Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008577.1 Hibiscus syriacus cultivar Beakdansim tig00111506_pilon, 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: 1329373
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:319950 original size:2 final size:2
Alignment explanation
Indices: 319943--319986 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
319933 ATGTGAAGAA
319943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
319984 AT A
1 AT A
319987 ATAAGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:320178 original size:12 final size:12
Alignment explanation
Indices: 320161--320185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
320151 AATTAACTCA
320161 AATTTTTACTTG
1 AATTTTTACTTG
320173 AATTTTTACTTG
1 AATTTTTACTTG
320185 A
1 A
320186 CTCAGTCAAA
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
AATTTTTACTTG
Found at i:322468 original size:24 final size:25
Alignment explanation
Indices: 322414--322468 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
322404 GAACGTTCGG
*
322414 TTATGTTCGTTTATATGCATTTAGT
1 TTATGTTCGTTTATATGCATTCAGT
* *
322439 TT-TGTTCGTTTATGTGCGTTCA-T
1 TTATGTTCGTTTATATGCATTCAGT
322462 TTATGTT
1 TTATGTT
322469 TAACCTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.12
24 21 0.81
25 2 0.08
ACGTcount: A:0.15, C:0.09, G:0.18, T:0.58
Consensus pattern (25 bp):
TTATGTTCGTTTATATGCATTCAGT
Found at i:323992 original size:10 final size:10
Alignment explanation
Indices: 323977--324051 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
323967 GGGTCTCCAA
323977 CGTTTATGTT
1 CGTTTATGTT
323987 CGTTTATGTT
1 CGTTTATGTT
323997 CG----TGTT
1 CGTTTATGTT
*
324003 CATTTATGTT
1 CGTTTATGTT
*
324013 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
324024 ATGTTTGTGTT
1 -CGTTTATGTT
324035 CGTTTATGTT
1 CGTTTATGTT
324045 CGTTTAT
1 CGTTTAT
324052 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:324008 original size:16 final size:16
Alignment explanation
Indices: 323983--324047 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
323973 CCAACGTTTA
323983 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
323999 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
324015 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
324031 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
324047 T
1 T
324048 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:324138 original size:16 final size:16
Alignment explanation
Indices: 324117--324149 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
324107 AAAAAATTTT
324117 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
324133 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
324149 T
1 T
324150 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:346729 original size:37 final size:36
Alignment explanation
Indices: 346654--346729 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
346644 TTTTTATATT
*
346654 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
346690 TTTAATTTTTTTAAAAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAAAAAATTATATAAATATTAT-CAA
346727 TTT
1 TTT
346730 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 18 0.51
37 17 0.49
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:348614 original size:22 final size:22
Alignment explanation
Indices: 348575--348616 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
348565 GAGTTTGAAA
*
348575 ATATTTGATAAATCGAAAAATG
1 ATATTTGATAAATAGAAAAATG
348597 ATATTT-ATAAATAAGAAAAA
1 ATATTTGATAAAT-AGAAAAA
348617 ATATGATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (22 bp):
ATATTTGATAAATAGAAAAATG
Found at i:350611 original size:36 final size:36
Alignment explanation
Indices: 350564--350634 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
350554 ACATTGAAAT
350564 GATTGGCAATGGAGAGTAAAACTCAACAATGTATAG
1 GATTGGCAATGGAGAGTAAAACTCAACAATGTATAG
*
350600 GATTGGCAATGGAGGGTAAAACTCAACAATGTATA
1 GATTGGCAATGGAGAGTAAAACTCAACAATGTATA
350635 TTTGAGGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (36 bp):
GATTGGCAATGGAGAGTAAAACTCAACAATGTATAG
