Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 178 of 193
Found at i:55592152 original size:21 final size:22
Alignment explanation
Indices: 55592103--55592157 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
55592093 ACTTAAATTT
* *
55592103 TAAATTTTAAAAAATAGAAAGAT
1 TAAATTCT-AAAAATAGAAAGAC
55592126 TAAATTCCTAAAAATA-AAA-AC
1 TAAATT-CTAAAAATAGAAAGAC
55592147 TAAATTCTAAA
1 TAAATTCTAAA
55592158 TTTATAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 5 0.17
21 7 0.24
22 3 0.10
23 13 0.45
24 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (22 bp):
TAAATTCTAAAAATAGAAAGAC
Found at i:55595324 original size:16 final size:16
Alignment explanation
Indices: 55595303--55595334 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55595293 TCATTAAATA
55595303 AATTAATTAAAAATTT
1 AATTAATTAAAAATTT
*
55595319 AATTAATTGAAAATTT
1 AATTAATTAAAAATTT
55595335 TAAATTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTAATTAAAAATTT
Found at i:55595772 original size:28 final size:27
Alignment explanation
Indices: 55595729--55595802 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 27
55595719 ATTTTTGAAA
55595729 ATTAAAAAATTCAAAAAATA-TATAAATT
1 ATTAAAAAATT-AAAAAATATTA-AAATT
* *
55595757 ATTTTAAAAATTAAAAATTATTAAAATT
1 A-TTAAAAAATTAAAAAATATTAAAATT
55595785 ATTAAAAAATTATAAAAA
1 ATTAAAAAATTA-AAAAA
55595803 ATAATTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 10 0.26
28 18 0.46
29 11 0.28
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTAAAAAATTAAAAAATATTAAAATT
Found at i:55595779 original size:10 final size:10
Alignment explanation
Indices: 55595766--55595804 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
55595756 TATTTTAAAA
55595766 ATTAAAAATT
1 ATTAAAAATT
55595776 ATT-AAAATT
1 ATTAAAAATT
55595785 ATTAAAAAATT
1 ATT-AAAAATT
*
55595796 ATAAAAAAT
1 ATTAAAAAT
55595805 AATTTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 9 0.35
10 9 0.35
11 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:55599143 original size:26 final size:25
Alignment explanation
Indices: 55599107--55599158 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
55599097 AATAATGATG
*
55599107 GAGGAAATATTGACTCAAGAAGTTCT
1 GAGGAAATATTGACTCAA-AAGGTCT
*
55599133 GAGGGAATATTGACTCAAAAGGTCT
1 GAGGAAATATTGACTCAAAAGGTCT
55599158 G
1 G
55599159 GATTGATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (25 bp):
GAGGAAATATTGACTCAAAAGGTCT
Found at i:55608016 original size:14 final size:14
Alignment explanation
Indices: 55607997--55608023 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55607987 TGAGTTTCTC
55607997 AACTCCTCATGCAA
1 AACTCCTCATGCAA
55608011 AACTCCTCATGCA
1 AACTCCTCATGCA
55608024 GTGTGAGTTG
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:0.33, C:0.37, G:0.07, T:0.22
Consensus pattern (14 bp):
AACTCCTCATGCAA
Found at i:55610583 original size:13 final size:13
Alignment explanation
Indices: 55610550--55610588 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
55610540 ATTTTAAAAA
*
55610550 ATAAAATTATTTC
1 ATAAAATTATGTC
*
55610563 ATTAAAATAATGTC
1 A-TAAAATTATGTC
55610577 ATAAAATTATGT
1 ATAAAATTATGT
55610589 TTTTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (13 bp):
ATAAAATTATGTC
Found at i:55619491 original size:88 final size:88
Alignment explanation
Indices: 55619342--55619519 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
55619332 ATGCTAAACT
*
55619342 AACCCTTCTATCAGTAGTTTTATGGTGGTATGACCCCCACCAACTTCTAATGTACAGCTCTATTT
1 AACCCTTCTATCAGTAGTTTTACGGTGGTATGACCCCCACCAACTTCTAATGTACAGCTCTATTT
55619407 TACAATAAACTTACCCTGCCAGA
66 TACAATAAACTTACCCTGCCAGA
55619430 AACCCTTCTATCAGTAGTTTTACGGTGGTATGACCCCCACCAACTTCTAATGTACAGCTCTATTT
1 AACCCTTCTATCAGTAGTTTTACGGTGGTATGACCCCCACCAACTTCTAATGTACAGCTCTATTT
55619495 TACAATAAACTTACCCTGCCAGA
66 TACAATAAACTTACCCTGCCAGA
55619518 AA
1 AA
55619520 AGATTAAACT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (88 bp):
AACCCTTCTATCAGTAGTTTTACGGTGGTATGACCCCCACCAACTTCTAATGTACAGCTCTATTT
TACAATAAACTTACCCTGCCAGA
Found at i:55623592 original size:138 final size:137
Alignment explanation
Indices: 55623227--55623626 Score: 613
Period size: 137 Copynumber: 2.9 Consensus size: 137
55623217 GAGAACATAG
* *
55623227 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATT
* * *
55623292 ACTATAAAAAATTATATTAATTAATTTCAGTCAAAATATAAAAGATATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACAT-AAAATTAATATTCTTT
55623357 TGAAAAAA
130 TGAAAAAA
* *
55623365 ATATAATTAATATATGAA-TTGATTCATATAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATT
**
55623429 AATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATAAAATTTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATAAAA-TTAATATTCTTT
*
55623494 TGAAAAGA
130 TGAAAAAA
* * ** * *
55623502 ATATAATTAATATATTAATTTCATTCATACAAAATATTAGCTATATATAATTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATT
*
55623567 AATATAAACAATTATATTAATTAATTTCAGTAAAAATATAAAAGACATAAAAATTAATAT
66 AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACAT-AAAATTAATAT
55623627 AATTCCTTTT
Statistics
Matches: 239, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
136 4 0.02
137 122 0.51
138 109 0.46
139 4 0.02
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (137 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATAAAATTAATATTCTTTT
GAAAAAA
Found at i:55630042 original size:2 final size:2
Alignment explanation
Indices: 55630025--55630079 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
55630015 TTAAACTATT
* * *
55630025 TA TA TA -A TT TA T- TA TA TA TA AA AA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55630064 TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA T
55630080 TTTTAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 41 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55630079 original size:25 final size:25
Alignment explanation
Indices: 55630024--55630079 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
55630014 ATTAAACTAT
*
55630024 TTATATAATTTATTATATATAAAAA
1 TTATATAATATATTATATATAAAAA
* * *
55630049 TAATAT-ATATATATATATATATATA
1 TTATATAATATAT-TATATATAAAAA
55630074 TTATAT
1 TTATAT
55630080 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATATAATATATTATATATAAAAA
Found at i:55630966 original size:323 final size:322
Alignment explanation
Indices: 55630370--55631019 Score: 1248
Period size: 323 Copynumber: 2.0 Consensus size: 322
55630360 ATACCAGTTA
55630370 AAAAAAAGGCTTTCCGTTATCAATTTAATGGTGAGTGATCAAAATAGGAACAAATTCAAGAATTA
1 AAAAAAAGGCTTTCCGTTATCAATTTAATGGTGAGTGATCAAAATAGGAACAAATTCAAGAATTA
*
55630435 GTGCCTAAATTGAAAAAAATTAAAGTTGGGTGATCGATATGAACATGGGAATATTGGGTGACAAT
66 GTGCCTAAATTGAAAAAAATTAAAGTTGGGTGATCGATAGGAACATGGGAATATTGGGTGACAAT
*
55630500 TTCTATAATTTACCCTATTATTAATTTTTTGTACTTTGAAACCCCAATTTTTTTTATAAAGGATG
131 TTCTATAATTTACCCTATTATTAATTTTTTGTACTTTGAAACCCCAATTTTTTTTATAAAAGATG
55630565 TACTATTTCGGGATTGAAAACGGTGAAATTTCAAGAAATTTGGAAATTGAGTCTAATAAAGAATG
196 TACTATTTCGGGATTGAAAACGGTGAAATTTCAAGAAATTTGGAAATTGAGTCTAATAAAGAATG
55630630 TTTACAAAAGAGAAATTGATGAAAAGTATTGTAGATGTAGAAAAGTGACAAAGGATTAAATT
261 TTTACAAAAGAGAAATTGATGAAAAGTATTGTAGATGTAGAAAAGTGACAAAGGATTAAATT
*
55630692 AAAAAAA-GCTTTCCGTTATCAATTTAATGGTGAGTGATCAAAATAGGAACAAATTCAAGTATTA
1 AAAAAAAGGCTTTCCGTTATCAATTTAATGGTGAGTGATCAAAATAGGAACAAATTCAAGAATTA
55630756 GTGCCTAAATTGAAAAAAAATTAAAGTTGGGTGATCGATAGGAACATGGGAATATTGGGTGACAA
66 GTGCCTAAATTG-AAAAAAATTAAAGTTGGGTGATCGATAGGAACATGGGAATATTGGGTGACAA
55630821 TTTCTATAATTTACCCTATTATTAATTTTTTGTACTTTGAAACCCCAATTTTTTTTTATAAAAGA
130 TTTCTATAATTTACCCTATTATTAATTTTTTGTACTTTGAAACCCCAA-TTTTTTTTATAAAAGA
55630886 TGTACTATTTCGGGATTGAAAACGGTGAAATTTCAAGAAATTTGGAAATTGAGTCTAATAAAGAA
194 TGTACTATTTCGGGATTGAAAACGGTGAAATTTCAAGAAATTTGGAAATTGAGTCTAATAAAGAA
55630951 TGTTTACAAAAGAGAAATTGATGAAAAGTATTGTAGATGTAGAAAAGTGACAAAGGATTAAATT
259 TGTTTACAAAAGAGAAATTGATGAAAAGTATTGTAGATGTAGAAAAGTGACAAAGGATTAAATT
55631015 AAAAA
1 AAAAA
55631020 GTTTGAGGAT
Statistics
Matches: 323, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
321 68 0.21
322 106 0.33
323 149 0.46
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (322 bp):
AAAAAAAGGCTTTCCGTTATCAATTTAATGGTGAGTGATCAAAATAGGAACAAATTCAAGAATTA
GTGCCTAAATTGAAAAAAATTAAAGTTGGGTGATCGATAGGAACATGGGAATATTGGGTGACAAT
TTCTATAATTTACCCTATTATTAATTTTTTGTACTTTGAAACCCCAATTTTTTTTATAAAAGATG
TACTATTTCGGGATTGAAAACGGTGAAATTTCAAGAAATTTGGAAATTGAGTCTAATAAAGAATG
TTTACAAAAGAGAAATTGATGAAAAGTATTGTAGATGTAGAAAAGTGACAAAGGATTAAATT
Found at i:55634236 original size:10 final size:10
Alignment explanation
Indices: 55634221--55634293 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
55634211 CAAAAATTAC
55634221 AAAATAATTT
1 AAAATAATTT
55634231 AAAATAATTTT
1 AAAATAA-TTT
* *
55634242 CAAA-AATTC
