Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold134
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: 811437
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 4 of 5
Found at i:527020 original size:24 final size:25
Alignment explanation
Indices: 526936--527026 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 25
526926 AAGCCACCCT
** * *
526936 TTGTTTGTCAAAAATAATGGTTACTT
1 TTGTTTGTCAAAAATGGTGGTCA-TG
* *
526962 TGTGTTTGTCAAAAATGGTGGTTTCTTT
1 T-TGTTTGTCAAAAATGGTGG--TCATG
*
526990 TTATTTGTCAAAAATGGTGG-CATG
1 TTGTTTGTCAAAAATGGTGGTCATG
527014 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
527027 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
24 14 0.26
26 1 0.02
27 35 0.65
28 3 0.06
29 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (25 bp):
TTGTTTGTCAAAAATGGTGGTCATG
Found at i:531890 original size:16 final size:17
Alignment explanation
Indices: 531871--531911 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
531861 GAAAGAAAGG
531871 AAAG-AGAGAAGAAAAA
1 AAAGAAGAGAAGAAAAA
*
531887 AAAGAAAGAGAATAAAAA
1 AAAG-AAGAGAAGAAAAA
531905 AAA-AAGA
1 AAAGAAGA
531912 TTCATGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAGAAGAGAAGAAAAA
Found at i:531893 original size:20 final size:20
Alignment explanation
Indices: 531860--531911 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
531850 GTGGTAAGGG
* *
531860 AGAAAGAAAGGAAAGAGAGA-
1 AGAAAAAAAAGAAAGAGA-AT
531880 AGAAAAAAAAGAAAGAGAAT
1 AGAAAAAAAAGAAAGAGAAT
*
531900 AAAAAAAAAAGA
1 AGAAAAAAAAGA
531912 TTCATGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AGAAAAAAAAGAAAGAGAAT
Found at i:532907 original size:22 final size:22
Alignment explanation
Indices: 532882--532933 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
532872 TATTACTTTG
*
532882 AATTATTTGTCACGTAATAAGT
1 AATTATTTGTCACGTAATAAAT
*
532904 AATTGA-TTGTGACGTAATAAAT
1 AATT-ATTTGTCACGTAATAAAT
*
532926 ATTTATTT
1 AATTATTT
532934 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (22 bp):
AATTATTTGTCACGTAATAAAT
Found at i:532951 original size:17 final size:17
Alignment explanation
Indices: 532926--532964 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
532916 CGTAATAAAT
532926 ATTTATTTAAATTTTTA
1 ATTTATTTAAATTTTTA
* * *
532943 ATTTTTTTATATTTTTT
1 ATTTATTTAAATTTTTA
532960 ATTTA
1 ATTTA
532965 CATTATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTATTTAAATTTTTA
Found at i:535311 original size:233 final size:233
Alignment explanation
Indices: 534896--535361 Score: 801
Period size: 233 Copynumber: 2.0 Consensus size: 233
534886 TAATAATTAT
* *
534896 AATATTAGATTTTTACACATCTATAAAATTGGGTAAATTTTTTATTTTTTATTTTGAAAAATAAT
1 AATACTAGATTTTTACACATCTACAAAATTGGGTAAATTTTTTATTTTTTATTTTGAAAAATAAT
*
534961 ATATTAAAGCTTAAAACGATTGTAGTCTTTTTCAAATAAAAAAGCAAAGAGTGTTATTATTAAAT
66 ATATTAAAGCTTAAAAAGATTGTAGTCTTTTTCAAATAAAAAAGCAAAGAGTGTTATTATTAAAT
*
535026 AAAAAATATAAACAATTAATTATTATTTTAAAAGAAAAGATAAAAACACTCTTAATTTTATTTTT
131 AAAAAATATAAACAATTAATTATTATTTTAAAAGAAAAGACAAAAACACTCTTAATTTTATTTTT
*
535091 ATTTTGAGAATTTATTTGGACTTTTTGTAATTCTTAGA
196 ATTTTGAGAATTCATTTGGACTTTTTGTAATTCTTAGA
*
535129 AATACTAGATTTTTACACATCTACAAAATTGGGTAAATTTTTTATTTTTTTTTTTGAAAAATAAT
1 AATACTAGATTTTTACACATCTACAAAATTGGGTAAATTTTTTATTTTTTATTTTGAAAAATAAT
* * *
535194 ATATTAAAGCTTAAAAAGATTGTTAGTCTTTTTCAAA-CAAAAATC-AAGAAGTTTTATTATTAA
66 ATATTAAAGCTTAAAAAGATTG-TAGTCTTTTTCAAATAAAAAAGCAAAG-AGTGTTATTATTAA
*
535257 ATAAAAAATATAAACAATTAATTATTATTTTAAAAGAAAAGACAAAAGCACTCTTAATTTTATTT
129 ATAAAAAATATAAACAATTAATTATTATTTTAAAAGAAAAGACAAAAACACTCTTAATTTTATTT
*
535322 TTATTTTGAGAATTCATTTGGATTTTTTGTAATTCTTAGA
194 TTATTTTGAGAATTCATTTGGACTTTTTGTAATTCTTAGA
535362 TTAAGCTAGT
Statistics
Matches: 220, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
232 3 0.01
233 203 0.92
234 14 0.06
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (233 bp):
AATACTAGATTTTTACACATCTACAAAATTGGGTAAATTTTTTATTTTTTATTTTGAAAAATAAT
ATATTAAAGCTTAAAAAGATTGTAGTCTTTTTCAAATAAAAAAGCAAAGAGTGTTATTATTAAAT
AAAAAATATAAACAATTAATTATTATTTTAAAAGAAAAGACAAAAACACTCTTAATTTTATTTTT
ATTTTGAGAATTCATTTGGACTTTTTGTAATTCTTAGA
Found at i:538337 original size:4 final size:4
Alignment explanation
Indices: 538328--538358 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
538318 CAAGGTACTT
538328 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
538359 GAATTTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:539384 original size:2 final size:2
Alignment explanation
Indices: 539379--539412 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
539369 AATTTGATCC
539379 AT AT AT AT 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 AT AT AT AT
539413 TGATTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:540281 original size:21 final size:22
Alignment explanation
Indices: 540252--540298 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
540242 CTAACATTCT
540252 CACCCAATA-CATCACCTAACA
1 CACCCAATAGCATCACCTAACA
* *
540273 CACCTAATATGCTTCACCTAACA
1 CACCCAATA-GCATCACCTAACA
540296 CAC
1 CAC
540299 TTAACAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.38, C:0.40, G:0.02, T:0.19
Consensus pattern (22 bp):
CACCCAATAGCATCACCTAACA
Found at i:544011 original size:34 final size:35
Alignment explanation
Indices: 543972--544053 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 35
543962 AAATATCTTG
* * *
543972 CTCACCTAACATATTACCTAATACACCTAATAT-C
1 CTCACCTAACACATCACCTAACACACCTAATATGC
* *
544006 CTCACCAAATACATCACCTAACACACCTAATATGC
1 CTCACCTAACACATCACCTAACACACCTAATATGC
*
544041 TTCACCTAACACA
1 CTCACCTAACACA
544054 CTTAACAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 28 0.72
35 11 0.28
ACGTcount: A:0.39, C:0.35, G:0.01, T:0.24
Consensus pattern (35 bp):
CTCACCTAACACATCACCTAACACACCTAATATGC
Found at i:544037 original size:21 final size:22
Alignment explanation
Indices: 544008--544054 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
543998 CTAATATCCT
544008 CACCAAATA-CATCACCTAACA
1 CACCAAATAGCATCACCTAACA
* *
544029 CACCTAATATGCTTCACCTAACA
1 CACCAAATA-GCATCACCTAACA
544052 CAC
1 CAC
544055 TTAACAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.40, C:0.38, G:0.02, T:0.19
Consensus pattern (22 bp):
CACCAAATAGCATCACCTAACA
Found at i:553249 original size:970 final size:956
Alignment explanation
Indices: 551281--553157 Score: 2478
Period size: 970 Copynumber: 1.9 Consensus size: 956
551271 CAGCTGAGGG
* * *
551281 TAAACTAAAGCGGCTACGGAGGAAATCCGTAGC-TTTACTCAACATCCCAACCACGCTAGTCTTG
1 TAAACT-AAGAGGCTATGGAGGAAA--CGTAGCTTTTACTCAACATCCCAACCACACTAGTCTTG
* * * * *
551345 ATGTTCTGCAGAAAATCTGAAAATGCATCACCACTGTAGTCTTTATATTCTTCTTGCTTTACTGA
63 ATGTTCTGCAGAAAAGCCGAAAATGCATCACCACTGAAGTCTTTATATTCTTCTAGCTTTACCGA
* * *
551410 GGATTCGGAACTTCGTGGGGATCCCTGATATCCAAACTCAACATCTGTAAGACATTTGTTTATTA
128 AGATTCGGAACTTCGGGGGGATCCCTGATATCCAAACTCAACATCTGTAAGACAATTGTTTATTA
* * *
551475 AAAGCTGAATAAGTAAACGATGCATCAAATATTGAAAAGTTATAGAAAAGCAATGTGCAAAACTT
193 AAAGCTAAATAAGTAAAAGATGCATCAAATATTGAAAAGTAATAGAAAAGCAATGTGCAAAACTT
551540 CTCACTGCTCTGCATGGACTGGATGAAATCCATATAAGCTGAATTGTTCAGGACAGCAATCCATA
258 CTCACTGCTCTGCATGGACTGGATGAAATCCATATAAGCTGAATTGTTCAGGACAGCAATCCATA
551605 CAATCGGATCGGCAGCAACAACAGACTGAAAGGAAAACCAAAACCATCAACCGAGTTATATTTCA
323 CAATCGGATCGGCAGCAACAACAGACTGAAAGGAAAACCAAAACCATCAACCGAGTTATATTTCA
* ** * *
551670 TAAATTATAGGTAAAGGAAGTAAATCTTAAAATGAAGGGTACTAAAATCAAAAACCAAATAAAGC
388 TAAATTATAGGTAAAGGAAGAAAATCTTAAAATGAAGAATAATAAAATCAAAAACCAAATAAAGA
551735 ATCCTAGCATTTTTTTATTTTTTTCAAAGTATGGAAGACCATGTTGCTCTGAGCCTTTCATTTTT
453 ATCCTAGCATTTTTTTATTTTTTTCAAAGTATGGAAGACCATGTTGCTCTGAGCCTTTCATTTTT
*
551800 CTTAAAGTGCCTGTGTTCAATGGAATTGATAACCATGTCTAATGCATATTCAGACACATGAAGGA
518 CTTAAAGTGCCTGTGTTCAATGGAATTGACAACCATGTCTAATGCATATTCAGACACATGAAGGA
* ** * * *
551865 CCCTCCAAATACATGAAAAAAGTTTAAAAAGTTTGAACATTCCTATATCAGTCAAATACCGTATT
583 CCCTCCAAATACATAAAAAAAACTTAAAAAG-ATGAACATTCCTATAGCAGTCAAATACCATATT