Found at i:358522 original size:326 final size:328
Alignment explanation
Indices: 357896--358550 Score: 1216
Period size: 326 Copynumber: 2.0 Consensus size: 328
357886 AAAAAAAATC
357896 ACAATTCAGAATATACTTGTCTGAGAAAAGAACAGACAGATCTTCAGAAGCCTAAGCACATATCA
1 ACAATTCAGAATATACTTGTCTGAGAAAAGAACAGACAGATCTTCAGAAGCCTAAGCACATATCA
357961 ATAATTAGCTCATTCACCCACCTCCCCAGTAGCTGTATCCCAACAAATAGTCCGATTGTCTTTGG
66 ATAATTAGCTCATTCACCCACCTCCCCAGTAGCTGTATCCCAACAAATAGTCCGATTGTCTTTGG
358026 CACATGTGAGTAAATAAGAGCTGTCAGAGGGACACCATGCCATTGCATTACACCTGGAACAATAG
131 CACATGTGAGTAAATAAGAGCTGTCAGAGGGACACCATGCCATTGCATTACACCTGGAACAATAG
358091 ACGGATAAATCAAATATCAGAACCAAAAATAAAACAATTCCTATTTAACTTCGGACCACAAAAGA
196 ACGGATAAATCAAATATCAGAACCAAAAATAAAACAATTCCTATTTAACTTCGGACCACAAAAGA
358156 CCTAGAAAAATATGCCTAAATAGAATGGAGAGATGGATAACTATAAAAAAATTAATGCAT-TACA
261 CCTAGAAAAATATGCCTAAATAGAATGGAGAGATGGATAACTATAAAAAAATTAATGCATATACA
358220 AGG
326 AGG
358223 ACAATTCAGAATATACTTGTCTGAG-AAAGAACAGACAGATCTTCAGAAGCCTAAAGCACATATC
1 ACAATTCAGAATATACTTGTCTGAGAAAAGAACAGACAGATCTTCAGAAGCCT-AAGCACATATC
358287 AATAATTAGCTCATTCACCCACCTCCCCAGTAGCTGTATCCCAACAAATAGT-CGATTGTCTTTG
65 AATAATTAGCTCATTCACCCACCTCCCCAGTAGCTGTATCCCAACAAATAGTCCGATTGTCTTTG
358351 GCACATGTGAGTAAATAAGAGCTGTCAGAGGGACACCATGCCATTGCAATTACACCTGGAACAAT
130 GCACATGTGAGTAAATAAGAGCTGTCAGAGGGACACCATGCCATTGC-ATTACACCTGGAACAAT
358416 AGACACGGATAAATCAAATATCAGAACCAAAAATAAAACAATTCCTATTTAACTTCGGACCACAA
194 AG--ACGGATAAATCAAATATCAGAACCAAAAATAAAACAATTCCTATTTAACTTCGGACCACAA
358481 AAGACCTAG-AAAATAATGCCT-AA-A-AATGGAGAGATGGATAACTATAAAAAAATTAATGCAT
257 AAGACCTAGAAAAAT-ATGCCTAAATAGAATGGAGAGATGGATAACTATAAAAAAATTAATGCAT
358542 ATACAAGG
321 ATACAAGG
358550 A
1 A
358551 GAGACAATAT
Statistics
Matches: 322, Mismatches: 0, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
326 123 0.38
327 116 0.36
328 7 0.02
329 76 0.24
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.22
Consensus pattern (328 bp):
ACAATTCAGAATATACTTGTCTGAGAAAAGAACAGACAGATCTTCAGAAGCCTAAGCACATATCA
ATAATTAGCTCATTCACCCACCTCCCCAGTAGCTGTATCCCAACAAATAGTCCGATTGTCTTTGG
CACATGTGAGTAAATAAGAGCTGTCAGAGGGACACCATGCCATTGCATTACACCTGGAACAATAG
ACGGATAAATCAAATATCAGAACCAAAAATAAAACAATTCCTATTTAACTTCGGACCACAAAAGA
CCTAGAAAAATATGCCTAAATAGAATGGAGAGATGGATAACTATAAAAAAATTAATGCATATACA
AGG
Found at i:364626 original size:12 final size:12
Alignment explanation
Indices: 364609--364633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
364599 AAGATAAAAT
364609 TTATACATTAGA
1 TTATACATTAGA
364621 TTATACATTAGA
1 TTATACATTAGA
364633 T
1 T
364634 CAAAGTTTGT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTATACATTAGA
Found at i:365244 original size:25 final size:24
Alignment explanation
Indices: 365200--365249 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
365190 ATTTAATATT
* *
365200 TAAATAAAATTATAGTAAAATTTA
1 TAAAAAAAATTATAGTAAAAATTA
365224 TAAAAAAAATATATA-TAAAAAATTA
1 TAAAAAAAAT-TATAGT-AAAAATTA
365249 T
1 T
365250 TATATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAAAAAAATTATAGTAAAAATTA
Found at i:371542 original size:24 final size:24
Alignment explanation
Indices: 371515--371565 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
371505 TCTTTAGAAA
371515 AAAAATAAAAA-AAAATAAATT-T
1 AAAAATAAAAATAAAATAAATTAT
*
371537 ATAAAATAAAAATATAATAAATTAT
1 A-AAAATAAAAATAAAATAAATTAT
371562 AAAA
1 AAAA
371566 CTATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 10 0.40
24 12 0.48
25 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATAAAAATAAAATAAATTAT
Found at i:371573 original size:24 final size:24
Alignment explanation
Indices: 371516--371565 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
371506 CTTTAGAAAA
*
371516 AAAATAAAAA-AAAATAAATTTAT
1 AAAATAAAAATATAATAAATTTAT
371539 AAAATAAAAATATAATAAA-TTAT
1 AAAATAAAAATATAATAAATTTAT
371562 AAAA
1 AAAA
371566 CTATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATAAAAATATAATAAATTTAT
Found at i:372388 original size:21 final size:21
Alignment explanation
Indices: 372349--372388 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
372339 TTATTCACAT
* * *