1 AAAATAATTT
55634251 AAAATAATTT
1 AAAATAATTT
*
55634261 -TAA-AATTT
1 AAAATAATTT
55634269 AAAAT-ATTT
1 AAAATAATTT
55634278 ATAAA-AATTTT
1 A-AAATAA-TTT
55634289 AAAAT
1 AAAAT
55634294 TTATATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
8 5 0.10
9 14 0.29
10 20 0.41
11 10 0.20
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAATAATTT
Found at i:55634254 original size:20 final size:19
Alignment explanation
Indices: 55634226--55634293 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
55634216 ATTACAAAAT
55634226 AATTTAAAATAATTTTCAAA
1 AATTTAAAATAATTTT-AAA
*
55634246 AATTCAAAATAATTTT-AA
1 AATTTAAAATAATTTTAAA
55634264 AATTTAAAAT-ATTTATAAA
1 AATTTAAAATAATTT-TAAA
55634283 AATTTTAAAAT
1 AA-TTTAAAAT
55634294 TTATATCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.09
18 12 0.28
19 4 0.09
20 23 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTAAAATAATTTTAAA
Found at i:55634295 original size:18 final size:19
Alignment explanation
Indices: 55634226--55634298 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 19
55634216 ATTACAAAAT
55634226 AATTTAAAATAATTT-TCAAA
1 AATTTAAAAT-ATTTAT-AAA
*
55634246 AATTCAAAATAATTT-T-AA
1 AATTTAAAAT-ATTTATAAA
55634264 AATTTAAAATATTTATAAA
1 AATTTAAAATATTTATAAA
*
55634283 AATTTTAAA-ATTTATA
1 AATTTAAAATATTTATA
55634299 TCTTTAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.08
18 19 0.40
19 10 0.21
20 15 0.31
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTAAAATATTTATAAA
Found at i:55634312 original size:27 final size:27
Alignment explanation
Indices: 55634243--55634310 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
55634233 AATAATTTTC
* *
55634243 AAAA-ATTCAAAATAATTTTAAAATTT
1 AAAATATTTAAAAAAATTTTAAAATTT
*
55634269 AAAATATTTATAAAAATTTTAAAATTT
1 AAAATATTTAAAAAAATTTTAAAATTT
* *
55634296 -ATATCTTTAAAAAAA
1 AAAATATTTAAAAAAA
55634311 ATAAAAATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 16 0.46
27 19 0.54
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
AAAATATTTAAAAAAATTTTAAAATTT
Found at i:55634342 original size:18 final size:17
Alignment explanation
Indices: 55634302--55634343 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
55634292 ATTTATATCT
*
55634302 TTAAAAAAAATAAAAAT
1 TTAAAAAAAATAAAAAG
55634319 TCTAAAAAAATATAAAAAG
1 T-TAAAAAAA-ATAAAAAG
55634338 TTAAAA
1 TTAAAA
55634344 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 13 0.59
19 8 0.36
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
TTAAAAAAAATAAAAAG
Found at i:55637626 original size:59 final size:58
Alignment explanation
Indices: 55637551--55637722 Score: 195
Period size: 59 Copynumber: 2.9 Consensus size: 58
55637541 TTAATATAAC
*
55637551 ATTTGATATTTGAACTTGACACTTTTTTCTAATTTGGTACTTAAACTTTTTTTGACCCA
1 ATTTG-TACTTGAACTTGACACTTTTTTCTAATTTGGTACTTAAACTTTTTTTGACCCA
* * ** *
55637610 ATTTGTTACTTGAACTTGACACTTTTTCCTAATTTAGTTTTTAAACTATTTTTTGACCCT
1 ATTTG-TACTTGAACTTGACACTTTTTTCTAATTTGGTACTTAAACT-TTTTTTGACCCA
* * *
55637670 ATTTAGTACCTAAACTTGACA-TGTTTTTCTAATTTGGTATCTT-AGCTTTTTTT
1 ATTT-GTACTTGAACTTGACACT-TTTTTCTAATTTGGTA-CTTAAACTTTTTTT
55637723 TAATATTCAA
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 48 0.51
60 44 0.46
61 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (58 bp):
ATTTGTACTTGAACTTGACACTTTTTTCTAATTTGGTACTTAAACTTTTTTTGACCCA
Found at i:55637723 original size:60 final size:61
Alignment explanation
Indices: 55637563--55637723 Score: 190
Period size: 60 Copynumber: 2.7 Consensus size: 61
55637553 TTGATATTTG
* *
55637563 AACTTGACACTTTTTTCTAATTTGGTA-CTTAAAC-TTTTTTTGACCCAATTTGTTACTTG
1 AACTTGACACTTTTTTCTAATTTGGTATCTTAAACTTTTTTTTGACCCAATTTGTTACCTA
* * * * *
55637622 AACTTGACACTTTTTCCTAATTTAGT-TTTTAAACTATTTTTTGACCCTATTTAG-TACCTA
1 AACTTGACACTTTTTTCTAATTTGGTATCTTAAACTTTTTTTTGACCCAATTT-GTTACCTA
*
55637682 AACTTGACA-TGTTTTTCTAATTTGGTATCTT-AGCTTTTTTTT
1 AACTTGACACT-TTTTTCTAATTTGGTATCTTAAACTTTTTTTT
55637724 AATATTCAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
59 31 0.36
60 50 0.59
61 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (61 bp):
AACTTGACACTTTTTTCTAATTTGGTATCTTAAACTTTTTTTTGACCCAATTTGTTACCTA
Found at i:55637965 original size:32 final size:31
Alignment explanation
Indices: 55637899--55637966 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
55637889 AATAGATACT
*
55637899 AAATTAAGAAAAAAAATCAAATTCAAGTATC
1 AAATTAAGAAAAAAAATCAAATTCAAGTACC
* * **
55637930 AAATTAAGAAAAACATATCAAGTTTGAGTACC
1 AAATTAAGAAAAA-AAATCAAATTCAAGTACC
55637962 AAATT
1 AAATT
55637967 GGTTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (31 bp):
AAATTAAGAAAAAAAATCAAATTCAAGTACC
Found at i:55647329 original size:61 final size:61
Alignment explanation
Indices: 55647234--55647416 Score: 318
Period size: 61 Copynumber: 3.0 Consensus size: 61
55647224 AGGCATCATT
* *
55647234 GTTGTCTTATTGAGAATGCTTTTGTGCTTGATGTGTAAGGAAATAGAGAGTTTCTAACACA
1 GTTGTCTTATTGAGAATGCTCTTGTGCTTGATGTGTAAGGACATAGAGAGTTTCTAACACA
*
55647295 GTTGTCTTATTGAGAATGCTCTTGTGCTTGATGTGTAAGGACATGGAGAGTTTCTAACACA
1 GTTGTCTTATTGAGAATGCTCTTGTGCTTGATGTGTAAGGACATAGAGAGTTTCTAACACA
55647356 GTTGTCTTATTGAGAATGCTCTTGTGC-T--TGTGTAAGGACATAGAGAGTTTCTAACACA
1 GTTGTCTTATTGAGAATGCTCTTGTGCTTGATGTGTAAGGACATAGAGAGTTTCTAACACA
55647414 GTT
1 GTT
55647417 TTATGCTGCG
Statistics
Matches: 118, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
58 32 0.27
60 1 0.01
61 85 0.72
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (61 bp):
GTTGTCTTATTGAGAATGCTCTTGTGCTTGATGTGTAAGGACATAGAGAGTTTCTAACACA
Found at i:55649790 original size:15 final size:15
Alignment explanation
Indices: 55649770--55649804 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
55649760 AAAGAATTGT
55649770 TAAATAAAATGTTTA
1 TAAATAAAATGTTTA
55649785 TAAATAAAATGTTTA
1 TAAATAAAATGTTTA
55649800 TAAAT
1 TAAAT
55649805 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
TAAATAAAATGTTTA
Found at i:55659880 original size:17 final size:18
Alignment explanation
Indices: 55659850--55659894 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
55659840 ACAAAATTTA
*
55659850 TTTTAAAAAGTTATAAAT
1 TTTTTAAAAGTTATAAAT
55659868 TTTTTAAAA-TTATAAAT
1 TTTTTAAAAGTTATAAAT
55659885 TTTATTAAAA
1 TTT-TTAAAA
55659895 ATAACAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAGTTATAAAT
Found at i:55659994 original size:13 final size:12
Alignment explanation
Indices: 55659976--55660020 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
55659966 TCGAAATTTT
55659976 TATTTTTTAATAA
1 TATTTTTTAAT-A
55659989 TATTTTTT--TA
1 TATTTTTTAATA
55659999 TGATTTTTTAATA
1 T-ATTTTTTAATA
55660012 T-TTTTTTAA
1 TATTTTTTAA
55660021 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.07
11 16 0.55
13 11 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTTTTTAATA
Found at i:55659998 original size:21 final size:20
Alignment explanation
Indices: 55659972--55660025 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
55659962 TAGGTCGAAA
55659972 TTTTTAT-TTTTTAATAATATT
1 TTTTTATATTTTT--TAATATT
55659993 TTTTTATGATTTTTTAATATT
1 TTTTTAT-ATTTTTTAATATT
*
55660014 TTTTTAAATTTT
1 TTTTTATATTTT
55660026 AAAAAGCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 20 0.67
23 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTATATTTTTTAATATT
Found at i:55660024 original size:10 final size:11
Alignment explanation
Indices: 55659976--55660025 Score: 52
Period size: 10 Copynumber: 4.5 Consensus size: 11
55659966 TCGAAATTTT
55659976 TATTTTTTAATAA
1 TATTTTTT--TAA
55659989 TATTTTTTT-A
1 TATTTTTTTAA
55659999 TGA-TTTTTTAA
1 T-ATTTTTTTAA
55660010 TATTTTTTTAA
1 TATTTTTTTAA
55660021 -ATTTT
1 TATTTT
55660026 AAAAAGCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 14 0.41
11 12 0.35
13 8 0.24
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTTTTTTAA
Found at i:55681301 original size:23 final size:22
Alignment explanation
Indices: 55681275--55681320 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
55681265 TATAATAAAT
*
55681275 TTAATATAATGAAATATATATAA
1 TTAATATAATCAAATATAT-TAA
* *
55681298 TTAATGTAGTCAAATATATTAA
1 TTAATATAATCAAATATATTAA
55681320 T
1 T
55681321 GCGCCGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (22 bp):
TTAATATAATCAAATATATTAA
Found at i:55692404 original size:57 final size:59
Alignment explanation
Indices: 55692334--55692458 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 59
55692324 TACACCATAG
* * *
55692334 GTCACTCAACTATTG-TC-TCTT-TTTTTTGGTCATACAGCTATCAATTTTTTTAATTTA
1 GTCACCCAACTATTGCTCTTCTTCTTTTTTGGTCACACAACTATC-ATTTTTTTAATTTA
* * *
55692391 GTCACCCAACTATTGCCTCTTTTTCTTTTTTGGTCACCCAACTATCATTTTTTTAATTTG
1 GTCACCCAACTATTG-CTCTTCTTCTTTTTTGGTCACACAACTATCATTTTTTTAATTTA
55692451 GTCACCCA
1 GTCACCCA
