAAT
1 AATTCGAAT
*
53540309 AACTCGAAT
1 AATTCGAAT
53540318 AATTCGAAT
1 AATTCGAAT
53540327 AATTCGAAT
1 AATTCGAAT
53540336 A
1 A
53540337 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53540598 original size:30 final size:31
Alignment explanation
Indices: 53540550--53540609 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
53540540 AAACCTTTTA
* *
53540550 TTTTCCCCCCAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
53540580 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
53540610 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:53549221 original size:18 final size:18
Alignment explanation
Indices: 53549193--53549246 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
53549183 TATATTATTT
*
53549193 TTTAAAAAATA-AAGTAA
1 TTTAAAAAATATAAATAA
*
53549210 TTATAAATAATATAAATAA
1 TT-TAAAAAATATAAATAA
53549229 TTTAAAAAA-AT-AATAA
1 TTTAAAAAATATAAATAA
53549245 TT
1 TT
53549247 GAACTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.22
17 4 0.12
18 14 0.44
19 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATATAAATAA
Found at i:53550922 original size:4 final size:4
Alignment explanation
Indices: 53550913--53550945 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
53550903 GCTACAATAA
53550913 AACT AACT AACT AACT AACT AACT AACT AACT A
1 AACT AACT AACT AACT AACT AACT AACT AACT A
53550946 TCAAATTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
AACT
Found at i:53551221 original size:22 final size:22
Alignment explanation
Indices: 53551196--53551237 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53551186 TTAATATCGC
*
53551196 GATACCCAAACTTCGATATCAT
1 GATACCCAAACTTCAATATCAT
*
53551218 GATACCCAATCTTCAATATC
1 GATACCCAAACTTCAATATC
53551238 GCAATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (22 bp):
GATACCCAAACTTCAATATCAT
Found at i:53558584 original size:34 final size:34
Alignment explanation
Indices: 53558546--53558722 Score: 131
Period size: 34 Copynumber: 5.1 Consensus size: 34
53558536 CAACTAGTGT
* *
53558546 TGGGCACAACCATCGTCGGTTGTCCGACTAGCGC
1 TGGGCACAACCATCGTCGGTTATCTGACTAGCGC
* * * * * *
53558580 TGGGCGCAA-CTTCTGTCAGTTTATCTAACCAGCGT
1 TGGGCACAACCATC-GTC-GGTTATCTGACTAGCGC
* * * * * *
53558615 TGGGTACAATCATCGTCTGTTATCCGATTAGCAC
1 TGGGCACAACCATCGTCGGTTATCTGACTAGCGC
* ** ** *
53558649 TGGGCGCAACTTTCGTCAATTTATCTGACTAGTGC
1 TGGGCACAACCATCGTC-GGTTATCTGACTAGCGC
*
53558684 TGGGCACAACCATCGTCGGTTATCTGACTAGCAC
1 TGGGCACAACCATCGTCGGTTATCTGACTAGCGC
53558718 TGGGC
1 TGGGC
53558723 GCAAAACATT
Statistics
Matches: 102, Mismatches: 37, Indels: 8
0.69 0.25 0.05
Matches are distributed among these distances:
33 3 0.03
34 50 0.49
35 46 0.45
36 3 0.03
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (34 bp):
TGGGCACAACCATCGTCGGTTATCTGACTAGCGC
Found at i:53558655 original size:69 final size:69
Alignment explanation
Indices: 53558544--53558726 Score: 242
Period size: 69 Copynumber: 2.7 Consensus size: 69
53558534 TTCAACTAGT
* * *
53558544 GTTGGGCACAACCATCGTCGGTTGTCCGACTAGCGCTGGGCGCAAC-TTCTGTCAGTTTATCTAA
1 GTTGGGCACAACCATCGTCGGTTATCCGACTAGCACTGGGCGCAACTTTC-GTCAATTTATCTAA
53558608 CCAGC
65 CCAGC
* * * * *
53558613 GTTGGGTACAATCATCGTCTGTTATCCGATTAGCACTGGGCGCAACTTTCGTCAATTTATCTGAC
1 GTTGGGCACAACCATCGTCGGTTATCCGACTAGCACTGGGCGCAACTTTCGTCAATTTATCTAAC
* *
53558678 TAGT
66 CAGC
* *
53558682 GCTGGGCACAACCATCGTCGGTTATCTGACTAGCACTGGGCGCAA
1 GTTGGGCACAACCATCGTCGGTTATCCGACTAGCACTGGGCGCAA
53558727 AACATTGTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
69 94 0.97
70 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (69 bp):
GTTGGGCACAACCATCGTCGGTTATCCGACTAGCACTGGGCGCAACTTTCGTCAATTTATCTAAC
CAGC
Found at i:53569025 original size:21 final size:21
Alignment explanation
Indices: 53568999--53569039 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53568989 AGACGAGCAA
* *
53568999 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
53569020 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
53569040 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:53573124 original size:29 final size:27
Alignment explanation
Indices: 53573091--53573169 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 27
53573081 AGAAATCTCA
* *
53573091 AATTTTATATGAATTTTGGTTTAATGTAT
1 AATTTTATATAAATTTTGATTT--TGTAT
53573120 AATTTTACATATAAATTTTGATTTTGTAT
1 AATTTT--ATATAAATTTTGATTTTGTAT
* *
53573149 AATTTTAT-GAAATTTAGATTT
1 AATTTTATATAAATTTTGATTT
53573170 GATTCAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.25
27 2 0.05
29 17 0.39
31 14 0.32
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (27 bp):
AATTTTATATAAATTTTGATTTTGTAT
Found at i:53573139 original size:31 final size:29
Alignment explanation
Indices: 53573097--53573155 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
53573087 CTCAAATTTT
* *
53573097 ATATGAATTTTGGTTTAATGTATAATTTTAC
1 ATATAAATTTTGATTT--TGTATAATTTTAC
53573128 ATATAAATTTTGATTTTGTATAATTTTA
1 ATATAAATTTTGATTTTGTATAATTTTA
53573156 TGAAATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
31 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (29 bp):
ATATAAATTTTGATTTTGTATAATTTTAC
Found at i:53580591 original size:43 final size:43
Alignment explanation
Indices: 53580521--53580603 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
53580511 ATATTCTAGA
* * * *
53580521 AAGGACAGAAATCAACTAAAGTGAAATCGCAATAGAGAAACCT
1 AAGGAAAGAAATCAACTAAAATAAAATCACAATAGAGAAACCT
* *
53580564 AAGGAAAGAAATCAATTAAAATAAAATCACAATCGAGAAA
1 AAGGAAAGAAATCAACTAAAATAAAATCACAATAGAGAAA
53580604 TCTACTGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.57, C:0.13, G:0.16, T:0.14
Consensus pattern (43 bp):
AAGGAAAGAAATCAACTAAAATAAAATCACAATAGAGAAACCT
Found at i:53583655 original size:5 final size:5
Alignment explanation
Indices: 53583645--53583680 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
53583635 TCAGGTTTGC
53583645 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
53583681 TACCCCACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:53586554 original size:79 final size:79
Alignment explanation
Indices: 53586240--53586555 Score: 398
Period size: 79 Copynumber: 4.0 Consensus size: 79
53586230 GGCTCTCATG
* * * * *
53586240 ACTTTTTGCACAAGGTTTAAAGTTGGTAGGTTGCCAATGAGGTACATTGGTGCTCCTTTTGTTTC
1 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTGCCAATGAGGTACTTTGGTGCTCCTCTTGTTTC
* **
53586305 TCGAAAGCAATCTC
66 TCGGAAGCTGTCTC
* * *
53586319 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTACCAATGAGGTACCTTGGTGCACCTCTTGTTTC
