Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015054.1 Kokia drynarioides strain JFW-HI SEQ_130098, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 570327
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 497 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:457039 original size:17 final size:17
Alignment explanation
Indices: 457017--457050 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
457007 AAGAAAACAG
457017 AAAGAAA-CGAAAACAAA
1 AAAGAAAGC-AAAACAAA
457034 AAAGAAAGCAAAACAAA
1 AAAGAAAGCAAAACAAA
457051 TATAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAAGCAAAACAAA
Found at i:463823 original size:47 final size:45
Alignment explanation
Indices: 463762--463858 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 45
463752 ATTAATGTAC
* * * *
463762 ACAATGGTCGAACATTAACTCTTAAGATTTTTAAATTTTAATTTTGT
1 ACAATGCTCAAACATTAACTCGTAAGA--TTTAAATTTTAATTTTAT
* * *
463809 ACAATGCTCAAACATTCACTCGTAGGATTTGAATTTTAATTTTAT
1 ACAATGCTCAAACATTAACTCGTAAGATTTAAATTTTAATTTTAT
463854 ACAAT
1 ACAAT
463859 TTTAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 21 0.49
47 22 0.51
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (45 bp):
ACAATGCTCAAACATTAACTCGTAAGATTTAAATTTTAATTTTAT
Found at i:478464 original size:4 final size:4
Alignment explanation
Indices: 478455--478519 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
478445 AAATAAACGG
* * *
478455 GAAA GAAA GAAA GAAAA GAAG GAAA GAAA GGAA GAAG GAGAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
478505 G-AA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
478520 TGTAATGTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.80
5 7 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:478481 original size:17 final size:17
Alignment explanation
Indices: 478459--478519 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
478449 AAACGGGAAA
478459 GAAAGAAAGAAAAGAAG
1 GAAAGAAAGAAAAGAAG
*
478476 GAAAGAAAG-GAAGAAG
1 GAAAGAAAGAAAAGAAG
478492 GAGAAGAAAGAAAGAAGAAG
1 GA-AAGAAAG-AA-AAGAAG
478512 GAAAGAAA
1 GAAAGAAA
478520 TGTAATGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.21
17 16 0.42
19 6 0.16
20 8 0.21
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAAGAAG
Found at i:478484 original size:25 final size:25
Alignment explanation
Indices: 478455--478519 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
478445 AAATAAACGG
*
478455 GAAAGAAAGAAAGAAAAGAAGGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
* * *
478480 GAAAGGAAGAAGGAGAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
*
478505 G-AAGAAGGAAAGAAA
1 GAAAGAAAGAAAGAAA
478520 TGTAATGTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAGAAAGAAA
Found at i:482113 original size:45 final size:45
Alignment explanation
Indices: 481994--482119 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
481984 AATATCGCGA
* * * **
481994 TGACTCGTCAAACTCAGCCTGATATCTTTCCCTTGAGTATTGCGG
1 TGACTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
*
482039 TGACTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
1 TGACTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
** *
482084 TGGGTCGTCAAACTGAGGCTAATATCCTTGGCTTGA
1 TGACTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
482120 TGAGCTATGC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (45 bp):
TGACTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
Found at i:484369 original size:20 final size:21
Alignment explanation
Indices: 484344--484386 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
484334 TACTTACTAC
484344 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
484364 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
484385 TA
1 TA
484387 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:486708 original size:57 final size:56
Alignment explanation
Indices: 486583--486711 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 56
486573 GGTATGGATT
* *
486583 TTTTTTTGTTCAAGTTAGTCTCTAAACTTGTAATTGTTAATACATTGGGACTTGAA
1 TTTTTTTGTTCAAGTTAGTCCCTAAACTTGCAATTGTTAATACATTGGGACTTGAA
* * *
486639 TATTTTTT-TTCAAGTTAGTCCCTAAATTTGACAATTGTT-TTCACATTGGG-GTCT-AA
1 T-TTTTTTGTTCAAGTTAGTCCCTAAACTTG-CAATTGTTAAT-ACATTGGGACT-TGAA
486695 TTTTTTTGGTTCAAGTT
1 TTTTTTT-GTTCAAGTT
486712 GGTTCTTGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
55 6 0.10
56 26 0.42
57 30 0.48
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49
Consensus pattern (56 bp):
TTTTTTTGTTCAAGTTAGTCCCTAAACTTGCAATTGTTAATACATTGGGACTTGAA
Found at i:490889 original size:4 final size:4
Alignment explanation
Indices: 490880--490922 Score: 61
Period size: 4 Copynumber: 10.5 Consensus size: 4
490870 TTGTTAGGAT
490880 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AAGAC AAGAC A-AC AG
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC -AGAC -AGAC AGAC AG
490923 TTGTGGACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.08
4 25 0.68
5 9 0.24
ACGTcount: A:0.53, C:0.23, G:0.23, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:491190 original size:16 final size:16
Alignment explanation
Indices: 491165--491209 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
491155 TTTGTTCGCA
*
491165 GTAATGGAATAGAATT
1 GTAATAGAATAGAATT
*
491181 GTAATAGAATAAAATT
1 GTAATAGAATAGAATT
*
491197 ATAATAGAATAGA
1 GTAATAGAATAGA
491210 GCTATAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (16 bp):
GTAATAGAATAGAATT
Found at i:491467 original size:58 final size:58
Alignment explanation
Indices: 491405--491538 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 58
491395 TTTTAATAAG
* * *
491405 ATTATTATTAAATATAATTTAATAAAAATAATA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATATAAT-AAAATAATATA-TAATTTAATAACATTTTTAACATA