372349 ATAAATTATTATATGAATATC
1 ATAAATTATCACATCAATATC
372370 ATAAATTATCACATCAATA
1 ATAAATTATCACATCAATA
372389 ATATAACAGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAAATTATCACATCAATATC
Found at i:372394 original size:21 final size:20
Alignment explanation
Indices: 372347--372394 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
372337 TATTATTCAC
* * *
372347 ATATAAATTATTATATGAAT
1 ATATAAATTATCACATCAAT
372367 ATCATAAATTATCACATCAAT
1 AT-ATAAATTATCACATCAAT
372388 AATATAA
1 -ATATAA
372395 CAGCTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATAAATTATCACATCAAT
Found at i:376835 original size:64 final size:63
Alignment explanation
Indices: 376722--376842 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
376712 GCATAAATTC
* * * *
376722 CATTCGATGTTTGTATTTAAGGGGGTGCATCAATGCACTACTTGTGCATCGATACACTGATGA
1 CATTCGATGTTTGTATTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACACTGATGA
* * * *
376785 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATATACTTCATGTGCATCGATACAC
1 CATTCGATGTTTGTA-TTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACAC
376843 CTTGAACAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 14 0.29
64 35 0.71
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (63 bp):
CATTCGATGTTTGTATTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACACTGATGA
Found at i:388576 original size:34 final size:35
Alignment explanation
Indices: 388533--388619 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 35
388523 TCAATTTGAT
* *
388533 TATAAATTTAAATATTTAGAATT-ATTTTTCATATA
1 TATATATTTAAATATTTAG-ATTAATTTTTAATATA
*
388568 -ATATATTTAAGATATATAGATTAAATTTTTAATATA
1 TATATATTTAA-ATATTTAGATT-AATTTTTAATATA
* *
388604 TATATATATATATATT
1 TATATATTTAAATATT
388620 AAAATAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
34 12 0.29
35 7 0.17
36 15 0.36
37 8 0.19
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (35 bp):
TATATATTTAAATATTTAGATTAATTTTTAATATA
Found at i:388621 original size:22 final size:21
Alignment explanation
Indices: 388563--388621 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
388553 ATTATTTTTC
388563 ATATA-ATATATTTAAGATAT
1 ATATATATATATTTAAGATAT
* * * *
388583 ATAGATTAAATTTTTAATATAT
1 ATATA-TATATATTTAAGATAT
388605 ATATATATATATATTAA
1 ATATATATATAT-TTAA
388622 AATAATTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 20 0.69
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
ATATATATATATTTAAGATAT
Found at i:389439 original size:5 final size:5
Alignment explanation
Indices: 389429--389466 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
389419 AGTTGGCAAA
389429 CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT CTA
1 CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT CTA
389467 CTAATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
CTAAT
Found at i:390422 original size:23 final size:22
Alignment explanation
Indices: 390395--390443 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
390385 TCACCTAAGA
*
390395 TATTTATATACCTAAAATATTAT
1 TATTTAT-TACCTAAAATATCAT
*
390418 TATTT-TTATCTAAAATATCAT
1 TATTTATTACCTAAAATATCAT
390439 T-TTTA
1 TATTTA
390444 ACATTTTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.13
21 14 0.61
22 1 0.04
23 5 0.22
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTATTACCTAAAATATCAT
Found at i:391267 original size:23 final size:24
Alignment explanation
Indices: 391223--391267 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
391213 TATTAAGAGG
* *
391223 TAAATTTTTAAAGTCTTTAAAAAA
1 TAAATTTTTAAAGTCATAAAAAAA
*
391247 TAAATTTTT-AAGTGATAAAAA
1 TAAATTTTTAAAGTCATAAAAA
391268 TAAATTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (24 bp):
TAAATTTTTAAAGTCATAAAAAAA
Found at i:391392 original size:21 final size:21
Alignment explanation
Indices: 391362--391402 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
391352 CAAGAAACTA
*
391362 CTTGCTGGAGACGTTTTCGTT
1 CTTGCCGGAGACGTTTTCGTT
391383 CTTGCCGGAGACGTTTTCGT
1 CTTGCCGGAGACGTTTTCGT
391403 AAACTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.22, G:0.29, T:0.39
Consensus pattern (21 bp):