* * **
551930 CGACACCCACATCTAAATCCATATATGAAAGAAAATAAGGAGAAAGGATCAGAGGAAGTGATCCT
647 CAACACCCACATCTAAATACATATATGAAAGAAAATAAGGAGAAAGGATCAGAAAAAGTGATCCT
*
551995 AACAACACTATTAACAATCTGTAAGGAAGACCATTATTCAAACATGTAGAAAACCAACTGGAGGG
712 AACAACACTATCAACAATCTGTAAGGAAGACCATTATTCAAACATGTAGAAAACCAACTGGAGGG
* *
552060 TAAGCAATGATTGGGAAGACACATATAACATTTCCCAAGTCTCAAAAAACCAAAATTTTGGGGCG
777 TAAGCAATGATCGGGAAGACACATATAACATTTCCCAAGTCACAAAAAACCAAAATTTTGGGGCG
*
552125 AAACTCCTCTACCAGTTTCTATATAAAAAAGCAATTATGAATACTTTAAAACATAAAAAGTCATA
842 AAACTCCTCTACCAGTTTCTATATAAAAAAGCAATTATGAATAATTTAAAACAT-AAAAGTCATA
**** * * * ** *** *** * **
552190 TTCCGTATCAAAATTCTTTGATCCAGCACTTTGTTTTGCCTTTTCAGCTGAGGG
906 AAAAGTACCAAAA-TCTCTGATCCAGAACTTCATAAAGCAACTTCAAC--AGCC
* * * *
552244 TAAACTAAAGAGGCTATGGAGGAAATCCGTAGCTTTTACTCACCATCTCAACCTCACTTGTCTTG
1 TAAACT-AAGAGGCTATGGAGGAAA--CGTAGCTTTTACTCAACATCCCAACCACACTAGTCTTG
*
552309 ATGTTCTGCAGAAAAGCCGAAAATGCATCCCCACTGAAGTCTTTATATTCTTCTAGCTTTACCGA
63 ATGTTCTGCAGAAAAGCCGAAAATGCATCACCACTGAAGTCTTTATATTCTTCTAGCTTTACCGA
* * * *
552374 AGATTCGGAGCTTTGGGGGGGTCCCTGATCTCCAAACTCAACATCTGTAAGACAATTGTTT-TTA
128 AGATTCGGAACTTCGGGGGGATCCCTGATATCCAAACTCAACATCTGTAAGACAATTGTTTATTA
* * *
552438 AAA-CTAAATAAGTAAAAGATGCATCGAATTTTG-AAGGTAATAGAAAAGCAATGTGCAAAACTT
193 AAAGCTAAATAAGTAAAAGATGCATCAAATATTGAAAAGTAATAGAAAAGCAATGTGCAAAACTT
* * *
552501 CTCACTGCTCTTCATGGACTGGATGAAATCCATATAAGCTGAATTGTTCAGGGCAGCATTCCATA
258 CTCACTGCTCTGCATGGACTGGATGAAATCCATATAAGCTGAATTGTTCAGGACAGCAATCCATA
* * * *
552566 CATTCGGATCAGCAGCAATTGATGCAACGACAGACTGAAAGGAAACCCAAAACCATCAA-TGAAG
323 CAATCGGATC-G--GC-----A-GCAACAACAGACTGAAAGGAAAACCAAAACCATCAACCG-AG
* * * *
552630 TTATATTTTATAAATTATGGGTAAAGGCAGAAAATC-TAACAATGAAGAATAATAAAATCAACAA
378 TTATATTTCATAAATTATAGGTAAAGGAAGAAAATCTTAA-AATGAAGAATAATAAAATCAAAAA
** * * *
552694 CCAAATAAAGAATCCTAGTTTTTTTTTTTTTTTTTTAAAGTATGGAAGACCATGTTGCTCTGCGC
442 CCAAATAAAGAATCCTAGCATTTTTTTATTTTTTTCAAAGTATGGAAGACCATGTTGCTCTGAGC
* * ** *
552759 TTTTCATTTTTCTTAAAGTGTCTGTGTTTGATGGAATTGACACCCATGTCTAATGCATATTCAGA
507 CTTTCATTTTTCTTAAAGTGCCTGTGTTCAATGGAATTGACAACCATGTCTAATGCATATTCAGA
552824 CACATGAAGGACCCTCCAAATACATATAAAAAAAAAAACTTAAAAA-ATGAACATTCCTAT-GCA
572 CACATGAAGGACCCTCCAAATAC--AT---AAAAAAAACTTAAAAAGATGAACATTCCTATAGCA
* ** *
552887 GTCAAATGCCATATTCAACACTTAAACCTGAGT-TCAAATAACATATATGAAAGATAATAAGGAG
632 GTCAAATACCATATTCAACAC-----CCACA-TCT-AAAT-ACATATATGAAAGAAAATAAGGAG
*
552951 AAAGGATCAGAAAAAGTGATCCTAACAACACTATCAACAATCTGTAAGGAAGATCATTATTCAAA
689 AAAGGATCAGAAAAAGTGATCCTAACAACACTATCAACAATCTGTAAGGAAGACCATTATTCAAA
* *
553016 CATGTAGAAAACCAACTGGAGGGTAAGCTATGATCGGGTAGACACATATAACATTTCCCAAGTCA
754 CATGTAGAAAACCAACTGGAGGGTAAGCAATGATCGGGAAGACACATATAACATTTCCCAAGTCA
* * * * * *
553081 CAAGAATCCAAGA-TTTGGGGTCGAAACTCCTCTGCCGGTTTCTATATAATAAAGCAATTATGAA
819 CAAAAAACCAAAATTTTGGGG-CGAAACTCCTCTACCAGTTTCTATATAAAAAAGCAATTATGAA
553145 TAATTTAAAACAT
883 TAATTTAAAACAT
553158 GGGGTAAAAA
Statistics
Matches: 808, Mismatches: 80, Indels: 36
0.87 0.09 0.04
Matches are distributed among these distances:
961 99 0.12
962 27 0.03
963 37 0.05
964 141 0.17
969 5 0.01
970 229 0.28
972 22 0.03
973 13 0.02
975 13 0.02
977 4 0.00
978 12 0.01
979 206 0.25
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (956 bp):
TAAACTAAGAGGCTATGGAGGAAACGTAGCTTTTACTCAACATCCCAACCACACTAGTCTTGATG
TTCTGCAGAAAAGCCGAAAATGCATCACCACTGAAGTCTTTATATTCTTCTAGCTTTACCGAAGA
TTCGGAACTTCGGGGGGATCCCTGATATCCAAACTCAACATCTGTAAGACAATTGTTTATTAAAA
GCTAAATAAGTAAAAGATGCATCAAATATTGAAAAGTAATAGAAAAGCAATGTGCAAAACTTCTC
ACTGCTCTGCATGGACTGGATGAAATCCATATAAGCTGAATTGTTCAGGACAGCAATCCATACAA
TCGGATCGGCAGCAACAACAGACTGAAAGGAAAACCAAAACCATCAACCGAGTTATATTTCATAA
ATTATAGGTAAAGGAAGAAAATCTTAAAATGAAGAATAATAAAATCAAAAACCAAATAAAGAATC
CTAGCATTTTTTTATTTTTTTCAAAGTATGGAAGACCATGTTGCTCTGAGCCTTTCATTTTTCTT
AAAGTGCCTGTGTTCAATGGAATTGACAACCATGTCTAATGCATATTCAGACACATGAAGGACCC
TCCAAATACATAAAAAAAACTTAAAAAGATGAACATTCCTATAGCAGTCAAATACCATATTCAAC
ACCCACATCTAAATACATATATGAAAGAAAATAAGGAGAAAGGATCAGAAAAAGTGATCCTAACA
ACACTATCAACAATCTGTAAGGAAGACCATTATTCAAACATGTAGAAAACCAACTGGAGGGTAAG
CAATGATCGGGAAGACACATATAACATTTCCCAAGTCACAAAAAACCAAAATTTTGGGGCGAAAC
TCCTCTACCAGTTTCTATATAAAAAAGCAATTATGAATAATTTAAAACATAAAAGTCATAAAAAG
TACCAAAATCTCTGATCCAGAACTTCATAAAGCAACTTCAACAGCC
Found at i:554740 original size:17 final size:18
Alignment explanation
Indices: 554720--554762 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
554710 AAATTTAAAC
*
554720 ATTTAAATTA-TATTTTT
1 ATTTAAATTATTAATTTT
554737 ATTTAAA-TATTAATTTT
1 ATTTAAATTATTAATTTT
554754 A-TTAAATTA
1 ATTTAAATTA
554763 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAATTATTAATTTT
Found at i:558760 original size:18 final size:17
Alignment explanation
Indices: 558737--558775 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
558727 AAATTAATTA
558737 AATATTAT-TTATAATAAT
1 AATATTATATTA-AAT-AT
558755 AATATTATATTAAATAT
1 AATATTATATTAAATAT
558772 AATA
1 AATA
558776 ATTAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 11 0.55
19 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATTATATTAAATAT
Found at i:558773 original size:20 final size:18
Alignment explanation
Indices: 558716--558777 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 18
558706 GTGCCTTTAA
*
558716 AATATTTTTTAAAATTAATT
1 AATATTATTTAAAA-TAA-T
*
558736 AAATATTATTTATAATAAT
1 -AATATTATTTAAAATAAT
558755 AATATTATATTAAATATAAT
1 AATATTAT-TTAAA-ATAAT
558775 AAT
1 AAT
558778 TAAAAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.22
19 5 0.14
20 11 0.31
21 12 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATTATTTAAAATAAT
Found at i:559720 original size:21 final size:21
Alignment explanation
Indices: 559694--559733 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
559684 TGATACATTT
559694 ATTAAACATAAAATAAAATTC
1 ATTAAACATAAAATAAAATTC
*
559715 ATTAAATATAAAATAAAAT
1 ATTAAACATAAAATAAAAT
559734 AATAAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
ATTAAACATAAAATAAAATTC
Found at i:560337 original size:14 final size:14
Alignment explanation
Indices: 560314--560354 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
560304 TAAAATTTAT
560314 TATAATAAATATAAA
1 TATAA-AAATATAAA
560329 TATAAAAATATAAA
1 TATAAAAATATAAA
* *
560343 TTTTAAAATATA
1 TATAAAAATATA
560355 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATAAAAATATAAA
Found at i:561286 original size:28 final size:26
Alignment explanation
Indices: 561232--561290 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
561222 TATTATTTTA
*
561232 AATATAATATATAATTATGATATATT
1 AATATAATATATAATTATAATATATT
561258 AATATAATAAATATAA-TATAATATGATT
1 AATATAAT--ATATAATTATAATAT-ATT
561286 AATAT
1 AATAT
561291 TATTAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.28
27 7 0.24
28 14 0.48
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
AATATAATATATAATTATAATATATT
Found at i:562181 original size:16 final size:15
Alignment explanation
Indices: 562153--562193 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
562143 TTAATATAAA
562153 AAATTTATAAATATT
1 AAATTTATAAATATT
562168 AAATTTATTAAATATT
1 AAATTTA-TAAATATT
*
562184 ATATTT-TAAA
1 AAATTTATAAA
562194 AATAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTATAAATATT
Found at i:562753 original size:15 final size:15
Alignment explanation
Indices: 562729--562767 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
562719 AAATATAAAC
562729 ATAATA-TATATTAA
1 ATAATATTATATTAA
562743 ATAATATTATATTAA
1 ATAATATTATATTAA
562758 A-AATTATTAT
1 ATAA-TATTAT
562768 GTATTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATTATATTAA
Found at i:563503 original size:19 final size:20
Alignment explanation
Indices: 563467--563513 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
563457 CAACTTTTTA
*
563467 AATTAATATCATTAATTAA-
1 AATTAATATCAATAATTAAT
563486 ATATTAATAT-AATAATTAAT
