Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 1242643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 8
Found at i:354321 original size:8 final size:8
Alignment explanation
Indices: 354305--354343 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
354295 ACACATTAAT
354305 TATTCATA
1 TATTCATA
*
354313 TATTTATA
1 TATTCATA
* *
354321 TTTTGATA
1 TATTCATA
354329 TATTCATA
1 TATTCATA
354337 TATTCAT
1 TATTCAT
354344 GTGTGTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (8 bp):
TATTCATA
Found at i:354696 original size:19 final size:19
Alignment explanation
Indices: 354672--354725 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
354662 TTAGTGAGGG
* * *
354672 GAGAGAAGGAAGGAAACGA
1 GAGAGAAAGAAAGAAAAGA
354691 GAGAGAAAGAAAGAAAAGA
1 GAGAGAAAGAAAGAAAAGA
*
354710 AAGAGAAA-AAAGAAAA
1 GAGAGAAAGAAAGAAAA
354726 AAAAGAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 8 0.26
19 23 0.74
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (19 bp):
GAGAGAAAGAAAGAAAAGA
Found at i:354723 original size:18 final size:18
Alignment explanation
Indices: 354692--354739 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
354682 AGGAAACGAG
*
354692 AGAGAAAGAAAGAAAAGAA
1 AGAGAAA-AAAGAAAAAAA
354711 AGAGAAAAAAGAAAAAAA
1 AGAGAAAAAAGAAAAAAA
354729 AGAGAGAAAAA
1 AGAGA-AAAAA
354740 AATATTATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AGAGAAAAAAGAAAAAAA
Found at i:354724 original size:22 final size:21
Alignment explanation
Indices: 354696--354741 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
354686 AACGAGAGAG
*
354696 AAAGAAAGAAAAGAAAGAGAAA
1 AAAGAAAAAAAAGAAAGA-AAA
*
354718 AAAGAAAAAAAAGAGAGAAAA
1 AAAGAAAAAAAAGAAAGAAAA
354739 AAA
1 AAA
354742 TATTATGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAGAAAA
Found at i:354738 original size:9 final size:9
Alignment explanation
Indices: 354692--354739 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
354682 AGGAAACGAG
354692 AGAGAAAGAA
1 AGAGAAA-AA
354702 AGA-AAAGAA
1 AGAGAAA-AA
354711 AGAGAAAAA
1 AGAGAAAAA
*
354720 AGAAAAAAA
1 AGAGAAAAA
354729 AGAGAGAAAA
1 AGAGA-AAAA
354739 A
1 A
354740 AATATTATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 23 0.68
10 11 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AGAGAAAAA
Found at i:355773 original size:18 final size:16
Alignment explanation
Indices: 355748--355790 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
355738 AAAAGGATCT
355748 AATATCCAAAATTTGAC
1 AATATCCAAAATTT-AC
355765 AATTATCC-AAATTTAC
1 AA-TATCCAAAATTTAC
355781 AATATCCAAA
1 AATATCCAAA
355791 TCTACGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.21
16 6 0.25
17 8 0.33
18 5 0.21
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (16 bp):
AATATCCAAAATTTAC
Found at i:359465 original size:307 final size:303
Alignment explanation
Indices: 358862--359463 Score: 938
Period size: 304 Copynumber: 2.0 Consensus size: 303
358852 ATAGAGAACC
* * *
358862 TATCAACTATGACCAATGGCAATAAATCCACACGCTCAATTCCAAAATAGCTAAGTGAGATAGTG
1 TATCAACTATGACCAATGACAATAAATCCACACACTCAATTCCAAAATAGCTAAATGAGATAGTG
*
358927 ATAAACAAAAGCAATGAAAAGGAAAGTGGAAAAGCATAGAATTCAACTAGAATTCCAAGCACGAA
66 ATAAACAAAAGCAATGAAAAGGAAAGTGGAAAAGCATAGAATTCAACTAGAAGTCCAAGCACGAA
* * * *
358992 AAAATTAAAAGAAAAAAAAATTGAGATATATGCGTAAGGATTGAGGAATGCCTTTCTTTTCTTCG
131 AAAATT---AGAAAAAAAAATTGAGAAATATGCATAAGGATTGAGGAATACCTGTCTTTTCTTCG
* * * *
359057 TCTTTGATAACCGTTTCTTCAGATTTCATGGTCATGACTGAGTCAACTGCAGCTGCTCATACGCG
193 TCTTTGAGAACCGTTTCTTCAGATTTCATAGTCATGACTGACTCAACTGCAGCTACTCATACGCG
*
359122 AGACAAACATCTGTTACTATTGAAACGTGAAAAAAAAATATATATA
258 AGACAAACATCTGTTACTATTGAAACATGAAAAAAAAATATATATA
* *
359168 TATCAACTATGACCAATGACAAATAAATCCACACACTCAATTCCAAAATAGCTAAATGAGTTGGT
1 TATCAACTATGACCAATGAC-AATAAATCCACACACTCAATTCCAAAATAGCTAAATGAGATAGT
*
359233 GATAAACAAAAGCAATGAAAAGGAAAGTGGAAAAGCATAGAATTCAAGTAGAAGTCCAAGCACGA
65 GATAAACAAAAGCAATGAAAAGGAAAGTGGAAAAGCATAGAATTCAACTAGAAGTCCAAGCACG-
** *
359298 AAAAAATT-TTAAAAAAAATTGAGAAATATGCATAAGGATTGTGGAATACCTGTCTTTTCTTCAG
129 AAAAAATTAGAAAAAAAAATTGAGAAATATGCATAAGGATTGAGGAATACCTGTCTTTTCTTC-G
* *
359362 -CTTTGAGAACCGTTTCTTCAGATTTCATAGTCATGGCTGACTCAACTGCAGCTACTCATATGCG
193 TCTTTGAGAACCGTTTCTTCAGATTTCATAGTCATGACTGACTCAACTGCAGCTACTCATACGCG
*
359426 AGAGAAACATCTGTTACTATTGAAACATGAAAAAAAAA
258 AGACAAACATCTGTTACTATTGAAACATGAAAAAAAAA
359464 AAGAAAAAGA
Statistics
Matches: 271, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
304 141 0.52
305 1 0.00
306 19 0.07
307 102 0.38
308 8 0.03
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (303 bp):
TATCAACTATGACCAATGACAATAAATCCACACACTCAATTCCAAAATAGCTAAATGAGATAGTG
ATAAACAAAAGCAATGAAAAGGAAAGTGGAAAAGCATAGAATTCAACTAGAAGTCCAAGCACGAA
AAAATTAGAAAAAAAAATTGAGAAATATGCATAAGGATTGAGGAATACCTGTCTTTTCTTCGTCT
TTGAGAACCGTTTCTTCAGATTTCATAGTCATGACTGACTCAACTGCAGCTACTCATACGCGAGA
CAAACATCTGTTACTATTGAAACATGAAAAAAAAATATATATA
Found at i:362857 original size:37 final size:37
Alignment explanation
Indices: 362787--362859 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
362777 TATTCTTTTC
* *
362787 TTTGATTTGATTAGATTATATGTAGGTGATATATTGA
1 TTTGATTTGATTAGATTATATATAGATGATATATTGA
* *
362824 TTTGATTTGATTATATATATATATATATGTATATAT
1 TTTGATTTGATTAGAT-TATATATAGATG-ATATAT
362860 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 15 0.50
38 9 0.30
39 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (37 bp):
TTTGATTTGATTAGATTATATATAGATGATATATTGA
Found at i:363351 original size:2 final size:2
Alignment explanation
Indices: 363344--363393 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
363334 TTTCAACTTA
* *
363344 AT AT AT AT AC AT GT A- 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 AT AT AT
363385 AT AT AT AT A
1 AT AT AT AT A
363394 GTTATGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:367441 original size:40 final size:40
Alignment explanation
Indices: 367348--367450 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
367338 AAACTGATAC
* *
367348 AGTTAAGAGATGGAAAAGGTTGATCTAGACGAAAACAACA
1 AGTTAACAGATGGGAAAGGTTGATCTAGACGAAAACAACA
* * *
367388 AGTCAACAAATGGGAAAGGTTGATC-AGAAC-AAAATCGACA
1 AGTTAACAGATGGGAAAGGTTGATCTAG-ACGAAAA-CAACA
* *
367428 TGTTAATAGATGGGAAAGGTTGA
1 AGTTAACAGATGGGAAAGGTTGA
367451 CTAAGACAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 6 0.12
40 46 0.88
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (40 bp):
AGTTAACAGATGGGAAAGGTTGATCTAGACGAAAACAACA
Found at i:367621 original size:40 final size:40
Alignment explanation
Indices: 367577--367744 Score: 122
Period size: 40 Copynumber: 4.2 Consensus size: 40
367567 GTTTGATTGA
*
367577 GATGAAATTAACAAGTCACCAAATAAAAAGGGTTGACCAG
1 GATGAAATTAACAAGTCAACAAATAAAAAGGGTTGACCAG
** * * *
367617 GATGAAATCGATAAGTCAACAAATATAAAGGGGTTGACTAG
1 GATGAAATTAACAAGTCAACAAATA-AAAAGGGTTGACCAG
* * * * * * * *
367658 GA-CAAAATAATAAGTCAACAAATAAGAATGTTTAACCAA
1 GATGAAATTAACAAGTCAACAAATAAAAAGGGTTGACCAG
* * * * * * *
367697 GATGAAACTGACAAGTCAACGAACAAAGAGGGCTGACCAA
1 GATGAAATTAACAAGTCAACAAATAAAAAGGGTTGACCAG
*
367737 GATAAAAT
1 GATGAAAT
367745 GATAGGTTAA
Statistics
Matches: 95, Mismatches: 31, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
39 10 0.11
40 70 0.74
41 15 0.16
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.18
Consensus pattern (40 bp):
GATGAAATTAACAAGTCAACAAATAAAAAGGGTTGACCAG
Found at i:367943 original size:41 final size:41
Alignment explanation
Indices: 367884--368000 Score: 119
Period size: 41 Copynumber: 2.9 Consensus size: 41
367874 ACAATAGATG
* * *
367884 GAAAGGGTTGACTGGGACAAAACTT-ACTAGTCAACGAATAA
1 GAAAAGGTTGACTAGGACAAAA-TTAACTAGTCAACGAACAA
* *
367925 GAAAAGGTTGATTAGGACAAAATTAACTAGTCAATGAACAA
1 GAAAAGGTTGACTAGGACAAAATTAACTAGTCAACGAACAA
** * * * *
367966 GAAAACATTGACCAAGACAAAACTAACAAGTCAAC
1 GAAAAGGTTGACTAGGACAAAATTAACTAGTCAAC
368001 AAATGAGAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
40 2 0.03
41 60 0.97
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (41 bp):
GAAAAGGTTGACTAGGACAAAATTAACTAGTCAACGAACAA
Found at i:368639 original size:78 final size:78
Alignment explanation
Indices: 368472--368688 Score: 223
Period size: 78 Copynumber: 2.8 Consensus size: 78
368462 ATCAACAACC
** *
368472 GAAA-AAACTAATAACGAGCTAAAGAAGAAGAACATGGTA-AGGAATATGTAGTTTCTACAATTT
1 GAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGATAGAGGAATATGTAGTTTCTACAATTT
*
368535 TTCATTAATAGCT
66 TTCATCAATAGCT
* * * * * * *
368548 AAAACAAACTAATAATAAGCTGAAGAAAAAGAACATGATAGGGGGAATATGTAGTTTTTATAA-T
1 GAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGATA-GAGGAATATGTAGTTTCTACAATT
368612 TTTCATCAGCAT-G-T
65 TTTCATCA--ATAGCT
* * * *
368626 GAAACAAACTAATAAAAAGCTAAAGAAGAAGAATATGATAG-TGAATATGT-GCTTCTAAAATTT
1 GAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGATAGAGGAATATGTAGTTTCTACAATTT
368689 CCATCAACAC
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
75 7 0.06
76 13 0.11
77 31 0.27
78 44 0.38
79 19 0.16
80 2 0.02
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (78 bp):
GAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGATAGAGGAATATGTAGTTTCTACAATTT
TTCATCAATAGCT
Found at i:368706 original size:75 final size:75
Alignment explanation
Indices: 368447--368715 Score: 222
Period size: 78 Copynumber: 3.5 Consensus size: 75
368437 GGAACAGATG
* * ** *
368447 GTTTTTAAAATTTCCATCAACA-ACCGAAA-AAACTAATAACGAGCTAAAGAAGAAGAACATGGT
1 GTTTCTAAAATTTCCATCAACACA-CAAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGAT
368510 AAGGAATATGTA
65 -AGGAATATGTA
* * * * * * * *
368522 GTTTCTACAATTTTTCATTAATAGC-TAAAACAAACTAATAATAAGCTGAAGAAAAAGAACATGA
1 GTTTCTA-AAATTTCCATCAACA-CACAAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGA
368586 TAGGGGGAATATGTA
64 TA---GGAATATGTA
* * * * **** *
368601 GTTTTTATAATTTTCATCAGCATGTGAAACAAACTAATAAAAAGCTAAAGAAGAAGAATATGATA
1 GTTTCTAAAATTTCCATCAACACACAAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGATA
368666 GTGAATATGT-
66 G-GAATATGTA
* *
368676 GCTTCTAAAATTTCCATCAACACACAAAACAAACTGATAA
1 GTTTCTAAAATTTCCATCAACACACAAAACAAACTAATAA
368716 TGAGCTGAAG
Statistics
Matches: 151, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
75 37 0.25
76 23 0.15
77 29 0.19
78 46 0.30
79 16 0.11
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.26
Consensus pattern (75 bp):
GTTTCTAAAATTTCCATCAACACACAAAACAAACTAATAAAAAGCTAAAGAAGAAGAACATGATA
GGAATATGTA
Found at i:368727 original size:75 final size:75
Alignment explanation
Indices: 368447--368727 Score: 228
Period size: 75 Copynumber: 3.7 Consensus size: 75
368437 GGAACAGATG
* * ** *
368447 GTTTTTAAAATTTCCATCAACA-ACCGAAA-AAACTAATAACGAGCTAAAGAAGAAGAACATGGT
1 GTTTCTAAAATTTCCATCAACACA-CAAAACAAACTAATAATAAGCTAAAGAAGAAGAACATGAT
368510 AAGGAATATGTA
65 -AGGAATATGTA
* * * * * * *