1 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTGCCAATGAGGTACTTTGGTGCTCCTCTTGTTTC
*
53586384 TTGGAAGCTGTCTC
66 TCGGAAGCTGTCTC
* * * * * *
53586398 ACTTCTTGCACAAGGTTTAAAGTCGGTAGGCTGCTAGTGAGGTACTTCGGTGTTCCTCTTGTTTC
1 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTGCCAATGAGGTACTTTGGTGCTCCTCTTGTTTC
* *
53586463 TTGGAAGATGTCTC
66 TCGGAAGCTGTCTC
** * * *
53586477 ACTTCTTATACAAGGTTTAAAGTTGGTAAGCTGCTAGTGAGGTACTTTGGTGTTCCTCTTGTTTC
1 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTGCCAATGAGGTACTTTGGTGCTCCTCTTGTTTC
*
53586542 TCGGAAGTTGTCTC
66 TCGGAAGCTGTCTC
53586556 GATCTAACTG
Statistics
Matches: 209, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 209 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (79 bp):
ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTGCCAATGAGGTACTTTGGTGCTCCTCTTGTTTC
TCGGAAGCTGTCTC
Found at i:53586846 original size:76 final size:76
Alignment explanation
Indices: 53586751--53586898 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 76
53586741 TTCATATCAT
53586751 AAACCAAACAAAATAAATCATATAGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTA-A
1 AAACCAAACAAAATAAATCATATAGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAGA
53586815 AAATAAGTTGGG
66 AAA-AAGTTGGG
* * * * *
53586827 AAACCAAACAAAACT-AATCATGTGGTCCCTTATATGAACTCTCGAGGCCCAAAATATACATTAG
1 AAACCAAACAAAA-TAAATCATATAGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAG
53586891 AAAAAAGT
65 AAAAAAGT
53586899 CGAGACTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
76 60 0.92
77 5 0.08
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (76 bp):
AAACCAAACAAAATAAATCATATAGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAGA
AAAAAGTTGGG
Found at i:53588192 original size:24 final size:24
Alignment explanation
Indices: 53588144--53588202 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
53588134 TGCAAACATG
*
53588144 TAAACGGGAAGCTCTTTCGAGCCA
1 TAAACGGGAAGCTCTATCGAGCCA
53588168 TATAACGGGAAGCTC-ATCGAGCCA
1 TA-AACGGGAAGCTCTATCGAGCCA
*
53588192 TAATCGGGAAG
1 TAAACGGGAAG
53588203 TTCAAGCGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 8 0.25
24 12 0.38
25 12 0.38
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (24 bp):
TAAACGGGAAGCTCTATCGAGCCA
Found at i:53588212 original size:24 final size:24
Alignment explanation
Indices: 53588146--53588215 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
53588136 CAAACATGTA
**
53588146 AACGGGAAGCTCTTTCGAGCCATAT
1 AACGGGAAGCTC-AGCGAGCCATAT
*
53588171 AACGGGAAGCTCATCGAGCCATA-
1 AACGGGAAGCTCAGCGAGCCATAT
* *
53588194 ATCGGGAAGTTCAAGCGAGCCA
1 AACGGGAAGCTC-AGCGAGCCA
53588216 ATATCAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 10 0.25
24 18 0.45
25 12 0.30
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.17
Consensus pattern (24 bp):
AACGGGAAGCTCAGCGAGCCATAT
Found at i:53588288 original size:25 final size:25
Alignment explanation
Indices: 53588224--53588288 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
53588214 CAATATCAAG
* * **
53588224 AAGCTCGTGAGAGCCAAATATCGGG
1 AAGCTCGTGAGAGCTAAATAACGAC
* * *
53588249 ATGCTCATAAGAGCTAAATAACGAC
1 AAGCTCGTGAGAGCTAAATAACGAC
53588274 AAGCTCGTGAGAGCT
1 AAGCTCGTGAGAGCT
53588289 GTGATGTATC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (25 bp):
AAGCTCGTGAGAGCTAAATAACGAC
Found at i:53590478 original size:2 final size:2
Alignment explanation
Indices: 53590471--53590507 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53590461 CCCTACTTTA
53590471 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
53590508 ATATTTATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53590835 original size:18 final size:19
Alignment explanation
Indices: 53590800--53590851 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
53590790 TAAATTATTT
53590800 TTTTAATTAAGTAATAATA
1 TTTTAATTAAGTAATAATA
**
53590819 TTTTAA-TAAGTGCTAATA
1 TTTTAATTAAGTAATAATA
*
53590837 TTTT-ATTAATTAATA
1 TTTTAATTAAGTAATA
53590852 TTATAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.04
18 20 0.74
19 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAATTAAGTAATAATA
Found at i:53597607 original size:36 final size:36
Alignment explanation
Indices: 53597566--53597756 Score: 229
Period size: 36 Copynumber: 5.0 Consensus size: 36
53597556 GGTAGCTTTA
53597566 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
53597602 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
53597647 AGCTACACTTATCTGATCAAGTGAAAAAGTAATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
53597684 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
53597720 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
53597756 G
1 G
53597757 GTAGTTTAGC
Statistics
Matches: 135, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
36 98 0.73
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 29 0.21
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:53597667 original size:82 final size:82
Alignment explanation
Indices: 53597530--53597720 Score: 328
Period size: 82 Copynumber: 2.3 Consensus size: 82
53597520 TTTGAGTACT
*
53597530 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
53597595 GATAAGTGCTACACTTA
66 AATAAGTGCTACACTTA
*
53597612 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
53597677 AATAAGTGTTATACTTA
66 AATAAGTGCTACACTTA
*
53597694 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
53597721 CTATACTTAT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
AATAAGTGCTACACTTA
Found at i:53604514 original size:14 final size:13
Alignment explanation
Indices: 53604478--53604519 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
53604468 AGTCTCCAAT
53604478 TATAATAAATATGA
1 TATAATAAATAT-A
53604492 TATAATAAATATA
1 TATAATAAATATA
*
53604505 TCATAGTAAA-ATA
1 T-ATAATAAATATA
53604518 TA
1 TA
53604520 CCTGAGATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 6 0.23
14 19 0.73
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (13 bp):
TATAATAAATATA
Found at i:53604829 original size:15 final size:16
Alignment explanation
Indices: 53604809--53604839 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53604799 TAATAACAAT
53604809 AATTTAATCAT-AAAA
1 AATTTAATCATCAAAA
53604824 AATTTAATCATCAAAA
1 AATTTAATCATCAAAA
53604840 TACCATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTTAATCATCAAAA
Found at i:53608350 original size:30 final size:28
Alignment explanation