1 A-ATTAATATCAATAATTAAT
563506 AATTAATA
1 AATTAATA
563514 AAAATTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTAATATCAATAATTAAT
Found at i:563529 original size:19 final size:17
Alignment explanation
Indices: 563480--563534 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
563470 TAATATCATT
563480 AATTAAATATTAATATAA
1 AATTAAATATTAATA-AA
563498 TAATT-AATAATTAATAAA
1 -AATTAAAT-ATTAATAAA
563516 AATTTAACATATT-ATAAA
1 AA-TTAA-ATATTAATAAA
563534 A
1 A
563535 TATCACATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.06
18 13 0.41
19 15 0.47
20 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATATTAATAAA
Found at i:570076 original size:21 final size:21
Alignment explanation
Indices: 570050--570102 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
570040 GTTGCATTTT
570050 TTTCATTCAAAAAATACATTC-
1 TTTCATTCAAAAAATACA-TCA
* *
570071 TTTCA-TCTAACAAATATATCA
1 TTTCATTC-AAAAAATACATCA
570092 TTTCATTCAAA
1 TTTCATTCAAA
570103 GATACCGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTCATTCAAAAAATACATCA
Found at i:575150 original size:2 final size:2
Alignment explanation
Indices: 575143--575175 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
575133 TCATCGTAAA
575143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
575176 CATTTTCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:581171 original size:29 final size:30
Alignment explanation
Indices: 581083--581171 Score: 74
Period size: 32 Copynumber: 2.8 Consensus size: 30
581073 TCTTCAAGAG
*
581083 TTAAATAATTTATTTAGTTTAATAAATTTAAT
1 TTAAATTA-TTATTTA-TTTAATAAATTTAAT
* *
581115 TTAAAATTTTTAATTT-TTATAATTTAAA-TTGAT
1 TT-AAATTATT-ATTTATT-TAA--TAAATTTAAT
581148 TTAAATTATTATTTATTTAATAAA
1 TTAAATTATTATTTATTTAATAAA
581172 ATAATAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
29 4 0.09
31 9 0.19
32 16 0.34
33 14 0.30
34 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TTAAATTATTATTTATTTAATAAATTTAAT
Found at i:581219 original size:28 final size:28
Alignment explanation
Indices: 581162--581219 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
581152 ATTATTATTT
**
581162 ATTTAATAAAATAATAATTTTTATTTAA
1 ATTTAATAAAATAATAATTTTTATAAAA
581190 ATTTAATTATAAA-AATAATTTTTA-AAAA
1 ATTTAA-TA-AAATAATAATTTTTATAAAA
581218 AT
1 AT
581220 ATTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 10 0.38
29 13 0.50
30 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTAATAAAATAATAATTTTTATAAAA
Found at i:582876 original size:30 final size:31
Alignment explanation
Indices: 582842--582937 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 31
582832 ATTTTTTTAC
582842 TTAAA-ATTAAAAGGGTAAGTGTATTATTGG
1 TTAAACATTAAAAGGGTAAGTGTATTATTGG
* * * * **
582872 TTAAATC-TTAAGAGAGTAAGT-AAATATTTT
1 TTAAA-CATTAAAAGGGTAAGTGTATTATTGG
*
582902 TTAAACATTAAAAAGGTAAGTGTATTATTGG
1 TTAAACATTAAAAGGGTAAGTGTATTATTGG
582933 TTAAA
1 TTAAA
582938 TCTTAAGTAA
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
29 1 0.02
30 26 0.53
31 22 0.45
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.38
Consensus pattern (31 bp):
TTAAACATTAAAAGGGTAAGTGTATTATTGG
Found at i:582983 original size:29 final size:28
Alignment explanation
Indices: 582948--583010 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
582938 TCTTAAGTAA
*
582948 ATATTTTT-TAAACGTTAAAAAAATAAAT
1 ATATTTTTATAAACATT-AAAAAATAAAT
* *
582976 ATATTTTTATAAATATTTAAAAATAAAT
1 ATATTTTTATAAACATTAAAAAATAAAT
*
583004 ATCTTTT
1 ATATTTT
583011 ACTCTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (28 bp):
ATATTTTTATAAACATTAAAAAATAAAT
Found at i:589054 original size:34 final size:33
Alignment explanation
Indices: 589016--589088 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
589006 TTAATTCATG
*
589016 ATTTTTAGGAATCAAATCAATTATTTATTCTTGA
1 ATTTTTAGGAATCAAATCAATT-TTTATTATTGA
** * *
589050 ATTTTTTTGAATCAATTCTATTTTTATTATTGA
1 ATTTTTAGGAATCAAATCAATTTTTATTATTGA
*
589083 AATTTT
1 ATTTTT
589089 CTTAAGGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 15 0.45
34 18 0.55
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (33 bp):
ATTTTTAGGAATCAAATCAATTTTTATTATTGA
Found at i:589083 original size:33 final size:34
Alignment explanation
Indices: 589024--589088 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
589014 TGATTTTTAG
* *
589024 GAATCAAATCAATTATTTATTCTTGAATTTTTTT
1 GAATCAAATCAATTATTTATTATTGAAATTTTTT
* *
589058 GAATCAATTCTATT-TTTATTATTGAAATTTT
1 GAATCAAATCAATTATTTATTATTGAAATTTT
589089 CTTAAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (34 bp):
GAATCAAATCAATTATTTATTATTGAAATTTTTT
Found at i:601632 original size:21 final size:21
Alignment explanation
Indices: 601606--601662 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
601596 AAATTATCCA
601606 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
601627 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
601648 AATGTATCGATACAT
1 AATGTATCGATACAT
601663 CCTAAAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:601742 original size:19 final size:19
Alignment explanation
Indices: 601718--601804 Score: 123
Period size: 19 Copynumber: 4.9 Consensus size: 19
601708 AATTCAACAA
601718 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
601737 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
601756 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
601771 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
601788 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
601805 TTAGCTACTG
Statistics
Matches: 62, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.18
15 2 0.03
17 2 0.03
19 47 0.76
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:601776 original size:13 final size:13
Alignment explanation
Indices: 601758--601782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
601748 ACATAAGTTT
601758 TGTATCGATACAA
1 TGTATCGATACAA
601771 TGTATCGATACA
1 TGTATCGATACA
601783 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:601780 original size:32 final size:32
Alignment explanation
Indices: 601739--601801 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
601729 ACATAAGTTT
*
601739 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
601771 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
601802 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:601862 original size:13 final size:13
Alignment explanation
Indices: 601844--601871 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
601834 CATTTTTCTG
601844 TGTATCGATACAT
1 TGTATCGATACAT
601857 TGTATCGATACAT
1 TGTATCGATACAT
601870 TG
1 TG
601872 ATCTTTGTAT
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:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:601866 original size:33 final size:33
Alignment explanation
Indices: 601824--601890 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
601814 GCCAAGGAAA
**
601824 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTGATCTGTGTATCGATACAT
*
601857 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCTGTGTATCGATACAT
601890 T
1 T
601891 TGGAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTGATCTGTGTATCGATACAT
Found at i:605554 original size:104 final size:104
Alignment explanation
Indices: 605374--605582 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
605364 CTTATTTTCT
605374 TTTCTTTTTATTCTTCTCCATATAAGTTTTACGGATTTCTTTTATAACGAATTGCTGCAGAAGTC
1 TTTCTTTTTATTCTTCTCCATATAAGTTTTACGGATTTCTTTTATAACGAATTGCTGCAGAAGTC
605439 CTTTATAAAAGAATGATAATTTTGTTCTACACTACTCAG
66 CTTTATAAAAGAATGATAATTTTGTTCTACACTACTCAG
605478 TTTCTTTTTATTCTTCTCCATATAAGTTTTACGGATTTCTTTTATAACGAATTGCTGCAGAAGTC
1 TTTCTTTTTATTCTTCTCCATATAAGTTTTACGGATTTCTTTTATAACGAATTGCTGCAGAAGTC
605543 CTTTATAAAAGAATGATAATTTTGTTCTACACTACTCAG
66 CTTTATAAAAGAATGATAATTTTGTTCTACACTACTCAG
605582 T
1 T
605583 GCTCAGTGGA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44
Consensus pattern (104 bp):
TTTCTTTTTATTCTTCTCCATATAAGTTTTACGGATTTCTTTTATAACGAATTGCTGCAGAAGTC