* * *
491463 ATTATTATTAAATAGAATATAATAAAATAATATATGATTTAATAACATTTTTAATATA
1 ATTATTATTAAATATAATATAATAAAATAATATATAATTTAATAACATTTTTAACATA
491521 ATTATTATTAAAATATAA
1 ATTATTATT-AAATATAA
491539 ATTAGTAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 19 0.29
58 40 0.61
59 7 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAATATAATATAATAAAATAATATATAATTTAATAACATTTTTAACATA
Found at i:491547 original size:25 final size:25
Alignment explanation
Indices: 491519--491568 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
491509 ATTTTTAATA
*
491519 TAATTATTATTAAAATATAA-ATTAG
1 TAATAATT-TTAAAATATAATATTAG
*
491544 TAATAATTTTAATATATAATATTAG
1 TAATAATTTTAAAATATAATATTAG
491569 AAAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TAATAATTTTAAAATATAATATTAG
Found at i:497226 original size:32 final size:32
Alignment explanation
Indices: 497180--497252 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
497170 GGGATTTTAG
* * *
497180 TTTAGGTTTTAAAATTTTGGAGATTTTCGGGT
1 TTTAGGTTTCAAAATTTTAGAGATTTTCGGGA
* *
497212 TTTAGGTTTCAAAATTTTAGCGGTTTTCGGGA
1 TTTAGGTTTCAAAATTTTAGAGATTTTCGGGA
497244 TTTAGGTTT
1 TTTAGGTTT
497253 AGAGATATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.21, C:0.05, G:0.25, T:0.49
Consensus pattern (32 bp):
TTTAGGTTTCAAAATTTTAGAGATTTTCGGGA
Found at i:498204 original size:32 final size:32
Alignment explanation
Indices: 498168--498237 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
498158 ATTGAAAATT
*
498168 AAAATTA-TTTAATAATTTTATTATTTCAAAAA
1 AAAATTATTTTAATAATTTTA-CATTTCAAAAA
* *
498200 AAAATAATTTTAATAATTTTACATTTTAAAAA
1 AAAATTATTTTAATAATTTTACATTTCAAAAA
*
498232 ATAATT
1 AAAATT
498238 TAAAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAATTATTTTAATAATTTTACATTTCAAAAA
Found at i:498236 original size:20 final size:20
Alignment explanation
Indices: 498211--498248 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
498201 AAATAATTTT
* *
498211 AATAATTTTACATTTTAAAA
1 AATAATTTAAAATTTTAAAA
498231 AATAATTTAAAATTTTAA
1 AATAATTTAAAATTTTAA
498249 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATTTAAAATTTTAAAA
Found at i:498239 original size:28 final size:29
Alignment explanation
Indices: 498198--498258 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
498188 TTATTTCAAA
498198 AAAAAATAATTTTAATAATTTT-ACATTTT
1 AAAAAATAATTTTAA-AATTTTAACATTTT
*
498227 AAAAAATAA-TTTAAAATTTTAATATTTT
1 AAAAAATAATTTTAAAATTTTAACATTTT
498255 AAAA
1 AAAA
498259 TCATTTACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.20
28 15 0.50
29 9 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAAAATAATTTTAAAATTTTAACATTTT
Found at i:499419 original size:35 final size:37
Alignment explanation
Indices: 499379--499460 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 37
499369 TAAATTATTC
499379 ATATTTTACTATAAAATATT-TAT-AA-ATTTT-AATA
1 ATATTTTACT-TAAAATATTATATAAATATTTTCAATA
499413 TATATTTATACTTAAAATATTGATATAAATATTTTCAATA
1 -ATATTT-TACTTAAAATATT-ATATAAATATTTTCAATA
499453 ATATTTTA
1 ATATTTTA
499461 AGAATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
35 15 0.37
36 4 0.10
37 3 0.07
38 4 0.10
39 11 0.27
40 4 0.10
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (37 bp):
ATATTTTACTTAAAATATTATATAAATATTTTCAATA
Found at i:500345 original size:23 final size:22
Alignment explanation
Indices: 500318--500363 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
500308 TTAGTATTAT
* *
500318 TTAATATCACTACTTATATTAAA
1 TTAATATCACAAATTA-ATTAAA
500341 TTAATATCACAAATTAATTAAA
1 TTAATATCACAAATTAATTAAA
500363 T
1 T
500364 ATCAACCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAATATCACAAATTAATTAAA
Found at i:502030 original size:31 final size:31
Alignment explanation
Indices: 501995--502116 Score: 144
Period size: 31 Copynumber: 3.9 Consensus size: 31
501985 GAGTACTTTA
501995 AAAAATGTTTTACTC-TTATTTGAACACTTGC
1 AAAAA-GTTTTACTCGTTATTTGAACACTTGC
* *
502026 AAAAAGTTTTAGC-CGTTATTTGAGA-ATTTTC
1 AAAAAGTTTTA-CTCGTTATTTGA-ACACTTGC
*
502057 AAAAAGGTTTGACTC-TTATTTGAACACTTGC
1 AAAAA-GTTTTACTCGTTATTTGAACACTTGC
*
502088 AAAAAGTTTTAATCGTTATTTGAACACTT
1 AAAAAGTTTTACTCGTTATTTGAACACTT
502117 TGAAATGTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
30 15 0.19
31 55 0.71
32 7 0.09
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (31 bp):
AAAAAGTTTTACTCGTTATTTGAACACTTGC
Found at i:502048 original size:62 final size:62
Alignment explanation
Indices: 501980--502110 Score: 199
Period size: 62 Copynumber: 2.1 Consensus size: 62
501970 TGATATACTA
* * * *
501980 TATTTGAGTACTTTAAAAAATGTTTTACTCTTATTTGAACACTTGCAAAAAGTTTTAGCCGT
1 TATTTGAGAACTTTAAAAAAGGTTTGACTCTTATTTGAACACTTGCAAAAAGTTTTAACCGT
* * *
502042 TATTTGAGAATTTTCAAAAAGGTTTGACTCTTATTTGAACACTTGCAAAAAGTTTTAATCGT
1 TATTTGAGAACTTTAAAAAAGGTTTGACTCTTATTTGAACACTTGCAAAAAGTTTTAACCGT
502104 TATTTGA
1 TATTTGA
502111 ACACTTTGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (62 bp):
TATTTGAGAACTTTAAAAAAGGTTTGACTCTTATTTGAACACTTGCAAAAAGTTTTAACCGT
Found at i:504066 original size:13 final size:13
Alignment explanation
Indices: 504045--504082 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
504035 GATTTATCTG
504045 TATTA-TTTTTTA
1 TATTATTTTTTTA
*
504057 TATTATTTTTATA
1 TATTATTTTTTTA
*
504070 TAATATTTTTTTA
1 TATTATTTTTTTA
504083 AATATTATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTTTTTTA
Found at i:504067 original size:11 final size:12
Alignment explanation
Indices: 504045--504080 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
504035 GATTTATCTG
504045 TATTATTTTTTA
1 TATTATTTTTTA
504057 TATTATTTTTATA
1 TATTATTTTT-TA
*
504070 TAATATTTTTT
1 TATTATTTTTT
504081 TAAATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:506233 original size:24 final size:24