Indices: 53608272--53608351 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 28
53608262 TCCTTAACAC
* *
53608272 TTATAAATTCTATCAAATTAACTCCAAT
1 TTATAAATTCTATCAATTTAACCCCAAT
* *
53608300 TCTAAATAATT-TAATAAATTTAACCCTCACAT
1 T-TATA-AATTCT-ATCAATTTAACCC-CA-AT
53608332 TTATAAATTCTATCAATTTA
1 TTATAAATTCTATCAATTTA
53608352 GCTCTCAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
28 1 0.03
29 4 0.10
30 26 0.65
31 6 0.15
32 3 0.08
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.41
Consensus pattern (28 bp):
TTATAAATTCTATCAATTTAACCCCAAT
Found at i:53617287 original size:21 final size:21
Alignment explanation
Indices: 53617248--53617289 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53617238 TTTGCCTAAT
* *
53617248 ATATGAATTGGATTGAATTGA
1 ATATGAATTGGACTAAATTGA
*
53617269 ATATGAATTGTACTAAATTGA
1 ATATGAATTGGACTAAATTGA
53617290 GCTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (21 bp):
ATATGAATTGGACTAAATTGA
Found at i:53617795 original size:25 final size:25
Alignment explanation
Indices: 53617724--53617795 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
53617714 GTCCCGGTAT
*
53617724 ATGGCTCTTCGTGAGCTTCCTAATTA
1 ATGGCTCTTCG-GAGCTTCCCAATTA
* * * **
53617750 AAGGTTATTTTTGAGCTTCCCAATTA
1 ATGGCT-CTTCGGAGCTTCCCAATTA
53617776 ATGGCTCTTCGGAGCTTCCC
1 ATGGCTCTTCGGAGCTTCCC
53617796 GATATGGCTC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
25 11 0.32
26 21 0.62
27 2 0.06
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (25 bp):
ATGGCTCTTCGGAGCTTCCCAATTA
Found at i:53617889 original size:49 final size:50
Alignment explanation
Indices: 53617835--53617979 Score: 138
Period size: 49 Copynumber: 2.9 Consensus size: 50
53617825 TGGCTATCTA
* *
53617835 AAGTTTCCTGATTAATGGCTCTTCGGAGCTACCCGTTAT-TGGCTCGCAT
1 AAGTTTCCTGATTAATGGCTCTTAGGAGCTACCCGTTATATAGCTCGCAT
* * * * *
53617884 GAGTTTCCTGATT-ATAGCTCTTATGAGCTTCCCGTTATATAGCTCGGAT
1 AAGTTTCCTGATTAATGGCTCTTAGGAGCTACCCGTTATATAGCTCGCAT
* * *
53617933 AAGTTTCCCG-TTACATGGCTCATTTA--AGCTTCTCGTTATATAGCTCG
1 AAGTTTCCTGATTA-ATGGCTC--TTAGGAGCTACCCGTTATATAGCTCG
53617980 AAAGAGAGCT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
48 23 0.29
49 28 0.35
50 26 0.32
52 3 0.04
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (50 bp):
AAGTTTCCTGATTAATGGCTCTTAGGAGCTACCCGTTATATAGCTCGCAT
Found at i:53617903 original size:24 final size:25
Alignment explanation
Indices: 53617876--53617942 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
53617866 CCCGTTATTG
*
53617876 GCTCGCATGAGTTTCCTGAT-TATA
1 GCTCGCATGAGTTTCCCGATATATA
** * *
53617900 GCTCTTATGAGCTTCCCGTTATATA
1 GCTCGCATGAGTTTCCCGATATATA
* *
53617925 GCTCGGATAAGTTTCCCG
1 GCTCGCATGAGTTTCCCG
53617943 TTACATGGCT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (25 bp):
GCTCGCATGAGTTTCCCGATATATA
Found at i:53617940 original size:25 final size:25
Alignment explanation
Indices: 53617909--53617979 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
53617899 AGCTCTTATG
53617909 AGCTTCCCGTTATATAGCTCGGATA
1 AGCTTCCCGTTATATAGCTCGGATA
* * * ***
53617934 AGTTTCCCGTTACATGGCTCATTTA
1 AGCTTCCCGTTATATAGCTCGGATA
*
53617959 AGCTTCTCGTTATATAGCTCG
1 AGCTTCCCGTTATATAGCTCG
53617980 AAAGAGAGCT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (25 bp):
AGCTTCCCGTTATATAGCTCGGATA
Found at i:53622165 original size:139 final size:139
Alignment explanation
Indices: 53621915--53622206 Score: 512
Period size: 139 Copynumber: 2.1 Consensus size: 139
53621905 GTTACACTAG
* *
53621915 CACACGGGCGTGTGGCTTGGCTGTGTGACCTAAGTTAAAGAGTTAGATGGGTACCAACACAGGCT
1 CACACGGGCGTGTGGCTTGGCTATGTGACCTAAGTCAAAGAGTTAGATGGGTACCAACACAGGCT
*
53621980 GGGACACGGCCGTGTGCCCTATTTTGAATGCCCACATGGCCTGAGACATGGGCATGTCTCTTGGC
66 GGGACACGGCCGTGTGCCCTATTTTGAATGCCCACACGGCCTGAGACATGGGCATGTCTCTTGGC
53622045 CGTGTGAAC
131 CGTGTGAAC
* *
53622054 CACACGGGCGTGTGGCTTGGCTATGTGACTTAAGTCAGAGAGTTAGATGGGTACCAACACAGGCT
1 CACACGGGCGTGTGGCTTGGCTATGTGACCTAAGTCAAAGAGTTAGATGGGTACCAACACAGGCT
*
53622119 GGGACACGGCCGTGTGCCCTATTTTGAATGCCCACACGGCCTGAGACATGGGCGTGTCTCTTGGC
66 GGGACACGGCCGTGTGCCCTATTTTGAATGCCCACACGGCCTGAGACATGGGCATGTCTCTTGGC
*
53622184 TGTGTGAAC
131 CGTGTGAAC
*
53622193 CACATGGGCGTGTG
1 CACACGGGCGTGTG
53622207 TCCTCTGCAC
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 145 1.00
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.24
Consensus pattern (139 bp):
CACACGGGCGTGTGGCTTGGCTATGTGACCTAAGTCAAAGAGTTAGATGGGTACCAACACAGGCT
GGGACACGGCCGTGTGCCCTATTTTGAATGCCCACACGGCCTGAGACATGGGCATGTCTCTTGGC
CGTGTGAAC
Found at i:53623337 original size:14 final size:14
Alignment explanation
Indices: 53623318--53623344 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53623308 CATGATAAAA
53623318 TAAAATACAAGTGG
1 TAAAATACAAGTGG
53623332 TAAAATACAAGTG
1 TAAAATACAAGTG
53623345 TGCAAGAGAA
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:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:53624919 original size:12 final size:12
Alignment explanation
Indices: 53624902--53624929 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53624892 TGTAGAGATC
53624902 GAATTAAAGGAT
1 GAATTAAAGGAT
53624914 GAATTAAAGGAT
1 GAATTAAAGGAT
53624926 GAAT
1 GAAT
53624930 ATGAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
GAATTAAAGGAT
Found at i:53628920 original size:43 final size:43
Alignment explanation
Indices: 53628857--53628940 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
53628847 ATTGCTTGTT
* * * *
53628857 ATACCTTGTGTAATATGCTTCGCGAACTTTATAGTGCACCTTG
1 ATACCTTATGTAATAGGCTTCACGAACCTTATAGTGCACCTTG
* * *
53628900 ATACCTTATGTAATGGGCTTCACGGACCTTATAGTGTACCT
1 ATACCTTATGTAATAGGCTTCACGAACCTTATAGTGCACCT
53628941 CACGAACTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (43 bp):
ATACCTTATGTAATAGGCTTCACGAACCTTATAGTGCACCTTG
Found at i:53631363 original size:20 final size:21
Alignment explanation
Indices: 53631330--53631368 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
53631320 TAATTAAAAA
53631330 TTACTATATTTATTAAATATT
1 TTACTATATTTATTAAATATT
*
53631351 TTACTAT-TTTATTGAATA
1 TTACTATATTTATTAAATA
53631369 ATATGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (21 bp):
TTACTATATTTATTAAATATT
Found at i:53632055 original size:14 final size:14
Alignment explanation
Indices: 53632036--53632071 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
53632026 TTGTTTCACT
*
53632036 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
53632050 GAAAATGATTTCTG
1 GAAAATGATTTCTG
53632064 GAAAATGA