CTTGCCGGAGACGTTTTCGTT
Found at i:394534 original size:22 final size:22
Alignment explanation
Indices: 394509--394572 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
394499 TTAGTATATC
394509 AAATATATTTATATTTTAATAA
1 AAATATATTTATATTTTAATAA
* * * *
394531 AAATAT-TTAAAAGTATGAATAA
1 AAATATATTTATA-TTTTAATAA
394553 AAATATATTTATATATTTAA
1 AAATATATTTATAT-TTTAA
394573 ATGTATGAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
21 4 0.13
22 20 0.65
23 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
AAATATATTTATATTTTAATAA
Found at i:395678 original size:18 final size:21
Alignment explanation
Indices: 395641--395683 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
395631 TTAGTAAAAG
395641 TTTATCTAAAATATTATTATT
1 TTTATCTAAAATATTATTATT
395662 TTTAT-TAAAAATATTATT-TT
1 TTTATCT-AAAATATTATTATT
395682 TT
1 TT
395684 GATATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATCTAAAATATTATTATT
Found at i:396335 original size:28 final size:28
Alignment explanation
Indices: 396295--396377 Score: 139
Period size: 28 Copynumber: 3.0 Consensus size: 28
396285 ATGACGTTGC
396295 TTTCAAACACTGACTCAACGACATAATG
1 TTTCAAACACTGACTCAACGACATAATG
*
396323 TTTCAAATACTGACTCAACGACATAATG
1 TTTCAAACACTGACTCAACGACATAATG
* *
396351 TTTCAAACACTGACTTAACGACGTAAT
1 TTTCAAACACTGACTCAACGACATAAT
396378 ATAAATAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (28 bp):
TTTCAAACACTGACTCAACGACATAATG
Found at i:396686 original size:15 final size:15
Alignment explanation
Indices: 396666--396698 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
396656 TGTTTTACTC
396666 AAATTTTTAACGTTA
1 AAATTTTTAACGTTA
*
396681 AAA-TTTTACCGTTA
1 AAATTTTTAACGTTA
396695 AAAT
1 AAAT
396699 AAAATTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (15 bp):
AAATTTTTAACGTTA
Found at i:402617 original size:34 final size:33
Alignment explanation
Indices: 402558--402641 Score: 150
Period size: 34 Copynumber: 2.5 Consensus size: 33
402548 TATATATATA
402558 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
*
402591 TTTATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATAT-TTTTATATTAAT
402625 TATATATATAATATTTT
1 TATATATATAATATTTT
402642 CGGGTTCGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 20 0.42
34 28 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:402978 original size:64 final size:64
Alignment explanation
Indices: 402894--403091 Score: 342
Period size: 64 Copynumber: 3.1 Consensus size: 64
402884 TCTTTCATCT
*
402894 TTATTCTTACGAATGAAAGTGGATGGAGCTTTTACTTATCTTACACATTTTTATAAATCATATA
1 TTATACTTACGAATGAAAGTGGATGGAGCTTTTACTTATCTTACACATTTTTATAAATCATATA
*
402958 TTATACTTACGAATGAAAGTGGATGAAGCTTTTACTTATCTTACACATTTTTATAAATCATATA
1 TTATACTTACGAATGAAAGTGGATGGAGCTTTTACTTATCTTACACATTTTTATAAATCATATA
* * **
403022 TTATACTTACGAATGAAAATGGATGGAACTTTTACTTATCTTACACATTTTTATATGTCATATA
1 TTATACTTACGAATGAAAGTGGATGGAGCTTTTACTTATCTTACACATTTTTATAAATCATATA
403086 TTATAC
1 TTATAC
403092 ATGCTTATAT
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 127 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (64 bp):
TTATACTTACGAATGAAAGTGGATGGAGCTTTTACTTATCTTACACATTTTTATAAATCATATA
Found at i:409649 original size:23 final size:24
Alignment explanation
Indices: 409623--409667 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
409613 CATTAAATTA
409623 TTTAAAAATA-TAAATTAAAATGT
1 TTTAAAAATATTAAATTAAAATGT
409646 TTTAAAAATATTAAATTAAAAT
1 TTTAAAAATATTAAATTAAAAT
409668 AATTATTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTAAAAATATTAAATTAAAATGT
Found at i:419513 original size:18 final size:18
Alignment explanation
Indices: 419490--419541 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
419480 AGAATTTCAT
*
419490 GGTGGCTGCCGTGGCTAC
1 GGTGGCCGCCGTGGCTAC
419508 GGTGGCCGCCGTGGCTAC
1 GGTGGCCGCCGTGGCTAC
* *
419526 GGAGGCCGCAGTGGCT
1 GGTGGCCGCCGTGGCT
419542 GAGGCCGCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.08, C:0.29, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTGGCCGCCGTGGCTAC
Found at i:424597 original size:2 final size:2
Alignment explanation