55692459 CCTAATTGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 14 0.24
59 2 0.03
60 24 0.41
61 18 0.31
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (59 bp):
GTCACCCAACTATTGCTCTTCTTCTTTTTTGGTCACACAACTATCATTTTTTTAATTTA
Found at i:55696544 original size:15 final size:15
Alignment explanation
Indices: 55696524--55696566 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
55696514 ATCTAGCCAT
*
55696524 CATAGCTTTCTTAAC
1 CATAGCTCTCTTAAC
55696539 CATAGCTCTCTTAAC
1 CATAGCTCTCTTAAC
*
55696554 CATAGCTCACTTA
1 CATAGCTCTCTTA
55696567 TCTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (15 bp):
CATAGCTCTCTTAAC
Found at i:55696711 original size:22 final size:23
Alignment explanation
Indices: 55696677--55696729 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
55696667 GCTGGGGAAA
* * *
55696677 CAGTAAGCACACACAGTGC-AAT
1 CAGTAGGCGCACACAGCGCAAAT
* *
55696699 TAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCGCACACAGCGCAAAT
55696722 CAGTAGGC
1 CAGTAGGC
55696730 ACACGAAGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (23 bp):
CAGTAGGCGCACACAGCGCAAAT
Found at i:55696865 original size:23 final size:23
Alignment explanation
Indices: 55696682--55696869 Score: 109
Period size: 23 Copynumber: 8.1 Consensus size: 23
55696672 GGAAACAGTA
*
55696682 AGCACACACAGTGC-AATTAGTAG
1 AGCACACACAGTGCTAATCAG-AG
* * * *
55696705 -GCGCACATAGCGCAAATCAGTAG
1 AGCACACACAGTGCTAATCAG-AG
* *
55696728 -GCACACGA-AGTGCGAAACAGTAG
1 AGCACAC-ACAGTGCTAATCAG-AG
* * *
55696751 -GCACACAAAGTGCGAAACAGAG
1 AGCACACACAGTGCTAATCAGAG
* * * *
55696773 AGTACACAAAGTACTGATCAGAG
1 AGCACACACAGTGCTAATCAGAG
*
55696796 AGCACACACAATGCTAATAACAGAG
1 AGCACACACAGTGCTAAT--CAGAG
* *
55696821 AGCACGAGAC-GTGCTAAACAGAG
1 AGCAC-ACACAGTGCTAATCAGAG
*
55696844 AGCACACACAGTGATAATCAGAG
1 AGCACACACAGTGCTAATCAGAG
55696867 AGC
1 AGC
55696870 GCGCTAGTGT
Statistics
Matches: 133, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
22 16 0.12
23 97 0.73
24 1 0.01
25 16 0.12
26 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
AGCACACACAGTGCTAATCAGAG
Found at i:55701659 original size:16 final size:16
Alignment explanation
Indices: 55701622--55701664 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
55701612 TAATTTATTA
*
55701622 AATAAAA-ATGATGTT
1 AATAAAATATTATGTT
*
55701637 AATTAAAATATTATTTT
1 AA-TAAAATATTATGTT
55701654 AATAAAATATT
1 AATAAAATATT
55701665 TAAATTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.58
17 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
AATAAAATATTATGTT
Found at i:55706384 original size:20 final size:18
Alignment explanation
Indices: 55706359--55706403 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
55706349 GTTTTTGAAT
*
55706359 AAATTTTGTAAGATTTTGTA
1 AAATTTTG-AA-ATTTTATA
*
55706379 AAATTTTGAAATTTTATG
1 AAATTTTGAAATTTTATA
55706397 AAATTTT
1 AAATTTT
55706404 ATTTTTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
AAATTTTGAAATTTTATA
Found at i:55709297 original size:3 final size:3
Alignment explanation
Indices: 55709289--55709324 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55709279 ATGCTCATAC
55709289 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
55709325 TATGGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:55709379 original size:39 final size:39
Alignment explanation
Indices: 55709325--55709403 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
55709315 GGAGGAGGAG
*
55709325 TATGGTTATTGGGAAGATAATGAATATGAAGAGTATTGA
1 TATGGTTATAGGGAAGATAATGAATATGAAGAGTATTGA
* * *
55709364 TATGGTTATAGGGAAGATTATGATTATGAAGAGTTTTGA
1 TATGGTTATAGGGAAGATAATGAATATGAAGAGTATTGA
55709403 T
1 T
55709404 GTGATTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.37
Consensus pattern (39 bp):
TATGGTTATAGGGAAGATAATGAATATGAAGAGTATTGA
Found at i:55709679 original size:19 final size:19
Alignment explanation
Indices: 55709638--55709679 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
55709628 AGTTAAATTG
*
55709638 AAAATTCATAAAAAATTTC
1 AAAATTCATAAAAAATTTA
*
55709657 AAAATTTAT-AAAAATTATA
1 AAAATTCATAAAAAATT-TA
55709676 AAAA
1 AAAA
55709680 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATTCATAAAAAATTTA
Found at i:55709813 original size:19 final size:19
Alignment explanation
Indices: 55709759--55709815 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
55709749 ACAAAATTGG
*
55709759 GTTTTCAATAAGAATTTGT
1 GTTTTCATTAAGAATTTGT
*
55709778 GTATTTGATT-AGAAATTTGT
1 GT-TTTCATTAAG-AATTTGT
55709798 GTTTTCATTAAGAATTTG
1 GTTTTCATTAAGAATTTG
55709816 AGTAAATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.49
Consensus pattern (19 bp):
GTTTTCATTAAGAATTTGT
Found at i:55711040 original size:14 final size:13
Alignment explanation
Indices: 55711003--55711037 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
55710993 ATAAATAAAT
*
55711003 TTTTTTAATTTAA
1 TTTTTTAATTGAA
55711016 TATTTTTAATTGAA
1 T-TTTTTAATTGAA
55711030 TTTTTTAA
1 TTTTTTAA
55711038 ATTTTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TTTTTTAATTGAA
Found at i:55714660 original size:28 final size:28
Alignment explanation
Indices: 55714641--55714715 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
55714631 TATTAAGATG
*
55714641 ATTATATAAAA-AATTAAATAAATAAAAA
1 ATTATATAAAATAATTAAAT-ATTAAAAA
*
55714669 ATTATATAAAATTATTAAATATTAAAAA
1 ATTATATAAAATAATTAAATATTAAAAA
* *
55714697 TATAATAT-AAATATTTAAA
1 -ATTATATAAAATAATTAAA
55714716 AAAATTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 27 0.68
29 13 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
ATTATATAAAATAATTAAATATTAAAAA
Found at i:55714667 original size:16 final size:16
Alignment explanation
Indices: 55714646--55714678 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55714636 AGATGATTAT
55714646 ATAAAAAATTAAATAA
1 ATAAAAAATTAAATAA
*
55714662 ATAAAAAATTATATAA
1 ATAAAAAATTAAATAA
55714678 A
1 A
55714679 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAAATTAAATAA
Found at i:55715230 original size:15 final size:14
Alignment explanation
Indices: 55715186--55715235 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
55715176 AATTCATATA
55715186 ATTTTT-AT-TTTT
1 ATTTTTCATGTTTT
55715198 ATTTTTCATGTTTAT
1 ATTTTTCATGTTT-T
*
55715213 ATTTTTTATGATTTT
1 ATTTTTCATG-TTTT
*
55715228 ATTATTCA
1 ATTTTTCA
55715236 AAATAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 3 0.10
15 17 0.55
16 3 0.10
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (14 bp):
ATTTTTCATGTTTT
Found at i:55717686 original size:17 final size:18
Alignment explanation
Indices: 55717657--55717692 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
55717647 TATATTTTTG
55717657 TAAATTTATGTTTTTAAT
1 TAAATTTATGTTTTTAAT
55717675 TAAATTTA-GTTTTTAAT
1 TAAATTTATGTTTTTAAT
55717692 T
1 T
55717693 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TAAATTTATGTTTTTAAT
Found at i:55717894 original size:32 final size:32
Alignment explanation
Indices: 55717818--55717895 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
55717808 TATTTACTTC
55717818 ATTATAATTATTT-TTTTAATTTTTAATGAACT
1 ATTA-AATTATTTATTTTAATTTTTAATGAACT
* * * *
55717850 -TTATATTTTTTATTTTGAATTTTTTAT-AATT
1 ATTAAATTATTTATTTT-AATTTTTAATGAACT
55717881 ATTAAATTATTTATT
1 ATTAAATTATTTATT
55717896 GATGTGATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 6 0.16
31 10 0.27
32 21 0.57
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (32 bp):
ATTAAATTATTTATTTTAATTTTTAATGAACT
Found at i:55719029 original size:2 final size:2
Alignment explanation
Indices: 55719022--55719047 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55719012 CCAAAATGTA
55719022 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
55719048 TGTGAGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55720516 original size:13 final size:13
Alignment explanation
Indices: 55720498--55720537 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
55720488 TTTATGAGTT
55720498 TATTCATTTATGA
1 TATTCATTTATGA
* *
55720511 TATTCATAGTGTGA
1 TATTCAT-TTATGA
55720525 TATTCATTTATGA
1 TATTCATTTATGA
55720538 CTCGTATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTCATTTATGA
Found at i:55723028 original size:23 final size:22
Alignment explanation
Indices: 55722998--55723103 Score: 86
Period size: 25 Copynumber: 4.5 Consensus size: 22
55722988 ACACTAGCGC
55722998 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGTCT-GT
*
55723021 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GTCTGT
* * *
55723046 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTCTGT
* *
55723069 GCTCTCTGTTTCCCAGCACTTTTGT
1 GCTCTCTGTTT---AGCACGTCTGT
55723094 GCTCTCTGTT
1 GCTCTCTGTT
55723104 AGTACTTTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
23 31 0.43
24 1 0.01
25 32 0.44
26 8 0.11