Alignment explanation
Indices: 506201--506266 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
506191 AAACTCTGTT
506201 TAGGCTCGTAAGAGCTAACCATTC
1 TAGGCTCGTAAGAGCTAACCATTC
* *
506225 TAGGCTCGTAAAAGCTAACCATTT
1 TAGGCTCGTAAGAGCTAACCATTC
* **
506249 TGGGCTCGTGTGAGCTAA
1 TAGGCTCGTAAGAGCTAA
506267 AGTTATCTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (24 bp):
TAGGCTCGTAAGAGCTAACCATTC
Found at i:506287 original size:25 final size:23
Alignment explanation
Indices: 506203--506299 Score: 72
Period size: 24 Copynumber: 4.0 Consensus size: 23
506193 ACTCTGTTTA
* *
506203 GGCTCGTAAGAGCTAACCA-TTCTA
1 GGCTCGTATGAGCTAA--ATTTCTG
**
506227 GGCTCGTAAAAGCTAACCATTT-TG
1 GGCTCGTATGAGCTAA--ATTTCTG
*
506251 GGCTCGTGTGAGCTAAAGTTATCTG
1 GGCTCGTATGAGCTAAA-TT-TCTG
*
506276 GGCTTGTATGAGCTAAATTTCTG
1 GGCTCGTATGAGCTAAATTTCTG
506299 G
1 G
506300 AAGACTCAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 7 0.11
24 35 0.56
25 19 0.31
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCTCGTATGAGCTAAATTTCTG
Found at i:510560 original size:54 final size:53
Alignment explanation
Indices: 510502--510630 Score: 134
Period size: 54 Copynumber: 2.4 Consensus size: 53
510492 ACATCCAAAC
* * *
510502 AACAAAAATAACAACCAAAACAGCAGTAAAAAAAAC-ATCAAACAACATTAAAAA
1 AACAAAAATAACAACCAAAACAACAGCAAAAAAAACAATC-AA-AACAGTAAAAA
* * * *
510556 AACAAAAATAGCAACAAAAATAACAGCAAAAACAACAATCAAAACAGTAAAAA
1 AACAAAAATAACAACCAAAACAACAGCAAAAAAAACAATCAAAACAGTAAAAA
*
510609 AAGCACGAAAATAACAAACAAA
1 AA-CA--AAAATAACAACCAAA
510631 TATAATTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
53 12 0.20
54 34 0.56
55 3 0.05
56 12 0.20
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (53 bp):
AACAAAAATAACAACCAAAACAACAGCAAAAAAAACAATCAAAACAGTAAAAA
Found at i:510573 original size:12 final size:12
Alignment explanation
Indices: 510556--510599 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
510546 ACATTAAAAA
*
510556 AACAAAAATAGC
1 AACAAAAATAAC
510568 AACAAAAATAAC
1 AACAAAAATAAC
* *
510580 AGCAAAAACAAC
1 AACAAAAATAAC
510592 AATCAAAA
1 AA-CAAAA
510600 CAGTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAAAAATAAC
Found at i:510591 original size:21 final size:21
Alignment explanation
Indices: 510485--510593 Score: 64
Period size: 20 Copynumber: 5.1 Consensus size: 21
510475 AAAACGCATA
*
510485 AAAAATAACATC-CAAACAAC
1 AAAAATAACATCAAAAACAAC
* **
510505 AAAAATAACAACCAAAACAGCAGT
1 AAAAATAAC-ATCAAAA-A-CAAC
* **
510529 AAAAAAAACATCAAACAACATT
1 AAAAATAACATCAAA-AACAAC
510551 AAAAA-AACA--AAAATAGCAAC
1 AAAAATAACATCAAAA-A-CAAC
*
510571 AAAAATAACAGCAAAAACAAC
1 AAAAATAACATCAAAAACAAC
510592 AA
1 AA
510594 TCAAAACAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 16 0.23
21 16 0.23
22 11 0.16
23 11 0.16
24 11 0.16
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (21 bp):
AAAAATAACATCAAAAACAAC
Found at i:516359 original size:25 final size:26
Alignment explanation
Indices: 516325--516375 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
516315 ATATCATTAA
*
516325 ATAATTAAAAAAAACCAT-AAATAAT
1 ATAATGAAAAAAAACCATAAAATAAT
*
516350 ATAATGAAAAAAATCCATAAAATAAT
1 ATAATGAAAAAAAACCATAAAATAAT
516376 TTCTCCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (26 bp):
ATAATGAAAAAAAACCATAAAATAAT
Found at i:516947 original size:6 final size:6
Alignment explanation
Indices: 516926--516960 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
516916 TTAAAATTTG
516926 ATTAAA TATATAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA -AT-TAAA ATTAAA ATTAAA ATTAAA ATT
516961 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:524889 original size:22 final size:22
Alignment explanation
Indices: 524848--524889 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
524838 AAGCTTATAT
* *
524848 AACTTATTAATTATGGAAAAGA
1 AACTTATTAATTAAGAAAAAGA
524870 AACTTATTAATTAAGAAAAA
1 AACTTATTAATTAAGAAAAA
524890 ATCATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (22 bp):
AACTTATTAATTAAGAAAAAGA
Found at i:537064 original size:61 final size:61
Alignment explanation
Indices: 536969--537091 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
536959 CCACAACAAG
536969 TTATCTCCCTTACACCACGCATCCACTCTCCACCATCGCCAGTTCTCTCCCTTCCAGCACC
1 TTATCTCCCTTACACCACGCATCCACTCTCCACCATCGCCAGTTCTCTCCCTTCCAGCACC
537030 TTATCTCCCTTACACCACGCATCCACTCTCCACCATCGCCAGTTCTCTCCCTTCCAGCACC
1 TTATCTCCCTTACACCACGCATCCACTCTCCACCATCGCCAGTTCTCTCCCTTCCAGCACC
537091 T
1 T
537092 GTCCAATCTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.18, C:0.49, G:0.07, T:0.27
Consensus pattern (61 bp):
TTATCTCCCTTACACCACGCATCCACTCTCCACCATCGCCAGTTCTCTCCCTTCCAGCACC
Found at i:537250 original size:63 final size:62
Alignment explanation
Indices: 537053--537317 Score: 239
Period size: 63 Copynumber: 4.2 Consensus size: 62
537043 ACCACGCATC
* * * * * *
537053 CACTCTCCACCATCGCCAGTTCTCTCCCTTCCAGC-ACCTGTCCAATC-TCTACCACTACCAATT
1 CACTCTCCACCACCACCAGTTCTCTCCCTTCCA-CAACC-ATCCACTCTTC-ACCTCCACCAATT
* * * * * * *
537116 CACTCTCCACCACAACCAGTTCTCTCTC-ACCATCATCCGTCCACTCTTCACCTCCACTAGTT
1 CACTCTCCACCACCACCAGTTCTCTCCCTTCCA-CAACCATCCACTCTTCACCTCCACCAATT
* * * *
537178 CACTTTCCACCACCACCAGTTCTCTCCCTTCCACAACTCAACCACTCTTCACTTCTACCAATT
1 CACTCTCCACCACCACCAGTTCTCTCCCTTCCACAAC-CATCCACTCTTCACCTCCACCAATT
* * * * * * *
537241 CACTATCCACCACTATCAGTTCTTTCCCTTCTACCACCAGTCCACTCTCCACCTCCACCAATT
1 CACTCTCCACCACCACCAGTTCTCTCCCTTCCACAACCA-TCCACTCTTCACCTCCACCAATT
537304 CACTCTCCACCACC
1 CACTCTCCACCACC
537318 TCCGATTCTC
Statistics
Matches: 162, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
62 50 0.31
63 112 0.69
ACGTcount: A:0.22, C:0.47, G:0.04, T:0.27
Consensus pattern (62 bp):