Indices: 424590--424625 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
424580 TTCCATCCTC
424590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
424626 TATTGACCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424767 original size:2 final size:2
Alignment explanation
Indices: 424762--424799 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
424752 ACAAGTCATA
424762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
424800 CAAACCCACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:434211 original size:23 final size:23
Alignment explanation
Indices: 434181--434232 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
434171 TTGATCATTT
434181 TTATCCCTTATAATTCCATCATA
1 TTATCCCTTATAATTCCATCATA
434204 TTATCCCTTATAATTCCATCATA
1 TTATCCCTTATAATTCCATCATA
434227 TTATCC
1 TTATCC
434233 ATAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATCCCTTATAATTCCATCATA
Found at i:438970 original size:2 final size:2
Alignment explanation
Indices: 438958--438989 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
438948 TATTTTACAA
438958 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
438990 ATACAATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:439519 original size:60 final size:59
Alignment explanation
Indices: 439446--439578 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 59
439436 ATATGATGGT
* * * * * * *
439446 CATTTTGTAACTTTTAATAGTCGGATGACTCAACAAAGTAGTATCCTATAATCGGAAGAC
1 CATTTTATAACTTTTAATAATCGAAAGACTCAACAAAATAATACCCTATAATCGG-AGAC
* * *
439506 CATTTTATAACTTTTAATAATTGAAAGACTCAACAAAATAATACCCTATAGTCGGGGAC
1 CATTTTATAACTTTTAATAATCGAAAGACTCAACAAAATAATACCCTATAATCGGAGAC
439565 CATTGTTAT-ACTTT
1 CATT-TTATAACTTT
439579 ACTCTTATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 12 0.19
60 50 0.81
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAATCGAAAGACTCAACAAAATAATACCCTATAATCGGAGAC
Found at i:440450 original size:25 final size:25
Alignment explanation
Indices: 440405--440452 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
440395 TAAGAAAAAA
*
440405 TAAATTGAAAAAATTATTTAAAACC
1 TAAATTGAAAAAATTAATTAAAACC
*
440430 TAAATTGCAGAAAA-TAATTAAAA
1 TAAATTG-AAAAAATTAATTAAAA
440453 TATATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (25 bp):
TAAATTGAAAAAATTAATTAAAACC
Found at i:440481 original size:19 final size:19
Alignment explanation
Indices: 440441--440510 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 19
440431 AAATTGCAGA
440441 AAATAATTAAAATATATAAAAT
1 AAAT-ATTAAAA-AT-TAAAAT
440463 AAATATTAAAAATTAAAAT
1 AAATATTAAAAATTAAAAT
* * * *
440482 -ATTATTGAAAATTTATAT
1 AAATATTAAAAATTAAAAT
440500 AAATATTAAAA
1 AAATATTAAAA
440511 TGTTACACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
18 14 0.34
19 14 0.34
20 2 0.05
21 7 0.17
22 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (19 bp):
AAATATTAAAAATTAAAAT
Found at i:440483 original size:15 final size:16
Alignment explanation
Indices: 440445--440486 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
440435 TGCAGAAAAT
440445 AATTAAAATA-TATAA
1 AATTAAAATATTATAA
440460 AA-T-AAATATTA-AA
1 AATTAAAATATTATAA
440473 AATTAAAATATTAT
1 AATTAAAATATTAT
440487 TGAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAAAATATTATAA
Found at i:443440 original size:13 final size:13
Alignment explanation
Indices: 443422--443449 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
443412 AGACCCTTGA
443422 CTATTTAATTAGT
1 CTATTTAATTAGT
443435 CTATTTAATTAGT
1 CTATTTAATTAGT
443448 CT
1 CT
443450 TTGGTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.54
Consensus pattern (13 bp):
CTATTTAATTAGT
Found at i:452323 original size:16 final size:16
Alignment explanation
Indices: 452301--452361 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
452291 TAATAAATAA
*
452301 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
452317 TCGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
452333 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
452349 ACGAACATAAACG
1 ACGAACATAAACG
452362 TTAGAGACCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.56, C:0.23, G:0.11, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:454671 original size:27 final size:29