CTTTATAAAAGAATGATAATTTTGTTCTACACTACTCAG
Found at i:606719 original size:11 final size:11
Alignment explanation
Indices: 606680--606752 Score: 69
Period size: 11 Copynumber: 6.6 Consensus size: 11
606670 AGTTCGTATT
606680 TAATTTATTTA
1 TAATTTATTTA
*
606691 TATTTATATTTA
1 TAATT-TATTTA
606703 -AATTTATTTA
1 TAATTTATTTA
606713 TAATTTATTTA
1 TAATTTATTTA
*
606724 AAATTCT-TTTA
1 TAATT-TATTTA
* * *
606735 TTATTAAATTA
1 TAATTTATTTA
606746 TAATTTA
1 TAATTTA
606753 ATAATAACGT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 6 0.12
11 36 0.73
12 7 0.14
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTTATTTA
Found at i:606725 original size:21 final size:22
Alignment explanation
Indices: 606676--606725 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
606666 ATTAAGTTCG
*
606676 TATTT-AATTTATTTATATTTA
1 TATTTAAATTTATTTATAATTA
606697 TATTTAAATTTATTTATAATT-
1 TATTTAAATTTATTTATAATTA
606718 TATTTAAA
1 TATTTAAA
606726 ATTCTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTAAATTTATTTATAATTA
Found at i:606929 original size:12 final size:12
Alignment explanation
Indices: 606912--606954 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
606902 TTGTTTATAA
606912 ATATATTCAATT
1 ATATATTCAATT
*
606924 ATATATTC-ATGA
1 ATATATTCAAT-T
*
606936 ATATATTTAATT
1 ATATATTCAATT
606948 ATATATT
1 ATATATT
606955 TTATAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (12 bp):
ATATATTCAATT
Found at i:607235 original size:12 final size:12
Alignment explanation
Indices: 607220--607267 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
607210 TCTAATTATA
*
607220 TTTATATAGATT
1 TTTATATAAATT
*
607232 TTTATTTAAAAGTT
1 TTTATAT-AAA-TT
*
607246 TTTAAATAAATT
1 TTTATATAAATT
607258 TTTATATAAA
1 TTTATATAAA
607268 AAATAATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 17 0.59
13 5 0.17
14 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (12 bp):
TTTATATAAATT
Found at i:615260 original size:4 final size:4
Alignment explanation
Indices: 615251--615279 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
615241 TCCATTAAGT
615251 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
615280 TATTATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:627121 original size:11 final size:10
Alignment explanation
Indices: 627102--627138 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
627092 GTTAACAATT
627102 TATATATTCA
1 TATATATTCA
627112 TATCATATTCA
1 TAT-ATATTCA
627123 TATATA-T-A
1 TATATATTCA
627131 TATATATT
1 TATATATT
627139 ATCATAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 6 0.24
11 10 0.40
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (10 bp):
TATATATTCA
Found at i:627192 original size:18 final size:18
Alignment explanation
Indices: 627169--627208 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
627159 ATTTTATATT
* *
627169 TATATAAATTTTGATACA
1 TATATAAATTTTAAGACA
627187 TATATAAATTTTAAGACA
1 TATATAAATTTTAAGACA
627205 TATA
1 TATA
627209 ATCATATCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
TATATAAATTTTAAGACA
Found at i:631029 original size:19 final size:20
Alignment explanation
Indices: 631007--631050 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
630997 ACATTATTAA
631007 AAAATAA-TTATTTCATATT
1 AAAATAATTTATTTCATATT
631026 AAAATAATTTATTTCATATT
1 AAAATAATTTATTTCATATT
*
631046 TAAAT
1 AAAAT
631051 TTTAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATAATTTATTTCATATT
Found at i:631436 original size:15 final size:15
Alignment explanation
Indices: 631399--631436 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
631389 TATTTTTATT
* *
631399 TTTATATTTTTAATA
1 TTTATAATTTTAACA
631414 TTTA-AATTTTAACA
1 TTTATAATTTTAACA
631428 TTTATAATT
1 TTTATAATT
631437 ATTTATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATAATTTTAACA
Found at i:635535 original size:2 final size:2
Alignment explanation
Indices: 635528--635552 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
635518 CTAGTTTTAC
635528 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
635553 AACAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:636478 original size:12 final size:12
Alignment explanation
Indices: 636461--636490 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
636451 AAATTTACTG
636461 TATAAAAATTTA
1 TATAAAAATTTA
*
636473 TATAAACATTTA
1 TATAAAAATTTA
636485 TATAAA
1 TATAAA
636491 TTAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (12 bp):
TATAAAAATTTA
Found at i:636729 original size:22 final size:21
Alignment explanation
Indices: 636701--636773 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 21
636691 ATATTAATTT
636701 TTATAAAATTAAATTAAATATA
1 TTATAAAATTAAATTAAA-ATA
**
636723 TTATAAAATTTTA-TAAAA-A
1 TTATAAAATTAAATTAAAATA
*
636742 TTAAAAAACTT-AATTAAAATA
1 TTATAAAA-TTAAATTAAAATA
636763 -TATAAAATTAA
1 TTATAAAATTAA
636774 TTTTTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
19 11 0.26
20 15 0.36
21 5 0.12
22 11 0.26
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
TTATAAAATTAAATTAAAATA
Found at i:636749 original size:19 final size:19
Alignment explanation
Indices: 636722--636797 Score: 55
Period size: 19 Copynumber: 3.8 Consensus size: 19
636712 AATTAAATAT
*
636722 ATTATAAAATTTTATAAAA
1 ATTAAAAAATTTTATAAAA
* *
636741 ATTAAAAAACTTAATTAAAA
1 ATTAAAAAATTTTA-TAAAA
*
636761 TATATAAAATTAATTTT-TTAAA
1 -AT-TAAAA--AATTTTATAAAA
*
636783 ATTAAAAAATATTAT
1 ATTAAAAAATTTTAT
636798 TATAATAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.11
19 12 0.27
20 10 0.23
21 4 0.09
22 9 0.20
24 4 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAAAAATTTTATAAAA
Found at i:636996 original size:10 final size:10
Alignment explanation
Indices: 636939--637030 Score: 59
Period size: 10 Copynumber: 9.1 Consensus size: 10
636929 ATACGACGAA
*
636939 TTTAAATTAT
1 TTTATATTAT
636949 TTTACTA--AT
1 TTTA-TATTAT
636958 TTTATA-TAT
1 TTTATATTAT
* *
636967 ATATATAATAT
1 -TTTATATTAT
636978 TTT-TATTAT
1 TTTATATTAT
636987 TTTATATTAT
1 TTTATATTAT
*
636997 ATTATATTTTAT
1 -TT-TATATTAT
637009 TTTA-ATTATT
1 TTTATATTA-T
637019 TTTATATATAT
1 TTTATAT-TAT
637030 T
1 T
637031 CATTCTAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
8 2 0.03
9 19 0.29
10 24 0.36
11 12 0.18
12 9 0.14
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATATTAT
Found at i:637001 original size:15 final size:14
Alignment explanation
Indices: 636981--637030 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
636971 ATAATATTTT
636981 TATTATTTTATATTA
1 TATTATTTT-TATTA
*
636996 TATTATATTTTATTT
1 TATTAT-TTTTATTA
637011 TAATTATTTTTATATA
1 T-ATTATTTTTAT-TA
637027 TATT
1 TATT
637031 CATTCTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 20 0.67
16 10 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTTTTATTA
Found at i:637010 original size:31 final size:31
Alignment explanation
Indices: 636946--637030 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
636936 GAATTTAAAT
* *
636946 TATTTTACTAATTTTATA-TATA-TATATAA
1 TATTTTAATTATTTTATATTATATTATATAA
* **
636975 TATTTTTATTATTTTATATTATATTATATTT
1 TATTTTAATTATTTTATATTATATTATATAA
637006 TATTTTAATTATTTT-TATATATATT
1 TATTTTAATTATTTTATAT-TATATT
637031 CATTCTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.32
30 7 0.15
31 25 0.53
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTTTAATTATTTTATATTATATTATATAA
Found at i:643815 original size:28 final size:28
Alignment explanation
Indices: 643761--643825 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
643751 GATTCAAATC
**
643761 AATTTAATTAAAAAAATTATTTAATTTT
1 AATTTAATTAAAAAAATTAAATAATTTT
643789 AATTTAATTAAAAAAATTAAA-ATATTTT
1 AATTTAATTAAAAAAATTAAATA-ATTTT
643817 ACA-TTAATT
1 A-ATTTAATT
643826 TTTTTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 31 0.94
29 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTTAATTAAAAAAATTAAATAATTTT
Found at i:647386 original size:9 final size:9