368522 GTTTCTACAATTTTTCATTAATAGC-TAAAACAAACTAATAATAAGCTGAAGAAAAAGAACATGA
1 GTTTCTA-AAATTTCCATCAACA-CACAAAACAAACTAATAATAAGCTAAAGAAGAAGAACATGA
368586 TAGGGGGAATATGTA
64 TA---GGAATATGTA
* * * * **** * *
368601 GTTTTTATAATTTTCATCAGCATGTGAAACAAACTAATAAAAAGCTAAAGAAGAAGAATATGATA
1 GTTTCTAAAATTTCCATCAACACACAAAACAAACTAATAATAAGCTAAAGAAGAAGAACATGATA
368666 GTGAATATGT-
66 G-GAATATGTA
* * * *
368676 GCTTCTAAAATTTCCATCAACACACAAAACAAACTGATAATGAGCTGAAGAA
1 GTTTCTAAAATTTCCATCAACACACAAAACAAACTAATAATAAGCTAAAGAA
368728 TAACATGATG
Statistics
Matches: 160, Mismatches: 37, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
75 46 0.29
76 23 0.14
77 29 0.18
78 46 0.29
79 16 0.10
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (75 bp):
GTTTCTAAAATTTCCATCAACACACAAAACAAACTAATAATAAGCTAAAGAAGAAGAACATGATA
GGAATATGTA
Found at i:369485 original size:60 final size:59
Alignment explanation
Indices: 369421--369564 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 59
369411 AATAACTTGG
** * * *
369421 ATGAAACCAAAAACCTAAATAATGATTTGGGTGAA-ACCAGGACTTAATGAAATGGCCTGA
1 ATGAAACCAAAAACCTAAA-AATGAGCTGGG-CAAGACCAAGACTCAATGAAATGGCCTGA
* * * *
369481 ATGAAACTAAAAACCTAAACAATAAGCTGGGCAAGATCAAGACTCAATGAAATGGCCTGG
1 ATGAAACCAAAAACCTAAA-AATGAGCTGGGCAAGACCAAGACTCAATGAAATGGCCTGA
* *
369541 ACGAAATCAAAAACCTAAAAATGA
1 ATGAAACCAAAAACCTAAAAATGA
369565 CAATATATGA
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
59 6 0.09
60 63 0.91
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (59 bp):
ATGAAACCAAAAACCTAAAAATGAGCTGGGCAAGACCAAGACTCAATGAAATGGCCTGA
Found at i:370827 original size:109 final size:108
Alignment explanation
Indices: 370567--370895 Score: 310
Period size: 109 Copynumber: 3.0 Consensus size: 108
370557 CTTTGGTTGG
* * * ** *
370567 CTCAAAAATTTCAAAACTAATAGGATACATGCCCCATTTT--CT-TAAGCATGAGTG-GATTAGA
1 CTCAAAAATTTCAAAACTAATAGGATACATGCCTCATTTTCCCTGGAA-CA--AATGAG-CCAGG
* * * *
370628 TCATATAAAATATGAATTCCTTTGAAAATCAGACAAATTTGATGTCGCTAG
62 TCATATAAAACATAAATTTCTTTGAAAATCAGACAAATTTGATGT---T-T
* * * *
370679 CTCAAAATTTTCAAAACTAATAGGATACATGCCTCATTTT-CCTAGGCACAAAT-AGACCGGGTT
1 CTCAAAAATTTCAAAACTAATAGGATACATGCCTCATTTTCCCT-GGAACAAATGAG-CCAGGTC
* *
370742 ATATAAAACATAATTTTTTTTTGAAAATCAGACAAATTTGATGTTT
64 ATATAAAACATAA-ATTTCTTTGAAAATCAGACAAATTTGATGTTT
* * * * *
370788 CTTAAAAATTTCAAAACTGATAGGATACATGCCTTATTTTCCCTGGAACGAATGAGTCAGGTCAT
1 CTCAAAAATTTCAAAACTAATAGGATACATGCCTCATTTTCCCTGGAACAAATGAGCCAGGTCAT
* *
370853 ATAAAACATAAATTTCTTTGAAAATTAGACAAATTTTATGTTT
66 ATAAAACATAAATTTCTTTGAAAATCAGACAAATTTGATGTTT
370896 TTTCAAGTTT
Statistics
Matches: 181, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
108 28 0.15
109 60 0.33
110 6 0.03
112 55 0.30
113 29 0.16
114 2 0.01
115 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (108 bp):
CTCAAAAATTTCAAAACTAATAGGATACATGCCTCATTTTCCCTGGAACAAATGAGCCAGGTCAT
ATAAAACATAAATTTCTTTGAAAATCAGACAAATTTGATGTTT
Found at i:372509 original size:2 final size:2
Alignment explanation
Indices: 372502--372527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
372492 AAAATTCAAG
372502 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
372528 TTCAAGAAAA
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:378997 original size:27 final size:27
Alignment explanation
Indices: 378961--379018 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
378951 CACCATATTT
** *
378961 TCCTACTCAATTTCCATACCCGTCATA
1 TCCTACTCAACCTCCATACCCATCATA
378988 TCCTACTCAACCTCCATACCCATCATA
1 TCCTACTCAACCTCCATACCCATCATA
379015 TCCT
1 TCCT
379019 GTCACGACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.41, G:0.02, T:0.31
Consensus pattern (27 bp):
TCCTACTCAACCTCCATACCCATCATA
Found at i:382420 original size:19 final size:19
Alignment explanation
Indices: 382396--382462 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
382386 CAGTAGCTAA
382396 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
382415 TTATG--T--AT-CAATAC
1 TTATGTATCGATACAATAC
* *
382429 AT-TGTATCGATACAACAC
1 TTATGTATCGATACAATAC
382447 TTATGTATCGATACAA
1 TTATGTATCGATACAA
382463 ATCGTTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
13 2 0.05
14 7 0.18
15 3 0.08
17 3 0.08
18 6 0.15
19 18 0.46
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:382440 original size:32 final size:32
Alignment explanation
Indices: 382399--382461 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
382389 TAGCTAATTA
*
382399 TGTATCGATACAATACTTATGTATCAATACAT
1 TGTATCGATACAACACTTATGTATCAATACAT
*
382431 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCAATACA
382462 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCAATACAT
Found at i:382873 original size:75 final size:75
Alignment explanation
Indices: 382750--383081 Score: 373
Period size: 75 Copynumber: 4.4 Consensus size: 75
382740 GTGTCTACAT
* *
382750 TTGTAGTTATCGTGCAGATTATCTC-GAGTTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAA
1 TTGTAGTTATCATGCATATTATCTCGGA-TTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAA
*
382814 ATATTTATTGA
65 ACATTTATTGA
* * * * * * *
382825 TTGTAATTATCATCCAAATTATCTCGGGTTAGTTGTTCATAATAGTACTGTGAAATATGCTGAAA
1 TTGTAGTTATCATGCATATTATCTCGGATTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAA
* *
382890 CATTTGTTCA
66 CATTTATTGA
* * * * *** *
382900 TTGTAGTTATCGTGCATATTATCTTGAATTAGTTGTTGATAGTAGTAATGTGAAATACATAGCAA
1 TTGTAGTTATCATGCATATTATCTCGGATTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAA
*
382965 CATTTGTT-A
66 CATTTATTGA
* * * * *
382974 GTTATAGTTATCGTGCATATTATTTCAGATTAGTTATTGATAGTAGTACTGTGAAATATGCAGAA
1 -TTGTAGTTATCATGCATATTATCTCGGATTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAA
383039 ACATTTATTGA
65 ACATTTATTGA
*
383050 TTGTAGTTAT-AGTGCAGATTATCTCGGATTAG
1 TTGTAGTTATCA-TGCATATTATCTCGGATTAG
383082 GGTTTCATCT
Statistics
Matches: 210, Mismatches: 43, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
74 1 0.00
75 207 0.99
76 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (75 bp):
TTGTAGTTATCATGCATATTATCTCGGATTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAA
CATTTATTGA
Found at i:383021 original size:150 final size:150
Alignment explanation
Indices: 382750--383081 Score: 414
Period size: 150 Copynumber: 2.2 Consensus size: 150
382740 GTGTCTACAT
* * **
382750 TTGTAGTTATCGTGCAGATTATCTCGAGTTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAA
1 TTGTAGTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTAATGTGAAATACACAGAAA
* * * * *
382815 TATTTATTGATTGTAATTATCATCCAAATTATCTCGGGTTAGTTGTTCATAATAGTACTGTGAAA
66 CATTTATTGATTATAATTATCATCCAAATTATCTCAGATTAGTTATTCATAATAGTACTGTGAAA
* *
382880 TATGCTGAAACATTTGTTCA
131 TATGCAGAAACATTTATTCA
* * * *
382900 TTGTAGTTATCGTGCATATTATCTTGAATTAGTTGTTGATAGTAGTAATGTGAAATACATAGCAA
1 TTGTAGTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTAATGTGAAATACACAGAAA
* * * * * * * *
382965 CATTTGTT-AGTTATAGTTATCGTGCATATTATTTCAGATTAGTTATTGATAGTAGTACTGTGAA
66 CATTTATTGA-TTATAATTATCATCCAAATTATCTCAGATTAGTTATTCATAATAGTACTGTGAA
*
383029 ATATGCAGAAACATTTATTGA
130 ATATGCAGAAACATTTATTCA
* *
383050 TTGTAGTTATAGTGCAGATTATCTCGGATTAG
1 TTGTAGTTATCGTGCAGATTATCTCGAATTAG
383082 GGTTTCATCT
Statistics
Matches: 153, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
149 1 0.01
150 152 0.99
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (150 bp):
TTGTAGTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTAATGTGAAATACACAGAAA
CATTTATTGATTATAATTATCATCCAAATTATCTCAGATTAGTTATTCATAATAGTACTGTGAAA
TATGCAGAAACATTTATTCA
Found at i:384078 original size:28 final size:28
Alignment explanation
Indices: 384046--384101 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
384036 TTCTAAACTA
*
384046 AAGAACAAGAAAAATAAAATTGATAAGT
1 AAGAACAAGAAAAATAAAACTGATAAGT
384074 AAGAACAAGAAAAATAAAACTGATAAGT
1 AAGAACAAGAAAAATAAAACTGATAAGT
384102 CGAGGCTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.16
Consensus pattern (28 bp):
AAGAACAAGAAAAATAAAACTGATAAGT
Found at i:384330 original size:28 final size:29
Alignment explanation
Indices: 384292--384349 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
384282 CATTCTGAAC
384292 TAAAGAACAAGAAAAATAAAACTGATAAG
1 TAAAGAACAAGAAAAATAAAACTGATAAG
384321 TAAA-AACAAGAAAAATAAAACTGATAAG
1 TAAAGAACAAGAAAAATAAAACTGATAAG
384349 T
1 T
384350 CAAGGCTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.66, C:0.07, G:0.12, T:0.16
Consensus pattern (29 bp):
TAAAGAACAAGAAAAATAAAACTGATAAG
Found at i:384358 original size:248 final size:248
Alignment explanation
Indices: 383918--384635 Score: 1132
Period size: 248 Copynumber: 2.9 Consensus size: 248
383908 ATACACATAA
* * *
383918 AATAATAACCTCTTCCTATTAAATAGAAACAAATACTTGAGACTAGGACTT-ACAATTACAATAA
1 AATAATAACCTCTTCCTATTAAATAGAAACAACTACTTGAGACTAGGA-TTCACAATCACAATCA
* * * **
383982 GGTGCAACTAAATAGCTGGCACTTATCCACGTTATTAAAACAAAAATTGACTCATTCTAAACTAA
65 CGTGCAACTAAATAACTAGCACTTATCCACGTTACCAAAACAAAAATTGACTCATTCTAAACTAA
*
384047 AGAACAAGAAAAATAAAATTGATAAGTAAGAACAAGAAAAATAAAACTGATAAGTCGAGGCTTGC
130 AGAACAAGAAAAATAAAAATGATAAGTAAGAACAAGAAAAATAAAACTGATAAGTCGAGGCTTGC
* *
384112 ATAGCTTGCTTAACTCATGGCTTCATGTGCTGTAATATTTGCATCAGGACTGAC
195 ATAGCTTGCTTAACTCATGGCTTCATGTGCTATAATATTTGCATCAGGACTAAC
* *
384166 AATAATAACCTCTTCCTATTATATAGTAACAACTACTTGAGACTAGGATTCACAATCACAATCAC
1 AATAATAACCTCTTCCTATTAAATAGAAACAACTACTTGAGACTAGGATTCACAATCACAATCAC
*
384231 GTGCAACTAAATAACTAGCACTTATCCACGTTACCAAAACAAAAATTGACTCATTCTGAACTAAA
66 GTGCAACTAAATAACTAGCACTTATCCACGTTACCAAAACAAAAATTGACTCATTCTAAACTAAA
* * *
384296 GAACAAGAAAAATAAAACTGATAAGTAAAAACAAGAAAAATAAAACTGATAAGTCAAGGCTTGCA
131 GAACAAGAAAAATAAAAATGATAAGTAAGAACAAGAAAAATAAAACTGATAAGTCGAGGCTTGCA
* *
384361 TAGCTTGCTTAACTCATGGCTTCATGTTCTATAATATTTGCATCATGACTAAC
196 TAGCTTGCTTAACTCATGGCTTCATGTGCTATAATATTTGCATCAGGACTAAC
* * * *
384414 AATAACAACCTCTTCCTATTAAATAGCAACAACTACTTGAGACCAGGACTCACAATCACAATCAC
1 AATAATAACCTCTTCCTATTAAATAGAAACAACTACTTGAGACTAGGATTCACAATCACAATCAC
* *
384479 ATGCAACTAAATAACTAGCACTTATCCACATTACCAAAACAAAAATTGACTCATTCTAAACTAAA
66 GTGCAACTAAATAACTAGCACTTATCCACGTTACCAAAACAAAAATTGACTCATTCTAAACTAAA
* * * * * *
384544 GAAAAATAAAAATAAAAATGATAAATAAGAACACGAAAAATAAAACAGATAAGTCGAGGATTGCA
131 GAACAAGAAAAATAAAAATGATAAGTAAGAACAAGAAAAATAAAACTGATAAGTCGAGGCTTGCA
384609 TAGCTTGCTTAACTCATGGCTTACATG
196 TAGCTTGCTTAACTCATGGCTT-CATG
384636 ATCTTGCATG
Statistics
Matches: 433, Mismatches: 35, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
247 2 0.00
248 427 0.99
249 4 0.01
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (248 bp):
AATAATAACCTCTTCCTATTAAATAGAAACAACTACTTGAGACTAGGATTCACAATCACAATCAC
GTGCAACTAAATAACTAGCACTTATCCACGTTACCAAAACAAAAATTGACTCATTCTAAACTAAA
GAACAAGAAAAATAAAAATGATAAGTAAGAACAAGAAAAATAAAACTGATAAGTCGAGGCTTGCA
TAGCTTGCTTAACTCATGGCTTCATGTGCTATAATATTTGCATCAGGACTAAC
Found at i:393455 original size:19 final size:19