1 GAAAATGA
53632072 CTTACTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:53634469 original size:18 final size:19
Alignment explanation
Indices: 53634433--53634473 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53634423 ATTTATTTTA
53634433 AAAAATAATCAAAGAAAAG
1 AAAAATAATCAAAGAAAAG
*
53634452 AAAAAT-ATCCAAAGAAAGG
1 AAAAATAAT-CAAAGAAAAG
53634471 AAA
1 AAA
53634474 GTTTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAATAATCAAAGAAAAG
Found at i:53635618 original size:91 final size:91
Alignment explanation
Indices: 53635463--53635671 Score: 242
Period size: 91 Copynumber: 2.3 Consensus size: 91
53635453 TTAAAGGTGT
* * * *
53635463 AAAAGGCCCTCAAACTTTTTCAAAAAAAAGCAATTAAAGCCCTCATCTTTTTTTGCACTCAATTG
1 AAAAGGCCCTCAAACTTCTTCAAAAAAAACCAATTAAAGCCATCATCTTTTTTTCCACTCAATTG
53635528 AGCACTT-AATCTTTCAAAATGCATCA
66 AGCACTTGAA-CTTTCAAAATGCATCA
* ** * *
53635554 AAAAGGCCCTCAAACTTCTTCCAAAAAAAACCAA-TAAAGTCATTGTTTTTTTTTCCATTCAATT
1 AAAAGGCCCTCAAACTTCTT-CAAAAAAAACCAATTAAAGCCATCATCTTTTTTTCCACTCAATT
* **
53635618 GGGTGCTTGAACTTTCAAAATGCATCA
65 GAGCACTTGAACTTTCAAAATGCATCA
* * **
53635645 AAAAGACCCTAAAAAATCTTCAAAAAA
1 AAAAGGCCCTCAAACTTCTTCAAAAAA
53635672 GCAATTAATC
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
90 7 0.07
91 79 0.79
92 14 0.14
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.30
Consensus pattern (91 bp):
AAAAGGCCCTCAAACTTCTTCAAAAAAAACCAATTAAAGCCATCATCTTTTTTTCCACTCAATTG
AGCACTTGAACTTTCAAAATGCATCA
Found at i:53635840 original size:18 final size:19
Alignment explanation
Indices: 53635795--53635850 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
53635785 TAGAATTTTT
53635795 TTTATAAAAATCGTAAAAA
1 TTTATAAAAATCGTAAAAA
* * * *
53635814 ATAAAAAAAAT-GTAAAAG
1 TTTATAAAAATCGTAAAAA
*
53635832 TTTATAAAAATCATAAAAA
1 TTTATAAAAATCGTAAAAA
53635851 AATTATAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (19 bp):
TTTATAAAAATCGTAAAAA
Found at i:53636097 original size:12 final size:12
Alignment explanation
Indices: 53636080--53636117 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
53636070 TTATGTGGTG
53636080 AAAAATAATAAA
1 AAAAATAATAAA
53636092 AAAAATAA-AAA
1 AAAAATAATAAA
53636103 TAAAAATCAATAAA
1 -AAAAAT-AATAAA
53636117 A
1 A
53636118 GTTGTAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.13
12 14 0.61
13 3 0.13
14 3 0.13
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:53636185 original size:20 final size:20
Alignment explanation
Indices: 53636160--53636224 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
53636150 TACGATAATT
53636160 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
**
53636180 TTTAT-ATTTTTTTAC-ATT
1 TTTATAATTTTTTTACGAAA
* *
53636198 TTGTATAATTTTCTTATG-AA
1 TT-TATAATTTTTTTACGAAA
53636218 TTTATAA
1 TTTATAA
53636225 AATTTTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 3 0.08
19 18 0.50
20 15 0.42
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:53636236 original size:28 final size:29
Alignment explanation
Indices: 53636201--53636298 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
53636191 TTACATTTTG
53636201 TATAATTTTCTTATGA-ATTTATAAAATTT
1 TATAATTTT-TTATGACATTTATAAAATTT
* *
53636230 TAT-ATTTTTT-T-ACATTTCTATATATTT
1 TATAATTTTTTATGACATTTATA-AAATTT
* **
53636257 TATAATTTTTTACGATTTTTATAAAATTT
1 TATAATTTTTTATGACATTTATAAAATTT
*
53636286 TACAATTTTTTAT
1 TATAATTTTTTAT
53636299 TTTTTTACGA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
25 1 0.02
26 7 0.13
27 10 0.18
28 12 0.22
29 19 0.35
30 6 0.11
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (29 bp):
TATAATTTTTTATGACATTTATAAAATTT
Found at i:53636267 original size:10 final size:10
Alignment explanation
Indices: 53636180--53636344 Score: 59
Period size: 10 Copynumber: 17.4 Consensus size: 10
53636170 TTTTACGAAA
53636180 TTTAT-ATTT
1 TTTATAATTT
53636189 TTT-TACATTT
1 TTTATA-ATTT
*
53636199 TGTATAATTT
1 TTTATAATTT
53636209 TCTTATGAA---
1 T-TTAT-AATTT
**
53636218 TTTATAAAAT
1 TTTATAATTT
53636228 TTTAT-ATTT
1 TTTATAATTT
53636237 TTT-TACA-TT
1 TTTATA-ATTT
* *
53636246 TCTAT-ATAT
1 TTTATAATTT
53636255 TTTATAATTT
1 TTTATAATTT
**
53636265 TTTACGA-TT
1 TTTATAATTT
**
53636274 TTTATAAAAT
1 TTTATAATTT
*
53636284 TTTACAATTT
1 TTTATAATTT
53636294 TTTAT--TTT
1 TTTATAATTT
**
53636302 TTTACGA-TT
1 TTTATAATTT
*
53636311 TTTATATTTT
1 TTTATAATTT
*
53636321 TTTGTAATTT
1 TTTATAATTT
* *
53636331 TTGATAAATT
1 TTTATAATTT
53636341 TTTA
1 TTTA
53636345 ATATTTAAAT
Statistics
Matches: 112, Mismatches: 27, Indels: 33
0.65 0.16 0.19
Matches are distributed among these distances:
7 2 0.02
8 14 0.12
9 31 0.28
10 58 0.52
11 5 0.04
12 2 0.02
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (10 bp):
TTTATAATTT
Found at i:53636305 original size:28 final size:28
Alignment explanation
Indices: 53636218--53636297 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
53636208 TTCTTATGAA
*
53636218 TTTATAAAATTTTATATTTTTTTACATT
1 TTTATAAAATTTTATAATTTTTTACATT
* *
53636246 TCTAT-ATATTTTATAATTTTTTACGATT
1 TTTATAAAATTTTATAATTTTTTAC-ATT
*
53636274 TTTATAAAATTTTACAATTTTTTA
1 TTTATAAAATTTTATAATTTTTTA
53636298 TTTTTTTACG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 17 0.39
28 11 0.25
29 16 0.36
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTATAAAATTTTATAATTTTTTACATT
Found at i:53636314 original size:56 final size:54
Alignment explanation
Indices: 53636170--53636323 Score: 155
Period size: 56 Copynumber: 2.7 Consensus size: 54
53636160 TTTATAATTT
* * *
53636170 TTTTACGAAATTTATATTTTTTTACATTTTGTATAATTTTCTTATGAATTTATAAAA
1 TTTTAC-AATTTTTTATTTTTTTACATTTT-TATAATTTT-TTACGAATTTATAAAA
* * ** * * *
53636227 TTTTATATTTTTTTACATTTCTATATATTTTATAATTTTTTACGATTTTTATAAAA
1 TTTTACAATTTTTTATTTTTTTACAT-TTTTATAATTTTTTACGA-ATTTATAAAA
*
53636283 TTTTACAATTTTTTATTTTTTTACGATTTTTATATTTTTTT
1 TTTTACAATTTTTTATTTTTTTAC-ATTTTTATAATTTTTT
53636324 GTAATTTTTG
Statistics
Matches: 77, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
55 5 0.06
56 62 0.81
57 10 0.13
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (54 bp):
TTTTACAATTTTTTATTTTTTTACATTTTTATAATTTTTTACGAATTTATAAAA
Found at i:53636331 original size:56 final size:55
Alignment explanation
Indices: 53636155--53636344 Score: 143
Period size: 56 Copynumber: 3.3 Consensus size: 55
53636145 TTTCGTACGA
** * *
53636155 TAATTTTTATAATTTTTTTACGAAATTTATATTTTTTTACATTTTGTATAATTTTCTTATG
1 TAATTTTTATAA-AATTTTAC-AATTTTTTATTTTTTTACATTTT-TAT-ATTTT-TT-TG
* * ** * * * *