CACTCTCCACCACCACCAGTTCTCTCCCTTCCACAACCATCCACTCTTCACCTCCACCAATT
Found at i:537325 original size:21 final size:21
Alignment explanation
Indices: 537098--537340 Score: 73
Period size: 21 Copynumber: 11.6 Consensus size: 21
537088 ACCTGTCCAA
* *
537098 TCTCTACCACTACCAATTCAC
1 TCTCCACCACCACCAATTCAC
* * *
537119 TCTCCACCACAACCAGTTCTC
1 TCTCCACCACCACCAATTCAC
* * *
537140 TCT-CACCATCATCC-GTCCAC
1 TCTCCACCACCA-CCAATTCAC
* * * *
537160 TCTTCACCTCCACTAGTTCAC
1 TCTCCACCACCACCAATTCAC
* * *
537181 TTTCCACCACCACCAGTTCTC
1 TCTCCACCACCACCAATTCAC
* * *
537202 TC-CCTTCCACAACTCAA-CCAC
1 TCTCC-ACCACCAC-CAATTCAC
* ** *
537223 TCTTCACTTCTACCAATTCAC
1 TCTCCACCACCACCAATTCAC
* * * * **
537244 TATCCACCACTATCAGTTCTT
1 TCTCCACCACCACCAATTCAC
* * * *
537265 TC-CCTTCTACCACCAGTCCAC
1 TCTCC-ACCACCACCAATTCAC
*
537286 TCTCCACCTCCACCAATTCAC
1 TCTCCACCACCACCAATTCAC
* * *
537307 TCTCCACCACCTCCGATTCTC
1 TCTCCACCACCACCAATTCAC
* *
537328 TCTTCTCCACCAC
1 TCTCCACCACCAC
537341 TCGTCCACAC
Statistics
Matches: 156, Mismatches: 57, Indels: 18
0.68 0.25 0.08
Matches are distributed among these distances:
20 21 0.13
21 130 0.83
22 5 0.03
ACGTcount: A:0.22, C:0.47, G:0.03, T:0.28
Consensus pattern (21 bp):
TCTCCACCACCACCAATTCAC
Found at i:537340 original size:63 final size:61
Alignment explanation
Indices: 537053--537354 Score: 221
Period size: 63 Copynumber: 4.8 Consensus size: 61
537043 ACCACGCATC
* * * * * * *
537053 CACTCTCCACCATC-GCCAGTTCTCTCCCTTCCAGCACCTGTCCAATCTCTACCACTACCAATT
1 CACTCTCCACCA-CAACCAGTTCTCTCTC-TCCACCACC-GTCCACTCTCCACCTCCACCAATT
* * * * *
537116 CACTCTCCACCACAACCAGTTCTCTCTCACCATCATCCGTCCACTCTTCACCTCCACTAGTT
1 CACTCTCCACCACAACCAGTTCTCTCTCTCCACCA-CCGTCCACTCTCCACCTCCACCAATT
* * * * ** * * *
537178 CACTTTCCACCACCACCAGTTCTCTCCCTTCCACAACTCAACCACTCTTCACTTCTACCAATT
1 CACTCTCCACCACAACCAGTTCTCTCTC-TCCACCAC-CGTCCACTCTCCACCTCCACCAATT
* * * * * *
537241 CACTATCCACCACTATCAGTTCTTTCCCTTCTACCACCAGTCCACTCTCCACCTCCACCAATT
1 CACTCTCCACCACAACCAGTTCTCTCTC-TCCACCACC-GTCCACTCTCCACCTCCACCAATT
** *
537304 CACTCTCCACCACCTCC-GATTCTCTCTTCTCCACCACTCGTCCACACTCCA
1 CACTCTCCACCACAACCAG-TTCTCTC-TCTCCACCAC-CGTCCACTCTCCA
537355 ACACCATCAG
Statistics
Matches: 189, Mismatches: 42, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
62 51 0.27
63 136 0.72
64 2 0.01
ACGTcount: A:0.21, C:0.47, G:0.04, T:0.27
Consensus pattern (61 bp):
CACTCTCCACCACAACCAGTTCTCTCTCTCCACCACCGTCCACTCTCCACCTCCACCAATT
Found at i:537441 original size:105 final size:105
Alignment explanation
Indices: 537246--537450 Score: 232
Period size: 105 Copynumber: 2.0 Consensus size: 105
537236 CAATTCACTA
* * * * * * *
537246 TCCACCACTATCAGTTCTTTCCCTTCTACCACCAGTCCACTCTCCACCTCCACCAATTCACTCTC
1 TCCAACACCATCAGTTCTTACCCCTCCACCACCAGTACACTCTCCACCTCAACCAATTCACTCTC
* * ** *
537311 CACCACCTCCGATTCTCTCTTCTCCACCACTCGTCCACAC
66 CACCACCACAGATTCTCTCCCCTCCACCACCCGTCCACAC
* * * *
537351 TCCAACACCATCAGTTCTTACCCCTCCACCATCAGTACACTCTCCACCTCAACCAGTTCACTTTT
1 TCCAACACCATCAGTTCTTACCCCTCCACCACCAGTACACTCTCCACCTCAACCAATTCACTCTC
* *
537416 CATCACCACTAG-TTCTTTCCCCTCCACCACCCGTC
66 CACCACCAC-AGATTCTCTCCCCTCCACCACCCGTC
537451 TACTTTCTAC
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
105 80 0.99
106 1 0.01
ACGTcount: A:0.20, C:0.48, G:0.04, T:0.27
Consensus pattern (105 bp):
TCCAACACCATCAGTTCTTACCCCTCCACCACCAGTACACTCTCCACCTCAACCAATTCACTCTC
CACCACCACAGATTCTCTCCCCTCCACCACCCGTCCACAC
Found at i:537515 original size:24 final size:24
Alignment explanation
Indices: 537436--537507 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
537426 AGTTCTTTCC
* * * *
537436 CCTCCACCACCCGTCTACTTTCTA
1 CCTCCACCACCTGTCCACTCTCCA
* *
537460 CTTCCACCATCTGTCCACTCTCCA
1 CCTCCACCACCTGTCCACTCTCCA
537484 CCTCCACCACCTGTCCACTCTCCA
1 CCTCCACCACCTGTCCACTCTCCA
537508 TGTCCACCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.17, C:0.53, G:0.04, T:0.26
Consensus pattern (24 bp):
CCTCCACCACCTGTCCACTCTCCA
Found at i:537883 original size:21 final size:21
Alignment explanation
Indices: 537859--537912 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
537849 CCACGCGTCC
* *
537859 ACTCTTCAACTCCACTAGTCA
1 ACTCTTCAACTCCACCAATCA
* *
537880 ACTCTTCGACTCCACCAATCT
1 ACTCTTCAACTCCACCAATCA
*
537901 ACTCTCCAACTC
1 ACTCTTCAACTC
537913 TGTCAGTCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.43, G:0.04, T:0.28
Consensus pattern (21 bp):
ACTCTTCAACTCCACCAATCA
Found at i:537884 original size:63 final size:63
Alignment explanation
Indices: 537730--537884 Score: 157
Period size: 63 Copynumber: 2.5 Consensus size: 63
537720 ACTCTATCAA
* * * * * * * * * **
537730 TCCATTCTCCAACTCCACCAGTCGACTCTCCTTCACTATCAGTTTTTTCTCTTTTACCACGCG
1 TCCACTCTTCAACTCCACCAGTCAACTCTCCGTCACCACCAGTTCTTTCCCCTCCACCACGCG
* * * * *
537793 TCCACTTTTCGACTTCACCAATCCACTCTCCGTCACCACCAGTTCTTTCCCCTCCACCACGCG
1 TCCACTCTTCAACTCCACCAGTCAACTCTCCGTCACCACCAGTTCTTTCCCCTCCACCACGCG
*
537856 TCCACTCTTCAACTCCACTAGTCAACTCT
1 TCCACTCTTCAACTCCACCAGTCAACTCT
537885 TCGACTCCAC
Statistics
Matches: 71, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.19, C:0.43, G:0.07, T:0.32
Consensus pattern (63 bp):
TCCACTCTTCAACTCCACCAGTCAACTCTCCGTCACCACCAGTTCTTTCCCCTCCACCACGCG
Found at i:537926 original size:42 final size:42
Alignment explanation
Indices: 537875--537954 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
537865 CAACTCCACT
* *
537875 AGTCAACTCTTC-GACTCCACCAATCTACTCTCCAACTCTGTC
1 AGTCAACTCTCCAG-CTCCACCAATCCACTCTCCAACTCTGTC
* **
537917 AGTCTACTCTCCAGCTCCATTAATCCACTCTCCAACTC
1 AGTCAACTCTCCAGCTCCACCAATCCACTCTCCAACTC
537955 CACCATTCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.41, G:0.06, T:0.29
Consensus pattern (42 bp):
AGTCAACTCTCCAGCTCCACCAATCCACTCTCCAACTCTGTC
Found at i:537946 original size:21 final size:21