Alignment explanation
Indices: 393417--393456 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
393407 TAAATATGGA
*
393417 ATTATAATTAAATTAAAAT
1 ATTATAATTAAAATAAAAT
* *
393436 ATTATATTTAAAATATAAT
1 ATTATAATTAAAATAAAAT
393455 AT
1 AT
393457 GAGAAAACTT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATAATTAAAATAAAAT
Found at i:394605 original size:30 final size:30
Alignment explanation
Indices: 394571--394641 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
394561 TGATCAGGGG
394571 GAAACCTTCAATTGAAAAGATAACCAAGGT
1 GAAACCTTCAATTGAAAAGATAACCAAGGT
* * *
394601 GAAA-CTTTAATTGAATAGATAACTAAGGT
1 GAAACCTTCAATTGAAAAGATAACCAAGGT
* *
394630 AAAACTTTCAAT
1 GAAACCTTCAAT
394642 CAAGAGAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (30 bp):
GAAACCTTCAATTGAAAAGATAACCAAGGT
Found at i:394898 original size:31 final size:31
Alignment explanation
Indices: 394848--394916 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
394838 TAGGATGAAT
* *
394848 CCTATTAGTTACAAGGATGATTAAAGCGAAA
1 CCTATTAATTACAAAGATGATTAAAGCGAAA
* ** *
394879 CCTATTAATTAGAAAGATGATTAGGGCTAAA
1 CCTATTAATTACAAAGATGATTAAAGCGAAA
394910 CCTATTA
1 CCTATTA
394917 GCCAAAAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (31 bp):
CCTATTAATTACAAAGATGATTAAAGCGAAA
Found at i:394972 original size:30 final size:30
Alignment explanation
Indices: 394907--394991 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
394897 GATTAGGGCT
* *
394907 AAACCTATTAGCCAAAAAGATGACTAAGGGA
1 AAACCTATTAGTC-AAAAGATGACCAAGGGA
*
394938 AAACCTATTAGTCAAAAGGTGACCAAGGCG-
1 AAACCTATTAGTCAAAAGATGACCAAGG-GA
*
394968 AAACCTGTTAGTCAGAAAGATGAC
1 AAACCTATTAGTCA-AAAGATGAC
394992 TAGGGCAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 26 0.55
31 21 0.45
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (30 bp):
AAACCTATTAGTCAAAAGATGACCAAGGGA
Found at i:395002 original size:30 final size:31
Alignment explanation
Indices: 394873--395003 Score: 133
Period size: 31 Copynumber: 4.3 Consensus size: 31
394863 GATGATTAAA
* * *
394873 GCGAAACCTATTAATTAGAAAGATGATTAGG
1 GCGAAACCTATTAGTCAGAAAGATGACTAGG
* * *
394904 GCTAAACCTATTAGCCAAAAAGATGACTAAGG
1 GCGAAACCTATTAGTCAGAAAGATGACT-AGG
* * * *
394936 G-AAAACCTATTAGTCA-AAAGGTGACCAAG
1 GCGAAACCTATTAGTCAGAAAGATGACTAGG
*
394965 GCGAAACCTGTTAGTCAGAAAGATGACTAGG
1 GCGAAACCTATTAGTCAGAAAGATGACTAGG
394996 GC-AAACCT
1 GCGAAACCT
395004 TAAGTTAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
29 3 0.04
30 27 0.33
31 47 0.58
32 4 0.05
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (31 bp):
GCGAAACCTATTAGTCAGAAAGATGACTAGG
Found at i:395082 original size:31 final size:30
Alignment explanation
Indices: 395027--395111 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
395017 TGATGATGGT
*
395027 AAAACTTTAT-GTTA-AAAGGATGACT-CGAGC
1 AAAACTTAATAGTTAGAAA-GATGACTAC-A-C
395057 AAAACTTAATAGTTAGAAAGATGACTAACAC
1 AAAACTTAATAGTTAGAAAGATGACT-ACAC
* *
395088 AAAACCTATTAGTTAGAAA-ATGAC
1 AAAACTTAATAGTTAGAAAGATGAC
395112 CAGGGCAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 14 0.29
31 29 0.60
32 4 0.08
33 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (30 bp):
AAAACTTAATAGTTAGAAAGATGACTACAC
Found at i:395121 original size:30 final size:31
Alignment explanation
Indices: 395055--395127 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
395045 GATGACTCGA
* *
395055 GCAAAACTTAATAGTTAGAAAGATGACTAAC
1 GCAAAACCTAATAGTTAGAAAGATGACCAAC
* * **
395086 ACAAAACCTATTAGTTAGAAA-ATGACCAGG
1 GCAAAACCTAATAGTTAGAAAGATGACCAAC
395116 GCAAAACCTAAT
1 GCAAAACCTAAT
395128 GGTCATTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (31 bp):
GCAAAACCTAATAGTTAGAAAGATGACCAAC
Found at i:395380 original size:56 final size:57
Alignment explanation
Indices: 395300--395434 Score: 141
Period size: 56 Copynumber: 2.4 Consensus size: 57
395290 CTTGGGCTTA
* *
395300 TGCCAATTT-AAATTAGAATGAAACCTATCT-GCTACTTTTAAGCTTTCA-CATCTTGG
1 TGCCAATTTCAAATGAG-ATGAAACCTAT-TAGCTACTCTTAAGCTTTCATCATCTTGG
* * * * *
395356 TGCCAATTTCAACTGAGATGAAACCTATTAGTTGCTCTTAAGCTTTTATCATTTTGG
1 TGCCAATTTCAAATGAGATGAAACCTATTAGCTACTCTTAAGCTTTCATCATCTTGG
* * *
395413 TGCTAATTTCAATTGGGATGAA
1 TGCCAATTTCAAATGAGATGAA
395435 CTTATCAGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
55 1 0.02
56 34 0.52
57 31 0.47
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (57 bp):
TGCCAATTTCAAATGAGATGAAACCTATTAGCTACTCTTAAGCTTTCATCATCTTGG
Found at i:395433 original size:57 final size:55
Alignment explanation
Indices: 395337--395458 Score: 145
Period size: 56 Copynumber: 2.2 Consensus size: 55
395327 TCTGCTACTT
*
395337 TTAAGCTTTCACATCTTGGTGCCAATTTCAACTGAGATGAAACCTATTAGTTGCTC
1 TTAAGCTTTCACATCTTGGTGCCAATTTCAACTGAGATG-AACCTATCAGTTGCTC
* * * * * * *
395393 TTAAGCTTTTATCATTTTGGTGCTAATTTCAATTGGGATGAACTTATCAGTTGCTT
1 TTAAGCTTTCA-CATCTTGGTGCCAATTTCAACTGAGATGAACCTATCAGTTGCTC
*
395449 TTAGGCTTTC
1 TTAAGCTTTC
395459 TCATTTGAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 31 0.56
57 24 0.44
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (55 bp):
TTAAGCTTTCACATCTTGGTGCCAATTTCAACTGAGATGAACCTATCAGTTGCTC
Found at i:396950 original size:12 final size:12
Alignment explanation
Indices: 396928--396977 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
396918 AATTATTTAA
396928 ATTATTTTTAAAT
1 ATTA-TTTTAAAT
396941 ATTATTTTAAGAT
1 ATTATTTTAA-AT
396954 A--ATTTTAAAT
1 ATTATTTTAAAT
396964 ATT-TTATTAAAT
1 ATTATT-TTAAAT
396976 AT
1 AT
396978 AAAATATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 3 0.09
11 9 0.27
12 14 0.42
13 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
ATTATTTTAAAT
Found at i:405358 original size:19 final size:20
Alignment explanation
Indices: 405330--405375 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
405320 TTATATTTAA
*
405330 TATTTATTT-ATAGTAAAAT
1 TATTTTTTTAATAGTAAAAT
*
405349 TATTTTTTTAATAGTTAAAT
1 TATTTTTTTAATAGTAAAAT
405369 T-TTTTTT
1 TATTTTTT
405376 AATTAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TATTTTTTTAATAGTAAAAT
Found at i:411151 original size:3 final size:3
Alignment explanation
Indices: 411143--411174 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
411133 TCCATGGCGA
411143 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
411175 GCTTGCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:419870 original size:12 final size:12
Alignment explanation
Indices: 419853--419877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
419843 ATAATCTATT
419853 TGAACTTGTGTC
1 TGAACTTGTGTC
419865 TGAACTTGTGTC
1 TGAACTTGTGTC
419877 T
1 T
419878 ATACTTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TGAACTTGTGTC
Found at i:419918 original size:30 final size:30
Alignment explanation
Indices: 419864--419921 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
419854 GAACTTGTGT
* **
419864 CTGAACTTGTGTCTATACTTGTTTCTACAC
1 CTGAACTTGTGTCTAAACCCGTTTCTACAC
419894 CTGAACTTGTGTCTAAACCCGTTTCTAC
1 CTGAACTTGTGTCTAAACCCGTTTCTAC
419922 GCTTGTAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (30 bp):
CTGAACTTGTGTCTAAACCCGTTTCTACAC
Found at i:424292 original size:6 final size:7
Alignment explanation
Indices: 424277--424301 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
424267 CATTACTTAG
424277 TTTTATT
1 TTTTATT
424284 TTTTATT
1 TTTTATT
424291 TTTTATT
1 TTTTATT
424298 TTTT
1 TTTT
424302 GGGTAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:424550 original size:4 final size:4
Alignment explanation
Indices: 424541--424572 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
424531 CATTAAGTAA
424541 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
424573 GAGGAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:426809 original size:16 final size:17
Alignment explanation
Indices: 426790--426822 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
426780 CAAGAATAGG
426790 AATAAAAAAAGG-CAAA
1 AATAAAAAAAGGACAAA
*
426806 AATAAAACAAGGACAAA
1 AATAAAAAAAGGACAAA
426823 CACTGCATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
AATAAAAAAAGGACAAA
Found at i:428327 original size:21 final size:21
Alignment explanation
Indices: 428302--428361 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
428292 AAATTATAAT
428302 TTTAATTAAATTTATTTTAAA
1 TTTAATTAAATTTATTTTAAA
* * *
428323 TTTAAGTAAAAATT-TTTAAAA
1 TTTAA-TTAAATTTATTTTAAA
428344 TTT--TTAAAATTTATTTTA
1 TTTAATT-AAATTTATTTTA
428362 TTTTTTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 5 0.17
20 4 0.13
21 14 0.47
22 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAATTAAATTTATTTTAAA
Found at i:428345 original size:9 final size:9
Alignment explanation
Indices: 428331--428355 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
428321 AATTTAAGTA
428331 AAAATTTTT
1 AAAATTTTT
428340 AAAATTTTT
1 AAAATTTTT
428349 AAAATTT
1 AAAATTT
428356 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:432762 original size:16 final size:16
Alignment explanation
Indices: 432741--432804 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
432731 ACTTCATTTA
* *
432741 AGTTCGAGTCATTTCG
1 AGTTCGAATCATTTTG
*
432757 AGTTCGGATCATTTTG
1 AGTTCGAATCATTTTG
* * *
432773 GGTTCAAATCATTTTA
1 AGTTCGAATCATTTTG
432789 AGTTCGAATCATTTTG
1 AGTTCGAATCATTTTG
432805 GATTCGTGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (16 bp):
AGTTCGAATCATTTTG
Found at i:432810 original size:16 final size:16
Alignment explanation
Indices: 432759--432810 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
432749 TCATTTCGAG
* *
432759 TTCGGATCATTTTGGG
1 TTCGAATCATTTTGGA
* *
432775 TTCAAATCATTTT-AA
1 TTCGAATCATTTTGGA
432790 GTTCGAATCATTTTGGA
1 -TTCGAATCATTTTGGA
432807 TTCG
1 TTCG
432811 TGTTTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.44
Consensus pattern (16 bp):
TTCGAATCATTTTGGA
Found at i:442031 original size:61 final size:60
Alignment explanation
Indices: 441850--442271 Score: 213
Period size: 61 Copynumber: 7.2 Consensus size: 60
441840 TGCAGCACTA
* * * * * * * *
441850 GACTTAAAGATGATAAGGATGAAAAAAGTGCCAATGTGCTGATTCAAGG-TCAATGACATT-
1 GACTTAAA-ATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCT-AACGATATTG
* * * * * *
441910 GATCTTAAAA-GATGCAAAGAATAATAAAGGTGTCAATATGCTGATTCACGGCTAGCGATATCG
1 GA-CTTAAAATGA-G--AAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAACGATATTG
*
441973 GACTTGAAAATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAATGATATTG
1 GACTT-AAAATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAACGATATTG
* * ** * * *
442034 G--TT----TTA-AA-AATGACAAAGGTGCTGATGTGTTGATTCAAAGCTAACGACATTG
1 GACTTAAAATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAACGATATTG
* * * * * * * *
442086 GACTTGAAGATTAGAAAAATGATAAAGGTGCCAATATATTAATTTAAGGCCAGCGATATTAG
1 GACTT-AAAATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAACGATATT-G