Alignment explanation
Indices: 647374--647407 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
647364 TAAATATATC
647374 ATATTAATT
1 ATATTAATT
647383 ATATTAATT
1 ATATTAATT
*
647392 ATATTTATAT
1 ATATTAAT-T
647402 ATATTA
1 ATATTA
647408 TATCATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTAATT
Found at i:648138 original size:2 final size:2
Alignment explanation
Indices: 648131--648155 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
648121 GATAACTTAT
648131 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
648156 TATATATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:648221 original size:6 final size:6
Alignment explanation
Indices: 648208--648271 Score: 83
Period size: 6 Copynumber: 10.7 Consensus size: 6
648198 CTTAGGTCGC
* * * *
648208 ATATAT ACATAT ACATAC ATATAT CTATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
648256 ATATAT ATATAA ATAT
1 ATATAT ATATAT ATAT
648272 TGAAAATCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:648240 original size:4 final size:4
Alignment explanation
Indices: 648208--648271 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
648198 CTTAGGTCGC
* * * *
648208 ATAT ATAC ATAT ACAT ACAT ATAT CTAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
648256 ATAT ATAT ATAA ATAT
1 ATAT ATAT ATAT ATAT
648272 TGAAAATCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:648265 original size:10 final size:10
Alignment explanation
Indices: 648208--648271 Score: 83
Period size: 10 Copynumber: 6.4 Consensus size: 10
648198 CTTAGGTCGC
*
648208 ATATATACAT
1 ATATATATAT
* *
648218 ATACATACAT
1 ATATATATAT
*
648228 ATATCTATAT
1 ATATATATAT
648238 ATATATATAT
1 ATATATATAT
648248 ATATATATAT
1 ATATATATAT
*
648258 ATATATATAA
1 ATATATATAT
648268 ATAT
1 ATAT
648272 TGAAAATCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 48 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:649378 original size:22 final size:21
Alignment explanation
Indices: 649323--649378 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
649313 ATATGATATG
649323 AATATAATATAAAAATACTTAA
1 AATATAA-ATAAAAATACTTAA
* *
649345 AATATGATTAAAAATA-TAATAA
1 AATATAAATAAAAATACT--TAA
649367 AATATAAATAAA
1 AATATAAATAAA
649379 TAAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 19 0.68
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AATATAAATAAAAATACTTAA
Found at i:651131 original size:25 final size:26
Alignment explanation
Indices: 651103--651155 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
651093 AAATATATTT
651103 TATTAAAATTTATTTA-TAAAAATAA
1 TATTAAAATTTATTTATTAAAAATAA
** * *
651128 TATTTTAATTTTTTTATTATAAATAA
1 TATTAAAATTTATTTATTAAAAATAA
651154 TA
1 TA
651156 AAATAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TATTAAAATTTATTTATTAAAAATAA
Found at i:651975 original size:26 final size:24
Alignment explanation
Indices: 651934--651982 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
651924 ATTAAAATTT
*
651934 TAAATATAAATATATTTTTTATAC
1 TAAATATAAATATATTTATTATAC
*
651958 TAAATATATCATATTATTTATTATA
1 TAAATATA-AATA-TATTTATTATA
651983 TTATTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TAAATATAAATATATTTATTATAC
Found at i:652227 original size:13 final size:13
Alignment explanation
Indices: 652193--652231 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
652183 TATTAATTTC
*
652193 ATTTATTATTATT
1 ATTTATTATTAAT
652206 ATTTATTATTAAT
1 ATTTATTATTAAT
652219 ATTTATTA-TAAT
1 ATTTATTATTAAT
652231 A
1 A
652232 AATCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATTATTAAT
Found at i:653189 original size:11 final size:11
Alignment explanation
Indices: 653169--653255 Score: 65
Period size: 11 Copynumber: 8.0 Consensus size: 11
653159 GAGCGTTTAC
653169 AATA-AATATA
1 AATATAATATA
653179 AATATAATATA
1 AATATAATATA
* *
653190 ATTAT-ATGATG
1 AATATAAT-ATA
*
653201 AGTATAATATA
1 AATATAATATA
*
653212 AAAATAAT-TAA
1 AATATAATAT-A
* *
653223 AATATGATAAA
1 AATATAATATA
653234 AATATAATA-A
1 AATATAATATA
653244 AATATAAATATA
1 AATAT-AATATA
653256 TAAACATCTT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 13 0.22
11 44 0.73
12 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (11 bp):
AATATAATATA
Found at i:653244 original size:21 final size:20
Alignment explanation
Indices: 653209--653248 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
653199 TGAGTATAAT
*
653209 ATAAAAATAATTAAAATATG
1 ATAAAAATAAATAAAATATG
653229 ATAAAAATATAATAAAATAT
1 ATAAAAATA-AATAAAATAT
653249 AAATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
ATAAAAATAAATAAAATATG
Found at i:653886 original size:11 final size:10
Alignment explanation
Indices: 653860--653890 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
653850 AATTTAATTA
*
653860 TTAAAATTAT
1 TTAAAAATAT
653870 TTAAAAATAT
1 TTAAAAATAT
653880 TTAAAAATAT
1 TTAAAAATAT
653890 T
1 T
653891 AATAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:654141 original size:15 final size:15
Alignment explanation
Indices: 654123--654161 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
654113 TTTACCTATA
654123 ATTTTTTTAAAAAAT
1 ATTTTTTTAAAAAAT
654138 ATTTTTTTAAAAAAT
1 ATTTTTTTAAAAAAT
654153 ATTATTTTT
1 ATT-TTTTT
654162 TTCCCACGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTTTAAAAAAT
Found at i:654296 original size:21 final size:21
Alignment explanation
Indices: 654245--654298 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
654235 TAATACTAAT
654245 TTAATTAATAAATTTATAAAA
1 TTAATTAATAAATTTATAAAA
654266 --AATTTAAATAAATTTA-AAATA
1 TTAA-TT-AATAAATTTATAAA-A
654287 TTAATTAATAAA
1 TTAATTAATAAA
654299 ATAAAGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
19 2 0.07
20 5 0.18
21 17 0.61
22 2 0.07
23 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAATTAATAAATTTATAAAA
Found at i:655323 original size:2 final size:2
Alignment explanation
Indices: 655316--655344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
655306 AATGATTTCC
655316 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 T
655345 TAATAGCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:657335 original size:2 final size:2
Alignment explanation
Indices: 657328--657363 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
657318 TGCATGATGA
*
657328 AT AT AT AT AA 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 AT AT AT AT AT
657364 GAAGTTGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:657619 original size:23 final size:22
Alignment explanation
Indices: 657589--657659 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
657579 TATGATATGT
657589 ATATAATATATAAAATAATTAAA
1 ATATAATATATAAAATAA-TAAA
* *
657612 ATATAATATA-ATATATGATAAA
1 ATATAATATATA-AAATAATAAA
*
657634 ATATAAATATATAAATATGATAAA
1 ATAT-AATATATAAA-ATAATAAA
657658 AT
1 AT
657660 TTTTTGTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 9 0.22
23 21 0.51
24 11 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (22 bp):
ATATAATATATAAAATAATAAA
Found at i:657641 original size:28 final size:25
Alignment explanation
Indices: 657588--657660 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 25
657578 ATATGATATG
*
657588 TATATAATATAT-AAAATAATTAAAATA
1 TATATAATATATGATAA-AATT-AAA-A
657615 TAATATAATATATGATAAAA-TATAAA
1 T-ATATAATATATGATAAAATTA-AAA
657641 TATATAA-ATATGATAAAATT
1 TATATAATATATGATAAAATT
657661 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
24 11 0.27
25 7 0.17
26 3 0.07
27 4 0.10
28 13 0.32
29 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
TATATAATATATGATAAAATTAAAA
Found at i:659280 original size:28 final size:30
Alignment explanation
Indices: 659240--659300 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
659230 TTTTAAATTA
*
659240 ATTTTAAAAATTAT-A-TTAATTATTATAT
1 ATTTTAAAAATTATCATTTAATTATTAAAT
** *
659268 ATTTTAATCATTATCATTTTATTATTAAAT
1 ATTTTAAAAATTATCATTTAATTATTAAAT
659298 ATT
1 ATT