Alignment explanation
Indices: 537922--537971 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
537912 CTGTCAGTCT
* **
537922 ACTCTCCAGCTCCATTAATCC
1 ACTCTCCAACTCCACCAATCC
*
537943 ACTCTCCAACTCCACCATTCC
1 ACTCTCCAACTCCACCAATCC
537964 ACTCTCCA
1 ACTCTCCA
537972 TCACTGTCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.48, G:0.02, T:0.26
Consensus pattern (21 bp):
ACTCTCCAACTCCACCAATCC
Found at i:538028 original size:21 final size:21
Alignment explanation
Indices: 537998--538043 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
537988 CACATGTCGG
**
537998 CTCTCAAACTTTATCAATCCA
1 CTCTCAAACTCAATCAATCCA
* *
538019 CTCTCTAACTCAATCAGTCCA
1 CTCTCAAACTCAATCAATCCA
538040 CTCT
1 CTCT
538044 TTATCACCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.37, G:0.02, T:0.33
Consensus pattern (21 bp):
CTCTCAAACTCAATCAATCCA
Found at i:538105 original size:21 final size:21
Alignment explanation
Indices: 538080--538232 Score: 119
Period size: 21 Copynumber: 7.3 Consensus size: 21
538070 ACCAAGTGTT
* *
538080 CACTCTTCAACTCCATCAGTC
1 CACTCTTCAACTCCACCAATC
** *
538101 CACTCTTTGACTCTACCAATC
1 CACTCTTCAACTCCACCAATC
* *
538122 CACTCTCCAAATCCACCAATC
1 CACTCTTCAACTCCACCAATC
* * * * ***
538143 TATTCTCCAACTCTATTTATC
1 CACTCTTCAACTCCACCAATC
* *
538164 CACTCCTCAACTCCACCAGTC
1 CACTCTTCAACTCCACCAATC
*
538185 CACTCTTCAAC-CCTATCAATC
1 CACTCTTCAACTCC-ACCAATC
* *
538206 CACTCTTCAACTCCAGCAGTC
1 CACTCTTCAACTCCACCAATC
538227 CACTCT
1 CACTCT
538233 CCGTCACCAC
Statistics
Matches: 99, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
20 2 0.02
21 95 0.96
22 2 0.02
ACGTcount: A:0.25, C:0.42, G:0.03, T:0.29
Consensus pattern (21 bp):
CACTCTTCAACTCCACCAATC
Found at i:538126 original size:42 final size:42
Alignment explanation
Indices: 538080--538232 Score: 171
Period size: 42 Copynumber: 3.6 Consensus size: 42
538070 ACCAAGTGTT
* ** *
538080 CACTCTTCAACTCCATCAGTCCACTCTTTGACTCTACCAATC
1 CACTCTTCAACTCCACCAGTCCACTCTTCAACTCTATCAATC
* * * * * * **
538122 CACTCTCCAAATCCACCAATCTATTCTCCAACTCTATTTATC
1 CACTCTTCAACTCCACCAGTCCACTCTTCAACTCTATCAATC
* *
538164 CACTCCTCAACTCCACCAGTCCACTCTTCAACCCTATCAATC
1 CACTCTTCAACTCCACCAGTCCACTCTTCAACTCTATCAATC
*
538206 CACTCTTCAACTCCAGCAGTCCACTCT
1 CACTCTTCAACTCCACCAGTCCACTCT
538233 CCGTCACCAC
Statistics
Matches: 87, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.25, C:0.42, G:0.03, T:0.29
Consensus pattern (42 bp):
CACTCTTCAACTCCACCAGTCCACTCTTCAACTCTATCAATC
Found at i:538234 original size:84 final size:84
Alignment explanation
Indices: 538080--538234 Score: 202
Period size: 84 Copynumber: 1.8 Consensus size: 84
538070 ACCAAGTGTT
* * ** * *
538080 CACTCTTCAACTCCATCAGTCCACTCTTTGACTCTACCAATCCACTCTCCAAATCCACCAATCTA
1 CACTCCTCAACTCCACCAGTCCACTCTTCAACCCTACCAATCCACTCTCCAAATCCACCAATCCA
*
538145 TTCTCCAACTCTATTTATC
66 CTCTCCAACTCTATTTATC
* * * * *
538164 CACTCCTCAACTCCACCAGTCCACTCTTCAACCCTATCAATCCACTCTTCAACTCCAGCAGTCCA
1 CACTCCTCAACTCCACCAGTCCACTCTTCAACCCTACCAATCCACTCTCCAAATCCACCAATCCA
538229 CTCTCC
66 CTCTCC
538235 GTCACCACAG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 59 1.00
ACGTcount: A:0.25, C:0.43, G:0.03, T:0.28
Consensus pattern (84 bp):
CACTCCTCAACTCCACCAGTCCACTCTTCAACCCTACCAATCCACTCTCCAAATCCACCAATCCA
CTCTCCAACTCTATTTATC
Found at i:538274 original size:63 final size:63
Alignment explanation
Indices: 538204--538616 Score: 316
Period size: 63 Copynumber: 6.5 Consensus size: 63
538194 ACCCTATCAA
* * * * *
538204 TCCACTCTTCAACTCCAGCAGTCCACTCTCCGTCACCA-CAGATTCTTTCTCCTCCATCACGCG
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAG-TTCTTTCTCCTCCACCACACG
* * * * * * * *
538267 TCTACTCTCCAACTCCACCAGTTCACTGTCCAACTCCATCAGTCCACTTTTCACCTCCACCAC-C
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAGT--TC-TTTCTCCTCCACCACAC
538331 TG
63 -G
* * * * * * *
538333 TCCACTCTCCACCTTCACTAGTTCACTCTCCATCACCACCAGTTCTCTCCCCTCCACCACACT
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAGTTCTTTCTCCTCCACCACACG
* * * ** * *
538396 TCCACTCTCCAACTCCACCAATCCACTCTCCGTCATCACTGGTTC--TCTCCATTCCACTACATG
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAGTTCTTTCTCC--TCCACCACACG
* * * *
538459 TCCACTCTCCAACTCCATCAGTCCATTCTTCGTCACCACC-GATTCTTT-TCTCTCCACCACACG
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAG-TTCTTTCTC-CTCCACCACACG
* * * * * * * * **
538522 TCTAATCTCCAACTCCACCAATCCACTCTACACCACCACCAGTTCTCTCCCCTCCACTACGTG
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAGTTCTTTCTCCTCCACCACACG
**
538585 TCCACTCTTTAACTCCACCAGTCCACTCTCCA
1 TCCACTCTCCAACTCCACCAGTCCACTCTCCA
538617 ACTCTATCAA
Statistics
Matches: 273, Mismatches: 63, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
61 4 0.01
62 1 0.00
63 206 0.75
64 9 0.03
65 4 0.01
66 49 0.18
ACGTcount: A:0.21, C:0.46, G:0.06, T:0.27
Consensus pattern (63 bp):
TCCACTCTCCAACTCCACCAGTCCACTCTCCATCACCACCAGTTCTTTCTCCTCCACCACACG
Found at i:538282 original size:24 final size:21
Alignment explanation
Indices: 538255--538308 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
538245 ATTCTTTCTC
538255 CTCCATCACGCGTCTACTCTCCAA
1 CTCCATCA-G-GTC-ACTCTCCAA
* * *
538279 CTCCACCAGTTCACTGTCCAA
1 CTCCATCAGGTCACTCTCCAA
538300 CTCCATCAG
1 CTCCATCAG
538309 TCCACTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.62
22 2 0.08
23 1 0.04
24 7 0.27
ACGTcount: A:0.22, C:0.44, G:0.09, T:0.24
Consensus pattern (21 bp):
CTCCATCAGGTCACTCTCCAA
Found at i:538345 original size:24 final size:24
Alignment explanation
Indices: 538308--538415 Score: 65
Period size: 24 Copynumber: 4.9 Consensus size: 24
538298 AACTCCATCA
* *
538308 GTCCACTTTTCACCTCCACCACCT
1 GTCCACTCTCCACCTCCACCACCT
* *
538332 GTCCACTCTCCACCTTCACTA---
1 GTCCACTCTCCACCTCCACCACCT