* * * * *
442148 G-CTT-AAA-GATG-A-CA--A-AAA--TGCCAATGTGCTGATTCAAGGC-AAGTGACATTG
1 GACTTAAAATGA-GAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAA-CGATATTG
* * * * **
442199 GACTTGAAGATGAGAAGAATGATAAGGGTGCCGATATGTTGATTCAAGGCCAGTGATATTG
1 GACTT-AAAATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAACGATATTG
442260 GACTTAAAATGA
1 GACTTAAAATGA
442272 CAAAGGCACC
Statistics
Matches: 272, Mismatches: 58, Indels: 64
0.69 0.15 0.16
Matches are distributed among these distances:
51 3 0.01
52 63 0.23
53 2 0.01
54 10 0.04
55 4 0.01
56 1 0.00
57 1 0.00
58 3 0.01
59 12 0.04
60 11 0.04
61 113 0.42
62 39 0.14
63 8 0.03
64 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (60 bp):
GACTTAAAATGAGAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCTAACGATATTG
Found at i:442135 original size:113 final size:112
Alignment explanation
Indices: 441935--442315 Score: 397
Period size: 113 Copynumber: 3.4 Consensus size: 112
441925 AAAGAATAAT
* * ** * * * *
441935 AAAGGTGTCAATATGCTGATTCACGGCTAGCGATATCGGACTTGAAAATGAGAAGAATGATAAAG
1 AAAGGTGCCAATGTGCTGATTCAAAGCAAGCGACATTGGACTTGAAGATGAGAAGAATGATAAAG
* * *
442000 GTGCCAATATGTTGATTCAAGGCTAATGATATTGGTTTTAAAAATGAC
66 GTGCCAATATGTTGATTCAAGGCCAGTGATATTGG-CTTAAAAATGAC
** * * *
442048 AAAGGTGCTGATGTGTTGATTCAAAGCTAA-CGACATTGGACTTGAAGATTAGAAAAATGATAAA
1 AAAGGTGCCAATGTGCTGATTCAAAGC-AAGCGACATTGGACTTGAAGATGAGAAGAATGATAAA
* * * * *
442112 GGTGCCAATATATTAATTTAAGGCCAGCGATATTAGGCTTAAAGATGAC
65 GGTGCCAATATGTTGATTCAAGGCCAGTGATATT-GGCTTAAAAATGAC
** * * *
442161 AAAAATGCCAATGTGCTGATTCAAGGCAAGTGACATTGGACTTGAAGATGAGAAGAATGATAAGG
1 AAAGGTGCCAATGTGCTGATTCAAAGCAAGCGACATTGGACTTGAAGATGAGAAGAATGATAAAG
*
442226 GTGCCGATATGTTGATTCAAGGCCAGTGATATTGGACTT-AAAATGAC
66 GTGCCAATATGTTGATTCAAGGCCAGTGATATTGG-CTTAAAAATGAC
** * * * * * *
442273 AAAGGCACCAGTATGCTGATTCAAGGCCAGCAATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAAGCAAGCGACATTGGACTT
442316 AAAAATGACA
Statistics
Matches: 217, Mismatches: 47, Indels: 9
0.79 0.17 0.03
Matches are distributed among these distances:
112 44 0.20
113 170 0.78
114 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (112 bp):
AAAGGTGCCAATGTGCTGATTCAAAGCAAGCGACATTGGACTTGAAGATGAGAAGAATGATAAAG
GTGCCAATATGTTGATTCAAGGCCAGTGATATTGGCTTAAAAATGAC
Found at i:442187 original size:52 final size:52
Alignment explanation
Indices: 442104--442420 Score: 187
Period size: 52 Copynumber: 5.9 Consensus size: 52
442094 GATTAGAAAA
* * ** * *
442104 ATGATAAAGGTGCCAATATATTAATTTAAGGCCAGCGATATTAGG-CTTAAAG
1 ATGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAG
* * * * * *
442156 ATGACAAAAATGCCAATGTGCTGATTCAAGGCAAGTGACATTGGACTTGAAG
1 ATGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* * * *
442208 ATGAGAAGAATGATAAGGGTGCCGATATGTTGATTCAAGGCCAGTGATATTGGACTTAAA-
1 AT--G-A-CA--A-AA--GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* ** * * *
442268 ATGACAAAGGCACCAGTATGCTGATTCAAGGCCAGCAATATTGGACTTAAAA
1 ATGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* * * * *
442320 ATGACAAAGGTGACAATATGCTGA-TCTAAGGCTAACGATATTAGACTT-AAG
1 ATGACAAAAGTGCCAATATGCTGATTC-AAGGCCAGCGATATTGGACTTAAAG
* * * *
442371 AAAGA-AAAATGTGCCAATGTGTTGTTTCAAGGCCAGCGACT-TTGGACTTA
1 -ATGACAAAA-GTGCCAATATGCTGATTCAAGGCCAGCGA-TATTGGACTTA
442421 TAAAGAAATG
Statistics
Matches: 201, Mismatches: 47, Indels: 33
0.72 0.17 0.12
Matches are distributed among these distances:
51 44 0.22
52 106 0.53
53 4 0.02
54 2 0.01
55 1 0.00
56 2 0.01
57 1 0.00
58 2 0.01
59 2 0.01
60 2 0.01
61 35 0.17
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (52 bp):
ATGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
Found at i:442559 original size:33 final size:32
Alignment explanation
Indices: 442488--442802 Score: 303
Period size: 33 Copynumber: 9.7 Consensus size: 32
442478 TAGAAAGAGA
* * * *
442488 TGCCACCAACTTATATGGGCTTTTGAGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
* *
442520 TGCCATCAACTTGTGTGGGCTTTTGAAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAA-GGGT
* * *
442553 TACCATCGACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AAGGGT
* * *
442586 TGCCACCGACTGGTGTGGACTTTTAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AAGGGT
* *
442619 TGCCACTGACTTGTGTGGGCTTTAG-AAGAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAG-GGT
* *
442651 TGCCACCGACTTATGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AAGGGT
* *
442684 TGCCACCGACTTCTGTAGGCTTTTG-AAGAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAAG-GGT
* * * *
442716 TGCCACCAACTTGTATGGGCTTTAAGGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-TGAAAGGGT
* **
442749 TGCCACCGACTTGTGTGAGC-TTTGAGAAGAAT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AAGGGT
*
442781 TGCCACCGACTTATGTGGGCTT
1 TGCCACCGACTTGTGTGGGCTT
442803 AAAAGGAAAA
Statistics
Matches: 236, Mismatches: 37, Indels: 19
0.81 0.13 0.07
Matches are distributed among these distances:
31 7 0.03
32 96 0.41
33 125 0.53
34 8 0.03
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTTGAAAGGGT
Found at i:442670 original size:98 final size:96
Alignment explanation
Indices: 442505--442791 Score: 341
Period size: 98 Copynumber: 2.9 Consensus size: 96
442495 AACTTATATG
* * *
442505 GGCTTTT-GAGAGGGTTGCCA-TCAACTTGTGTGGGCTTTTGAAAGGGGTTACCATCGACTTGTG
1 GGCTTTTAGA-AGGGTTGCCACT-AACTTGTGTGGGCTTTAG-AA-GGGTTGCCACCGACTTGTG
*
442568 TGGGCTTTAGAGAAGGGTTGCCACCGACTGGTGT-
62 TGGGCTTTAGAGAAGGGTTGCCACCGACTGCTGTA
* *
442602 GGACTTTTAAGAAGGGTTGCCACTGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTATGT
1 GG-CTTTT-AGAAGGGTTGCCACTAACTTGTGTGGGCTTTAGAAG-GGTTGCCACCGACTTGTGT
*
442667 GGGCTTTAGAGAAGGGTTGCCACCGACTTCTGTA
63 GGGCTTTAGAGAAGGGTTGCCACCGACTGCTGTA
* *
442701 GGCTTTT-GAAGAGGTTGCCACCAACTTGTATGGGCTTTAAGGAAGGGTTGCCACCGACTTGTGT
1 GGCTTTTAGAAG-GGTTGCCACTAACTTGTGTGGGCTTT-A-GAAGGGTTGCCACCGACTTGTGT
* **
442765 GAGCTTT-GAGAAGAATTGCCACCGACT
63 GGGCTTTAGAGAAGGGTTGCCACCGACT
442792 TATGTGGGCT
Statistics
Matches: 167, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
96 4 0.02
97 44 0.26
98 84 0.50
99 32 0.19
100 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (96 bp):
GGCTTTTAGAAGGGTTGCCACTAACTTGTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGG
CTTTAGAGAAGGGTTGCCACCGACTGCTGTA
Found at i:442680 original size:65 final size:64
Alignment explanation
Indices: 442488--442802 Score: 332
Period size: 65 Copynumber: 4.8 Consensus size: 64
442478 TAGAAAGAGA
* * * * * * *
442488 TGCCACCAACTTATATGGGCTTTTG-AGAGGGTTGCCATCAACTTGTGTGGGCTTTTGAA-AGGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGA-GGTTGCCACCGACTTGTGTGGGC-TTT-AAGAAGG
442551 GT
63 GT
* * * *
442553 TACCATCGACTTGTGTGGGCTTTAG-AGAAGGGTTGCCACCGACTGGTGTGGACTTTTAAGAAGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAG-A-GGTTGCCACCGACTTGTGTGGGC-TTTAAGAAGG
442617 GT
63 GT
* *
442619 TGCCACTGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTATGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTA-AGAAGGGT
* * * * *
442684 TGCCACCGACTTCTGTAGGCTTTTGAAGAGGTTGCCACCAACTTGTATGGGCTTTAAGGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAA-GAAGGGT
* * *
442749 TGCCACCGACTTGTGTGAGCTTTGAGAAGA-ATTGCCACCGACTTATGTGGGCTT
1 TGCCACCGACTTGTGTGGGCTTT-AGAAGAGGTTGCCACCGACTTGTGTGGGCTT
442803 AAAAGGAAAA
Statistics
Matches: 212, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
64 5 0.02
65 147 0.69
66 58 0.27
67 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (64 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGT
Found at i:442846 original size:33 final size:33
Alignment explanation
Indices: 442800--442958 Score: 155
Period size: 33 Copynumber: 4.8 Consensus size: 33
442790 CTTATGTGGG
*
442800 CTTAAAAGGAAAAAA-CTGCCACAGAGTTATGGA
1 CTTAAAA-GAAAAAAGGTGCCACAGAGTTATGGA
* * * *
442833 TTTAAAAGAAAAAAGGTGTCATAGAGTTATGAA
1 CTTAAAAGAAAAAAGGTGCCACAGAGTTATGGA
* * * *
442866 CTTAAAA-AGAAAAGGTTCCACGGAGTTGTGGA
1 CTTAAAAGAAAAAAGGTGCCACAGAGTTATGGA
* *
442898 CTTTAAAAG-AAAAATGTGCCA-TGAAGTTATGGA
1 C-TTAAAAGAAAAAAGGTGCCACAG-AGTTATGGA
*
442931 CTTAAAAGAAAAAAGGTGCCATAGAGTT
1 CTTAAAAGAAAAAAGGTGCCACAGAGTT
442959 TGAAGAAGAA
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
32 34 0.34
33 65 0.65
34 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (33 bp):
CTTAAAAGAAAAAAGGTGCCACAGAGTTATGGA
Found at i:442934 original size:65 final size:64
Alignment explanation
Indices: 442818--442942 Score: 164
Period size: 65 Copynumber: 1.9 Consensus size: 64
442808 GAAAAAACTG
*
442818 CCACAGAGTTATGGATTTAAAAGAAAAAAGGTGTCATAGAGTTATGAACTTAAAAAGAAAAGGTT
1 CCACAGAGTTATGGATTTAAAAGAAAAAAGGTGCCATAGAGTTATGAACTT-AAAAGAAAAGGTT
* * * *
442883 CCACGGAGTTGTGGACTTTAAAAG-AAAAATGTGCCAT-GAAGTTATGGACTTAAAAGAAAA
1 CCACAGAGTTATGGA-TTTAAAAGAAAAAAGGTGCCATAG-AGTTATGAACTTAAAAGAAAA
442943 AAGGTGCCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
64 10 0.19
65 35 0.66
66 8 0.15
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (64 bp):
CCACAGAGTTATGGATTTAAAAGAAAAAAGGTGCCATAGAGTTATGAACTTAAAAGAAAAGGTT
Found at i:444015 original size:221 final size:221
Alignment explanation
Indices: 443632--444075 Score: 888
Period size: 221 Copynumber: 2.0 Consensus size: 221
443622 TTTTTTTTTA
443632 CAAAAGGCTTATTTGACAATAAAAATATATGGTTTGATTTATTTCTGACAAGAAAAGCAAACAAA
1 CAAAAGGCTTATTTGACAATAAAAATATATGGTTTGATTTATTTCTGACAAGAAAAGCAAACAAA
443697 ACGGTCTGGTGACTGGAAAAGTGATGTAATTTTGGATCATTGATGCCATTGATAATTATGACACG
66 ACGGTCTGGTGACTGGAAAAGTGATGTAATTTTGGATCATTGATGCCATTGATAATTATGACACG
443762 AATGTTTTTCTGATGCCTCTCGAGATCTTTCCCGAATAATCAACCTGATCGGTATAAGTCAACCT
131 AATGTTTTTCTGATGCCTCTCGAGATCTTTCCCGAATAATCAACCTGATCGGTATAAGTCAACCT
443827 TAGAGGCCGTTAAGATTTCCCTGTGT
196 TAGAGGCCGTTAAGATTTCCCTGTGT
443853 CAAAAGGCTTATTTGACAATAAAAATATATGGTTTGATTTATTTCTGACAAGAAAAGCAAACAAA
1 CAAAAGGCTTATTTGACAATAAAAATATATGGTTTGATTTATTTCTGACAAGAAAAGCAAACAAA
443918 ACGGTCTGGTGACTGGAAAAGTGATGTAATTTTGGATCATTGATGCCATTGATAATTATGACACG
66 ACGGTCTGGTGACTGGAAAAGTGATGTAATTTTGGATCATTGATGCCATTGATAATTATGACACG
443983 AATGTTTTTCTGATGCCTCTCGAGATCTTTCCCGAATAATCAACCTGATCGGTATAAGTCAACCT
131 AATGTTTTTCTGATGCCTCTCGAGATCTTTCCCGAATAATCAACCTGATCGGTATAAGTCAACCT
444048 TAGAGGCCGTTAAGATTTCCCTGTGT
196 TAGAGGCCGTTAAGATTTCCCTGTGT
444074 CA
1 CA
444076 TTCTATATTT
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 223 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (221 bp):
CAAAAGGCTTATTTGACAATAAAAATATATGGTTTGATTTATTTCTGACAAGAAAAGCAAACAAA
ACGGTCTGGTGACTGGAAAAGTGATGTAATTTTGGATCATTGATGCCATTGATAATTATGACACG
AATGTTTTTCTGATGCCTCTCGAGATCTTTCCCGAATAATCAACCTGATCGGTATAAGTCAACCT
TAGAGGCCGTTAAGATTTCCCTGTGT
Found at i:444447 original size:26 final size:27
Alignment explanation
Indices: 444418--444471 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