53636216 -AA--TTTATAAAATTTTATATTTTTTTACATTTCTATATATTTTATAATTTTTTA
1 TAATTTTTATAAAATTTTACAATTTTTTATTTTTTTACAT-TTTTATATTTTTTTG
**
53636269 CGATTTTTATAAAATTTTACAATTTTTTATTTTTTTACGATTTTTATATTTTTTTG
1 TAATTTTTATAAAATTTTACAATTTTTTATTTTTTTAC-ATTTTTATATTTTTTTG
*
53636325 TAATTTTTGATAAATTTTTA
1 TAATTTTT-ATAAAATTTTA
53636345 ATATTTAAAT
Statistics
Matches: 99, Mismatches: 24, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
53 1 0.01
54 3 0.03
55 4 0.04
56 62 0.63
57 20 0.20
58 7 0.07
60 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (55 bp):
TAATTTTTATAAAATTTTACAATTTTTTATTTTTTTACATTTTTATATTTTTTTG
Found at i:53636332 original size:19 final size:18
Alignment explanation
Indices: 53636283--53636323 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
53636273 TTTTATAAAA
53636283 TTTTACAATTTTTTATTT
1 TTTTACAATTTTTTATTT
*
53636301 TTTTACGATTTTTATATTT
1 TTTTACAATTTTT-TATTT
53636320 TTTT
1 TTTT
53636324 GTAATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTACAATTTTTTATTT
Found at i:53636573 original size:14 final size:15
Alignment explanation
Indices: 53636533--53636571 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
53636523 GAGCTTAATT
*
53636533 GTTTTTTTTTTAAAG
1 GTTTTTTTTTAAAAG
53636548 GTTTTTTTTTAAAAG
1 GTTTTTTTTTAAAAG
53636563 GTTTTTTTT
1 GTTTTTTTT
53636572 AATTTGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (15 bp):
GTTTTTTTTTAAAAG
Found at i:53642232 original size:56 final size:56
Alignment explanation
Indices: 53642146--53642261 Score: 232
Period size: 56 Copynumber: 2.1 Consensus size: 56
53642136 CCTGTTATAA
53642146 TTGACAATACAAAGGCCATATATTAAATAACACTAACAAATAAGGTAAAGTACTCC
1 TTGACAATACAAAGGCCATATATTAAATAACACTAACAAATAAGGTAAAGTACTCC
53642202 TTGACAATACAAAGGCCATATATTAAATAACACTAACAAATAAGGTAAAGTACTCC
1 TTGACAATACAAAGGCCATATATTAAATAACACTAACAAATAAGGTAAAGTACTCC
53642258 TTGA
1 TTGA
53642262 ATAAACAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.24
Consensus pattern (56 bp):
TTGACAATACAAAGGCCATATATTAAATAACACTAACAAATAAGGTAAAGTACTCC
Found at i:53647468 original size:29 final size:29
Alignment explanation
Indices: 53647427--53647503 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
53647417 TTTGCCTCAG
*
53647427 ATTACATTTTAGTCACTTATGTTTGAAAT
1 ATTACGTTTTAGTCACTTATGTTTGAAAT
53647456 ATTACGTTTTAGTCACTTATGTTTGAAAT
1 ATTACGTTTTAGTCACTTATGTTTGAAAT
*
53647485 GTTACGTTTTAGTCACTTA
1 ATTACGTTTTAGTCACTTA
53647504 CGTTATCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (29 bp):
ATTACGTTTTAGTCACTTATGTTTGAAAT
Found at i:53654633 original size:12 final size:12
Alignment explanation
Indices: 53654618--53654642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53654608 GGAGAAGCCC
53654618 TAAAAGAACATA
1 TAAAAGAACATA
53654630 TAAAAGAACATA
1 TAAAAGAACATA
53654642 T
1 T
53654643 GTTCTTTTTG
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:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (12 bp):
TAAAAGAACATA
Found at i:53655059 original size:18 final size:18
Alignment explanation
Indices: 53655033--53655073 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
53655023 AATTTTTTAT
*
53655033 TTATTATTA-TATTA-TA
1 TTATTATCATTATTACTA
53655049 -TATTATCATTATTACTA
1 TTATTATCATTATTACTA
53655066 TTATTATC
1 TTATTATC
53655074 TCCATATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 2 0.10
18 7 0.33
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATCATTATTACTA
Found at i:53655172 original size:5 final size:5
Alignment explanation
Indices: 53655162--53655195 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
53655152 ATACATATGT
53655162 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTT
53655196 CCTAACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:53659069 original size:30 final size:30
Alignment explanation
Indices: 53659035--53659093 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
53659025 CTTAACAAGC
53659035 AAATGCCTCTAAAATAATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* *
53659065 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
53659094 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:53664797 original size:32 final size:32
Alignment explanation
Indices: 53664756--53664828 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
53664746 AATGATATTA
53664756 GATATTGAATTTATTATGTTTTAAGCTTGTTG
1 GATATTGAATTTATTATGTTTTAAGCTTGTTG
*
53664788 GATATTGAATTTATTATGTTTTAAGTTTGTTG
1 GATATTGAATTTATTATGTTTTAAGCTTGTTG
53664820 GATATTGAA
1 GATATTGAA
53664829 ATGATTGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.27, C:0.01, G:0.19, T:0.52
Consensus pattern (32 bp):
GATATTGAATTTATTATGTTTTAAGCTTGTTG
Found at i:53664997 original size:48 final size:48
Alignment explanation
Indices: 53664929--53665021 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
53664919 CCTCTTTTTC
53664929 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTATTT
1 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTATTT
53664977 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTA
1 TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTA
53665022 ATACTTTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (48 bp):
TTGAAATTCTAGCAGAGGAGGCCAAGAGAGGAAATAAGCCTTCTATTT
Found at i:53666206 original size:20 final size:19
Alignment explanation
Indices: 53666161--53666206 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
53666151 AAAACAAGAC
53666161 TAGAAAAATAAATCATTTT
1 TAGAAAAATAAATCATTTT
* *
53666180 TAAAAAAATAAATTATTTT
1 TAGAAAAATAAATCATTTT
53666199 TCAGAAAA
1 T-AGAAAA
53666207 TATTTTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (19 bp):
TAGAAAAATAAATCATTTT
Found at i:53681701 original size:21 final size:21
Alignment explanation
Indices: 53681675--53681730 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
53681665 AACAACGGTG
*
53681675 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGATATTGTA
*
53681696 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATATTGTA
*
53681717 ACGGTGAGATTAGA
1 GCGGTGAGATTAGA
53681731 ACAATGGTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.36, T:0.32
Consensus pattern (21 bp):
GCGGTGAGATTAGATATTGTA
Found at i:53682512 original size:29 final size:29
Alignment explanation
Indices: 53682448--53682541 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
53682438 CAGATTAATT
53682448 TTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTATTTTTAAAATACACTACATATA
53682477 TATTTTTATTTTTAAAATACACTACATATA