* *
538353 GTTCACTCTCCA--T-CACCACCA
1 GTCCACTCTCCACCTCCACCACCT
*
538374 GT--TCTCTCC-CCTCCACCACACT
1 GTCCACTCTCCACCTCCACCAC-CT
*
538396 -TCCACTCTCCAACTCCACCA
1 GTCCACTCTCCACCTCCACCA
538416 ATCCACTCTC
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
18 4 0.06
19 7 0.11
20 1 0.02
21 20 0.31
22 1 0.02
23 6 0.09
24 25 0.39
ACGTcount: A:0.19, C:0.51, G:0.04, T:0.26
Consensus pattern (24 bp):
GTCCACTCTCCACCTCCACCACCT
Found at i:538376 original size:21 final size:21
Alignment explanation
Indices: 538270--538426 Score: 95
Period size: 21 Copynumber: 7.3 Consensus size: 21
538260 TCACGCGTCT
538270 ACTCTCCAACTCCACCAGTTC
1 ACTCTCCAACTCCACCAGTTC
* * *
538291 ACTGTCCAACTCCATCAGTCC
1 ACTCTCCAACTCCACCAGTTC
* * * *
538312 ACTTTTCACCTCCACCACCTGTCC
1 ACTCTCCAACTCCACCA---GTTC
* * *
538336 ACTCTCCACCTTCACTAGTTC
1 ACTCTCCAACTCCACCAGTTC
* *
538357 ACTCTCCATCACCACCAGTT-
1 ACTCTCCAACTCCACCAGTTC
* *
538377 -CTCTCC-CCTCCACCACACTTCC
1 ACTCTCCAACTCCA-C-CAGTT-C
* *
538399 ACTCTCCAACTCCACCAATCC
1 ACTCTCCAACTCCACCAGTTC
538420 ACTCTCC
1 ACTCTCC
538427 GTCATCACTG
Statistics
Matches: 105, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
18 4 0.04
19 7 0.07
20 4 0.04
21 58 0.55
22 3 0.03
23 7 0.07
24 22 0.21
ACGTcount: A:0.21, C:0.50, G:0.04, T:0.25
Consensus pattern (21 bp):
ACTCTCCAACTCCACCAGTTC
Found at i:538619 original size:21 final size:21
Alignment explanation
Indices: 538585--538657 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
538575 CCACTACGTG
** *
538585 TCCACTCTTTAACTCCACCAG
1 TCCACTCTCCAACTCCACCAA
* *
538606 TCCACTCTCCAACTCTATCAA
1 TCCACTCTCCAACTCCACCAA
*
538627 TCCATTCTCCAACTCCACCAA
1 TCCACTCTCCAACTCCACCAA
*
538648 TCGACTCTCC
1 TCCACTCTCC
538658 GTCACCACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.25, C:0.45, G:0.03, T:0.27
Consensus pattern (21 bp):
TCCACTCTCCAACTCCACCAA
Found at i:538718 original size:105 final size:105
Alignment explanation
Indices: 538527--538718 Score: 251
Period size: 105 Copynumber: 1.8 Consensus size: 105
538517 ACACGTCTAA
*
538527 TCTCCAACTCCACCAATCCACTCTACACCACCACCAGTTCTCTCCCCTCCACTACGTGTCCACTC
1 TCTCCAACTCCACCAATCCACTCTACACCACCACCAATTCTCTCCCCTCCACTACGTGTCCACTC
* * *
538592 TTTAACTCCACCAGTCCACTCTCCAACTCTATCAATCCAT
66 TTCAACTCCACCAATCAACTCTCCAACTCTATCAATCCAT
* * ** * * *
538632 TCTCCAACTCCACCAATCGACTCTCCGTCACCACTAATTCTCTCTCCTCTA-TCACGTGTCCACT
1 TCTCCAACTCCACCAATCCACTCTACACCACCACCAATTCTCTCCCCTCCACT-ACGTGTCCACT
* *
538696 CTTCAGCTCCACTAATCAACTCT
65 CTTCAACTCCACCAATCAACTCT
538719 TCGACTTCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 1 0.01
105 72 0.99
ACGTcount: A:0.23, C:0.45, G:0.05, T:0.28
Consensus pattern (105 bp):
TCTCCAACTCCACCAATCCACTCTACACCACCACCAATTCTCTCCCCTCCACTACGTGTCCACTC
TTCAACTCCACCAATCAACTCTCCAACTCTATCAATCCAT
Found at i:538733 original size:105 final size:105
Alignment explanation
Indices: 538527--538760 Score: 247
Period size: 105 Copynumber: 2.2 Consensus size: 105
538517 ACACGTCTAA
*
538527 TCTCCAACTCCACCAATCCACTCTACACCACCACCAGTTCTCTCCCCTCCACTACGTGTCCACTC
1 TCTCCAACTCCACCAATCCACTCTACACCACCACCAATTCTCTCCCCTCCACTACGTGTCCACTC
* * * * *
538592 TTTAACTCCACCAGTCCACTCTCCAACTCTATCAATCCAT
66 TTCAACTCCACCAATCAACTCTCCAACTCTACCAATCCAC
* * ** * * *
538632 TCTCCAACTCCACCAATCGACTCTCCGTCACCACTAATTCTCTCTCCTCTA-TCACGTGTCCACT
1 TCTCCAACTCCACCAATCCACTCTACACCACCACCAATTCTCTCCCCTCCACT-ACGTGTCCACT
* * * *
538696 CTTCAGCTCCACTAATCAACTCTTCGACT-TCACCAATCCAC
65 CTTCAACTCCACCAATCAACTCTCCAACTCT-ACCAATCCAC
* * * *
538737 TCTTCAACTCAACCAGTCCTCTCT
1 TCTCCAACTCCACCAATCCACTCT
538761 TTAACTCCAT
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
104 2 0.02
105 103 0.98
ACGTcount: A:0.23, C:0.44, G:0.05, T:0.28
Consensus pattern (105 bp):
TCTCCAACTCCACCAATCCACTCTACACCACCACCAATTCTCTCCCCTCCACTACGTGTCCACTC
TTCAACTCCACCAATCAACTCTCCAACTCTACCAATCCAC
Found at i:538760 original size:21 final size:21
Alignment explanation
Indices: 538690--538767 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
538680 CTATCACGTG
* * *
538690 TCCACTCTTCAGCTCCACTAA
1 TCCACTCTTCAACTCAACCAA
* *
538711 TCAACTCTTCGACTTC-ACCAA
1 TCCACTCTTCAAC-TCAACCAA
*
538732 TCCACTCTTCAACTCAACCAG
1 TCCACTCTTCAACTCAACCAA
* *
538753 TCCTCTCTTTAACTC
1 TCCACTCTTCAACTC
538768 CATATCCAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.24, C:0.41, G:0.04, T:0.31
Consensus pattern (21 bp):
TCCACTCTTCAACTCAACCAA
Found at i:538814 original size:159 final size:159
Alignment explanation
Indices: 538613--538929 Score: 386
Period size: 159 Copynumber: 2.0 Consensus size: 159
538603 CAGTCCACTC
* * *
538613 TCCAACTCTATCAATCCATTCTCCAACTCCACCAATCGACTCTCCGTCACCACTAA-TTCTCTCT
1 TCCAACTCTATCAATCCACTCTCCAACTCCACCAATCGACTCTCCATCACCAC-AAGTTCTCTCC
* * * * * *
538677 CCTCTATCACGTGTCCACTCTTCAGCTCCACTAATCAACTCTTCGACTTCACCAATCCACTCT-T
65 CCTCCACCACGTGTCCACTCTCCAGCTCCACTAATCAACTCTCCGAATCCACCAATCCACTCTCT
* *
538741 CAACTCAACCAGTCCTCTCTTTAACTCCATA
130 -AACTCAACCAGTCCACTCTCTAACTCCATA
* * * * * * *
538772 TCCAACTCTATTAATCCACTCTCCAATTTCGCCAATCTACTCTCTATCACCACAAGTTCTTTCCC
1 TCCAACTCTATCAATCCACTCTCCAACTCCACCAATCGACTCTCCATCACCACAAGTTCTCTCCC
* * * *
538837 CTCCACCATGTGTCTACTCTCCAGCTCCACTAGTCGACTCTCCGAATCCACCAATCCACTCTCTA
66 CTCCACCACGTGTCCACTCTCCAGCTCCACTAATCAACTCTCCGAATCCACCAATCCACTCTCTA
* *
538902 ACTCTACCAGTTCACTCTCTAACTCCAT
131 ACTCAACCAGTCCACTCTCTAACTCCAT
538930 CAATCCATTC
Statistics
Matches: 132, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
158 2 0.02
159 129 0.98
160 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.05, T:0.30
Consensus pattern (159 bp):
TCCAACTCTATCAATCCACTCTCCAACTCCACCAATCGACTCTCCATCACCACAAGTTCTCTCCC
CTCCACCACGTGTCCACTCTCCAGCTCCACTAATCAACTCTCCGAATCCACCAATCCACTCTCTA