444408 TGCTTTTGCC
444418 TTTGTACTTTTTTTCATTTTT-CTTTT
1 TTTGTACTTTTTTTCATTTTTACTTTT
* **
444444 TTTGTGCTTTTTTTTTTTTTTACTTTT
1 TTTGTACTTTTTTTCATTTTTACTTTT
444471 T
1 T
444472 CAGCATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.80
Consensus pattern (27 bp):
TTTGTACTTTTTTTCATTTTTACTTTT
Found at i:444469 original size:16 final size:16
Alignment explanation
Indices: 444425--444472 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
444415 GCCTTTGTAC
444425 TTTTTTTCATTTTTCTT
1 TTTTTTTC-TTTTTCTT
*
444442 TTTTTGTGCTTTTT-TT
1 TTTTT-TTCTTTTTCTT
444458 TTTTTTTACTTTTTC
1 TTTTTTT-CTTTTTC
444473 AGCATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
17 10 0.38
18 2 0.08
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTCTT
Found at i:446292 original size:27 final size:27
Alignment explanation
Indices: 446254--446308 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
446244 TCTGTCAAAC
446254 TATGTTGAAAGTAATGGATAAGGAGTT
1 TATGTTGAAAGTAATGGATAAGGAGTT
446281 TATGTTGAAAGTAATGGATAAGGAGTT
1 TATGTTGAAAGTAATGGATAAGGAGTT
446308 T
1 T
446309 CTCATCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.35
Consensus pattern (27 bp):
TATGTTGAAAGTAATGGATAAGGAGTT
Found at i:452933 original size:14 final size:16
Alignment explanation
Indices: 452904--452935 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
452894 GGTTAAAATC
452904 AATTGTAGACAAAGTT
1 AATTGTAGACAAAGTT
452920 AATTGTA-A-AAAGTT
1 AATTGTAGACAAAGTT
452934 AA
1 AA
452936 CATTTTAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (16 bp):
AATTGTAGACAAAGTT
Found at i:453508 original size:19 final size:21
Alignment explanation
Indices: 453465--453514 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
453455 TAACAATTTA
453465 TATCGATACAAACAGTAAATG
1 TATCGATACAAACAGTAAATG
* *
453486 TATCGATACATA-AGT-ATTG
1 TATCGATACAAACAGTAAATG
453505 TATCGATACA
1 TATCGATACA
453515 GTATATCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 11 0.41
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
TATCGATACAAACAGTAAATG
Found at i:453642 original size:20 final size:19
Alignment explanation
Indices: 453617--453690 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
453607 TTTACCCAGA
*
453617 TGTATCAATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
453637 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
453657 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
*
453677 TGTATTGATACATT
1 TGTATCGATACATT
453691 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:463316 original size:33 final size:33
Alignment explanation
Indices: 463271--463336 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
463261 AAATTCCCAG
*
463271 ATGTATCGATACAAAGA-TCAATGTATCGATACA
1 ATGTATCAATACAAAGAGT-AATGTATCGATACA
**
463304 ATGTATCAATACATTGAGTAATGTATCGATACA
1 ATGTATCAATACAAAGAGTAATGTATCGATACA
463337 TTCCCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCAATACAAAGAGTAATGTATCGATACA
Found at i:463406 original size:32 final size:31
Alignment explanation
Indices: 463355--463433 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 31
463345 GCAGTAGCTT
* *
463355 TGTAGTGATACATTGTATCGATACAACACTTA
1 TGTA-TGATACATTTTATCGATACAAAACTTA
463387 TGTACTGATACATTTTATCGATACAAAACTTA
1 TGTA-TGATACATTTTATCGATACAAAACTTA
463419 TGTATCGATACATTT
1 TGTAT-GATACATTT
463434 ACTGTTTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 1 0.02
32 42 0.98
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (31 bp):
TGTATGATACATTTTATCGATACAAAACTTA
Found at i:463426 original size:19 final size:19
Alignment explanation
Indices: 463368--463453 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 19
463358 AGTGATACAT
*
463368 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
463387 TGTA-CTGATAC---A-TT-
1 TGTATC-GATACAAAACTTA
463401 T-TATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
** *
463419 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACT-TA
463440 TGTATCGATACAAA
1 TGTATCGATACAAA
463454 TTGTTGAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
13 7 0.13
14 2 0.04
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 19 0.37
20 3 0.06
21 13 0.25
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:469612 original size:24 final size:24
Alignment explanation
Indices: 469584--469631 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
469574 CGGACGGTGT
469584 TCATCTTCTGCTTCTACTTGATGA
1 TCATCTTCTGCTTCTACTTGATGA
*
469608 TCATCTTTTGCTTCTACTTGATGA
1 TCATCTTCTGCTTCTACTTGATGA
469632 GCTTCATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.12, T:0.48
Consensus pattern (24 bp):
TCATCTTCTGCTTCTACTTGATGA
Found at i:470173 original size:12 final size:12
Alignment explanation
Indices: 470156--470181 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
470146 TTTATATTAA
470156 ATATATATTTAC
1 ATATATATTTAC
470168 ATATATATTTAC
1 ATATATATTTAC
470180 AT
1 AT
470182 CAAAATTTAC
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:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATATTTAC
Found at i:470813 original size:30 final size:31
Alignment explanation
Indices: 470757--470835 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 31
470747 TATCAATGAA
*
470757 TAAAACCTCAAACAATATAAATTAGGCAATC
1 TAAAACCTCAAACAATATAAAGTAGGCAATC
* *
470788 TAAAA-CTCAACCAATCTAAAGTAGGCAATC
1 TAAAACCTCAAACAATATAAAGTAGGCAATC
***
470818 TAAATTATCAAACAATAT
1 TAAAACCTCAAACAATAT
470836 GTTTTCTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 26 0.65
31 14 0.35
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.24
Consensus pattern (31 bp):
TAAAACCTCAAACAATATAAAGTAGGCAATC
Found at i:472144 original size:12 final size:12
Alignment explanation
Indices: 472124--472161 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
472114 TTTAAAAATT
*
472124 TATAT-TTTATA
1 TATATATTTAAA
472135 TATATATTTAAA
1 TATATATTTAAA
472147 TATATA-TTAAA
1 TATATATTTAAA
472158 TATA
1 TATA
472162 AATATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATATTTAAA
Found at i:472149 original size:14 final size:14
Alignment explanation
Indices: 472112--472153 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
472102 ATTTTTTATT
* *
472112 TATTTAAAAATTTA
1 TATTTAAATATATA
*
472126 TATTT-TATATATA
1 TATTTAAATATATA
472139 TATTTAAATATATA
1 TATTTAAATATATA
472153 T
1 T
472154 TAAATATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTTAAATATATA
Found at i:472374 original size:25 final size:24
Alignment explanation
Indices: 472346--472392 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
472336 ATTGTGGTGA
* *
472346 TGCCTATGCCAATGCCCGGTGCCGG
1 TGCCGATGCCAAT-CCCAGTGCCGG
*
472371 TGCCGGTGCCAATCCCAGTGCC
1 TGCCGATGCCAATCCCAGTGCC
472393 AGACAACATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.13, C:0.38, G:0.30, T:0.19
Consensus pattern (24 bp):
TGCCGATGCCAATCCCAGTGCCGG
Found at i:472879 original size:22 final size:22
Alignment explanation
Indices: 472854--472903 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
472844 TGTTATATAC
472854 TTATATGATATTTACATTAT-TT
1 TTATATGATA-TTACATTATATT
* *
472876 TTATATTATATTATATTATATT
1 TTATATGATATTACATTATATT
472898 TTATAT
1 TTATAT
472904 AAAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATATGATATTACATTATATT
Found at i:472922 original size:37 final size:37
Alignment explanation
Indices: 472881--472955 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
472871 TATTTTTATA
*
472881 TTATATTATATT-ATATTTTATATAAAA-TATTAATTTT
1 TTATATTATATTCA-A-TTTATATAAAATTATTAAATTT
* *
472918 TTATATTCTATTCAATTTATTTAAAATTATTAAATTT
1 TTATATTATATTCAATTTATATAAAATTATTAAATTT
472955 T
1 T
472956 ATACCATACC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 10 0.30
37 22 0.67
38 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (37 bp):
TTATATTATATTCAATTTATATAAAATTATTAAATTT
Found at i:474211 original size:18 final size:18
Alignment explanation
Indices: 474172--474213 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
474162 AGTCTCAGTT
*
474172 GAAGAAGAAGATGTCGAA
1 GAAGAAGAAGATGTCAAA
*
474190 GAAGAAGGAGATG-CAAA
1 GAAGAAGAAGATGTCAAA
474207 GGAAGAA
1 -GAAGAA
474214 TTAGAAGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.52, C:0.05, G:0.36, T:0.07
Consensus pattern (18 bp):
GAAGAAGAAGATGTCAAA
Found at i:474378 original size:2 final size:2
Alignment explanation
Indices: 474371--474406 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
474361 TTCCTTCTTT
*
474371 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
474407 GTGATGAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:476105 original size:8 final size:8
Alignment explanation
Indices: 476079--476180 Score: 59
Period size: 8 Copynumber: 11.9 Consensus size: 8
476069 TTATTATAAT
476079 TATATTTA
1 TATATTTA
*
476087 -AAATATTA
1 TATAT-TTA
476095 TATATTTA
1 TATATTTA
476103 TATAAATTT-
1 TAT--ATTTA
476112 TAATATATTA
1 T-ATAT-TTA
476122 -ATATTT-
1 TATATTTA
476128 TATATTATA
1 TATATT-TA
*
476137 TAAATTTCAA
1 TATATTT--A
476147 TATATTTA
1 TATATTTA
476155 TATATTTAAA
1 TATATTT--A
476165 TAATATTTA
1 T-ATATTTA
476174 TATATTT
1 TATATTT
476181 TAATTATTTG
Statistics
Matches: 75, Mismatches: 4, Indels: 30
0.69 0.04 0.28
Matches are distributed among these distances:
7 10 0.13
8 31 0.41
9 13 0.17
10 15 0.20
11 6 0.08
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (8 bp):
TATATTTA
Found at i:476113 original size:27 final size:27
Alignment explanation
Indices: 476083--476179 Score: 90
Period size: 32 Copynumber: 3.4 Consensus size: 27
476073 TATAATTATA
*
476083 TTTAAAATATTATATATTTATATAAAT
1 TTTAATATATTATATATTTATATAAAT
476110 TTTAATATATTAATATTTTATATTATATAAAT
1 TTTAATATATT-ATA---TAT-TTATATAAAT
* *
476142 TTCAATATATTTATATATTTAAAT-AAT
1 TTTAATATA-TTATATATTTATATAAAT
476169 ATTT-ATATATT
1 -TTTAATATATT
476180 TTAATTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
26 2 0.03
27 18 0.31
28 10 0.17
29 3 0.05
31 3 0.05
32 21 0.36
33 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTAATATATTATATATTTATATAAAT
Found at i:476113 original size:42 final size:40
Alignment explanation
Indices: 476049--476127 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 40
476039 TTCACTATTT
** *
476049 ATATTATATTTTATAATTTTTTATTATAATT-ATATTTAAA
1 ATATTATATTTTATAAAATTTTAATAT-ATTAATATTTAAA
476089 ATATTATATATTTATATAAATTTTAATATATTAATATTT
1 ATATTATAT-TTTATA-AAATTTTAATATATTAATATTT
476128 TATATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 9 0.27
41 9 0.27
42 15 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (40 bp):
ATATTATATTTTATAAAATTTTAATATATTAATATTTAAA
Found at i:476133 original size:40 final size:39
Alignment explanation
Indices: 476046--476138 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 39
476036 TTTTTCACTA
** *
476046 TTTATATTATAT-TTTATAATTTTTTATTATAATTATAT