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTCTGT
Found at i:55723071 original size:48 final size:45
Alignment explanation
Indices: 55722998--55723125 Score: 132
Period size: 48 Copynumber: 2.7 Consensus size: 45
55722988 ACACTAGCGC
* * *
55722998 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTAT-TAGCACTGTGTGT
1 GCTCTCTG-TTAGCAC-TTTGGTGCTCTCTGTT-TCCAGCACT-TGTGT
*
55723046 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTCCCAGCACTTTTGT
1 GCTCTCTG-TTAGCACTTTG-GTGCTCTCTGTTT-CCAGCACTTGTGT
* *
55723094 GCTCTCTGTTAGTACTTTGGTACTCTCTGTTT
1 GCTCTCTGTTAGCACTTTGGTGCTCTCTGTTT
55723126 GTTCCGTATA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
46 12 0.17
47 13 0.19
48 39 0.56
49 6 0.09
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (45 bp):
GCTCTCTGTTAGCACTTTGGTGCTCTCTGTTTCCAGCACTTGTGT
Found at i:55723110 original size:21 final size:22
Alignment explanation
Indices: 55722998--55723122 Score: 99
Period size: 23 Copynumber: 5.4 Consensus size: 22
55722988 ACACTAGCGC
* * *
55722998 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCAC-TTTTGT
*
55723021 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TTTGT
55723046 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
55723069 GCTCTCTGTTTCCCAGCACTTTTGT
1 GCTCTCTGATT---AGCACTTTTGT
* *
55723094 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGATTAGCACTTTTGT
*
55723115 ACTCTCTG
1 GCTCTCTG
55723123 TTTGTTCCGT
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
21 16 0.19
22 1 0.01
23 30 0.35
24 3 0.03
25 28 0.33
26 8 0.09
ACGTcount: A:0.10, C:0.26, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTTTGT
Found at i:55723743 original size:12 final size:13
Alignment explanation
Indices: 55723715--55723748 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
55723705 TTAATTGGAA
*
55723715 AAATTAATTTAAT
1 AAATAAATTTAAT
55723728 AAATAAATTT-AT
1 AAATAAATTTAAT
55723740 AAATAAATT
1 AAATAAATT
55723749 AACTAACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATAAATTTAAT
Found at i:55734679 original size:237 final size:240
Alignment explanation
Indices: 55734333--55734787 Score: 652
Period size: 237 Copynumber: 1.9 Consensus size: 240
55734323 TCAGAATTGA
* * * *
55734333 TTTATTACTGATTTAAGAAAAATATAAGTACATGAAGAAATGTGTCTGACACAAAATATATTATG
1 TTTATTACTGATTTAAAAAAAATATAAGTACATGAAGAAAGGTGTATGACACAAAATATATTATA
*
55734398 CATGAATTATTTTGACTTTTAATAAATCATAAAACACATAGTTCAATAATCCATCAAAATTCATT
66 CATGAATTATTTTGACTTTTAATAAATCATAAAACACATAGTTCAATAATCCACCAAAATTCATT
55734463 TATTCCCGATTTAAAAAAATA-TAAATAATTGAAGAAATGTGTAACACAAAATATATTATATATG
131 TATTCCCGATTTAAAAAAATATTAAATAATTGAAGAAATGTGTAACACAAAATATATTATATATG
55734527 AA-TATTTTGACTTTTAATAAACCATGGTTTAATAATTCATTTGG
196 AATTATTTTGACTTTTAATAAACCATGGTTTAATAATTCATTTGG
* * * *
55734571 TTTATTCCTGATTTAAAAAAATATATAAGTGCAT-AA-AGAGGTGTAT-ACCATAAAATATATTA
1 TTTATTACTGATTTAAAAAAA-ATATAAGTACATGAAGAAAGGTGTATGA-CACAAAATATATTA
* * * * ** *
55734633 TATATTATATT-TTTTGACTTTTGATAAATCATAAAACACATAGTTCAATACTCTGCCAAAATTG
64 TACATGA-ATTATTTTGACTTTTAATAAATCATAAAACACATAGTTCAATAATCCACCAAAATTC
* * * * *
55734697 GTTTATTCCTGATTTGAAAAAATATTAAGTACTTGAAGAAATGTGTAACACAAAATATATTATAT
128 ATTTATTCCCGATTTAAAAAAATATTAAATAATTGAAGAAATGTGTAACACAAAATATATTATAT
55734762 ATGAATTATTTTGACTTTTAATAAAC
193 ATGAATTATTTTGACTTTTAATAAAC
55734788 TATAAATCAC
Statistics
Matches: 191, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
236 1 0.01
237 92 0.48
238 67 0.35
239 31 0.16
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (240 bp):
TTTATTACTGATTTAAAAAAAATATAAGTACATGAAGAAAGGTGTATGACACAAAATATATTATA
CATGAATTATTTTGACTTTTAATAAATCATAAAACACATAGTTCAATAATCCACCAAAATTCATT
TATTCCCGATTTAAAAAAATATTAAATAATTGAAGAAATGTGTAACACAAAATATATTATATATG
AATTATTTTGACTTTTAATAAACCATGGTTTAATAATTCATTTGG
Found at i:55734717 original size:127 final size:126
Alignment explanation
Indices: 55734269--55734799 Score: 444
Period size: 126 Copynumber: 4.3 Consensus size: 126
55734259 GTAACACAAA
* * * * * *
55734269 ATATGGATTATTTTAACTTTTAATAAA-TACTAAAACACATGGTTTAATCATTCAT--CAGAATT
1 ATATGAATTATTTTGACTTTTAATAAACTA-TAAAACACATAGTTCAAT-ACTC-TGCCAAAATT
* * * * *
55734331 GATTTATTACTGATTTAAGAAAAATA-TAAGTACATGAAGAAATGTGTCTGACACAAAATATATT
63 GGTTTATTCCTGATTTAA-AAAAATATTAAGTACATAAAGAAA--TGTATAACACAAAATATATT
55734395 AT
125 AT
** * *** **
55734397 GCATGAATTATTTTGACTTTTAATAAA-TCATAAAACACATAGTTCAATAATCCATCAAAATTCA
1 ATATGAATTATTTTGACTTTTAATAAACT-ATAAAACACATAGTTCAATACTCTGCCAAAATTGG
* * * *
55734461 TTTATTCCCGATTTAAAAAAATA-TAAATA-ATTGAAGAAATGTGTAACACAAAATATATTAT
65 TTTATTCCTGATTTAAAAAAATATTAAGTACA-TAAAGAAATGTATAACACAAAATATATTAT
* * * *
55734522 ATATGAA-TATTTTGAC-TTT--T--A--AT-AAAC-CATGGTTTAATAAT-T--C--ATTTGGT
1 ATATGAATTATTTTGACTTTTAATAAACTATAAAACACATAGTTCAATACTCTGCCAAAATTGGT
* ** * *
55734572 TTATTCCTGATTTAAAAAAATATATAAGTGCATAAAGAGGTGTATACCATAAAATATATTAT
66 TTATTCCTGATTTAAAAAAATAT-TAAGTACATAAAGAAATGTATAACACAAAATATATTAT
* *
55734634 ATATTATATT-TTTTGACTTTTGATAAA-TCATAAAACACATAGTTCAATACTCTGCCAAAATTG
1 ATATGA-ATTATTTTGACTTTTAATAAACT-ATAAAACACATAGTTCAATACTCTGCCAAAATTG
* * * *
55734697 GTTTATTCCTGATTTGAAAAAATATTAAGTACTTGAAGAAATGTGTAACACAAAATATATTAT
64 GTTTATTCCTGATTTAAAAAAATATTAAGTACATAAAGAAATGTATAACACAAAATATATTAT
*
55734760 ATATGAATTATTTTGACTTTTAATAAACTATAAATCACAT
1 ATATGAATTATTTTGACTTTTAATAAACTATAAAACACAT
55734800 TATCTAGTAA
Statistics
Matches: 329, Mismatches: 49, Indels: 52
0.77 0.11 0.12
Matches are distributed among these distances:
110 25 0.08
112 34 0.10
113 9 0.03
114 4 0.01
115 12 0.04
116 5 0.02
117 2 0.01
118 1 0.00
119 1 0.00
120 2 0.01
121 5 0.02
122 11 0.03
123 4 0.01
124 9 0.03
125 29 0.09
126 62 0.19
127 52 0.16
128 61 0.19
129 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (126 bp):
ATATGAATTATTTTGACTTTTAATAAACTATAAAACACATAGTTCAATACTCTGCCAAAATTGGT
TTATTCCTGATTTAAAAAAATATTAAGTACATAAAGAAATGTATAACACAAAATATATTAT
Found at i:55741277 original size:23 final size:21
Alignment explanation
Indices: 55741250--55741291 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
55741240 TAATCTTTTA
55741250 AAAATTAAAAAAATATATATTAT
1 AAAA-TAAAAAAAT-TATATTAT
*
55741273 AAAATAATAAAATTATATT
1 AAAATAAAAAAATTATATT
55741292 TTTACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATAAAAAAATTATATTAT
Found at i:55743485 original size:24 final size:23
Alignment explanation
Indices: 55743453--55743498 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
55743443 AATCTCATTT
55743453 TTTTTATTTTATTACTAGTATATC
1 TTTTTATTTTATTA-TAGTATATC
*
55743477 TTTTTATTTTATTATATTATAT
1 TTTTTATTTTATTATAGTATAT
55743499 TTTATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATTTTATTATAGTATATC
Found at i:55743508 original size:23 final size:24
Alignment explanation
Indices: 55743453--55743509 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
55743443 AATCTCATTT
*
55743453 TTTTTATTTTATTACTAGTATATC
1 TTTTAATTTTATTACTAGTATATC
* *
55743477 TTTTTATTTTATTA-TATTATAT-
1 TTTTAATTTTATTACTAGTATATC
55743499 TTTATAATTTT
1 TTT-TAATTTT
55743510 TTTAAAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 3 0.10
23 13 0.43
24 14 0.47
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTAATTTTATTACTAGTATATC
Found at i:55744129 original size:14 final size:14
Alignment explanation
Indices: 55744110--55744165 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
55744100 ATGGTGTGAA
55744110 TTTAATTTTTATAT
1 TTTAATTTTTATAT
55744124 TTTAATTTGGTTAT-T
1 TTTAATTT--TTATAT
*
55744139 TTTATATTTTTTAAAT
1 TTTA-A-TTTTTATAT
*
55744155 TTTAAATTTTA
1 TTTAATTTTTA
55744166 AAATTTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 13 0.37
15 9 0.26
16 10 0.29
17 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:55744187 original size:15 final size:14
Alignment explanation
Indices: 55744147--55744188 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
55744137 TTTTTATATT
55744147 TTTTAAATTTTAAA
1 TTTTAAATTTTAAA
55744161 TTTTAAAATTTTGAAA
1 TTTT-AAATTTT-AAA
*
55744177 TTTTAATTTTTA
1 TTTTAAATTTTA
55744189 TTTAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 5 0.20
15 13 0.52
16 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTTAAATTTTAAA
Found at i:55744221 original size:40 final size:41
Alignment explanation
Indices: 55744135--55744222 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 41
55744125 TTAATTTGGT
* *
55744135 TATTTTT-ATATTTTTTAAATTTTAAATTTTAAAATTTTGA
1 TATTTTTAATATTTTTTAAATATTAAATATTAAAATTTTGA
* *
55744175 -AATTTTAAT-TTTTATTTAATATTAAATATTAAAA-TTTGA
1 TATTTTTAATATTTT-TTAAATATTAAATATTAAAATTTTGA
55744214 TATTTTTAA
1 TATTTTTAA
55744223 AATATTATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
39 14 0.35
40 26 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (41 bp):