Alignment explanation
Indices: 454621--454706 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 29
454611 TAGACGAAAA
*
454621 ATTAAAATTAAAATAATTAAAATTTTAAAT
1 ATTAAAATT-AAATTATTAAAATTTTAAAT
* *
454651 ATT-AAA-TAAATTATTACAA--TTATAT
1 ATTAAAATTAAATTATTAAAATTTTAAAT
*
454676 TTTAAAATTAAATTAGTTAAAATTTTAAAT
1 ATTAAAATTAAATTA-TTAAAATTTTAAAT
454706 A
1 A
454707 AATTATAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
25 7 0.16
26 3 0.07
27 17 0.39
28 6 0.14
29 3 0.07
30 8 0.18
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTAAAATTAAATTATTAAAATTTTAAAT
Found at i:454697 original size:15 final size:14
Alignment explanation
Indices: 454621--454699 Score: 67
Period size: 15 Copynumber: 5.6 Consensus size: 14
454611 TAGACGAAAA
*
454621 ATTAAAATTAAAATA
1 ATTAAAATT-AAATT
454636 ATTAAAATTTTAAA-T
1 ATTAAAA--TTAAATT
454651 ATT-AAA-TAAATT
1 ATTAAAATTAAATT
* *
454663 ATTACAATTATATT
1 ATTAAAATTAAATT
454677 -TTAAAATTAAATT
1 ATTAAAATTAAATT
454690 AGTTAAAATT
1 A-TTAAAATT
454700 TTAAATAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
11 4 0.08
12 4 0.08
13 13 0.25
14 8 0.15
15 18 0.35
16 3 0.06
17 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (14 bp):
ATTAAAATTAAATT
Found at i:487917 original size:21 final size:21
Alignment explanation
Indices: 487891--487936 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
487881 AACCTGTAAA
487891 TGATCTGACTTGTTATTGAAC
1 TGATCTGACTTGTTATTGAAC
487912 TGATCTGACTTGTTATTGAAC
1 TGATCTGACTTGTTATTGAAC
487933 TGAT
1 TGAT
487937 TTAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (21 bp):
TGATCTGACTTGTTATTGAAC
Found at i:488886 original size:2 final size:2
Alignment explanation
Indices: 488879--488906 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
488869 CCTTGCCACT
488879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
488907 ATTGTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:489934 original size:6 final size:6
Alignment explanation
Indices: 489914--489952 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
489904 ATTCCTAGCC
489914 AATTAT ATATATAT AATTAT AATTAT AATTAT AATTAT A
1 AATTAT A-AT-TAT AATTAT AATTAT AATTAT AATTAT A
489953 CTTTATACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.74
7 4 0.13
8 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTAT
Found at i:489946 original size:18 final size:20
Alignment explanation
Indices: 489914--490045 Score: 80
Period size: 20 Copynumber: 6.5 Consensus size: 20
489904 ATTCCTAGCC
489914 AATTATATATATATAATTAT
1 AATTATATATATATAATTAT
489934 AATTATA-AT-TATAATTAT
1 AATTATATATATATAATTAT
* * *
489952 ACTT-TATACTTTATACTT-T
1 AATTATATA-TATATAATTAT
489971 ATATATATATATATATATATTAT
1 A-AT-TATATATATATA-ATTAT
* *
489994 AGTT-TATATACTTATACTTTAT
1 AATTATATATA--TATA-ATTAT
* *
490016 ATTTATATTTATATACATTAT
1 AATTATATATATATA-ATTAT
490037 -A-TATATATA
1 AATTATATATA
490046 AAAGTATATA
Statistics
Matches: 88, Mismatches: 13, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.02
18 13 0.15
19 12 0.14
20 20 0.23
21 16 0.18
22 18 0.20
23 7 0.08
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.53
Consensus pattern (20 bp):
AATTATATATATATAATTAT
Found at i:489960 original size:7 final size:6
Alignment explanation
Indices: 489919--490029 Score: 78
Period size: 6 Copynumber: 16.8 Consensus size: 6
489909 TAGCCAATTA
* * * * *
489919 TATATA TATAAT TATAAT TATAAT TATAAT TATACTT TATACTT TATACTT
1 TATATT TATATT TATATT TATATT TATATT TATA-TT TATA-TT TATA-TT
*
489970 TATATAT ATATATA TATATAT TATAGTT TATATACT TATACTT TATATT
1 TATAT-T -TATATT TATAT-T TATA-TT TATAT--T TATA-TT TATATT
490019 TATATT TATAT
1 TATATT TATAT
490030 ACATTATATA
Statistics
Matches: 92, Mismatches: 5, Indels: 16
0.81 0.04 0.14
Matches are distributed among these distances:
6 46 0.50
7 34 0.37
8 11 0.12
9 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.55
Consensus pattern (6 bp):
TATATT
Found at i:489977 original size:2 final size:2
Alignment explanation
Indices: 489970--490142 Score: 74