1 TTTATATTATATATTTATAAAATTTTAATATAATTATAT
*
476084 TTAAAATATTATATATTTATATAAATTTTAATAT-ATTAATAT
1 TT--TATATTATATATTTATA-AAATTTTAATATAATT-ATAT
476126 TTTATATTATATA
1 TTTATATTATATA
476139 AATTTCAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
38 2 0.04
40 19 0.42
41 9 0.20
42 15 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (39 bp):
TTTATATTATATATTTATAAAATTTTAATATAATTATAT
Found at i:476141 original size:32 final size:33
Alignment explanation
Indices: 476088--476162 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 33
476078 TTATATTTAA
* *
476088 AATATTATATATTTATATAAATTTTAATATATT
1 AATATTTTATATTTATATAAATTTCAATATATT
476121 AATATTTTATA-TTATATAAATTTCAATATATT
1 AATATTTTATATTTATATAAATTTCAATATATT
*
476153 TATATATTTA
1 AATAT-TTTA
476163 AATAATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 24 0.63
33 14 0.37
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
AATATTTTATATTTATATAAATTTCAATATATT
Found at i:476180 original size:27 final size:26
Alignment explanation
Indices: 476079--476180 Score: 83
Period size: 27 Copynumber: 4.0 Consensus size: 26
476069 TTATTATAAT
476079 TATATTT-AA-AATATTATATATTTA
1 TATATTTAAATAATATTATATATTTA
*
476103 TATAAATTTTAAT-ATATTA-ATATTT-
1 TAT--ATTTAAATAATATTATATATTTA
*
476128 TATA-TTATATAA-ATTTCAATATATTTA
1 TATATTTAAATAATA-TT--ATATATTTA
476155 TATATTTAAATAATATTTATATATTT
1 TATATTTAAATAATA-TTATATATTT
476181 TAATTATTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
22 5 0.08
23 4 0.06
24 3 0.05
25 4 0.06
26 16 0.25
27 20 0.32
28 7 0.11
29 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (26 bp):
TATATTTAAATAATATTATATATTTA
Found at i:476195 original size:19 final size:19
Alignment explanation
Indices: 476079--476180 Score: 72
Period size: 19 Copynumber: 5.4 Consensus size: 19
476069 TTATTATAAT
476079 TATATTT-AA-AATA-TTA
1 TATATTTAAATAATATTTA
*
476095 TATATTTATATAA-ATTT-
1 TATATTTAAATAATATTTA
*
476112 TAATATATTAATATTTTATATTATA
1 T-ATAT-TTAA-A--TAATATT-TA
* *
476137 TAAATTTCAAT-ATATTTA
1 TATATTTAAATAATATTTA
476155 TATATTTAAATAATATTTA
1 TATATTTAAATAATATTTA
476174 TATATTT
1 TATATTT
476181 TAATTATTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
16 7 0.10
17 3 0.04
18 19 0.28
19 22 0.33
20 2 0.03
22 3 0.04
23 6 0.09
24 4 0.06
25 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTTAAATAATATTTA
Found at i:476204 original size:17 final size:17
Alignment explanation
Indices: 476047--476204 Score: 55
Period size: 17 Copynumber: 9.2 Consensus size: 17
476037 TTTTCACTAT
*
476047 TTATATTATATTTTATAA
1 TTAT-TTATATATTATAA
* * *
476065 TTTTTTAT-TATAATTA
1 TTATTTATATATTATAA
*
476081 -TATTTAAAATATTAT-A
1 TTATTT-ATATATTATAA
*
476097 -TATTTATATAAATTTTAA
1 TTATTTATAT--ATTATAA
* *
476115 TATATTAATATTTTAT-A
1 T-TATTTATATATTATAA
*
476132 TTA--TATAAATT-TCAA
1 TTATTTATATATTAT-AA
476147 TATATTTATATATT-TAAA
1 T-TATTTATATATTAT-AA
*
476165 TAATATTTATATATTTTAA
1 T--TATTTATATATTATAA
* *
476184 TTATTTGTATATTATAT
1 TTATTTATATATTATAA
476201 TTAT
1 TTAT
476205 AGAATATCTA
Statistics
Matches: 106, Mismatches: 20, Indels: 29
0.68 0.13 0.19
Matches are distributed among these distances:
13 1 0.01
14 5 0.05
15 9 0.08
16 16 0.15
17 32 0.30
18 18 0.17
19 16 0.15
20 9 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TTATTTATATATTATAA
Found at i:477353 original size:22 final size:20
Alignment explanation
Indices: 477328--477372 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
477318 TAATTCTTAA
* *
477328 TTTTTAATTTATATTAGAAAT
1 TTTTTAATGTAAATTA-AAAT
477349 TTTTTACATGTAAATTAAAAT
1 TTTTTA-ATGTAAATTAAAAT
477370 TTT
1 TTT
477373 ATTTAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTAATGTAAATTAAAAT
Found at i:477854 original size:37 final size:40
Alignment explanation
Indices: 477799--477873 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
477789 GTTTAACGAC
* *
477799 TTAAATTATTATT-AAA-A-TAATAAAAAATTATTTTTAT
1 TTAAATTATAATTAAAATATTAATAAAAAAATATTTTTAT
477836 TTAAATT-TAATTATAAATATTAATAAAAAAATATTTTT
1 TTAAATTATAATTA-AAATATTAATAAAAAAATATTTTT
477874 TAATAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 4 0.12
37 7 0.22
38 3 0.09
39 1 0.03
40 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
TTAAATTATAATTAAAATATTAATAAAAAAATATTTTTAT
Found at i:478895 original size:14 final size:14
Alignment explanation
Indices: 478873--478902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
478863 TATTTAAATA
478873 ATATAAATATTTTT
1 ATATAAATATTTTT
*
478887 ATATTAATATTTTT
1 ATATAAATATTTTT
478901 AT
1 AT
478903 TTTTTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATAAATATTTTT
Found at i:480551 original size:20 final size:19
Alignment explanation
Indices: 480504--480552 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
480494 GCAAAGTATG
*
480504 CAAAGAAAGAGAAAAAATA
1 CAAAGAAATAGAAAAAATA
* *
480523 CAAATAAATAGAGAAAATAA
1 CAAAGAAATAGAAAAAAT-A
*
480543 TAAAGAAATA
1 CAAAGAAATA
480553 AATTATGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.12
Consensus pattern (19 bp):
CAAAGAAATAGAAAAAATA
Found at i:481029 original size:20 final size:21
Alignment explanation
Indices: 481001--481073 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
480991 TTCAACAATT
*
481001 TGTATCGATACAATAAGTGAA
1 TGTATCGATACAATAAGTAAA
481022 TG-ATCGATAC-ATAAGTAAA
1 TGTATCGATACAATAAGTAAA
* * ***
481041 TGTATTGATACATTTTTTAAA
1 TGTATCGATACAATAAGTAAA
481062 TGTATCGATACA
1 TGTATCGATACA
481074 TGATCGTGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.23
20 15 0.35
21 18 0.42
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (21 bp):
TGTATCGATACAATAAGTAAA
Found at i:481171 original size:50 final size:50
Alignment explanation
Indices: 481109--481251 Score: 162
Period size: 50 Copynumber: 2.8 Consensus size: 50
481099 TCTGGAATGA
*
481109 AAATGTATTGATACATTCTTCATTGTATCGATGCATTCAGGGTTTT-AACCC
1 AAATGTA-TGATACATTCTTCATTGTATCGATACATTCAGGGTTTTGAA-CC
* * ** *
481160 AAATGTATGATACATTTTTCATTGTATCAATACATTTTGAGTTTTTGAACC
1 AAATGTATGATACATTCTTCATTGTATCGATACATTCAG-GGTTTTGAACC
* * *
481211 AAATGTATCGATTCATTCTTCAATGTATCGATACATGCAGG
1 AAATGTAT-GATACATTCTTCATTGTATCGATACATTCAGG
481252 CAATTTTACA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
50 27 0.36
51 23 0.30
52 26 0.34
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (50 bp):
AAATGTATGATACATTCTTCATTGTATCGATACATTCAGGGTTTTGAACC
Found at i:483410 original size:8 final size:8
Alignment explanation
Indices: 483397--483421 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
483387 CTCCAATCCC
483397 ACTTTTAA
1 ACTTTTAA
483405 ACTTTTAA
1 ACTTTTAA
483413 ACTTTTAA
1 ACTTTTAA
483421 A
1 A
483422 TCTTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (8 bp):
ACTTTTAA
Found at i:486945 original size:62 final size:62
Alignment explanation
Indices: 486869--487678 Score: 765
Period size: 62 Copynumber: 13.2 Consensus size: 62
486859 TTTTAGCTCG
* * *
486869 TTAGTCCTCAAAGAGCAAGACGTCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGACACCCT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * ** * * **
486931 TTAGTCCTCAAAGAGCAAGACACCTTTTTTCTTTTCAAAACCCCACATAAGCTAGTGGCACATTT
1 TTAGTCCTCAAAGAGCAAGACGCC-TTTTTCTTTTC-AAAGCCCACACGAGTTGGTGGCAC-CCT
* * ** *
486996 TTAGTCCTCAAAGAGCAAGACGTCTTTTTCTTTTTAAAGCCTGCACGAGTTGGTGGAACCCT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * * * * * *
487058 GTAGTCCTCAAAAAGTAGGACACCTTTTTGTTTTCAAAGCCCACACGAATTGGTGGCACCCT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * ** * * *
487120 TTAGTCCTCAAAAAGCAGGACATCTTTTTCTTTTTAAATCCCACACGAGTTGGTGGCCCCCTT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC-T
* * * * *
487183 TTA-TCCTAAAAGAGTAAGACGCCTTTTTCTTTTCAAAACTCACACGAGTTTGTGGCACCCT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * * *
487244 TTAGTCCTCAAAGAGCAAGATGCCTTTTTTTTTTCAAAGCCCACACGAGTTGGTAGC-CTCTT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CCT
* * * * * *
487306 TTTGTCCTCAAAAAACAAGACACCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCCT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * * * * *
487368 TTAGTCCTTAAAGAGTAGGATGTCTTTTTCTTTTCAAAGCCCACGCGAGTTGGTGGC-CCCTT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC-T
* * * * * *
487430 TTTGTCCT--TA-A--AA-A-G-C-ATCT-TTTTCAAAGCCTACACAAGTTGGTGGCACCCT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * * * *
487482 TTAGTCCTCAAAGAGTAGGGCGCCTTTTT-TTTTCAAAGCCCACATGAATTGGTGGC-CCCAT
1 TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC-T
* * *
487543 TTTGTCCTCAAAGAGCAAGACGCAC-TTTTCTTTTCAAAGCCCACACGAGTTAGTGGCACCTT
1 TTAGTCCTCAAAGAGCAAGACGC-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* * ** * **
487605 TTAGTCCTCAAAGAAG-ATGACGCC-TTTTCTTTTAAAAGCCCACACGAGTTAATGGTACTTT
1 TTAGTCCTCAAAG-AGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
487666 TTAGTCCTCAAAG
1 TTAGTCCTCAAAG
487679 TTCAGGACAC
Statistics
Matches: 609, Mismatches: 116, Indels: 47
0.79 0.15 0.06
Matches are distributed among these distances:
52 32 0.05
53 5 0.01
54 2 0.00
55 2 0.00
56 1 0.00
57 2 0.00
59 2 0.00
60 5 0.01
61 104 0.17
62 366 0.60
63 36 0.06
64 29 0.05
65 23 0.04
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (62 bp):
TTAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT
Found at i:487478 original size:114 final size:112
Alignment explanation
Indices: 487334--487651 Score: 350
Period size: 123 Copynumber: 2.7 Consensus size: 112
487324 GACACCTTTT
* * *
487334 TCTTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTTAAAGAGTAGGATGTCTTTTTCT
1 TCTTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCTTTTT-T
* * * *
487399 TTTCAAAGCCCACGCGAGTTGGTGGCCCCTTTTTGTCCTTAAAAAGCA
65 TTTCAAAGCCCACACGAATTGGTGGCCCCATTTTGTCCTCAAAAAGCA
* *
487447 TCTTTTTCAAAGCCTACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGGCGCCTTTTTT
1 TCTTTTT-AAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCTTTTTT
*
487512 TTTCAAAGCCCACATGAATTGGTGGCCCCATTTTGTCCTCAAAGAGCAAGACGCA
65 TTTCAAAGCCCACACGAATTGGTGGCCCCATTTTGTCCTC--A-A--AA-A-GCA
* * * * *
487567 CTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCACCTTTTAGTCCTCAAAGAAG-ATGACGCCTT
1 ----TCTTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAG-AGTAGGACGCCTT
* *
487631 TTCTTTTAAAAGCCCACACGA
61 TTTTTTTCAAAGCCCACACGA
487652 GTTAATGGTA
Statistics
Matches: 172, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
113 43 0.25
114 51 0.30
115 1 0.01
116 1 0.01
118 2 0.01
119 1 0.01
120 3 0.02
123 62 0.36
124 8 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (112 bp):
TCTTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCTTTTTTT
TTCAAAGCCCACACGAATTGGTGGCCCCATTTTGTCCTCAAAAAGCA
Found at i:487668 original size:61 final size:62
Alignment explanation
Indices: 487450--487678 Score: 223
Period size: 61 Copynumber: 3.7 Consensus size: 62