ACTCAACCAGTCCACTCTCTAACTCCATA
Found at i:538910 original size:21 final size:21
Alignment explanation
Indices: 538883--538963 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 21
538873 ACTCTCCGAA
538883 TCCACCAATCCACTCTCTAAC
1 TCCACCAATCCACTCTCTAAC
* * *
538904 TCTACCAGTTCACTCTCTAAC
1 TCCACCAATCCACTCTCTAAC
* *
538925 TCCATCAATCCATTCTCTAAC
1 TCCACCAATCCACTCTCTAAC
*
538946 TCCACCATTCCACTCTCT
1 TCCACCAATCCACTCTCT
538964 GTCACCACCG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.25, C:0.43, G:0.01, T:0.31
Consensus pattern (21 bp):
TCCACCAATCCACTCTCTAAC
Found at i:538919 original size:42 final size:43
Alignment explanation
Indices: 538873--538962 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
538863 CCACTAGTCG
*
538873 ACTCTCCGAA-TCCACCAATCCACTCTCTAACTCTACCAGTT-C
1 ACTCTCCGAACTCCACCAATCCACTCTCTAACTCCACCA-TTCC
* * *
538915 ACTCT-CTAACTCCATCAATCCATTCTCTAACTCCACCATTCC
1 ACTCTCCGAACTCCACCAATCCACTCTCTAACTCCACCATTCC
538957 ACTCTC
1 ACTCTC
538963 TGTCACCACC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 5 0.12
42 36 0.88
ACGTcount: A:0.26, C:0.43, G:0.02, T:0.29
Consensus pattern (43 bp):
ACTCTCCGAACTCCACCAATCCACTCTCTAACTCCACCATTCC
Found at i:538963 original size:42 final size:42
Alignment explanation
Indices: 538883--538963 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
538873 ACTCTCCGAA
*
538883 TCCACCAATCCACTCTCTAACTCTACCAGTTCACTCTCTAAC
1 TCCACCAATCCACTCTCTAACTCCACCAGTTCACTCTCTAAC
* *
538925 TCCATCAATCCATTCTCTAACTCCACCA-TTCCACTCTCT
1 TCCACCAATCCACTCTCTAACTCCACCAGTT-CACTCTCT
538964 GTCACCACCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.25, C:0.43, G:0.01, T:0.31
Consensus pattern (42 bp):
TCCACCAATCCACTCTCTAACTCCACCAGTTCACTCTCTAAC
Found at i:539135 original size:21 final size:21
Alignment explanation
Indices: 539111--539172 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
539101 ACTCTTCGAT
539111 TCTACCAATCCACTCTCCAAA
1 TCTACCAATCCACTCTCCAAA
** * *
539132 TCTACCAGCCCATTCTCCAAG
1 TCTACCAATCCACTCTCCAAA
*
539153 TCTATCAATCCACTCTCCAA
1 TCTACCAATCCACTCTCCAA
539173 CTCCACTAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.42, G:0.03, T:0.26
Consensus pattern (21 bp):
TCTACCAATCCACTCTCCAAA
Found at i:539185 original size:21 final size:21
Alignment explanation
Indices: 539161--539231 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
539151 AGTCTATCAA
539161 TCCACTCTCCAACTCCACTAG
1 TCCACTCTCCAACTCCACTAG
* * *
539182 TCCACTTTCCAACCCCA-TCAA
1 TCCACTCTCCAACTCCACT-AG
* *
539203 ACCACTCTCTAACTCCACTAG
1 TCCACTCTCCAACTCCACTAG
539224 TCCACTCT
1 TCCACTCT
539232 ATGTCACCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.25, C:0.46, G:0.03, T:0.25
Consensus pattern (21 bp):
TCCACTCTCCAACTCCACTAG
Found at i:539193 original size:42 final size:42
Alignment explanation
Indices: 539076--539229 Score: 134
Period size: 42 Copynumber: 3.7 Consensus size: 42
539066 CCCTCCACGC
* * * * *
539076 ATCCACTCTCTAACTCCA-TCAGTTCACTCTT-CGATTCTACCA
1 ATCCACTCTCCAACTCCACT-AGTCCACT-TTCCAACTCTATCA
* * * * *
539118 ATCCACTCTCCAAATCTACCAGCCCA-TTCTCCAAGTCTATCA
1 ATCCACTCTCCAACTCCACTAGTCCACTT-TCCAACTCTATCA
* *
539160 ATCCACTCTCCAACTCCACTAGTCCACTTTCCAACCCCATCA
1 ATCCACTCTCCAACTCCACTAGTCCACTTTCCAACTCTATCA
* *
539202 AACCACTCTCTAACTCCACTAGTCCACT
1 ATCCACTCTCCAACTCCACTAGTCCACT
539230 CTATGTCACC
Statistics
Matches: 90, Mismatches: 18, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 85 0.94
43 2 0.02
ACGTcount: A:0.27, C:0.42, G:0.04, T:0.27
Consensus pattern (42 bp):
ATCCACTCTCCAACTCCACTAGTCCACTTTCCAACTCTATCA
Found at i:539612 original size:63 final size:63
Alignment explanation
Indices: 539468--539601 Score: 198
Period size: 63 Copynumber: 2.1 Consensus size: 63
539458 ATTATCCAAC
** *
539468 TCCACCACTTATCGACTCTTTAACTCTATCACTCCACTCTTCACCACATTCGATTCTCTCCCA
1 TCCACCACCCATCGACTCTTCAACTCTATCACTCCACTCTTCACCACATTCGATTCTCTCCCA
* * *
539531 TCCACCACCCATCGACTCTTCAACTCTATCACTCCACTTTTCACCAC-TATCGGTTCTCTCCTA
1 TCCACCACCCATCGACTCTTCAACTCTATCACTCCACTCTTCACCACAT-TCGATTCTCTCCCA
539594 TCCACCAC
1 TCCACCAC
539602 GCGTTTACTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 1 0.02
63 63 0.98
ACGTcount: A:0.22, C:0.43, G:0.04, T:0.31
Consensus pattern (63 bp):
TCCACCACCCATCGACTCTTCAACTCTATCACTCCACTCTTCACCACATTCGATTCTCTCCCA
Found at i:539717 original size:63 final size:63
Alignment explanation
Indices: 539650--539886 Score: 185
Period size: 63 Copynumber: 3.8 Consensus size: 63
539640 CCTTGCATTT
* * ** *
539650 ACTCTTCAACTCCACCAATCTACTATTCACCACCATC-AGTTCTCTCCCATTCACTA-AGTGTCC
1 ACTCTTCAACTCCACCAATCCACTATCCACCACCATCGA-TTCTCTCCCAACCACCACA-TGTCC
* * * *
539713 ACTCTCCAACTCCACCAGTCCACTCTCCACCACCATCGATTCTCTCTCAACCACCACATGTCC
1 ACTCTTCAACTCCACCAATCCACTATCCACCACCATCGATTCTCTCCCAACCACCACATGTCC
* * * * * * * * * * *
539776 ACTCTTCCACTCCATCAGTCCACTTTCCACCACCACCGGTTCTTTCCTC-TCCACTACGTGTTC
1 ACTCTTCAACTCCACCAATCCACTATCCACCACCATCGATTCTCTCC-CAACCACCACATGTCC
* * * * *
539839 ACTC-TCTAACTCCACTAGTCCACTCTCCATCACCACCGATTCTCTCCC
1 ACTCTTC-AACTCCACCAATCCACTATCCACCACCATCGATTCTCTCCC
539887 CTCCACTACG
Statistics
Matches: 142, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
62 3 0.02
63 136 0.96
64 3 0.02
ACGTcount: A:0.22, C:0.45, G:0.05, T:0.28
Consensus pattern (63 bp):
ACTCTTCAACTCCACCAATCCACTATCCACCACCATCGATTCTCTCCCAACCACCACATGTCC
Found at i:539767 original size:126 final size:125
Alignment explanation
Indices: 539650--539996 Score: 299
Period size: 126 Copynumber: 2.8 Consensus size: 125
539640 CCTTGCATTT
* * *
539650 ACTCTTCAACTCCACCAATCTACTATT-CACCACCATCAGTTCTCTCC-CATTCACTAAGTGTCC
1 ACTCTTCAACTCCACCAATCCACT-TTCCACCACCACCAGTTCTCTCCTC-TCCACTAAGTGTCC
*
539713 ACTCTCCAACTCCACCAGTCCACTCTCCACCACCATCGATTCTCTCTCAACCACCACATGTCC