Period size: 2 Copynumber: 86.0 Consensus size: 2
489960 CTTTATACTT
* *
489970 TA TA TA TA TA TA TA TA TA TA T- TA TA GTT TA TA TA CT- TA TA CTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA
* * * *
490013 TA TA TT TA TA TT TA TA TA CA T- TA TA TA TA TA TA -A AA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * * * *
490054 TA CA TA TA CTG TA TCG TA TA -A TG TA CA T- TA TA TA TA CA TG CA
1 TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
490096 TCA TA T- TA TCA TA -A TA TT TA TCA TA TA TA TA TA TA TA TA TA
1 T-A TA TA TA T-A TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
490137 TA TA TA
1 TA TA TA
490143 ATTGTTTCAA
Statistics
Matches: 125, Mismatches: 29, Indels: 34
0.66 0.15 0.18
Matches are distributed among these distances:
1 8 0.06
2 105 0.84
3 12 0.10
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:490016 original size:43 final size:43
Alignment explanation
Indices: 489956--490045 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
489946 AATTATACTT
* *
489956 TATACTTTATACTTTATATATATATATATATATATTATAGTTTA
1 TATACTTTATACTTTATATATATATATATATACATTATA-TATA
* *
490000 TATAC-TTATACTTTATATTTATATTTATATACATTATATATA
1 TATACTTTATACTTTATATATATATATATATACATTATATATA
490042 TATA
1 TATA
490046 AAAGTATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 7 0.17
43 30 0.71
44 5 0.12
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (43 bp):
TATACTTTATACTTTATATATATATATATATACATTATATATA
Found at i:490872 original size:15 final size:16
Alignment explanation
Indices: 490835--490873 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
490825 GTTTTGACAT
*
490835 GAACTGACATTAATCC
1 GAACTGAAATTAATCC
490851 GAACTGAAATTAA-CC
1 GAACTGAAATTAATCC
*
490866 GACCTGAA
1 GAACTGAA
490874 CCCGAACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (16 bp):
GAACTGAAATTAATCC
Found at i:494000 original size:29 final size:29
Alignment explanation
Indices: 493967--494045 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
493957 CTAAATTGAG
* *
493967 GTCATTACTTACATCATTTAATTAAAGAT
1 GTCATTGCTTACATCATTTAAGTAAAGAT
* *
493996 GTCATTGCTTACCTCATTTAAGTAATGAT
1 GTCATTGCTTACATCATTTAAGTAAAGAT
494025 GTCATTGCTTACATCAATTTA
1 GTCATTGCTTACATC-ATTTA
494046 GTTAGGTGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 39 0.89
30 5 0.11
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (29 bp):
GTCATTGCTTACATCATTTAAGTAAAGAT
Found at i:497124 original size:59 final size:59
Alignment explanation
Indices: 496997--497125 Score: 136
Period size: 59 Copynumber: 2.2 Consensus size: 59
496987 TAGTGACATT
* * * *
496997 ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGGGGGTGA
1 ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAACCATAGTTTGAGGATAA
* * ** *
497056 ATATAAAATGTTCAAAAGTTT-GGGATCAATTTAGAATGA-AAGCCATGGTTTGAGGATAAA
1 AT-TGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAA-CCATAGTTTGAGGAT-AA
497116 ATTGAAATGT
1 ATTGAAATGT
497126 AAAAGAAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.04
59 35 0.61
60 20 0.35
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (59 bp):
ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAACCATAGTTTGAGGATAA
Found at i:499277 original size:2 final size:2
Alignment explanation
Indices: 499270--499297 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
499260 CCAACCAGTG
499270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
499298 TCACGTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:499558 original size:3 final size:3
Alignment explanation
Indices: 499550--499646 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
499540 ACCGTTTGAC
499550 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
499598 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
499646 T
1 T
499647 TAAATCCACT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:503544 original size:2 final size:2
Alignment explanation
Indices: 503537--503568 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
503527 TCTAAATCAT
503537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