1 T-TTTTTATTTTTAAAATACACTACATATA
53682507 TTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTATTTTTAAAATACACTACATATA
53682536 TTTTTT
1 TTTTTT
53682542 TTATTGAAGC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 35 0.55
30 29 0.45
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTTTATTTTTAAAATACACTACATATA
Found at i:53684774 original size:24 final size:27
Alignment explanation
Indices: 53684720--53684771 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 27
53684710 AATGTGTATC
53684720 AATTCGAAAAAATAACATTTACTTTGT
1 AATTCGAAAAAATAACATTTACTTTGT
53684747 AATT-GAAAAAA-AA-A-TTACTTTGT
1 AATTCGAAAAAATAACATTTACTTTGT
53684770 AA
1 AA
53684772 ATTTTAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.44
24 1 0.04
25 2 0.08
26 7 0.28
27 4 0.16
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (27 bp):
AATTCGAAAAAATAACATTTACTTTGT
Found at i:53685064 original size:23 final size:22
Alignment explanation
Indices: 53685013--53685068 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
53685003 GGTCTCCATA
*
53685013 TTTTTCGTTTTAAGTAATTTAAT
1 TTTTTC-TTTTAAGTAATTTAAC
53685036 TGTTTTCTTTTATA-TAATTTTAAC
1 T-TTTTCTTTTA-AGTAA-TTTAAC
53685060 TTTTT-TTTT
1 TTTTTCTTTT
53685069 CATTCTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 4 0.14
23 13 0.45
24 12 0.41
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTTCTTTTAAGTAATTTAAC
Found at i:53685065 original size:24 final size:23
Alignment explanation
Indices: 53685013--53685065 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
53685003 GGTCTCCATA
53685013 TTTTTCGTTTTAAGTAATTTAAT
1 TTTTTCGTTTTAAGTAATTTAAT
53685036 TGTTTTC-TTTTATA-TAATTTTAACT
1 T-TTTTCGTTTTA-AGTAA-TTTAA-T
53685061 TTTTT
1 TTTTT
53685066 TTTCATTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
23 9 0.35
24 15 0.58
25 2 0.08
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (23 bp):
TTTTTCGTTTTAAGTAATTTAAT
Found at i:53686579 original size:23 final size:23
Alignment explanation
Indices: 53686549--53686596 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
53686539 CAAAACGATG
* *
53686549 AAATCTTAGTA-ACATTTTATTTT
1 AAATCTTAATATA-ATTATATTTT
53686572 AAATCTTAATATAATTATATTTT
1 AAATCTTAATATAATTATATTTT
53686595 AA
1 AA
53686597 TAGTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATCTTAATATAATTATATTTT
Found at i:53697606 original size:29 final size:29
Alignment explanation
Indices: 53697573--53697631 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
53697563 TCGTCCTTCC
53697573 TTTTCTATTTTTT-AATAAATGGCCCAATA
1 TTTTC-ATTTTTTGAATAAATGGCCCAATA
* *
53697602 TTTTCATTTTTTGCATAAATGGCCTAATA
1 TTTTCATTTTTTGAATAAATGGCCCAATA
53697631 T
1 T
53697632 GTTTATGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (29 bp):
TTTTCATTTTTTGAATAAATGGCCCAATA
Found at i:53704526 original size:17 final size:18
Alignment explanation
Indices: 53704452--53704530 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
53704442 AATTAGAAAA
*
53704452 AAATTTATAA-AAAATAAT
1 AAATTT-TAATAAAATTAT
53704470 AAATTTTAGA-AAAATTATT
1 AAATTTTA-ATAAAATTA-T
*
53704489 AAATTTTAATAAAAATAT
1 AAATTTTAATAAAATTAT
53704507 AAATTATT-AT-AAATTAT
1 AAATT-TTAATAAAATTAT
53704524 AAATTTT
1 AAATTTT
53704531 TTATAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.04
17 13 0.24
18 22 0.41
19 17 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
AAATTTTAATAAAATTAT
Found at i:53704534 original size:18 final size:17
Alignment explanation
Indices: 53704481--53704537 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
53704471 AATTTTAGAA
*
53704481 AAATTATTAAATTTTAAT
1 AAATTA-TAAATTTTTAT
* *
53704499 AAAAATATAAATTATTAT
1 -AAATTATAAATTTTTAT
53704517 AAATTATAAATTTTTTAT
1 AAATTATAAA-TTTTTAT
53704535 AAA
1 AAA
53704538 AATCATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 9 0.28
18 18 0.56
19 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTATAAATTTTTAT
Found at i:53704537 original size:36 final size:37
Alignment explanation
Indices: 53704455--53704583 Score: 104
Period size: 37 Copynumber: 3.5 Consensus size: 37
53704445 TAGAAAAAAA
53704455 TTTATAAAAAATAATAAATTTTAGAAAAATTATTAAATT
1 TTTAT-AAAAATAATAAATTTTA-AAAAATTATTAAATT
* *
53704494 TTAATAAAAAT-ATAAATTATT-ATAAATTA-TAAATTT
1 TTTATAAAAATAATAAATT-TTAAAAAATTATTAAA-TT
* ** * * *
53704530 TTTATAAAAATCATAAAAAATAAAAAAATT-GTAAAAT
1 TTTATAAAAATAAT-AAATTTTAAAAAATTATTAAATT
*
53704567 TTTATAAAAATCATAAA
1 TTTATAAAAATAATAAA
53704584 AAAATAACGA
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
35 4 0.05
36 22 0.29
37 25 0.33
38 21 0.28
39 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (37 bp):
TTTATAAAAATAATAAATTTTAAAAAATTATTAAATT
Found at i:53704583 original size:19 final size:19
Alignment explanation
Indices: 53704450--53704584 Score: 93
Period size: 19 Copynumber: 7.2 Consensus size: 19
53704440 CAAATTAGAA
* *
53704450 AAAAATTTATAAAAAATA-
1 AAAATTTTATAAAAATTAT
*
53704468 ATAAATTTTAGAAAAATTAT
1 A-AAATTTTATAAAAATTAT
*
53704488 TAAATTTTAATAAAAA-TAT
1 AAAATTTT-ATAAAAATTAT
53704507 -AAATTATTAT--AAATTAT
1 AAAATT-TTATAAAAATTAT
* *
53704524 AAATTTTTTATAAAAATCAT
1 AAA-ATTTTATAAAAATTAT
** * *
53704544 AAAA-AATAAAAAAATTGT
1 AAAATTTTATAAAAATTAT
*
53704562 AAAATTTTATAAAAATCAT
1 AAAATTTTATAAAAATTAT
53704581 AAAA
1 AAAA
53704585 AAATAACGAC
Statistics
Matches: 89, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
16 3 0.03
17 3 0.03
18 27 0.30
19 41 0.46
20 15 0.17
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAATTTTATAAAAATTAT
Found at i:53704790 original size:29 final size:28
Alignment explanation
Indices: 53704757--53704861 Score: 124
Period size: 28 Copynumber: 3.7 Consensus size: 28
53704747 TTACATTTTG
*
53704757 TATAATTTTCTTATGACTTTATAAAATTT
1 TATAATTTTTTTATGA-TTTATAAAATTT
* *
53704786 TATAATTTTTTTAT-ATTTCTATATATTT
1 TATAATTTTTTTATGATTTATA-AAATTT
53704814 TATAATTTTTTTATGATTTTTATAAAATTT
1 TATAATTTTTTTATGA--TTTATAAAATTT
*
53704844 TACAATTTTTTTAT-ATTT
1 TATAATTTTTTTATGATTT
53704862 TTTACGATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
27 8 0.12
28 20 0.30
29 15 0.23
30 18 0.27
31 5 0.08
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (28 bp):
TATAATTTTTTTATGATTTATAAAATTT
Found at i:53704799 original size:11 final size:10
Alignment explanation
Indices: 53704783--53704891 Score: 59
Period size: 10 Copynumber: 11.2 Consensus size: 10
53704773 CTTTATAAAA
53704783 TTTTATAATT
1 TTTTATAATT
53704793 TTTT-T-ATAT
1 TTTTATAAT-T
* *
53704802 TTCTAT-ATA
1 TTTTATAATT