659301 AATTAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 1 0.04
30 14 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTAAAAATTATCATTTAATTATTAAAT
Found at i:659491 original size:2 final size:2
Alignment explanation
Indices: 659474--659511 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
659464 CCATTCTGCA
*
659474 AT AT -T AT AT AT GT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
659512 TCTGCATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:660527 original size:6 final size:6
Alignment explanation
Indices: 660518--660573 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
660508 ATTTTATATT
* * * *
660518 TAAATA TAAATA T-AATA TAAATTT TAAATA T-ATTA AAAATT TAAATA
1 TAAATA TAAATA TAAATA TAAA-TA TAAATA TAAATA TAAATA TAAATA
660565 TAAATA TAA
1 TAAATA TAA
660574 TTTATATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
5 8 0.21
6 26 0.67
7 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATA
Found at i:660543 original size:24 final size:24
Alignment explanation
Indices: 660516--660590 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
660506 ATATTTTATA
660516 TTTAAATATAAATATAATATAAAT
1 TTTAAATATAAATATAATATAAAT
660540 TTTAAATAT--AT-T-A-A-AAA-
1 TTTAAATATAAATATAATATAAAT
* *
660557 TTTAAATATAAATATAATTTATAT
1 TTTAAATATAAATATAATATAAAT
*
660581 ATTAAATATA
1 TTTAAATATA
660591 TTATATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
17 9 0.22
18 3 0.07
19 3 0.07
20 2 0.05
21 2 0.05
22 2 0.05
23 2 0.05
24 18 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTAAATATAAATATAATATAAAT
Found at i:660547 original size:18 final size:18
Alignment explanation
Indices: 660519--660582 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 18
660509 TTTTATATTT
*
660519 AAATATAAATATAATATA
1 AAATTTAAATATAATATA
* *
660537 AATTTTAAATATATTA-A
1 AAATTTAAATATAATATA
660554 AAATTTAAATATAA-ATA
1 AAATTTAAATATAATATA
* *
660571 TAATTTATATAT
1 AAATTTAAATAT
660583 TAAATATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 1 0.03
17 24 0.63
18 13 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTAAATATAATATA
Found at i:660560 original size:41 final size:41
Alignment explanation
Indices: 660515--660593 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
660505 TATATTTTAT
*
660515 ATTTAAATATAAATATAATATAAATTTTAAATATATTAAAA
1 ATTTAAATATAAATATAATATAAATATTAAATATATTAAAA
* *
660556 ATTTAAATATAAATATAATTTATATATTAAATATATTA
1 ATTTAAATATAAATATAATATAAATATTAAATATATTA
660594 TATTAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (41 bp):
ATTTAAATATAAATATAATATAAATATTAAATATATTAAAA
Found at i:661638 original size:4 final size:4
Alignment explanation
Indices: 661629--661698 Score: 86
Period size: 4 Copynumber: 17.5 Consensus size: 4
661619 AACTTGCCTT
* * *
661629 TATA TATA TATA TATA TATA TATA TATA TATA TATG TATA TGTA TATG
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
661677 TATG TATG TATG TATA TATA TA
1 TATA TATA TATA TATA TATA TA
661699 CACTTGTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:661640 original size:6 final size:6
Alignment explanation
Indices: 661629--661698 Score: 86
Period size: 6 Copynumber: 11.7 Consensus size: 6
661619 AACTTGCCTT
* * *
661629 TATATA TATATA TATATA TATATA TATATA TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
661677 TATGTA TGTATG TATATA TATA
1 TATATA TATATA TATATA TATA
661699 CACTTGTTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:662508 original size:8 final size:8
Alignment explanation
Indices: 662483--662515 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
662473 AAAATAATTA
662483 AAATATGAT
1 AAATAT-AT
662492 AAA-ATAT
1 AAATATAT
662499 AAATATAT
1 AAATATAT
662507 AAATATAT
1 AAATATAT
662515 A
1 A
662516 TTTGAAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.22
8 15 0.65
9 3 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (8 bp):
AAATATAT
Found at i:662719 original size:2 final size:2
Alignment explanation
Indices: 662712--662744 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
662702 ACTAGTCTCT
662712 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 T
662745 GTATGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:662749 original size:4 final size:4
Alignment explanation
Indices: 662742--662776 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
662732 TATATATATA
662742 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
662777 AAATTTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:663540 original size:52 final size:52
Alignment explanation
Indices: 663484--663590 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
663474 AAAAAAGAAT
663484 AAAAATGCAAAATGAATTAAACTAAAATAAATAGCAATATCAAACACTAGCC
1 AAAAATGCAAAATGAATTAAACTAAAATAAATAGCAATATCAAACACTAGCC
* *
663536 AAAAATGCAAGATGAATTAAACTAAAATAAATAGCAATATCAAATACTAGCC
1 AAAAATGCAAAATGAATTAAACTAAAATAAATAGCAATATCAAACACTAGCC
663588 AAA
1 AAA
663591 GGTATAATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (52 bp):
AAAAATGCAAAATGAATTAAACTAAAATAAATAGCAATATCAAACACTAGCC
Found at i:663572 original size:27 final size:26
Alignment explanation
Indices: 663486--663572 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
663476 AAAAGAATAA
663486 AAATGCAAAATGAATTAAACTAAAAT
1 AAATGCAAAATGAATTAAACTAAAAT
* * * *
663512 AAATAGCAATATCAA--ACACTAGCCAA-
1 AAAT-GCAAAATGAATTAAACTA--AAAT
*
663538 AAATGCAAGATGAATTAAACTAAAAT
1 AAATGCAAAATGAATTAAACTAAAAT
663564 AAATAGCAA
1 AAAT-GCAA
663573 TATCAAATAC
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
25 15 0.33
26 12 0.26
27 19 0.41
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.20
Consensus pattern (26 bp):
AAATGCAAAATGAATTAAACTAAAAT
Found at i:664488 original size:15 final size:15
Alignment explanation
Indices: 664465--664495 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
664455 AAAATTATAA
664465 AAAAATTTAACATAT
1 AAAAATTTAACATAT
*
664480 AAAATTTTAACATAT
1 AAAAATTTAACATAT
664495 A
1 A
664496 TATTCACGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATTTAACATAT
Found at i:664818 original size:2 final size:2
Alignment explanation
Indices: 664811--664870 Score: 88
Period size: 2 Copynumber: 30.0 Consensus size: 2
664801 TGCATGAAGA
664811 AT AT AT AT AT AT AT AT AT AT AT GA- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
664853 GA- AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT
664871 GAAGTTGCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.04
2 50 0.93
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:664840 original size:20 final size:20
Alignment explanation
Indices: 664815--664870 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
664805 TGAAGAATAT
664815 ATATATATATATATATATGA
1 ATATATATATATATATATGA
664835 ATATATATATATATATATGA
1 ATATATATATATATATATGA
664855 ATATATATATATATAT
1 ATATATATATATATAT
664871 GAAGTTGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
ATATATATATATATATATGA
Found at i:665099 original size:19 final size:20
Alignment explanation
Indices: 665077--665146 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 20
665067 ATTATATAAT
*
665077 ATAAATATAATATATAAA-A
1 ATAAATATAAAATATAAATA
665096 AT-AAT-TAAAATATAATATA
1 ATAAATATAAAATATAA-ATA
*
665115 ATACATAATAAAATATAAATA
1 ATAAAT-ATAAAATATAAATA
665136 TATAAATATAA
1 -ATAAATATAA
665147 TAAAATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
17 9 0.21
18 4 0.10
19 5 0.12
20 2 0.05
21 7 0.17
22 15 0.36
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATATAAAATATAAATA
Found at i:665104 original size:10 final size:11
Alignment explanation
Indices: 665070--665240 Score: 59
Period size: 11 Copynumber: 15.0 Consensus size: 11
665060 TAATACGATT
665070 ATATAA-TATAA
1 ATATAATTA-AA
665081 ATATAATATATAA
1 ATATAAT-TA-AA
*
665094 AAATAATTAAA
1 ATATAATTAAA
*
665105 ATATAATATAAT
1 ATATAAT-TAAA
*
665117 ACATAA-TAAA
1 ATATAATTAAA
665127 ATATAAATATATAA
1 ATAT-AAT-TA-AA
665141 ATATAA-TAAA
1 ATATAATTAAA
*
665151 ATTTATATT--A