TATTTTTAATATTTTTTAAATATTAAATATTAAAATTTTGA
Found at i:55745221 original size:7 final size:8
Alignment explanation
Indices: 55745192--55745218 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
55745182 AGTTTATTGA
55745192 AAAATTAT
1 AAAATTAT
55745200 AAAATTAT
1 AAAATTAT
55745208 AAAATTAT
1 AAAATTAT
55745216 AAA
1 AAA
55745219 TTAGTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Found at i:55748642 original size:12 final size:12
Alignment explanation
Indices: 55748620--55748658 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
55748610 TATAATTGTC
55748620 CATTAAACCAAAT
1 CATT-AACCAAAT
*
55748633 CATTAACCAAAG
1 CATTAACCAAAT
55748645 CATTAACCAAAT
1 CATTAACCAAAT
55748657 CA
1 CA
55748659 ATACATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (12 bp):
CATTAACCAAAT
Found at i:55749221 original size:13 final size:14
Alignment explanation
Indices: 55749187--55749226 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55749177 AATATAAAAC
*
55749187 CTTAAACCCTAACT
1 CTTAAACCCTAAAT
*
55749201 CTTAAACCTTAAAT
1 CTTAAACCCTAAAT
55749215 C-TAAACCCTAAA
1 CTTAAACCCTAAA
55749227 CTCATACCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (14 bp):
CTTAAACCCTAAAT
Found at i:55749323 original size:49 final size:49
Alignment explanation
Indices: 55749200--55749311 Score: 224
Period size: 49 Copynumber: 2.3 Consensus size: 49
55749190 AAACCCTAAC
55749200 TCTTAAACCTTAAATCTAAACCCTAAACTCATACCCCATAATCTCAAAT
1 TCTTAAACCTTAAATCTAAACCCTAAACTCATACCCCATAATCTCAAAT
55749249 TCTTAAACCTTAAATCTAAACCCTAAACTCATACCCCATAATCTCAAAT
1 TCTTAAACCTTAAATCTAAACCCTAAACTCATACCCCATAATCTCAAAT
55749298 TCTTAAACCTTAAA
1 TCTTAAACCTTAAA
55749312 CTTTAACCCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (49 bp):
TCTTAAACCTTAAATCTAAACCCTAAACTCATACCCCATAATCTCAAAT
Found at i:55763227 original size:16 final size:18
Alignment explanation
Indices: 55763206--55763242 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55763196 TTTCTTTTAA
55763206 TATATTA-TAAA-TATTT
1 TATATTATTAAATTATTT
55763222 TATATTATTAAATTATTT
1 TATATTATTAAATTATTT
55763240 TAT
1 TAT
55763243 TACCCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTATTAAATTATTT
Found at i:55767447 original size:12 final size:12
Alignment explanation
Indices: 55767430--55767455 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55767420 GCTTAGGGAT
55767430 CAAGCATAAGGC
1 CAAGCATAAGGC
55767442 CAAGCATAAGGC
1 CAAGCATAAGGC
55767454 CA
1 CA
55767456 TGATGTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.23, T:0.08
Consensus pattern (12 bp):
CAAGCATAAGGC
Found at i:55769295 original size:23 final size:21
Alignment explanation
Indices: 55769268--55769320 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
55769258 ATGTGTAAGG
55769268 ATGGATTTTAAGCTTGTTGGAGA
1 ATGGATTTTAAGCTT-TTGGA-A
*
55769291 ATGGA-TTCAAGCTTTTGGAA
1 ATGGATTTTAAGCTTTTGGAA
55769311 ATGTGATTTT
1 ATG-GATTTT
55769321 GAGTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 10 0.38
23 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (21 bp):
ATGGATTTTAAGCTTTTGGAA
Found at i:55769318 original size:21 final size:22
Alignment explanation
Indices: 55769268--55769318 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
55769258 ATGTGTAAGG
*
55769268 ATGGATTTTAAGCTTGTTGGAGA
1 ATGGA-TTCAAGCTTGTTGGAGA
55769291 ATGGATTCAAGCTT-TTGGA-A
1 ATGGATTCAAGCTTGTTGGAGA
55769311 ATGTGATT
1 ATG-GATT
55769319 TTGAGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 9 0.35
22 8 0.31
23 5 0.19
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.39
Consensus pattern (22 bp):
ATGGATTCAAGCTTGTTGGAGA
Found at i:55771819 original size:12 final size:12
Alignment explanation
Indices: 55771770--55771826 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
55771760 ATATTTAATC
*
55771770 ATATAACAAATT
1 ATATAATAAATT
55771782 AT-TAATATAATT
1 ATATAATA-AATT
**
55771794 AATATAATTTATT
1 -ATATAATAAATT
*
55771807 ATTTAATAAATT
1 ATATAATAAATT
55771819 ATATAATA
1 ATATAATA
55771827 TTTTAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 4 0.11
12 22 0.63
13 5 0.14
14 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATAATAAATT
Found at i:55771837 original size:26 final size:25
Alignment explanation
Indices: 55771778--55771853 Score: 59
Period size: 26 Copynumber: 3.0 Consensus size: 25
55771768 TCATATAACA
55771778 AATTATTAATATAATTAATATAATTT
1 AATT-TTAATATAATTAATATAATTT
* *
55771804 ATTATTTAATA-AATTATATAATATTTT
1 AAT-TTTAATATAATTA-AT-ATAATTT
* *
55771831 AATTTTATTTTAA-TAATA-AATTT
1 AATTTTAATATAATTAATATAATTT
55771854 TAAAAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
23 4 0.10
24 1 0.03
25 7 0.17
26 17 0.43
27 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATTTTAATATAATTAATATAATTT
Found at i:55771855 original size:13 final size:14
Alignment explanation
Indices: 55771836--55771879 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
55771826 ATTTTAATTT
*
55771836 TATTTTAATAATAA
1 TATTTTAAAAATAA
55771850 -ATTTTAAAAATAA
1 TATTTTAAAAATAA
*
55771863 TATTTT-TAAATAA
1 TATTTTAAAAATAA
55771876 TATT
1 TATT
55771880 CTTCACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTTAAAAATAA
Found at i:55771927 original size:15 final size:15
Alignment explanation
Indices: 55771836--55771964 Score: 56
Period size: 15 Copynumber: 8.5 Consensus size: 15
55771826 ATTTTAATTT
55771836 TATTTTAATAAT-AA
1 TATTTTAATAATAAA
*
55771850 -ATTTTAAAAAT-AA
1 TATTTTAATAATAAA
*
55771863 TATTTTTA-AAT-AA
1 TATTTTAATAATAAA
*
55771876 TATTCTTCACATATTGAAA
1 TATT-TT-A-ATAAT-AAA
* *
55771895 -ATATTCAAT-ATTAA
1 TAT-TTTAATAATAAA
55771909 TATTTTAATAATAAA
1 TATTTTAATAATAAA
*
55771924 TATTTATTACAATTATAAA
1 TA-TT-TT--AATAATAAA
* *
55771943 TATATTAATAATACA
1 TATTTTAATAATAAA
55771958 TATTTTA
1 TATTTTA
55771965 TAGTATAAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
13 21 0.24
14 15 0.17
15 22 0.25
16 5 0.06
17 7 0.08
18 4 0.05
19 13 0.15
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.47
Consensus pattern (15 bp):
TATTTTAATAATAAA
Found at i:55772916 original size:29 final size:31
Alignment explanation
Indices: 55772864--55772925 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
55772854 ATCTCGAAAT
* *
55772864 TATATATAAATTTTAATTTATTGTACAATTA
1 TATATATAAACTTTAAGTTATTGTACAATTA
*
55772895 TATATATAAACTTT-AGTT-TTGTGCAATTA
1 TATATATAAACTTTAAGTTATTGTACAATTA
55772924 TA
1 TA
55772926 CATGTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.43
30 3 0.11
31 13 0.46
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (31 bp):
TATATATAAACTTTAAGTTATTGTACAATTA
Found at i:55777654 original size:29 final size:29
Alignment explanation
Indices: 55777612--55777675 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
55777602 TTCGATTGAC
*
55777612 GTGATATCCATTTAAATCAA-AATGCGGAT
1 GTGACATCCATTTAAAT-AAGAATGCGGAT
* **
55777641 GTGACATCTATTTAAATAAGAATGTTGAT
1 GTGACATCCATTTAAATAAGAATGCGGAT
55777670 GTGACA
1 GTGACA
55777676 AAAAAACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (29 bp):
GTGACATCCATTTAAATAAGAATGCGGAT
Found at i:55779606 original size:17 final size:17
Alignment explanation
Indices: 55779584--55779619 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55779574 TTGAGTTTGG
55779584 ATTTATCTTAAAATTAA
1 ATTTATCTTAAAATTAA
* *
55779601 ATTTATTTTTAAATTAA
1 ATTTATCTTAAAATTAA
55779618 AT
1 AT
55779620 AATAAGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATCTTAAAATTAA
Found at i:55780282 original size:3 final size:3
Alignment explanation
Indices: 55780274--55780306 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
55780264 TTAATTGATT
*
55780274 TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55780307 AAAGAGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:55781523 original size:31 final size:30
Alignment explanation
Indices: 55781479--55781631 Score: 163
Period size: 29 Copynumber: 5.1 Consensus size: 30
55781469 TAACCCCTTG
* * *
55781479 AACTTCTCCAAAATTACATTTTATGACCCCGA
1 AACTTC-CAAAAATTCCATTTT-TGACCCCAA
* *
55781511 AACATCCAAAAATTCCA-TTTT-CCCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
55781539 AACTTCCAAAAATTCCATTTTTGACCCCAAA
1 AACTTCCAAAAATTCCATTTTTGACCCC-AA
*
55781570 AACTTCCAAAAATTACATTTTTG-CCCTC-A
1 AACTTCCAAAAATTCCATTTTTGACCC-CAA
* *
55781599 AACTTTCAAAAATTCCATTTTT-ACCCCGA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
55781628 AACT
1 AACT
55781632 CTCGAAATGA
Statistics
Matches: 105, Mismatches: 10, Indels: 15
0.81 0.08 0.12
Matches are distributed among these distances:
28 22 0.21
29 34 0.32
30 10 0.10
31 34 0.32
32 5 0.05
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTGACCCCAA
Found at i:55781578 original size:59 final size:59
Alignment explanation