487440 AAAAGCATCT
* * * ** * * * * *
487450 TTTTCAAAGCCTACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGGCGC-CTTTTT
1 TTTTAAAAGCCCACACGAGTTAATGGCACCTTTTAGTCCTCAAAGAGCAAGACGCACTTTTC
* * * ** *
487511 TTTTCAAAGCCCACATGAATTGGTGGCCCCATTTT-GTCCTCAAAGAGCAAGACGCACTTTTC
1 TTTTAAAAGCCCACACGAGTTAATGGCACC-TTTTAGTCCTCAAAGAGCAAGACGCACTTTTC
* * *
487573 TTTTCAAAGCCCACACGAGTTAGTGGCACCTTTTAGTCCTCAAAGAAG-ATGACGC-CTTTTC
1 TTTTAAAAGCCCACACGAGTTAATGGCACCTTTTAGTCCTCAAAG-AGCAAGACGCACTTTTC
* *
487634 TTTTAAAAGCCCACACGAGTTAATGGTACTTTTTAGTCCTCAAAG
1 TTTTAAAAGCCCACACGAGTTAATGGCACCTTTTAGTCCTCAAAG
487679 TTCAGGACAC
Statistics
Matches: 145, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
61 93 0.64
62 50 0.34
63 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (62 bp):
TTTTAAAAGCCCACACGAGTTAATGGCACCTTTTAGTCCTCAAAGAGCAAGACGCACTTTTC
Found at i:487673 original size:123 final size:123
Alignment explanation
Indices: 487450--487678 Score: 291
Period size: 123 Copynumber: 1.9 Consensus size: 123
487440 AAAAGCATCT
* * * *
487450 TTTTCAAAGCCTACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGGCGCCTTTTTTTTT
1 TTTTCAAAGCCCACACAAGTTAGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCTTTTCTTTT
* * ** *
487515 CAAAGCCCACATGAATTGGTGGCCCCATTTTGTCCTCAAAGAGCAAGACGCACTTTTC
66 AAAAGCCCACACGAATTAATGGCCACATTTTGTCCTCAAAGAGCAAGACGCACTTTTC
* * *
487573 TTTTCAAAGCCCACACGAGTTAGTGGCACCTTTTAGTCCTCAAAGAAG-ATGACGCCTTTTCTTT
1 TTTTCAAAGCCCACACAAGTTAGTGGCACCCTTTAGTCCTCAAAG-AGTAGGACGCCTTTTCTTT
* * *
487637 TAAAAGCCCACACGAGTTAATGG-TACTTTTTAGTCCTCAAAG
65 TAAAAGCCCACACGAATTAATGGCCACATTTT-GTCCTCAAAG
487679 TTCAGGACAC
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
122 5 0.06
123 82 0.92
124 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (123 bp):
TTTTCAAAGCCCACACAAGTTAGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCTTTTCTTTT
AAAAGCCCACACGAATTAATGGCCACATTTTGTCCTCAAAGAGCAAGACGCACTTTTC
Found at i:487791 original size:43 final size:42
Alignment explanation
Indices: 487669--488070 Score: 456
Period size: 42 Copynumber: 9.5 Consensus size: 42
487659 GTACTTTTTA
** * *
487669 GTCCTCAAAGTTCAGGACACATTTTATTTCCTTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTCCTTT
* * *
487711 ATCCTCATAGAGTAGGACACACTTT-ATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACA-TTTCATTTCCTTTTTTCCTTT
* *
487753 GTCCTCAAAGAGCAAGACACATTTCATTTCCTCCTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCT-TTTTTCCTTT
* * *
487796 ATCCTCAAAGAGTAGGACACATTTTATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTCCTTT
* * *
487838 GTCCTCAAAGAGCAAGACACATTTCATTTACTCATTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCT-TTTTTCCTTT
* * *
487881 ATCCTCAAAGAGCAAGATACATTTCATTTCCTTATTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTT-TTTT-CCTTT
487925 GTCCTCAAAGAGCAGGACGTAC-TTT-ATTT-CTTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGAC--ACATTTCATTTCCTTTTT-TCCTTT
*
487967 GTCCTCAAAGAGCATGACACAGTTT-ATTTCCTTCTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACA-TTTCATTTCCTT-TTTTCCTTT
* * *
488010 GTCCTCAAAAAGCAGGACACACTTCATTTCCTTTTATCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTCCTTT
*
488052 GTCCTCGAAA-AGTAGGACA
1 GTCCTC-AAAGAGCAGGACA
488071 TACTGTTTTT
Statistics
Matches: 310, Mismatches: 35, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 148 0.48
43 125 0.40
44 27 0.09
45 3 0.01
46 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTCCTTT
Found at i:487822 original size:85 final size:84
Alignment explanation
Indices: 487669--488070 Score: 481
Period size: 85 Copynumber: 4.7 Consensus size: 84
487659 GTACTTTTTA
** * * *
487669 GTCCTCAAAGTTCAGGACACATTTTATTTCCTTTTTCCCTTTATCCTCATAGAGTAGGACACACT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTT-CCTTTATCCTCAAAGAGTAGGACACATT
487734 TTATTTCCTT-TTTTCCTTT
65 TTATTTCCTTATTTTCCTTT
*
487753 GTCCTCAAAGAGCAAGACACATTTCATTTCCTCCTTTTCCTTTATCCTCAAAGAGTAGGACACAT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCT--TTTTCCTTTATCCTCAAAGAGTAGGACACAT
487818 TTTATTTCCTT-TTTTCCTTT
64 TTTATTTCCTTATTTTCCTTT
* * * * *
487838 GTCCTCAAAGAGCAAGACACATTTCATTTACTCATTTTCCTTTATCCTCAAAGAGCAAGATACAT
1 GTCCTCAAAGAGCAGGACACATTTCATTT-C-CTTTTTCCTTTATCCTCAAAGAGTAGGACACAT
*
487903 TTCATTTCCTTATTTTCCCTTT
64 TTTATTTCCTTATTTT-CCTTT
* * * *
487925 GTCCTCAAAGAGCAGGACGTAC-TTT-ATTTCTTTTTCTCCTTTGTCCTCAAAGAGCATGACACA
1 GTCCTCAAAGAGCAGGAC--ACATTTCATTTCCTTTT-TCCTTTATCCTCAAAGAGTAGGACACA
* *
487988 GTTTATTTCCTTCTTTTCCTTT
63 TTTTATTTCCTTATTTTCCTTT
* * *
488010 GTCCTCAAAAAGCAGGACACACTTCATTTCCTTTTATCCTTTGTCCTCGAAA-AGTAGGACA
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTT-TCCTTTATCCTC-AAAGAGTAGGACA
488071 TACTGTTTTT
Statistics
Matches: 280, Mismatches: 26, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
83 2 0.01
84 30 0.11
85 165 0.59
86 51 0.18
87 27 0.10
88 3 0.01
89 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (84 bp):
GTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTCCTTTATCCTCAAAGAGTAGGACACATTT
TATTTCCTTATTTTCCTTT
Found at i:488169 original size:7 final size:7
Alignment explanation
Indices: 488157--488181 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
488147 CATTTCATTT
488157 TCCTTTG
1 TCCTTTG
488164 TCCTTTG
1 TCCTTTG
488171 TCCTTTG
1 TCCTTTG
488178 TCCT
1 TCCT
488182 CAAAGAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.12, T:0.56
Consensus pattern (7 bp):
TCCTTTG
Found at i:490871 original size:24 final size:21
Alignment explanation
Indices: 490828--490875 Score: 51
Period size: 24 Copynumber: 2.1 Consensus size: 21
490818 CATCAGATGC
**
490828 TTTTTTTAGAATTTTTTGAACA
1 TTTTTTTAGAATTTCATGAA-A
490850 TTTTTCTTAAGAATTTCATGAAA
1 TTTTT-TT-AGAATTTCATGAAA
490873 TTT
1 TTT
490876 CCTTTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
24 11 0.50
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (21 bp):
TTTTTTTAGAATTTCATGAAA
Found at i:491525 original size:79 final size:79
Alignment explanation
Indices: 491347--491801 Score: 478
Period size: 79 Copynumber: 5.8 Consensus size: 79
491337 TGAATTGATG
*
491347 TTTTATTTCTAAAACATCGATTTTCCACCATCG-GAGATACTCCAA-CCCGTTATTTCTCAGGGG
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAG-GATACTCCAACCCCGTTATTTCTGAGGGG
* *
491410 AT-GTCCAACCC-CA
65 ATACTCCAACCCTGA
* * * *
491423 GTTTTATTTCTAAAATATCGATTTTTCACCATCGAGGATACTTCAACCCCGTTATTTCTTAGGGG
1 -TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGG
*
491488 ATACTCCAACTCTGA
65 ATACTCCAACCCTGA
* * * * * * *
491503 TTTTATTTCTAAAACATTGATTTTTCACCATCAAGGATACTCCGACCCCGTTATTTCCGAAGAGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGA
*
491568 TACTCAAACCCTGA
66 TACTCCAACCCTGA
* * * * * * **
491582 TTTTATTTTTAAAACATCGATTTTCCACCATCGGGGGTACTCCAATCCTGTTATTTCTAATTGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGA
* *
491647 CACTCCAACTCCAG-
66 TACTCCAAC-CCTGA
* * *
491661 TTTTATTTCTAAAATATCGATTTTCCACCATC-AGGGATACTCCAACCCCATTATTT-TCGA-AG
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGA-GGATACTCCAACCCCGTTATTTCT-GAGGG
*
491723 GATACTCTAACCCTGA
64 GATACTCCAACCCTGA
* * * * *
491739 TTTTATTTCTAAAACA-CTAATTTTCTACCATCGGGGATAATCCAACCCCGTTATCTCTGAGGG
1 TTTTATTTCTAAAACATC-GATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGG
491802 AACATTCCGA
Statistics
Matches: 311, Mismatches: 55, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
77 44 0.14
78 79 0.25
79 184 0.59
80 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGA
TACTCCAACCCTGA
Found at i:497008 original size:2 final size:2
Alignment explanation
Indices: 496969--496993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
496959 TTCAACTTTC
496969 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
496994 CTTTCTTTCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:497527 original size:11 final size:11
Alignment explanation
Indices: 497511--497535 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
497501 GAAATAATCA
497511 TTTTATTTTAT
1 TTTTATTTTAT
497522 TTTTATTTTAT
1 TTTTATTTTAT
497533 TTT
1 TTT
497536 ATTCTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:497572 original size:15 final size:15
Alignment explanation
Indices: 497549--497579 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
497539 CTCATAAAAT
497549 AATTATTTTATTTTA
1 AATTATTTTATTTTA
*
497564 AATTTTTTTATTTTA
1 AATTATTTTATTTTA
497579 A
1 A
497580 TTAATCAAAC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
AATTATTTTATTTTA
Found at i:499355 original size:22 final size:22
Alignment explanation
Indices: 499323--499379 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
499313 ATTTTAATTC
*
499323 ATATTATTTT-AATTTAAAAATA
1 ATATAATTTTAAATTTAAAAA-A
* *
499345 ATTTAATTTTAAATTTTAAAAA
1 ATATAATTTTAAATTTAAAAAA
499367 ATATAA-TTTAAAT
1 ATATAATTTTAAAT
499380 AATTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 14 0.47
23 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAATTTTAAATTTAAAAAA
Found at i:499374 original size:15 final size:15
Alignment explanation
Indices: 499356--499406 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
499346 TTTAATTTTA
499356 AATTTTAAAAAATAT
1 AATTTTAAAAAATAT
* *
499371 AA-TTTAAATAATTT
1 AATTTTAAAAAATAT
*
499385 AAATTTAAATTAAATAT
1 AATTTTAAA--AAATAT
499402 AATTT
1 AATTT
499407 ATTTTAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
17 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAAAAAATAT
Found at i:499413 original size:36 final size:35
Alignment explanation
Indices: 499340--499421 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
499330 TTTAATTTAA
*
499340 AAATAATTTAATTTTAAATTTTAAAAAATATAATTT
1 AAATAATTTAAATTTAAA-TTTAAAAAATATAATTT
*
499376 AAATAATTTAAATTTAAA-TTAAATATAAT-TTATTT
1 AAATAATTTAAATTTAAATTTAAA-A-AATATAATTT
*
499411 TAATAATTTAA
1 AAATAATTTAA
499422 CAAAAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 5 0.12
35 16 0.39
36 20 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
AAATAATTTAAATTTAAATTTAAAAAATATAATTT
Found at i:500191 original size:167 final size:167
Alignment explanation
Indices: 499912--500250 Score: 549
Period size: 167 Copynumber: 2.0 Consensus size: 167
499902 AACACTTTCA
*
499912 TTTTGAAGTGACTGGATTTTCTGAGTAAGAAAGAAAATTCTTTCTCATCTATTTTCTTTTCTGCC
1 TTTTGAAGTGACTCGATTTTCTGAGTAAGAAAGAAAATTCTTTCTCATCTATTTTCTTTTCTGCC
* *
499977 AACCACTAATGAAAATATTTTTCCTTTTGGCCTTCCATTCATCCAATCCATCCTTTCAA-ATTTT
66 AACCACTAATGAAAATAATTTTCCTTTTGGCCTCCCATTCATCCAATCCATCCTTTCAATA-TTT
* *
500041 TTACTTTTCTAAGCATATCTTTAGATCGTTCATCTTCC
130 TTACTTTTCTAAGCACATCTTTAGATAGTTCATCTTCC
*
500079 TTTTGAAGTGACTCGATTTTCTGAGTAAGAAAAGAAAATTCTTTCTCATCTCTTTTCTTTTCTGC
1 TTTTGAAGTGACTCGATTTTCTGAGTAAG-AAAGAAAATTCTTTCTCATCTATTTTCTTTTCTGC
*
500144 CAACCACTAATG-AAATAATTTT-CTTTTCGGTCTCCCATTCATCCAATCCATCCTTTCAATATT