64 ACTCTCCAACTCCACCAGTCCACTCTCCACCACCA-CGATTCTCTCCCAACCACCACATGTCC
* * * * * * *
539776 ACTCTTCCACTCCATCAGTCCACTTTCCACCACCACCGGTTCTTTCCTCTCCACTACGTGTTCAC
1 ACTCTTCAACTCCACCAATCCACTTTCCACCACCACCAGTTCTCTCCTCTCCACTAAGTGTCCAC
* * * ** * *
539841 TCTCTAACTCCACTAGTCCACTCTCCATCACCACCGATTCTCTCCCCTCCACTACGA-GTTC
66 TCTCCAACTCCACCAGTCCACTCTCCACCACCA-CGATTCTCTCCCAACCACCAC-ATGTCC
* * * * * * * * * * **
539902 ACT-TTCCACCTCCACTAGTTCA-TTCACCACCACCACTAATTCTCCCCCCTCCACTATGCATCC
1 ACTCTT-CAACTCCACCAATCCACTT-TCCACCACCACCAGTTCTCTCCTCTCCACTAAGTGTCC
* * *
539965 ACTCTCCACCTCCACCAATTCACTCTCCACCA
64 ACTCTCCAACTCCACCAGTCCACTCTCCACCA
539997 TCGGTTCTCT
Statistics
Matches: 175, Mismatches: 41, Indels: 10
0.77 0.18 0.04
Matches are distributed among these distances:
125 6 0.03
126 167 0.95
127 2 0.01
ACGTcount: A:0.22, C:0.46, G:0.05, T:0.27
Consensus pattern (125 bp):
ACTCTTCAACTCCACCAATCCACTTTCCACCACCACCAGTTCTCTCCTCTCCACTAAGTGTCCAC
TCTCCAACTCCACCAGTCCACTCTCCACCACCACGATTCTCTCCCAACCACCACATGTCC
Found at i:539780 original size:21 final size:22
Alignment explanation
Indices: 539708--539780 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 22
539698 ATTCACTAAG
*
539708 TGTCCACTCTCCAA-CTCCACCA
1 TGTCCACTCT-CAACCACCACCA
* *
539730 -GTCCACTCTCCACCACCATCGA
1 TGTCCACTCTCAACCACCA-CCA
*
539752 T-T-CTCTCTCAACCACCA-CA
1 TGTCCACTCTCAACCACCACCA
539771 TGTCCACTCT
1 TGTCCACTCT
539781 TCCACTCCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 31 0.79
22 3 0.08
ACGTcount: A:0.22, C:0.48, G:0.05, T:0.25
Consensus pattern (22 bp):
TGTCCACTCTCAACCACCACCA
Found at i:539891 original size:63 final size:63
Alignment explanation
Indices: 539689--539996 Score: 278
Period size: 63 Copynumber: 4.9 Consensus size: 63
539679 CCACCATCAG
* * * * *
539689 TTCTCTCCCATTCACTAAGTGTCCACTCTCCAACTCCACCAGTCCACTCTCCACCACCATCGA
1 TTCTCTCCCCTCCACTACGTGTCCACTCTCCAACTCCACTAGTCCACTCTCCACCACCACCGA
* ** * * * *
539752 TTCTCTCTCAACCACCACATGTCCACTCTTCC-ACTCCA-TCAGTCCACTTTCCACCACCACCGG
1 TTCTCTCCCCTCCACTACGTGTCCACTC-TCCAACTCCACT-AGTCCACTCTCCACCACCACCGA
* * * * *
539815 TTCTTTCCTCTCCACTACGTGTTCACTCTCTAACTCCACTAGTCCACTCTCCATCACCACCGA
1 TTCTCTCCCCTCCACTACGTGTCCACTCTCCAACTCCACTAGTCCACTCTCCACCACCACCGA
* * * * * * * **
539878 TTCTCTCCCCTCCACTACGAGTTCACTTTCCACCTCCACTAGTTCATTCACCACCACCACTAA
1 TTCTCTCCCCTCCACTACGTGTCCACTCTCCAACTCCACTAGTCCACTCTCCACCACCACCGA
* * ** * * * *
539941 TTCTCCCCCCTCCACTATGCATCCACTCTCCACCTCCACCAATTCACTCTCCACCA
1 TTCTCTCCCCTCCACTACGTGTCCACTCTCCAACTCCACTAGTCCACTCTCCACCA
539997 TCGGTTCTCT
Statistics
Matches: 197, Mismatches: 44, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
62 2 0.01
63 191 0.97
64 4 0.02
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.27
Consensus pattern (63 bp):
TTCTCTCCCCTCCACTACGTGTCCACTCTCCAACTCCACTAGTCCACTCTCCACCACCACCGA
Found at i:540075 original size:18 final size:18
Alignment explanation
Indices: 540030--540077 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
540020 CATCCACTCT
* **
540030 TCACCACCAACAGTTCTC
1 TCACCACCACCAGTTCAA
* *
540048 TCCCCTCCACCAGTTCAA
1 TCACCACCACCAGTTCAA
540066 TCACCACCACCA
1 TCACCACCACCA
540078 CATAAACTAG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.50, G:0.04, T:0.19
Consensus pattern (18 bp):
TCACCACCACCAGTTCAA
Found at i:540120 original size:44 final size:43
Alignment explanation
Indices: 540020--540120 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 43
540010 CTCTATCAAA
* * *
540020 CATCCACTCTTCACCACCAACAGTTCTCTCCCCTCCACCAGTT
1 CATCCACTCTCCACCACAAACAGTTCTCTCCCCTCCACCAGCT
*
540063 CAAT-CAC-CACCACCACATAAACTAGTTCTCT-CCCTCCACCA-CT
1 C-ATCCACTCTCCACCAC--AAAC-AGTTCTCTCCCCTCCACCAGCT
540106 CATCCACTCTCCACC
1 CATCCACTCTCCACC
540121 TTCATTAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
42 9 0.19
43 9 0.19
44 21 0.45
45 8 0.17
ACGTcount: A:0.25, C:0.50, G:0.03, T:0.23
Consensus pattern (43 bp):
CATCCACTCTCCACCACAAACAGTTCTCTCCCCTCCACCAGCT
Found at i:544882 original size:37 final size:38
Alignment explanation
Indices: 544823--544896 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
544813 TGCAGCTTGT
* *
544823 TTTTGTGCTTCCATTGTCTAATTTCCCTCTATTTTCTA
1 TTTTGTGCTTCCATTGTATAATTTCCCTCAATTTTCTA
*
544861 TTTTGTGCTT-CATTGTATAATTTTCCTCAATTTTCT
1 TTTTGTGCTTCCATTGTATAATTTCCCTCAATTTTCT
544897 CCTGATGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 23 0.70
38 10 0.30
ACGTcount: A:0.15, C:0.20, G:0.08, T:0.57
Consensus pattern (38 bp):
TTTTGTGCTTCCATTGTATAATTTCCCTCAATTTTCTA
Found at i:548913 original size:29 final size:29
Alignment explanation
Indices: 548857--548913 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
548847 GGTCATTTTA
* *
548857 TGTCATTTTCATTATAGTTTTTAAATTTG
1 TGTCATTTTCATAATAGTTTATAAATTTG
*
548886 TGTCATTTTCATAAATA-TTTATATATTT
1 TGTCATTTTCAT-AATAGTTTATAAATTT
548914 TTTGGATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (29 bp):
TGTCATTTTCATAATAGTTTATAAATTTG
Found at i:560934 original size:22 final size:22
Alignment explanation
Indices: 560904--560952 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
560894 ATTAATTTTC
*
560904 AAAAACTCCATCTTCTATAATT
1 AAAATCTCCATCTTCTATAATT
* *
560926 AAAATCTCCATTTTCTATCATT
1 AAAATCTCCATCTTCTATAATT
560948 AAAAT
1 AAAAT
560953 TCATATTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATCTCCATCTTCTATAATT
Found at i:565300 original size:18 final size:19
Alignment explanation
Indices: 565279--565316 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
565269 ATAGTTCTAT
565279 TTTTTAA-AAAATTTAAAA
1 TTTTTAAGAAAATTTAAAA
565297 TTTTTAAGAAAATTTAAAA
1 TTTTTAAGAAAATTTAAAA
565316 T
1 T
565317 GTCTTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TTTTTAAGAAAATTTAAAA
Done.