Indices: 55781452--55781630 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 59
55781442 TCCTTAAATT
* ** ** * * *
55781452 ATCCAAAAATTATATTTTAACCCCTTGAACTTCTCCAAAATTACATTTTATGACCCCGAAAC
1 ATCCAAAAATTACATTTTTGCCCC-CAAACTTC-CAAAAATTCCATTTT-TGACCCCAAAAC
*
55781514 ATCCAAAAATTCCA-TTTT-CCCCCAAAACTTCCAAAAATTCCATTTTTGACCCCAAAAAC
1 ATCCAAAAATTACATTTTTGCCCCC-AAACTTCCAAAAATTCCATTTTTGACCCC-AAAAC
* * * *
55781573 TTCCAAAAATTACATTTTTGCCCTCAAACTTTCAAAAATTCCATTTTT-ACCCCGAAAC
1 ATCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAAC
55781631 TCTCGAAATG
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 11 0.11
59 34 0.34
60 36 0.36
61 7 0.07
62 12 0.12
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (59 bp):
ATCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAAC
Found at i:55781787 original size:28 final size:28
Alignment explanation
Indices: 55781750--55781811 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
55781740 CCAAATTTTG
55781750 CCAAAATTACCATTTTACCCTCGAG-AGT
1 CCAAAATTACCATTTTACCCTCGAGCA-T
55781778 CCAAAATTACCATTTTACCCTCGAGCAT
1 CCAAAATTACCATTTTACCCTCGAGCAT
55781806 CCAAAA
1 CCAAAA
55781812 AGTCTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCGAGCAT
Found at i:55781849 original size:146 final size:147
Alignment explanation
Indices: 55781597--55781969 Score: 413
Period size: 146 Copynumber: 2.6 Consensus size: 147
55781587 TTTTTGCCCT
* * * * * * * **
55781597 CAAA-CTTTCAAAAATT-CCATTTTTACCCC-GAAACTCTCGAAATGACCATTTTACCTCCAAAT
1 CAAACCTTTCCAAAATTACCATTTTTACCCCTGAGAGTC-CAAAATTACCATTTTACCCCCGAGC
* * * * *
55781659 GTCCAAAAA-TCCCGTTTTTGATCCCGATTTATCTAAAAATTACCGTTTTACCCTC-AAGTATCT
65 ATCCAAAAAGTCCCGTTTTTGATCCCGATTTATCCAAAAATTACCGTTTAACCCACGAA-CATCT
* *
55781722 AAAATTTCATTTTTAACCC
129 AAAATATCATTTTTAACCA
* *
55781741 CAAA-TTTTGCCAAAATTACCA-TTTTA-CCCTCGAGAGTCCAAAATTACCATTTTACCCTCGAG
1 CAAACCTTT-CCAAAATTACCATTTTTACCCCT-GAGAGTCCAAAATTACCATTTTACCCCCGAG
* *
55781803 CATCCAAAAAGTCTCTTTTTTGATCCCGATTCT-TCCAAAAATTACCGTTTAACCCACGAACATC
64 CATCCAAAAAGTCCCGTTTTTGATCCCGATT-TATCCAAAAATTACCGTTTAACCCACGAACATC
*
55781867 TAAAATATCATTTTTAACTA
128 TAAAATATCATTTTTAACCA
* * * *
55781887 CAAACCTTTCCAAAATTATCATTTTTGCCCCTGAGAGTCCAAAATTACCATTTTGCCCCCGAGTA
1 CAAACCTTTCCAAAATTACCATTTTTACCCCTGAGAGTCCAAAATTACCATTTTACCCCCGAGCA
55781952 TCCAAAAAGTCCCGTTTT
66 TCCAAAAAGTCCCGTTTT
55781970 CAGTCCCGAT
Statistics
Matches: 190, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
144 10 0.05
145 38 0.20
146 82 0.43
147 56 0.29
148 4 0.02
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (147 bp):
CAAACCTTTCCAAAATTACCATTTTTACCCCTGAGAGTCCAAAATTACCATTTTACCCCCGAGCA
TCCAAAAAGTCCCGTTTTTGATCCCGATTTATCCAAAAATTACCGTTTAACCCACGAACATCTAA
AATATCATTTTTAACCA
Found at i:55781959 original size:29 final size:29
Alignment explanation
Indices: 55781895--55781958 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
55781885 TACAAACCTT
* *
55781895 TCCAAAATTATCATTTTTGCCCCTGAGAG
1 TCCAAAATTACCATTTTTGCCCCCGAGAG
55781924 TCCAAAATTACCA-TTTTGCCCCCGAGTA-
1 TCCAAAATTACCATTTTTGCCCCCGAG-AG
55781952 TCCAAAA
1 TCCAAAA
55781959 AGTCCCGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (29 bp):
TCCAAAATTACCATTTTTGCCCCCGAGAG
Found at i:55784269 original size:6 final size:6
Alignment explanation
Indices: 55784258--55784296 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
55784248 TGATCAAAAT
*
55784258 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
55784297 TATGAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:55786063 original size:5 final size:5
Alignment explanation
Indices: 55786053--55786078 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55786043 ATATATATTG
55786053 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
55786079 CAAGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:55793058 original size:63 final size:63
Alignment explanation
Indices: 55792980--55793108 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
55792970 TGCGGCGAAA
55792980 GAAACAATGGGTATGAACGGTAGCACAAATCATTCATTCATTCATCAGGGTACATTCAGACAT
1 GAAACAATGGGTATGAACGGTAGCACAAATCATTCATTCATTCATCAGGGTACATTCAGACAT
55793043 GAAACAATGGGTATGAACGGTAGCACAAATCATTCATTCATTCATCAGGGTACATTCAGACAT
1 GAAACAATGGGTATGAACGGTAGCACAAATCATTCATTCATTCATCAGGGTACATTCAGACAT
55793106 GAA
1 GAA
55793109 CCTTCGTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (63 bp):
GAAACAATGGGTATGAACGGTAGCACAAATCATTCATTCATTCATCAGGGTACATTCAGACAT
Found at i:55797695 original size:165 final size:165
Alignment explanation
Indices: 55797423--55797754 Score: 592
Period size: 165 Copynumber: 2.0 Consensus size: 165
55797413 TCTACCACGA
* *
55797423 CCACCACCAGCCTGACCACCCCTCTCATCGCCGTCCCGATAAGGACCCACTTGAGAGTTAGTTGG
1 CCACCACCAGACTGACCACCCCTCGCATCGCCGTCCCGATAAGGACCCACTTGAGAGTTAGTTGG
*
55797488 GTTCCAGTTGGCCCCACTTTGCTCTTGGCCTATGGCCGCCTGATAAGGACCCTGATGATCAGCGC
66 GTTCCAGTTGGCCCCACTTTGCCCTTGGCCTATGGCCGCCTGATAAGGACCCTGATGATCAGCGC
* *
55797553 TGTAATCTCTACTTCTTGCTCTTGCTCTTCCTCTT
131 TGTAATCTCTACCTCTTCCTCTTGCTCTTCCTCTT
* *
55797588 CCACCACCAGACTGACCACCCCTCGCATCGCCGTCCTGATAAGGACCCACTTGAGAGTTGGTTGG
1 CCACCACCAGACTGACCACCCCTCGCATCGCCGTCCCGATAAGGACCCACTTGAGAGTTAGTTGG
55797653 GTTCCAGTTGGCCCCACTTTGCCCTTGGCCTATGGCCGCCTGATAAGGACCCTGATGATCAGCGC
66 GTTCCAGTTGGCCCCACTTTGCCCTTGGCCTATGGCCGCCTGATAAGGACCCTGATGATCAGCGC
*
55797718 TGTCATCTCTACCTCTTCCTCTTGCTCTTCCTCTT
131 TGTAATCTCTACCTCTTCCTCTTGCTCTTCCTCTT
55797753 CC
1 CC
55797755 TCTTCCTCTT
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 159 1.00
ACGTcount: A:0.16, C:0.36, G:0.20, T:0.28
Consensus pattern (165 bp):
CCACCACCAGACTGACCACCCCTCGCATCGCCGTCCCGATAAGGACCCACTTGAGAGTTAGTTGG
GTTCCAGTTGGCCCCACTTTGCCCTTGGCCTATGGCCGCCTGATAAGGACCCTGATGATCAGCGC
TGTAATCTCTACCTCTTCCTCTTGCTCTTCCTCTT
Found at i:55797738 original size:6 final size:6
Alignment explanation
Indices: 55797724--55797766 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
55797714 GCGCTGTCAT
* *
55797724 CTCTAC CTCTTC CTCTTG CTCTTC CTCTTC CTCTTC CTCTTC C
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC C
55797767 ACCACCATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.02, C:0.49, G:0.02, T:0.47
Consensus pattern (6 bp):
CTCTTC
Found at i:55798951 original size:27 final size:27
Alignment explanation
Indices: 55798897--55798951 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
55798887 GAAAATGCAT
***
55798897 ATTTATTTTCAAATGAATAACCTTTTA
1 ATTTATTTTCAAATGAATAACAAATTA
* *
55798924 ATTTATTTTCAAATTAATAATAAATTA
1 ATTTATTTTCAAATGAATAACAAATTA
55798951 A
1 A
55798952 ATGTAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTATTTTCAAATGAATAACAAATTA
Found at i:55799726 original size:28 final size:28
Alignment explanation
Indices: 55799653--55799743 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
55799643 CTCCTTTTTT
*
55799653 CTATTTAGGAGAATATATTATATATCTAT-
1 CTATTTA-G-GAATATATTATATATCTTTC
* * * *
55799682 ATATTTAGAAATTTATTATATATGTTTC
1 CTATTTAGGAATATATTATATATCTTTC
55799710 CTATTTAGGAATATATTATATATCTTTC
1 CTATTTAGGAATATATTATATATCTTTC
55799738 CTATTT
1 CTATTT
55799744 TTTACTTAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 15 0.29
28 31 0.60
29 6 0.12
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (28 bp):
CTATTTAGGAATATATTATATATCTTTC
Found at i:55799943 original size:30 final size:31
Alignment explanation
Indices: 55799902--55799966 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
55799892 TTTAAAGGCC
* * *
55799902 AAAATTTTTTTTAACAATTTTTAAGGGACTT
1 AAAATTTTTTTTAACAACTTTTAAGGAACCT
*
55799933 AAAATTTTTTTT-TCAACTTTTAAGGAACCT
1 AAAATTTTTTTTAACAACTTTTAAGGAACCT
55799963 AAAA
1 AAAA
55799967 CCCTATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (31 bp):
AAAATTTTTTTTAACAACTTTTAAGGAACCT
Found at i:55800758 original size:10 final size:9
Alignment explanation
Indices: 55800741--55800787 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
55800731 ATATTTCAAA
55800741 AAATAAAAT
1 AAATAAAAT
55800750 AAATAAAA-
1 AAATAAAAT
*
55800758 ATATAAAAT
1 AAATAAAAT
*
55800767 AATTAAAAT
1 AAATAAAAT
*
55800776 TAATAAATAT
1 AAATAAA-AT
55800786 AA
1 AA
55800788 TAGAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
8 7 0.23
9 20 0.67
10 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATAAAAT
Found at i:55800758 original size:17 final size:17
Alignment explanation
Indices: 55800738--55800774 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55800728 AAAATATTTC
55800738 AAAAAATAAAATAAATA
1 AAAAAATAAAATAAATA
* *
55800755 AAAATATAAAATAATTA
1 AAAAAATAAAATAAATA
55800772 AAA
1 AAA
55800775 TTAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAATAAAATAAATA
Found at i:55804037 original size:20 final size:20
Alignment explanation