53704811 TTTTATAATTT
1 TTTTATAA-TT
*
53704822 TTTTATGA-T
1 TTTTATAATT
**
53704831 TTTTATAAAA
1 TTTTATAATT
*
53704841 TTTTACAATT
1 TTTTATAATT
53704851 TTTT-TATATT
1 TTTTATA-ATT
**
53704861 TTTTACGA-T
1 TTTTATAATT
*
53704870 TTTTATATTT
1 TTTTATAATT
*
53704880 TTTTCTAATT
1 TTTTATAATT
53704890 TT
1 TT
53704892 AATAAAACTT
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
8 2 0.03
9 25 0.34
10 38 0.52
11 8 0.11
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:53704823 original size:9 final size:9
Alignment explanation
Indices: 53704783--53704984 Score: 58
Period size: 9 Copynumber: 21.6 Consensus size: 9
53704773 CTTTATAAAA
53704783 TTTTATAAT
1 TTTTATAAT
*
53704792 TTTTTTATAT
1 TTTTATA-AT
*
53704802 TTCTAT-AT
1 TTTTATAAT
53704810 ATTTTATAATTT
1 -TTTTATAA--T
*
53704822 TTTTATGAT
1 TTTTATAAT
*
53704831 TTTTATAAAA
1 TTTTAT-AAT
*
53704841 TTTTACAAT
1 TTTTATAAT
*
53704850 TTTTTTATAT
1 TTTTATA-AT
53704860 TTTT-TACGAT
1 TTTTATA--AT
*
53704870 TTTTATATTT
1 TTTTATA-AT
*
53704880 TTTTCTAAT
1 TTTTATAAT
* *
53704889 TTTAATAAA
1 TTTTATAAT
**
53704898 ACTT-TAAT
1 TTTTATAAT
*
53704906 ATTT-TAAT
1 TTTTATAAT
*
53704914 ATTTTATTAAAA
1 -TTTTA-T-AAT
*
53704926 TTTAATAAT
1 TTTTATAAT
* **
53704935 ATTTATAGC
1 TTTTATAAT
53704944 TTTTAT--T
1 TTTTATAAT
53704951 TATTT-TAATT
1 T-TTTATAA-T
53704961 TTTTATAATT
1 TTTTATAA-T
53704971 TTTTATAAT
1 TTTTATAAT
53704980 TTTTA
1 TTTTA
53704985 ATAAAAGCAG
Statistics
Matches: 141, Mismatches: 34, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
7 2 0.01
8 15 0.11
9 59 0.42
10 48 0.34
11 14 0.10
12 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53704872 original size:58 final size:58
Alignment explanation
Indices: 53704736--53704903 Score: 198
Period size: 58 Copynumber: 2.9 Consensus size: 58
53704726 AATTATGAAA
* * *
53704736 TTTATATTTCTTTACATTTTGTATAATTTTCTTATGA-CTTTATAAAATTTTATAATTTT
1 TTTATATTTCTTTACA-TTT-TATAATTTTTTTATGATTTTTATAAAATTTTACAATTTT
* *
53704795 TTTATATTTCTATATATTTTATAATTTTTTTATGATTTTTATAAAATTTTACAATTTT
1 TTTATATTTCTTTACATTTTATAATTTTTTTATGATTTTTATAAAATTTTACAATTTT
* * * *
53704853 TTTATATTT-TTTACGATTTT-TATATTTTTTTCTAATTTTAATAAAACTTTA
1 TTTATATTTCTTTAC-ATTTTATA-ATTTTTTTATGATTTTTATAAAATTTTA
53704904 ATATTTTAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
57 20 0.21
58 61 0.64
59 14 0.15
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (58 bp):
TTTATATTTCTTTACATTTTATAATTTTTTTATGATTTTTATAAAATTTTACAATTTT
Found at i:53704969 original size:10 final size:10
Alignment explanation
Indices: 53704956--53704988 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
53704946 TTATTTATTT
53704956 TAATTTTTTA
1 TAATTTTTTA
53704966 TAATTTTTTA
1 TAATTTTTTA
*
53704976 TAATTTTTAA
1 TAATTTTTTA
53704986 TAA
1 TAA
53704989 AAGCAGGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:53704984 original size:19 final size:19
Alignment explanation
Indices: 53704751--53704984 Score: 83
Period size: 19 Copynumber: 12.4 Consensus size: 19
53704741 ATTTCTTTAC
*
53704751 ATTTTGTATAATTTTCTTATG
1 ATTTT-TATAATTTT-TTATA
* **
53704772 A-CTTTATAAAATTTTATA
1 ATTTTTATAATTTTTTATA
* *
53704790 ATTTTT-TTATATTTCTAT-
1 ATTTTTATAAT-TTTTTATA
*
53704808 ATATTTTATAATTTTTTTATG
1 AT-TTTTATAA-TTTTTTATA
** *
53704829 ATTTTTATAAAATTTTACA
1 ATTTTTATAATTTTTTATA
* **
53704848 ATTTTTTTATATTTTTTACG
1 ATTTTTATA-ATTTTTTATA
* *
53704868 ATTTTTATATTTTTTTCTA
1 ATTTTTATAATTTTTTATA
* ***
53704887 ATTTTAATAAAACTTTA-A
1 ATTTTTATAATTTTTTATA
*
53704905 TATTTTAAT-ATTTTATTA-A
1 -ATTTTTATAATTTT-TTATA
* * *
53704924 AATTTAATAA-TATTTATA
1 ATTTTTATAATTTTTTATA
**
53704942 GCTTTTAT--TTATTTTA-A
1 ATTTTTATAATT-TTTTATA
*
53704959 TTTTTTATAATTTTTTATA
1 ATTTTTATAATTTTTTATA
53704978 ATTTTTA
1 ATTTTTA
53704985 ATAAAAGCAG
Statistics
Matches: 155, Mismatches: 42, Indels: 34
0.67 0.18 0.15
Matches are distributed among these distances:
17 11 0.07
18 36 0.23
19 71 0.46
20 33 0.21
21 4 0.03
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTTATAATTTTTTATA
Found at i:53705089 original size:83 final size:84
Alignment explanation
Indices: 53704995--53705158 Score: 213
Period size: 85 Copynumber: 2.0 Consensus size: 84
53704985 ATAAAAGCAG
** * *
53704995 GGGCTTAATTGCTTTTTTTTAAA-TTTGAGGGTCTTTTTGATACATTTTAAAAATTCAAGTACCC
1 GGGCTTAATTGCTTTTTTGAAAAGTTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATACCC
*
53705059 AATTGAGTGCAAAAAAAAT
66 AAATGAGTGCAAAAAAAAT
* * * * * *
53705078 GGGCTTAATTGCTTTTTTGAAAAGGTTTGAGAGTTTTTTTTATGCATTTTGAAAGTTTAAATACC
1 GGGCTTAATTGCTTTTTTGAAAA-GTTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATACC
53705143 CAAATGAGTGCAAAAA
65 CAAATGAGTGCAAAAA
53705159 GAAAAAACAA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 21 0.31
85 47 0.69
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (84 bp):
GGGCTTAATTGCTTTTTTGAAAAGTTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATACCC
AAATGAGTGCAAAAAAAAT
Found at i:53708643 original size:21 final size:21
Alignment explanation
Indices: 53708593--53708644 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
53708583 TACATTTGGG
*
53708593 TCATTCAA-TTTTTTTTAAAA
1 TCATTAAATTTTTTTTTAAAA
* *
53708613 T-AATATAATTTTTTTTTAAAT
1 TCATTA-AATTTTTTTTTAAAA
53708634 TCATTAAATTT
1 TCATTAAATTT
53708645 ATTAGATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 17 0.68
22 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (21 bp):
TCATTAAATTTTTTTTTAAAA
Found at i:53724013 original size:191 final size:195
Alignment explanation
Indices: 53723681--53724072 Score: 648
Period size: 191 Copynumber: 2.0 Consensus size: 195
53723671 TATTTAGATT
*
53723681 ATAAAAGTTATTTAATTCTAGCATTTGAGTACACCAAAACTTGCATACTAGTTAAATGATTACTT
1 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTG---ACTAG-TAAATGATTACTT
* * *
53723746 AAATGGTAGTGTCTTGAGAAGGGCATGTTGGTTCTTTTACAGAAGCAACTTCACTTACTGTTTCT
62 AAATGGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCT
53723811 TAAGCAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTC
127 TAAGCAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTC
53723876 AGGG
192 AGGG
*
53723880 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTG-C-A-T-AATGCTTACTTAAAT
1 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTGACTAGTAAATGATTACTTAAAT
* *
53723941 GGTGGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTGCCGGTTCTTAAG
66 GGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCTTAAG
*
53724006 CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAATTCCAGATGGCCAATTTCAGGG