1 ATATA-ATTAAA
* * *
665161 TTTTAATTATTA
1 ATATAATTA-AA
* *
665173 ACAT-ATCAAA
1 ATATAATTAAA
* *
665183 ATTTATATAAAA
1 ATATA-ATTAAA
665195 ATATAAATTAATAA
1 ATAT-AATT-A-AA
665209 ATATAATTAAA
1 ATATAATTAAA
*
665220 ATATAAATAAA
1 ATATAATTAAA
*
665231 A-ATTATTAAA
1 ATATAATTAAA
665241 TTTATTTTTT
Statistics
Matches: 122, Mismatches: 21, Indels: 35
0.69 0.12 0.20
Matches are distributed among these distances:
9 3 0.02
10 27 0.22
11 35 0.29
12 24 0.20
13 21 0.17
14 12 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAATTAAA
Found at i:665126 original size:22 final size:23
Alignment explanation
Indices: 665072--665152 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 23
665062 ATACGATTAT
665072 ATAATATAAATATAATATATAAAA
1 ATAATA-AAATATAATATATAAAA
* *
665096 ATAATTAAAATATAATATA-ATAC
1 ATAA-TAAAATATAATATATAAAA
*
665119 ATAATAAAATATAAATATATAAAT
1 ATAATAAAATAT-AATATATAAAA
665143 ATAATAAAAT
1 ATAATAAAAT
665153 TTATATTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.16
23 12 0.24
24 28 0.56
25 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATAAAATATAATATATAAAA
Found at i:665212 original size:14 final size:12
Alignment explanation
Indices: 665192--665233 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
665182 AATTTATATA
665192 AAAATATAAATT
1 AAAATATAAATT
665204 AATAA-ATATAATT
1 AA-AATATA-AATT
*
665217 AAAATATAAATA
1 AAAATATAAATT
665229 AAAAT
1 AAAAT
665234 TATTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATATAAATT
Found at i:666179 original size:22 final size:22
Alignment explanation
Indices: 666151--666194 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
666141 GAAACATTGA
666151 TTAAAAAT-TATTTATTTATTAT
1 TTAAAAATAT-TTTATTTATTAT
666173 TTAAAAATATTTTATTTATTAT
1 TTAAAAATATTTTATTTATTAT
666195 ATTTCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAAAATATTTTATTTATTAT
Found at i:666274 original size:14 final size:15
Alignment explanation
Indices: 666220--666274 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 15
666210 TGTAAAAATT
*
666220 ATATTAATTTTTATA
1 ATATTAATTATTATA
* *
666235 TCATTTTAATTATTATC
1 --ATATTAATTATTATA
666252 ATATT-ATTATTA-A
1 ATATTAATTATTATA
666265 ATATTAATTA
1 ATATTAATTA
666275 ATATTAGAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.16
14 11 0.34
15 4 0.12
17 12 0.38
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTAATTATTATA
Found at i:666363 original size:10 final size:11
Alignment explanation
Indices: 666338--666407 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 11
666328 TATATGATAT
666338 AAATATAATATA
1 AAATATAAT-TA
*
666350 TAAAAATAATTA
1 -AAATATAATTA
666362 AAATATAATATA
1 AAATATAAT-TA
* *
666374 ATATATGA-TA
1 AAATATAATTA
666384 AAATATGAATATA
1 AAATAT-AAT-TA
666397 TAAATATAATT
1 -AAATATAATT
666408 TATCGTATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
10 7 0.15
11 9 0.20
12 11 0.24
13 13 0.28
14 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAATATAATTA
Found at i:666381 original size:47 final size:48
Alignment explanation
Indices: 666309--666407 Score: 139
Period size: 47 Copynumber: 2.1 Consensus size: 48
666299 AGCTGGTGTA
* *
666309 AATTTAAATATAATACGATTATATGATATAAATAT-AATATATAAAAAT
1 AATTAAAATATAATACGAATATATGATA-AAATATGAATATATAAAAAT
* *
666357 AATTAAAATATAATA-TAATATATGATAAAATATGAATATATAAATAT
1 AATTAAAATATAATACGAATATATGATAAAATATGAATATATAAAAAT
666404 AATT
1 AATT
666408 TATCGTATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
46 6 0.13
47 26 0.57
48 14 0.30
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (48 bp):
AATTAAAATATAATACGAATATATGATAAAATATGAATATATAAAAAT
Found at i:667499 original size:16 final size:16
Alignment explanation
Indices: 667480--667515 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
667470 AATTTTTTAA
667480 ATGACTACATATTTGG
1 ATGACTACATATTTGG
*
667496 ATGACTACATGTTTGG
1 ATGACTACATATTTGG
667512 ATGA
1 ATGA
667516 ACTTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (16 bp):
ATGACTACATATTTGG
Found at i:668338 original size:84 final size:84
Alignment explanation
Indices: 668221--668402 Score: 310
Period size: 84 Copynumber: 2.2 Consensus size: 84
668211 TTATATATAT
* * * *
668221 ATATATATATATTTGTATATATAATATTCTCCATATAATCCATCTCCCCATACCATTGTGCATTC
1 ATATATATATATATGAATATATAATATTCTCCATACAATCAATCTCCCCATACCATTGTGCATTC
*
668286 AACACATTTCTGTAGATAA
66 AACACATTGCTGTAGATAA
*
668305 ATATATATATATATGAATATATAATATTCTCCATACAATCAATCTTCCCATACCATTGTGCATTC
1 ATATATATATATATGAATATATAATATTCTCCATACAATCAATCTCCCCATACCATTGTGCATTC
668370 AACACATTGCTGTAGATAA
66 AACACATTGCTGTAGATAA
668389 ATATATATATATAT
1 ATATATATATATAT
668403 ATAACTTATG
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (84 bp):
ATATATATATATATGAATATATAATATTCTCCATACAATCAATCTCCCCATACCATTGTGCATTC
AACACATTGCTGTAGATAA
Found at i:669387 original size:24 final size:24
Alignment explanation
Indices: 669356--669430 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
669346 ATATTTTATA
669356 TTTAAATATAAATATAATATAAAT
1 TTTAAATATAAATATAATATAAAT
669380 TTT-AA-AT--ATAT--TA-AAAT
1 TTTAAATATAAATATAATATAAAT
* *
669397 TTTAAATATAAATATAATTTATAT
1 TTTAAATATAAATATAATATAAAT
*
669421 ATTAAATATA
1 TTTAAATATA
669431 TCATATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
17 7 0.17
18 4 0.10
19 2 0.05
20 4 0.10
21 4 0.10
22 2 0.05
23 3 0.07
24 15 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAATATAAATATAATATAAAT
Found at i:669396 original size:17 final size:18
Alignment explanation
Indices: 669364--669413 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
669354 TATTTAAATA
669364 TAAATATAATATAAATTT
1 TAAATATAATATAAATTT
*
669382 TAAATATATTA-AAATTT
1 TAAATATAATATAAATTT
669399 TAAATATAAATATAA
1 TAAATAT-AATATAA
669414 TTTATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.46
18 13 0.46
19 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATAATATAAATTT
Found at i:669417 original size:17 final size:17
Alignment explanation
Indices: 669364--669416 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
669354 TATTTAAATA
669364 TAAATATAATATAAATTT
1 TAAATATAATAT-AATTT
* *
669382 TAAATATATTAAAATTT
1 TAAATATAATATAATTT
669399 TAAATATAAATATAATTT
1 TAAATAT-AATATAATTT
669417 ATATATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATATAATATAATTT
Found at i:669426 original size:18 final size:17
Alignment explanation
Indices: 669385--669431 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
669375 TAAATTTTAA
669385 ATATATTAAA-AT-TTT
1 ATATATTAAATATATTT
*
669400 AAATA-TAAATATAATTT
1 ATATATTAAATAT-ATTT
669417 ATATATTAAATATAT
1 ATATATTAAATATAT
669432 CATATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.15
15 6 0.23
17 9 0.35
18 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTAAATATATTT
Found at i:669438 original size:14 final size:13
Alignment explanation
Indices: 669398--669451 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
669388 TATTAAAATT
*
669398 TTAAATATAAATA
1 TTAAATATATATA
*
669411 -T-AATTTATATA
1 TTAAATATATATA
669422 TTAAATATATCATA
1 TTAAATATAT-ATA
*
669436 TTAATTATATATA
1 TTAAATATATATA
669449 TTA
1 TTA
669452 TATCATGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 8 0.24
12 2 0.06
13 12 0.35
14 12 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATATATATA
Found at i:669453 original size:23 final size:23
Alignment explanation
Indices: 669427--669473 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
669417 ATATATTAAA
669427 TATATCATATTAATTATATATAT
1 TATATCATATTAATTATATATAT
* * *
669450 TATATCATGTTTATTATTTATAT
1 TATATCATATTAATTATATATAT
669473 T
1 T
669474 TATTCTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATCATATTAATTATATATAT
Found at i:670253 original size:2 final size:2
Alignment explanation
Indices: 670248--670282 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
670238 TTTATATATA
670248 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
670283 ATGCTGATTG