Indices: 55804012--55804050 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
55804002 TTTGCCAAAT
55804012 ACTAATATTATAATGAGATA
1 ACTAATATTATAATGAGATA
55804032 ACTAATATTATAATGAGAT
1 ACTAATATTATAATGAGAT
55804051 GTTTGGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (20 bp):
ACTAATATTATAATGAGATA
Found at i:55819445 original size:29 final size:31
Alignment explanation
Indices: 55819393--55819473 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 31
55819383 GAATTAAAAC
* * * * *
55819393 AAATCAAAATTTTATGTATGAAATTGCACA-
1 AAATCAAAAGTTCATATATAAAATTACACAT
55819423 AAATCAAAA-TTCATATATAAAATTACACATT
1 AAATCAAAAGTTCATATATAAAATTACACA-T
55819454 AAA-CAAAAGTTCATATATAA
1 AAATCAAAAGTTCATATATAA
55819474 TTATAAGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 16 0.36
30 14 0.32
31 14 0.32
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (31 bp):
AAATCAAAAGTTCATATATAAAATTACACAT
Found at i:55820442 original size:19 final size:19
Alignment explanation
Indices: 55820410--55820449 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55820400 ATTCATACAC
*
55820410 AAAATAAAAATTTATGTAT
1 AAAATAAAAATTTATATAT
* *
55820429 AAAATTAAAGTTTATATAT
1 AAAATAAAAATTTATATAT
55820448 AA
1 AA
55820450 TTTTAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAATAAAAATTTATATAT
Found at i:55825158 original size:32 final size:33
Alignment explanation
Indices: 55825094--55825160 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
55825084 AATCGATAGC
*
55825094 AGATATTTTTTTAAAATATTGTTACTGTAAATTTT
1 AGATATTTTTTTAAAATATGGTTAC--TAAATTTT
* *
55825129 AGATTTTTTTTTAAATTATGGTTAC-AAATTTT
1 AGATATTTTTTTAAAATATGGTTACTAAATTTT
55825161 TTAAAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 7 0.24
35 22 0.76
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (33 bp):
AGATATTTTTTTAAAATATGGTTACTAAATTTT
Found at i:55826987 original size:15 final size:15
Alignment explanation
Indices: 55826941--55826991 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
55826931 AACAAAAAAT
*
55826941 AATATAAATTACTAA
1 AATATAAATAACTAA
* ** *
55826956 AATAT-GATATTTTA
1 AATATAAATAACTAA
55826970 AATATAAATAACTAA
1 AATATAAATAACTAA
55826985 AATATAA
1 AATATAA
55826992 TCTGAAAAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (15 bp):
AATATAAATAACTAA
Found at i:55853665 original size:34 final size:34
Alignment explanation
Indices: 55853571--55853665 Score: 84
Period size: 34 Copynumber: 2.8 Consensus size: 34
55853561 ATAGCAAATC
* * * *
55853571 TGCGAGCTCACCCAAAGTTGCGAGCTTAGCAAAGA
1 TGCGAGTTCA-CCAAAGCTGCGAGCTCACCAAAGA
* * * *
55853606 TGTGAGTTCACCAAATCTGCAAGCTCACCAAAGT
1 TGCGAGTTCACCAAAGCTGCGAGCTCACCAAAGA
*
55853640 TGCGAAGTT-ACCAAAGGTGCGAGCTC
1 TGCG-AGTTCACCAAAGCTGCGAGCTC
55853666 TATTAAGCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
34 35 0.74
35 12 0.26
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (34 bp):
TGCGAGTTCACCAAAGCTGCGAGCTCACCAAAGA
Found at i:55854899 original size:19 final size:18
Alignment explanation
Indices: 55854837--55854896 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
55854827 AGATGAGTAT
*
55854837 ATAAAAAATTTAAA-TAA
1 ATAAAAAATTAAAATTAA
55854854 ATAAAAAAGTATAAAATT-A
1 ATAAAAAA-T-TAAAATTAA
* *
55854873 TTAAATAATTAAAATTAA
1 ATAAAAAATTAAAATTAA
55854891 ATAAAA
1 ATAAAA
55854897 TAAATATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 15 0.44
18 7 0.21
19 11 0.32
20 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAAAAAATTAAAATTAA
Found at i:55858676 original size:195 final size:196
Alignment explanation
Indices: 55858230--55858677 Score: 489
Period size: 195 Copynumber: 2.3 Consensus size: 196
55858220 GAAACCGACG
* * * *
55858230 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGCGAGCAGCATCGTGAGTCA
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCATGACTCA
* *
55858295 GGAAATGAGAAAAGAAATATGGATCCTAAATGGATTAAGGCCCTAAGATGGTTGAGATTTTATGC
66 -G--A-GAGAAAAGAAATATGGATCCTAAATGGATTAAGGCCCTAAGATGGTAGAGA-TCTATGC
* * * * *
55858360 ATAAGTGCATATTCTCGACAGCTCGTGTAAGTAACATCTTTAGGGAATAGTTATATGCACAGATA
126 ATAAGTGCATACTCTCGACAGCTCGTGTAAGCAACATCTTTAGGGAACAGTTATATACACAGACA
* *
55858425 TCGTAT
191 CCGTAC
* * * * *
55858431 CGATGGCTGAGGTGCCGCATATATTGTGGGTCCTCGACAGCTCATGTGAGCAACATCATGACTC-
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCATGACTCA
* * *
55858495 G-G-G-AAAGAGATATGGATCCTAAATGGATTACAGGCCCTACGATGGCTAG-GA-CTATGC-TT
66 GAGAGAAAAGAAATATGGATCCTAAATGGATTA-AGGCCCTAAGATGG-TAGAGATCTATGCATA
* * *
55858554 ATTGCATACTCTCGACAGCTCGTGTGAGCAGCAT-TGTTAGGGAACAGTTTATATTACAGACAGA
129 AGTGCATACTCTCGACAGCTCGTGTAAGCAACATCT-TTAGGGAACAG-TTATA-TAC--ACAGA
55858618 CACCGTAC
189 CACCGTAC
* * *
55858626 CGATAGCTGGGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGCA
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCA
55858678 GCATTGAGTA
Statistics
Matches: 208, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
190 1 0.00
191 40 0.19
192 10 0.05
193 28 0.13
194 16 0.08
195 57 0.27
199 1 0.00
201 55 0.26
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (196 bp):
CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCATGACTCA
GAGAGAAAAGAAATATGGATCCTAAATGGATTAAGGCCCTAAGATGGTAGAGATCTATGCATAAG
TGCATACTCTCGACAGCTCGTGTAAGCAACATCTTTAGGGAACAGTTATATACACAGACACCGTA
C
Found at i:55861013 original size:32 final size:32
Alignment explanation
Indices: 55860977--55861044 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
55860967 TATTTTGATA
*
55860977 TTTGGTTA-AAATTTTTGGTAGCCACCAAAAAT
1 TTTGGTTACAAA-TTTTGGTAACCACCAAAAAT
* *
55861009 TTTGGTTACAAATTTTGGTAACCATCAGAAAT
1 TTTGGTTACAAATTTTGGTAACCACCAAAAAT
55861041 TTTG
1 TTTG
55861045 ATACCTGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 29 0.91
33 3 0.09
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (32 bp):
TTTGGTTACAAATTTTGGTAACCACCAAAAAT
Found at i:55861113 original size:19 final size:19
Alignment explanation
Indices: 55861084--55861131 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
55861074 AAAAAGTTTA
* *
55861084 ATTTTGATATCTGTTACAAG
1 ATTTTGGTATCTATTA-AAG
55861104 -TTTTGGTATCTATTAAAG
1 ATTTTGGTATCTATTAAAG
55861122 ATTTTGGTAT
1 ATTTTGGTAT
55861132 AAATTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (19 bp):
ATTTTGGTATCTATTAAAG
Found at i:55863947 original size:2 final size:2
Alignment explanation
Indices: 55863940--55863974 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55863930 CGACGTTGCG
55863940 TA TA TA TA 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 T
55863975 TACAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55865359 original size:18 final size:18
Alignment explanation
Indices: 55865336--55865376 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
55865326 ATAATTTTTA
55865336 AATTAAATAAATTT-AATT
1 AATTAAA-AAATTTAAATT
*
55865354 AATTAAAAATTTTAAATT
1 AATTAAAAAATTTAAATT
55865372 AATTA
1 AATTA
55865377 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAAAAATTTAAATT
Found at i:55869931 original size:17 final size:17
Alignment explanation
Indices: 55869900--55869999 Score: 112
Period size: 17 Copynumber: 5.9 Consensus size: 17
55869890 TCCAGCTTTT
* *
55869900 AATTT-TTTAAAATTTT
1 AATTTATTTTAAATTTA
*
55869916 AATTTATTTTAAATTTG
1 AATTTATTTTAAATTTA
55869933 AATTTATTTTTAAATTTA
1 AATTTA-TTTTAAATTTA
* * *
55869951 AATTCATTTTGAGTTTA
1 AATTTATTTTAAATTTA
* *
55869968 AATTTACTTTAAATTCA
1 AATTTATTTTAAATTTA
55869985 AATTTATTTTAAATT
1 AATTTATTTTAAATT
55870000 AAAAAAATTA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
16 5 0.07
17 50 0.71
18 15 0.21
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:55871937 original size:58 final size:58
Alignment explanation
Indices: 55871777--55872071 Score: 292
Period size: 58 Copynumber: 5.0 Consensus size: 58
55871767 CCTTGGAGGT
* * * *
55871777 CCCTAAATTATCCAAAAATTATATTTTTACCCTCAAACTTCCAAGAATTCTATTTTTGA
1 CCCTAAATT-TCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
* * * * * *
55871836 CCCAAAACTTTTCGAAAATAACATTTTTACCCTTGAACTTCCAAAAATTCTATTTTTGA
1 CCCTAAA-TTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
*
55871895 CCCTAAATTTCCAAAAATTATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAATTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
** * ** *
55871953 CCCTGACTTTTCC-AAAATTACCA-TTTTACCCTCAAACTTCTGAAAATTCCATTTTTGG
1 CCCT-AAATTTCCAAAAATTA-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
*** * *
55872011 CCACGTTTTTTTCCAAAAATTACCA-TTTTA-CCTCCGAACTTCTAAAAATCCCATTTTTGA
1 CC-C-TAAATTTCCAAAAATTA-CATTTTTACCCT-CGAACTTCCAAAAATTCCATTTTTGA
55872071 C
1 C
55872072 TTCGATTTTT
Statistics
Matches: 201, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
58 89 0.44
59 71 0.35
60 41 0.20
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
CCCTAAATTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
Found at i:55872008 original size:29 final size:29
Alignment explanation
Indices: 55871787--55872008 Score: 173
Period size: 29 Copynumber: 7.6 Consensus size: 29
55871777 CCCTAAATTA
**
55871787 TCCAAAAATTATATTTTTACCCTCAAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACT
* * *
55871816 TCCAAGAATTCTATTTTTGACCC-AAAACTT
1 TCCAAAAATTCCATTTTT-ACCCTCAAAC-T
* * ** **
55871846 TTCGAAAATAACATTTTTACCCTTGAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACT
* *
55871875 TCCAAAAATTCTATTTTTGACCCT-AAATT
1 TCCAAAAATTCCATTTTT-ACCCTCAAACT
** *
55871904 TCCAAAAATTATATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACT
* ***
55871933 TCCAAAAATTCCATTTTTGACCCTGACTTT
1 TCCAAAAATTCCATTTTT-ACCCTCAAACT
55871963 TCC-AAAATTACCA-TTTTACCCTCAAACT
1 TCCAAAAATT-CCATTTTTACCCTCAAACT
**
55871991 TCTGAAAATTCCATTTTT
1 TCCAAAAATTCCATTTTT
55872009 GGCCACGTTT
Statistics
Matches: 151, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
28 17 0.11
29 97 0.64
30 37 0.25
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCTCAAACT
Found at i:55872180 original size:28 final size:28
Alignment explanation
Indices: 55872122--55872183 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
55872112 TCAAACTTTC
* * *
55872122 CCAAAATGACCATTTTGCCATCGAGTGT
1 CCAAAATGACCATTTTACCACCGAGTAT
* * *
55872150 CCAAAATTACCATTTTACCCCCGGGTAT
1 CCAAAATGACCATTTTACCACCGAGTAT
55872178 CCAAAA
1 CCAAAA
55872184 ATCACATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CCAAAATGACCATTTTACCACCGAGTAT
Found at i:55888143 original size:16 final size:17
Alignment explanation
Indices: 55888109--55888145 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
55888099 TATAAATTAT
55888109 TAAATATTAAAATAAAA
1 TAAATATTAAAATAAAA
*
55888126 TAAATATTTAAA-AAAA
1 TAAATATTAAAATAAAA
55888142 TAAA
1 TAAA
55888146 AAATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATATTAAAATAAAA
Found at i:55888406 original size:12 final size:12
Alignment explanation
Indices: 55888389--55888429 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
55888379 TAAAGTTTAA
55888389 ATATTTAAAATT
1 ATATTTAAAATT
*
55888401 ATATTTCTAAAAAT
1 ATA-TT-TAAAATT
55888415 ATATTTAAAATT
1 ATATTTAAAATT
55888427 ATA
1 ATA
55888430 GATTTATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 12 0.48
13 4 0.16
14 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATTTAAAATT
Found at i:55890695 original size:21 final size:21
Alignment explanation
Indices: 55890669--55890729 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
55890659 CATGAAATTG
*
55890669 TTCTTGAGGTCTCGAGACATA
1 TTCTTGATGTCTCGAGACATA
55890690 TTCTTGATGTCTCGAGACATA
1 TTCTTGATGTCTCGAGACATA
55890711 TTCTTGATGTCTCGAGACA
1 TTCTTGATGTCTCGAGACA
55890730 CATGTCTAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (21 bp):
TTCTTGATGTCTCGAGACATA
Found at i:55894421 original size:25 final size:25
Alignment explanation
Indices: 55894383--55894437 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
55894373 TAAACGCATT
* *
55894383 GTTTT-ATTTAAACTGGAACTCCCC
1 GTTTTGATTGAAACTGAAACTCCCC
*
55894407 GTTTTGATTGAAACTGAAACTCCTC
1 GTTTTGATTGAAACTGAAACTCCCC
55894432 GTTTTG
1 GTTTTG
55894438 CTTATCCGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (25 bp):
GTTTTGATTGAAACTGAAACTCCCC
Found at i:55902577 original size:14 final size:16
Alignment explanation
Indices: 55902558--55902589 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55902548 ATTTGTTGTG
55902558 TTTTCA-ACA-AATTT
1 TTTTCACACAGAATTT
55902572 TTTTCACACAGAATTT
1 TTTTCACACAGAATTT
55902588 TT
1 TT
55902590 CTGCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.31, C:0.16, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTCACACAGAATTT
Found at i:55907577 original size:21 final size:20
Alignment explanation
Indices: 55907553--55907594 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
55907543 TGTTCTAATT
55907553 TATTATTA-ATTTCTACTAACA
1 TATTATTATATTTC-A-TAACA
*
55907574 TATTTTTATATTTCATAACA
1 TATTATTATATTTCATAACA
55907594 T
1 T
55907595 TTTCATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTATATTTCATAACA
Found at i:55910479 original size:34 final size:34
Alignment explanation
Indices: 55910423--55910526 Score: 118
Period size: 34 Copynumber: 3.0 Consensus size: 34
55910413 CAAGAATATG
* * * * *
55910423 AAAAGTTAATGAAGATGAAAGGTTAAAGATCAAG
1 AAAAATTAAAGAAGATGGAAGGTTAAAGATAAAA
* *
55910457 AGAGATTAAAGAAGATGGAAGGTTAAAGATAAAA
1 AAAAATTAAAGAAGATGGAAGGTTAAAGATAAAA
* *
55910491 AAAAATTAAAGAAGATTGAAGGTTAAAAGATGAAA
1 AAAAATTAAAGAAGATGGAAGGTT-AAAGATAAAA
55910526 A
1 A
55910527 GTTAAACATC
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
34 48 0.83
35 10 0.17
ACGTcount: A:0.57, C:0.01, G:0.23, T:0.19
Consensus pattern (34 bp):
AAAAATTAAAGAAGATGGAAGGTTAAAGATAAAA
Found at i:55911568 original size:21 final size:22
Alignment explanation
Indices: 55911543--55911585 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55911533 ATGAGAGGGA
55911543 GAGGGAGA-GGGACGATGGGGG
1 GAGGGAGAGGGGACGATGGGGG
*
55911564 GAGGGAGAGGGGACGGTGGGGG
1 GAGGGAGAGGGGACGATGGGGG
55911586 AAAGGGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.21, C:0.05, G:0.70, T:0.05
Consensus pattern (22 bp):
GAGGGAGAGGGGACGATGGGGG
Found at i:55928771 original size:6 final size:6
Alignment explanation
Indices: 55928744--55928786 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
55928734 AAATACAGAC
55928744 TTTATA TTATATA TTATATA TTTATA TTTATA TTTATA TTTAT
1 TTTATA TT-TATA TT-TATA TTTATA TTTATA TTTATA TTTAT
55928787 GAATGATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTATA
Found at i:55942219 original size:23 final size:23
Alignment explanation
Indices: 55942193--55942238 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
55942183 AAATCTAAAA
55942193 CTTAAAGAAAATATGATAACATG
1 CTTAAAGAAAATATGATAACATG
*
55942216 CTTAAAGAAAATATGATGACATG
1 CTTAAAGAAAATATGATAACATG
55942239 GCACAACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (23 bp):
CTTAAAGAAAATATGATAACATG
Found at i:55950137 original size:30 final size:30
Alignment explanation
Indices: 55950103--55950160 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55950093 GAGAGGGGAG
* * *
55950103 TAAAAGTTTTTGAAGGAAAGTAAAAAGTAA
1 TAAAAATTTTGGAAGAAAAGTAAAAAGTAA
*
55950133 TAAAAATTTTGGAATAAAAGTAAAAAGT
1 TAAAAATTTTGGAAGAAAAGTAAAAAGT
55950161 TTGGGATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (30 bp):
TAAAAATTTTGGAAGAAAAGTAAAAAGTAA
Found at i:55950962 original size:11 final size:11
Alignment explanation
Indices: 55950943--55950978 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
55950933 TGCAAACCAA
55950943 AAATTAATTTT
1 AAATTAATTTT
*
55950954 AAATAAATTTT
1 AAATTAATTTT
*
55950965 AATTTAATTTT
1 AAATTAATTTT
55950976 AAA
1 AAA
55950979 ATTTCCGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:55951729 original size:2 final size:2
Alignment explanation
Indices: 55951722--55951772 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
55951712 ACTACCTCCT
55951722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55951764 TA TA TA TA T
1 TA TA TA TA T
55951773 CAGTTGAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55967121 original size:24 final size:26
Alignment explanation
Indices: 55967094--55967142 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
55967084 TATAGAATAA
*
55967094 AATTTTAGAT-TTTTTTAAA-ATTTG
1 AATTTTAGATCATTTTTAAATATTTG
*
55967118 AATTTTATATCATTTTTAAATATTT
1 AATTTTAGATCATTTTTAAATATTT
55967143 ATTTTGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 8 0.38
26 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (26 bp):
AATTTTAGATCATTTTTAAATATTTG
Found at i:55967185 original size:25 final size:25
Alignment explanation
Indices: 55967139--55967196 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 25
55967129 ATTTTTAAAT
55967139 ATTTATTTTGAATATTTAATATTT-A
1 ATTT-TTTTGAATATTTAATATTTGA
55967164 ATTTTTTTGAAT-TTATATATATTTGA
1 ATTTTTTTGAATATT-TA-ATATTTGA
55967190 ATTTTTT
1 ATTTTTT
55967197 ATATAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.07
24 10 0.33
25 10 0.33
26 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (25 bp):
ATTTTTTTGAATATTTAATATTTGA
Found at i:55971352 original size:30 final size:30
Alignment explanation
Indices: 55971318--55971374 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
55971308 TAATTACTTA
55971318 AAAATATTTAA-AAT-TTATATTTTATATATC
1 AAAATA-TTAATAATATTAT-TTTTATATATC
55971348 AAAATATTAATAATATTATTTTTATAT
1 AAAATATTAATAATATTATTTTTATAT
55971375 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.16
30 17 0.68
31 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
AAAATATTAATAATATTATTTTTATATATC
Done.