131 CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTCAGGG
53724071 AT
1 AT
53724073 TCCATTTGTC
Statistics
Matches: 185, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
191 140 0.76
192 1 0.01
194 1 0.01
195 1 0.01
199 42 0.23
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (195 bp):
ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTGACTAGTAAATGATTACTTAAAT
GGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCTTAAG
CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTCAGGG
Found at i:53725544 original size:28 final size:28
Alignment explanation
Indices: 53725504--53725561 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
53725494 ATGTAGGGGG
*
53725504 TTAAAATGTTTTTACATGAAATCCTTTC
1 TTAAAATGTTTTTACATGAAAGCCTTTC
53725532 TTAAAATGTTTTTACATGAAAGCCTTTC
1 TTAAAATGTTTTTACATGAAAGCCTTTC
53725560 TT
1 TT
53725562 TCCTCTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (28 bp):
TTAAAATGTTTTTACATGAAAGCCTTTC
Found at i:53730718 original size:113 final size:110
Alignment explanation
Indices: 53730399--53730726 Score: 395
Period size: 113 Copynumber: 2.9 Consensus size: 110
53730389 GCACCAGAGG
* * * *
53730399 CATTTAAATTTTTTTTTTGATGCTGGCCAATAGATGGCCGGTACCAAGTACATTTTTCGGCTCCC
1 CATTTAAATTTTTTTTTTGGTGCTGGCCAGTAGATGGTCGGCACCAAGTACATTTTTCGGCTCCC
** * *
53730464 AAGAAACTTTTTTTTACTTTGGGACACTGACGGCCTGCACTAGTGT
66 AAGGCA-TTTTTTTTACTTTGGGACACTGATGGCCAGCACTAGTGT
*** * * * *
53730510 CATTTAAAAAGTTTTTTGGGTGCTAGCGAGTAGATGGTCGGCACCAAGTACATTTTTCGGTTCCC
1 CATTTAAATTTTTTTTTTGGTGCTGGCCAGTAGATGGTCGGCACCAAGTACATTTTTCGGCTCCC
*
53730575 AATGCATTTTTTTTACTTTGGGACACTGATGGCCAGCACTAGTGT
66 AAGGCATTTTTTTTACTTTGGGACACTGATGGCCAGCACTAGTGT
* * * * *
53730620 CATTTTAAATTTTTTTTTCTTGGTGCTGGCCAGTAAATGGTCGACACCAAGTCCATCTTTCAGCT
1 CA-TTTAAA-TTTTTTTT-TTGGTGCTGGCCAGTAGATGGTCGGCACCAAGTACATTTTTCGGCT
** * *
53730685 CTTAAGGCATTTTTTTTACTTTGGGACATTGATGGCCCGCAC
63 CCCAAGGCATTTTTTTTACTTTGGGACACTGATGGCCAGCAC
53730727 CACCTTTTTC
Statistics
Matches: 181, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
110 39 0.22
111 63 0.35
112 5 0.03
113 74 0.41
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (110 bp):
CATTTAAATTTTTTTTTTGGTGCTGGCCAGTAGATGGTCGGCACCAAGTACATTTTTCGGCTCCC
AAGGCATTTTTTTTACTTTGGGACACTGATGGCCAGCACTAGTGT
Found at i:53733877 original size:22 final size:22
Alignment explanation
Indices: 53733852--53733919 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
53733842 TTCTTATTCC
53733852 TAATTTAAAACACATTAAATTA
1 TAATTTAAAACACATTAAATTA
** * *
53733874 TAATACAATATACA-TACATATT-
1 TAATTTAAAACACATTA-A-ATTA
*
53733896 TATTTTAAAACACATTAAATTA
1 TAATTTAAAACACATTAAATTA
53733918 TA
1 TA
53733920 TTAATTGAAC
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
21 5 0.15
22 23 0.70
23 5 0.15
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATTTAAAACACATTAAATTA
Found at i:53734091 original size:20 final size:20
Alignment explanation
Indices: 53734068--53734106 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53734058 GATGAAATAT
*
53734068 ATAAATTAATATGGAAAAAC
1 ATAAATTAAAATGGAAAAAC
53734088 ATAAATTAAAATGGAAAAA
1 ATAAATTAAAATGGAAAAA
53734107 AAGACAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAATTAAAATGGAAAAAC
Found at i:53734141 original size:16 final size:17
Alignment explanation
Indices: 53734117--53734158 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
53734107 AAGACAACTT
*
53734117 AAATGAAATGAG-AAAA
1 AAATTAAATGAGAAAAA
53734133 AAATTAAATGAGAAAAA
1 AAATTAAATGAGAAAAA
53734150 AAATTAAAT
1 AAATTAAAT
53734159 TTAAATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AAATTAAATGAGAAAAA
Found at i:53734150 original size:15 final size:16
Alignment explanation
Indices: 53734117--53734151 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53734107 AAGACAACTT
53734117 AAATGAAATGAGAAAA
1 AAATGAAATGAGAAAA
*
53734133 AAATTAAATGAGAAAA
1 AAATGAAATGAGAAAA
53734149 AAA
1 AAA
53734152 ATTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAATGAAATGAGAAAA
Found at i:53734622 original size:5 final size:5
Alignment explanation
Indices: 53734612--53734711 Score: 65
Period size: 5 Copynumber: 18.4 Consensus size: 5
53734602 AAAAAAAATT
* * *
53734612 AATGA AATGAA ATATTA AATGA ATATGA AATGA AATGTA ATTTGT AATGA
1 AATGA AATG-A A-ATGA AATGA A-ATGA AATGA AATG-A A-ATGA AATGA
* * * *
53734662 ATATGA AATGA AATGA AATGA ATTTGT AATGA TTATGA AATGG AATGA
1 A-ATGA AATGA AATGA AATGA A-ATGA AATGA -AATGA AATGA AATGA
53734710 AA
1 AA
53734712 GTTTAAAAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
5 45 0.62
6 24 0.33
7 4 0.05
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (5 bp):
AATGA
Found at i:53734642 original size:11 final size:11
Alignment explanation
Indices: 53734613--53734703 Score: 77
Period size: 11 Copynumber: 8.7 Consensus size: 11
53734603 AAAAAAATTA
53734613 ATGAAATGAAAT
1 ATGAAATG-AAT
*
53734625 ATTAAATGAAT
1 ATGAAATGAAT
53734636 ATGAAATGAA-
1 ATGAAATGAAT
53734646 ATG---T-AAT
1 ATGAAATGAAT
* *
53734653 TTGTAATGAAT
1 ATGAAATGAAT
53734664 ATGAAATGAA-
1 ATGAAATGAAT
53734674 ATGAAATGAAT
1 ATGAAATGAAT
* * *
53734685 TTGTAATGATT
1 ATGAAATGAAT
53734696 ATGAAATG
1 ATGAAATG
53734704 GAATGAAAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
10 14 0.22
11 37 0.59
12 7 0.11
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (11 bp):
ATGAAATGAAT
Found at i:53734643 original size:28 final size:28
Alignment explanation
Indices: 53734612--53734680 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
53734602 AAAAAAAATT
53734612 AATGAAATGAAATATT-AAATGAATATGA
1 AATGAAATGAAAT-TTGAAATGAATATGA
* *
53734640 AATGAAATGTAATTTGTAATGAATATGA
1 AATGAAATGAAATTTGAAATGAATATGA
53734668 AATGAAATGAAAT
1 AATGAAATGAAAT
53734681 GAATTTGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (28 bp):
AATGAAATGAAATTTGAAATGAATATGA
Found at i:53734691 original size:32 final size:33
Alignment explanation
Indices: 53734630--53734711 Score: 130
Period size: 32 Copynumber: 2.5 Consensus size: 33
53734620 GAAATATTAA
53734630 ATGAATATGAAATGAAATGTAATTTGTAATGAAT
1 ATGAA-ATGAAATGAAATGTAATTTGTAATGAAT
*
53734664 ATGAAATGAAATGAAATG-AATTTGTAATGATT
1 ATGAAATGAAATGAAATGTAATTTGTAATGAAT
*
53734696 ATGAAATGGAATGAAA
1 ATGAAATGAAATGAAA
53734712 GTTTAAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 28 0.61
33 13 0.28
34 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (33 bp):
ATGAAATGAAATGAAATGTAATTTGTAATGAAT
Done.