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:670547 original size:18 final size:18
Alignment explanation
Indices: 670524--670564 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
670514 TGGTGGCAAA
670524 GGAAATCCTAACCAAA-CT
1 GGAAATCCTAA-CAAACCT
670542 GGAAATCCTAACAAACCT
1 GGAAATCCTAACAAACCT
670560 GGAAA
1 GGAAA
670565 AGCTTGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (18 bp):
GGAAATCCTAACAAACCT
Found at i:671103 original size:20 final size:20
Alignment explanation
Indices: 671029--671143 Score: 59
Period size: 20 Copynumber: 5.8 Consensus size: 20
671019 ATATGATATG
*
671029 AATATAATATAAA-AAATTAA
1 AATAT-ATATAAATATATTAA
* *
671049 AACATGATATAAAATATGATAAA
1 AATAT-ATAT-AAATAT-ATTAA
671072 ATATGAATATATAAATATATTAA
1 A-AT--ATATATAAATATATTAA
*
671095 AATATATAT---TAT-TT-T
1 AATATATATAAATATATTAA
671110 AAT-TAT-T-AATATATTAA
1 AATATATATAAATATATTAA
*
671127 AATTTATATAAATATAT
1 AATATATATAAATATAT
671144 AACATATTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
13 1 0.01
14 3 0.04
15 6 0.08
16 4 0.05
17 6 0.08
18 3 0.04
19 1 0.01
20 21 0.28
21 3 0.04
22 3 0.04
23 10 0.14
24 7 0.09
25 4 0.05
26 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (20 bp):
AATATATATAAATATATTAA
Found at i:671126 original size:15 final size:16
Alignment explanation
Indices: 671055--671158 Score: 69
Period size: 16 Copynumber: 6.8 Consensus size: 16
671045 TTAAAACATG
* *
671055 ATATAAAATATGATAAA
1 ATATTAAATAT-ATAAT
*
671072 ATA-TGAATATATAAAT
1 ATATTAAATATAT-AAT
*
671088 ATATTAAAATATATATT
1 ATATT-AAATATATAAT
* *
671105 ATTTTAATTAT-TAAT
1 ATATTAAATATATAAT
671120 ATATTAAA-AT-T--T
1 ATATTAAATATATAAT
*
671132 ATA-TAAATATATAAC
1 ATATTAAATATATAAT
671147 ATATTAAATATA
1 ATATTAAATATA
671159 ATAAAAATAC
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
11 4 0.06
12 6 0.09
13 1 0.01
14 3 0.04
15 14 0.21
16 23 0.34
17 10 0.15
18 7 0.10
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (16 bp):
ATATTAAATATATAAT
Found at i:671163 original size:9 final size:8
Alignment explanation
Indices: 671055--671163 Score: 57
Period size: 8 Copynumber: 13.1 Consensus size: 8
671045 TTAAAACATG
671055 ATATA-AA
1 ATATATAA
671062 ATATGATAA
1 ATAT-ATAA
*
671071 A-ATATGA
1 ATATATAA
671078 ATATATAA
1 ATATATAA
671086 ATATATTAA
1 ATATA-TAA
671095 A-ATATATA
1 ATATATA-A
* * *
671103 TTATTTTA
1 ATATATAA
*
671111 AT-TATTA
1 ATATATAA
671118 ATATATTAAA
1 ATATA-T-AA
671128 ATTTATATAA
1 A--TATATAA
671138 ATATATAA
1 ATATATAA
671146 CATAT-TAA
1 -ATATATAA
671154 ATATAATAA
1 ATAT-ATAA
671163 A
1 A
671164 AATACAAGTA
Statistics
Matches: 80, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
7 20 0.25
8 31 0.39
9 19 0.24
10 5 0.06
11 1 0.01
12 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (8 bp):
ATATATAA
Found at i:671899 original size:18 final size:18
Alignment explanation
Indices: 671872--671908 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
671862 TCAATTACTC
* *
671872 ACTTCTTAAAAACTCTCT
1 ACTTCATAAAAACTATCT
671890 ACTTCATAAAAACTATCT
1 ACTTCATAAAAACTATCT
671908 A
1 A
671909 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (18 bp):
ACTTCATAAAAACTATCT
Found at i:673385 original size:18 final size:18
Alignment explanation
Indices: 673330--673389 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
673320 ATATAATCAT
*
673330 AATATAAATTTTTAATAT-
1 AATAT-AATTTTAAATATA
* *
673348 ATTAAAATTTTAAATATA
1 AATATAATTTTAAATATA
673366 AATATAATTTATAAAT-TA
1 AATATAATTT-TAAATATA
673384 AATATA
1 AATATA
673390 TTATATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 11 0.31
18 19 0.54
19 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATAATTTTAAATATA
Found at i:673400 original size:18 final size:18
Alignment explanation
Indices: 673364--673416 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
673354 ATTTTAAATA
*
673364 TAAATATAATT-TATAAAT
1 TAAATAT-ATTATATTAAT
673382 TAAATATATTATATTAAT
1 TAAATATATTATATTAAT
* *
673400 TATATTTATATATATTA
1 TAAATATAT-TATATTA
673417 TATCATACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 20 0.67
19 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATATATTATATTAAT
Found at i:673679 original size:20 final size:19
Alignment explanation
Indices: 673654--673711 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
673644 AATAACAACA
673654 TAAAATTATAATTATTATTT
1 TAAAATTAT-ATTATTATTT
*
673674 TAAAATTATTATTTTTATTTT
1 TAAAATTA-TATTATTA-TTT
*
673695 TAATATTAT-TTATTATT
1 TAAAATTATATTATTATT
673712 AATATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 15 0.45
21 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAAATTATATTATTATTT
Found at i:673708 original size:16 final size:15
Alignment explanation
Indices: 673678--673730 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
673668 TTATTTTAAA
*
673678 ATTATTATTTTTATT
1 ATTAATATTTTTATT
*
673693 TTTAATATTATTTATT
1 ATTAATATT-TTTATT
*
673709 ATTAATATTTATTATA
1 ATTAATATTT-TTATT
673725 ATTAAT
1 ATTAAT
673731 TATAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTAATATTTTTATT
Found at i:673717 original size:25 final size:26
Alignment explanation
Indices: 673677--673747 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
673667 ATTATTTTAA
**
673677 AATTATTATTTTTATTT-TTA-ATATT
1 AATTATTATTAATATTTATTATA-ATT
*
673702 ATTTATTATTAATATTTATTATAATT
1 AATTATTATTAATATTTATTATAATT
*
673728 AATTA-TAATAATATTTATTA
1 AATTATTATTAATATTTATTA
673748 CATTTGTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 28 0.72
26 10 0.26
27 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
AATTATTATTAATATTTATTATAATT
Found at i:674429 original size:2 final size:2
Alignment explanation
Indices: 674422--674456 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
674412 AACTAGTGTT
674422 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
674457 CTGTGTGTGT
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:674744 original size:18 final size:18
Alignment explanation
Indices: 674721--674760 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
674711 GGTGGCAAAA
* *
674721 GAAATCCTAACCAATCTG
1 GAAATCCTAACAAACCTG
*
674739 GAAATCCTGACAAACCTG
1 GAAATCCTAACAAACCTG
674757 GAAA
1 GAAA
674761 AGCTTGTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (18 bp):
GAAATCCTAACAAACCTG
Found at i:675213 original size:11 final size:11
Alignment explanation
Indices: 675197--675259 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
675187 AATAAATTTT
675197 AATATAATATA
1 AATATAATATA
675208 AATATAATATA
1 AATATAATATA
675219 AA-ATAAT-TA
1 AATATAATATA
*
675228 AATTATAATAAA
1 AA-TATAATATA
675240 AATGATAAAATATA
1 AAT-AT--AATATA
675254 AATATA
1 AATATA
675260 TTAATATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
9 4 0.09
10 5 0.11
11 20 0.45
12 5 0.11
13 2 0.05
14 8 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATATAATATA
Found at i:675217 original size:16 final size:16
Alignment explanation
Indices: 675196--675267 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
675186 CAATAAATTT
675196 TAATATAATATAAATA
1 TAATATAATATAAATA
* *
675212 TAATATAAAATAATTA
1 TAATATAATATAAATA
675228 -AATTATAATA-AAA-A
1 TAA-TATAATATAAATA
* *
675242 TGATAAAATATAAATA
1 TAATATAATATAAATA
675258 T-AT-TAATATA
1 TAATATAATATA
675268 TTAAAATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 13 0.29
15 10 0.22
16 22 0.49
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
TAATATAATATAAATA
Found at i:675257 original size:20 final size:21
Alignment explanation
Indices: 675200--675259 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
675190 AAATTTTAAT
675200 ATAATATAAATAT-AATATAAA
1 ATAATA-AAATATAAATATAAA
*
675221 ATAATTAAAT-TATAATA-AAA
1 ATAATAAAATATA-AATATAAA
*
675241 ATGATAAAATATAAATATA
1 ATAATAAAATATAAATATA
675260 TTAATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 19 0.59
21 12 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATAAAATATAAATATAAA
Done.