65 CAACCACTAATGAAAATAATTTTCCTTTT-GGCCTCCCATTCATCCAATCCATCCTTTCAATATT
* *
500207 TTTACTTTTCTAAGCACATTTTTATATAGTTCATCTTCC
129 TTTACTTTTCTAAGCACATCTTTAGATAGTTCATCTTCC
500246 TTTTG
1 TTTTG
500251 TCAGATTATT
Statistics
Matches: 160, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
166 5 0.03
167 108 0.68
168 47 0.29
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (167 bp):
TTTTGAAGTGACTCGATTTTCTGAGTAAGAAAGAAAATTCTTTCTCATCTATTTTCTTTTCTGCC
AACCACTAATGAAAATAATTTTCCTTTTGGCCTCCCATTCATCCAATCCATCCTTTCAATATTTT
TACTTTTCTAAGCACATCTTTAGATAGTTCATCTTCC
Found at i:500637 original size:10 final size:10
Alignment explanation
Indices: 500608--500693 Score: 51
Period size: 10 Copynumber: 9.1 Consensus size: 10
500598 AATGGTGTAT
500608 TTTTATTATA
1 TTTTATTATA
500618 -TTTA-TATA
1 TTTTATTATA
500626 TTTTATTATA
1 TTTTATTATA
* *
500636 TTTAATGTAAA
1 TTTTAT-TATA
*
500647 TTATATT-TA
1 TTTTATTATA
500656 -TTTA--A-A
1 TTTTATTATA
*
500662 TTTTAATATA
1 TTTTATTATA
* *
500672 TTAATATTTTA
1 TT-TTATTATA
500683 TTTTATTATA
1 TTTTATTATA
500693 T
1 T
500694 AAATTTTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 18
0.66 0.13 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
8 7 0.12
9 10 0.18
10 20 0.36
11 14 0.25
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATTATA
Found at i:500687 original size:21 final size:19
Alignment explanation
Indices: 500661--500701 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
500651 ATTTATTTAA
500661 ATTTTAATATATTAATATTTT
1 ATTTTAATATA-TAA-ATTTT
*
500682 ATTTTATTATATAAATTTT
1 ATTTTAATATATAAATTTT
500701 A
1 A
500702 AAATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATATAAATTTT
Found at i:500740 original size:57 final size:56
Alignment explanation
Indices: 500604--500754 Score: 132
Period size: 57 Copynumber: 2.6 Consensus size: 56
500594 TATCAATGGT
* * *
500604 GTATTTTTATTATATTTATATATTTTATTATATTTAATGTAAATTATATTTATTTAA
1 GTATTTTTATTAT-TTTATTTATTTTATTATATTAAATGTAAAATATATTTATTTAA
* * *
500661 --ATTTTAATATATTAATATTTTATTTTATTATA-TAAATTTTAAAATATATATT-TTTAA
1 GTATTTTTAT-TATT-TTA-TTTATTTTATTATATTAAA-TGTAAAATATAT-TTATTTAA
500718 CGTATTTTTATTATTTTATTTATATTATATT-TATTAA
1 -GTATTTTTATTATTTTATTTAT-TT-TATTATATTAA
500755 TTCATATAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
55 8 0.11
56 8 0.11
57 33 0.44
58 8 0.11
59 11 0.15
60 7 0.09
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (56 bp):
GTATTTTTATTATTTTATTTATTTTATTATATTAAATGTAAAATATATTTATTTAA
Found at i:500743 original size:14 final size:15
Alignment explanation
Indices: 500720--500752 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
500710 ATTTTTAACG
*
500720 TATTTTTATTAT-TT
1 TATTTATATTATATT
500734 TATTTATATTATATT
1 TATTTATATTATATT
500749 TATT
1 TATT
500753 AATTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTATATTATATT
Found at i:508652 original size:21 final size:22
Alignment explanation
Indices: 508599--508656 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
508589 TTATATTTTT
*
508599 TATAATTAAAATTAAA-AAATA
1 TATAATTTAAATTAAATAAATA
*
508620 TATTATTT-AATTAAATAAATA
1 TATAATTTAAATTAAATAAATA
508641 -ATAATTTAAATTAAAT
1 TATAATTTAAATTAAAT
508657 CAAACCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATAATTTAAATTAAATAAATA
Found at i:511737 original size:13 final size:13
Alignment explanation
Indices: 511699--511738 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 13
511689 TATAGATTTT
511699 TAAATA-ATATTA
1 TAAATATATATTA
511711 T-AATATA-A-TA
1 TAAATATATATTA
511721 TAAATATATATTA
1 TAAATATATATTA
511734 TAAAT
1 TAAAT
511739 CAATAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.12
11 11 0.46
12 3 0.12
13 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATATATATTA
Found at i:512554 original size:372 final size:372
Alignment explanation
Indices: 511859--512603 Score: 1222
Period size: 372 Copynumber: 2.0 Consensus size: 372
511849 TATTCAACTA
*
511859 TTATCTCTTTTCCCATTTAAACCTTAGCATGAACCATTACTTATCTGAAAACAAAACACCTAAAT
1 TTATCTCTTTTCCCATTTAAACCTTAGCATCAACCATTACTTATCTGAAAACAAAACACCTAAAT
* ***
511924 TTTTTTTATTTGTCGTCTATTTGTTTACTTCTATTTGTTTTTAAATACCTTTCCTATTTAAAATC
66 TTTTTTTATTTGTCATCTATTTACCTACTTCTATTTGTTTTTAAATACCTTTCCTATTTAAAATC
* * *
511989 TAACAACACATAATTACTTAAGTATGGTGGTAAATCGAATATTTGTAATTTTTTAAATATCTAAA
131 TAACAACACATAATGACTTAAGTATGGTAGTAAATCAAATATTTGTAATTTTTTAAATATCTAAA
512054 CTCAAATCCACTTAATTTATTTGATATATGAAGTCTTTTATAATTCATTTACTATGTGAGTATTG
196 CTCAAATCCACTTAATTTATTTGATATATGAAGTCTTTTATAATTCATTTACTATGTGAGTATTG
* * * *
512119 CTATTTTAATCTAAATCTGATTTAAAGAATAATATTCATCGAATATCCAAATCCATTAAATATTT
261 CTATTTTAATCTAAATCCGATTTAAAGAACAATATTCATAGAATATCCAAATCCATAAAATATTT
*
512184 AAGTTTATTAAATCAAATTTTTAAAAATATAAAAATCAAACAATAAC
326 AAATTTATTAAATCAAATTTTTAAAAATATAAAAATCAAACAATAAC
* * * *
512231 TTATCTTTTTTCCCATTTAAACTTTAGCATCAAGCATTACTTATCTTAAAACAAAACACCTAAAT
1 TTATCTCTTTTCCCATTTAAACCTTAGCATCAACCATTACTTATCTGAAAACAAAACACCTAAAT
*
512296 TTTTTTTATTTGTCATCTATTTACCTACTTCTATTTGTTTTTAAATACTTTTCCTATTTAAAATC
66 TTTTTTTATTTGTCATCTATTTACCTACTTCTATTTGTTTTTAAATACCTTTCCTATTTAAAATC
* * *
512361 TAACGATACATAATGACTTAAGTATGGTAGTAAATCAAATATTTGTAATTTTTTTAATATCTAAA
131 TAACAACACATAATGACTTAAGTATGGTAGTAAATCAAATATTTGTAATTTTTTAAATATCTAAA
**
512426 CTTGAATCCACTTAATTTATTTGATATATGAAGTCTTTTATAATTCATTTACTATGTGAGTATTG
196 CTCAAATCCACTTAATTTATTTGATATATGAAGTCTTTTATAATTCATTTACTATGTGAGTATTG
* * * *
512491 TTATTTTAATTTGAATCCGATTTAGAGAACAATATTCATA-AGATATCCAAATCCATAAAATATT
261 CTATTTTAATCTAAATCCGATTTAAAGAACAATATTCATAGA-ATATCCAAATCCATAAAATATT
*
512555 TAAATTTATTAAATCAAATTTTTAAAAATATAAAAATCGAACAATAAC
325 TAAATTTATTAAATCAAATTTTTAAAAATATAAAAATCAAACAATAAC
512603 T
1 T
512604 AAATATGTAA
Statistics
Matches: 344, Mismatches: 28, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
371 1 0.00
372 343 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (372 bp):
TTATCTCTTTTCCCATTTAAACCTTAGCATCAACCATTACTTATCTGAAAACAAAACACCTAAAT
TTTTTTTATTTGTCATCTATTTACCTACTTCTATTTGTTTTTAAATACCTTTCCTATTTAAAATC
TAACAACACATAATGACTTAAGTATGGTAGTAAATCAAATATTTGTAATTTTTTAAATATCTAAA
CTCAAATCCACTTAATTTATTTGATATATGAAGTCTTTTATAATTCATTTACTATGTGAGTATTG
CTATTTTAATCTAAATCCGATTTAAAGAACAATATTCATAGAATATCCAAATCCATAAAATATTT
AAATTTATTAAATCAAATTTTTAAAAATATAAAAATCAAACAATAAC
Found at i:514981 original size:96 final size:96
Alignment explanation
Indices: 514853--515093 Score: 401
Period size: 96 Copynumber: 2.5 Consensus size: 96
514843 TATGAAAAAA
*
514853 GGGGTTGGAGTATCCCCTTGGAGGAATGGGTTGGAGTATCCCCGATGACAATAACTTAGGCAAAA
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGTTGGAGTATCCCCGATGACAATAACTTAGGCAAAA
514918 ATAAGGTTTGAATCTTGACAAGTTTAAAAGC
66 ATAAGGTTTGAATCTTGACAAGTTTAAAAGC
* * * *
514949 GGGGTTAGAGTATTCCCTCGGAGGAATAGGTTGGAGTATCCTCGATGACAATAACTTAGGCAAAA
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGTTGGAGTATCCCCGATGACAATAACTTAGGCAAAA
515014 ATAAGGTTTGAATCTTGACAAGTTTAAAAGC
66 ATAAGGTTTGAATCTTGACAAGTTTAAAAGC
** *
515045 ACGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGTGTATCCCCGATGA
1 GGGGTTGGAGTATCCCCTCGGAGGAAT-GGGTTGGAGTATCCCCGATGA
515094 ATAAAAATTT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 114 0.86
97 18 0.14
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (96 bp):
GGGGTTGGAGTATCCCCTCGGAGGAATGGGTTGGAGTATCCCCGATGACAATAACTTAGGCAAAA
ATAAGGTTTGAATCTTGACAAGTTTAAAAGC
Found at i:517272 original size:20 final size:20
Alignment explanation
Indices: 517247--517402 Score: 104
Period size: 20 Copynumber: 7.5 Consensus size: 20
517237 TTTTAACTAG
517247 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
517267 ATGTATCGATATATCTAGGTAAAAAGA
1 ATGTATCGATACAT-T--G---AAA-A
* * * *
517294 ATGTATTGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
517314 ATGTATCGATACA---ACAGA
1 ATGTATCGATACATTGA-AAA
* *
517332 ATGCATTGATACATT-AAAGA
1 ATGTATCGATACATTGAAA-A
* * *
517352 ATGTATCGATACATTTATAC
1 ATGTATCGATACATTGAAAA
517372 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
517392 ATGTATCGATA
1 ATGTATCGATA
517403 TATCTGGGTA
Statistics
Matches: 104, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.01
18 11 0.11
19 1 0.01
20 68 0.65
21 5 0.05
23 1 0.01
26 4 0.04
27 13 0.12
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:517333 original size:38 final size:38
Alignment explanation
Indices: 517291--517364 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
517281 CTAGGTAAAA
* * *
517291 AGAATGTATTGATACATTCATA-CATGTATCGATACAAC
1 AGAATGCATTGATACATT-AAAGAATGTATCGATACAAC
517329 AGAATGCATTGATACATTAAAGAATGTATCGATACA
1 AGAATGCATTGATACATTAAAGAATGTATCGATACA
517365 TTTATACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 2 0.06
38 30 0.94
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (38 bp):
AGAATGCATTGATACATTAAAGAATGTATCGATACAAC
Found at i:518122 original size:21 final size:21
Alignment explanation
Indices: 518096--518139 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
518086 CCTGCAACAA
*
518096 ATGTCAATTAGAAATATTGAT
1 ATGTCAATTACAAATATTGAT
*
518117 ATGTCAGTTACAAATATTGAT
1 ATGTCAATTACAAATATTGAT
518138 AT
1 AT
518140 ATTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGTCAATTACAAATATTGAT
Found at i:518330 original size:18 final size:18
Alignment explanation
Indices: 518308--518357 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
518298 AAATTAAATA
518308 ATAATTTAATTTTAATTT
1 ATAATTTAATTTTAATTT
* *
518326 TTAA-TAAATTTATAATTT
1 ATAATTTAATTT-TAATTT
*
518344 ATAATTTTATTTTA
1 ATAATTTAATTTTA
518358 TATTAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 6 0.24
18 14 0.56
19 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTTAATTTTAATTT
Found at i:518331 original size:24 final size:25
Alignment explanation
Indices: 518304--518351 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
518294 ATTAAAATTA
518304 AATAATAATT-TAATTT-TAATTTTT
1 AATAA-AATTATAATTTATAATTTTT
*
518328 AATAAATTTATAATTTATAATTTT
1 AATAAAATTATAATTTATAATTTT
518352 ATTTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.52
25 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATAAAATTATAATTTATAATTTTT
Found at i:518950 original size:53 final size:53
Alignment explanation
Indices: 518830--518954 Score: 135
Period size: 53 Copynumber: 2.4 Consensus size: 53
518820 TTTTATAAAA
* * * * *
518830 ACGAATTTAAATAGTAAATTCAAATATCCAAATATATTATCTGCATATGTAAT
1 ACGAATTTAAATAATAAATTCAAATATACAAATATATTATCTACATATATAAC
** * * *
518883 ACGAATTTCGATAATGAATT-AAGATATATAAATCTATTATCTACATATATAAC
1 ACGAATTTAAATAATAAATTCAA-ATATACAAATATATTATCTACATATATAAC
*
518936 GCGAATTTAAATAATAAAT
1 ACGAATTTAAATAATAAAT
518955 ATTCGAAAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
52 2 0.04
53 55 0.96
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (53 bp):
ACGAATTTAAATAATAAATTCAAATATACAAATATATTATCTACATATATAAC
Done.