503569 AAGAGAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:506063 original size:14 final size:14
Alignment explanation
Indices: 506044--506070 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
506034 TTTTTAAAAA
506044 AAAAATTAATATTT
1 AAAAATTAATATTT
506058 AAAAATTAATATT
1 AAAAATTAATATT
506071 ATATCAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAATTAATATTT
Found at i:516495 original size:14 final size:14
Alignment explanation
Indices: 516476--516503 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
516466 ATCATAACAA
516476 AATTATATAACTAT
1 AATTATATAACTAT
516490 AATTATATAACTAT
1 AATTATATAACTAT
516504 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:517208 original size:19 final size:19
Alignment explanation
Indices: 517183--517236 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
517173 AATCTATTTG
517183 ATTAAAATAATATAAATTA
1 ATTAAAATAATATAAATTA
* * ***
517202 TTTAAAATACTATTGTTTA
1 ATTAAAATAATATAAATTA
517221 ATTAAAATAATATAAA
1 ATTAAAATAATATAAA
517237 AATTATTAAA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTAAAATAATATAAATTA
Found at i:517939 original size:21 final size:20
Alignment explanation
Indices: 517915--517967 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
517905 AAAAAACCAG
*
517915 TTTTTAAAAAAAAACCGGATT
1 TTTTTAAAAAAAAACC-AATT
* *
517936 TTTTTAGATAAAAATCCAATT
1 TTTTTA-AAAAAAAACCAATT
517957 TTTTTAAAAAA
1 TTTTTAAAAAA
517968 CCAAATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (20 bp):
TTTTTAAAAAAAAACCAATT
Found at i:517966 original size:18 final size:18
Alignment explanation
Indices: 517944--517979 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
517934 TTTTTTTAGA
*
517944 TAAAAATCC-AATTTTTT
1 TAAAAAACCAAATTTTTT
517961 TAAAAAACCAAATTTTTT
1 TAAAAAACCAAATTTTTT
517979 T
1 T
517980 TGATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAAACCAAATTTTTT
Found at i:517993 original size:21 final size:21
Alignment explanation
Indices: 517933--517993 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
517923 AAAAAACCGG
* * *
517933 ATTTTTTTAGATAAAAATCCA
1 ATTTTTTTTGATAAAAAACAA
*
517954 A-TTTTTTT-A-AAAAACCAA
1 ATTTTTTTTGATAAAAAACAA
517972 ATTTTTTTTGATAAAAAACAA
1 ATTTTTTTTGATAAAAAACAA
517993 A
1 A
517994 AACCGATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 7 0.21
21 10 0.30
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (21 bp):
ATTTTTTTTGATAAAAAACAA
Found at i:518610 original size:21 final size:21
Alignment explanation
Indices: 518493--518630 Score: 59
Period size: 21 Copynumber: 6.7 Consensus size: 21
518483 ACGCGAAATA
**
518493 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
518513 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
518533 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
518554 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
518575 ATATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
518596 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
518616 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
518631 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:518692 original size:20 final size:20
Alignment explanation
Indices: 518598--518966 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
518588 GATTTTCCAT
* ** *
518598 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
518618 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
518638 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
518658 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
518678 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
518698 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
518718 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
518738 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
518758 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
518778 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
518798 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
518818 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
518838 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
518858 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
518878 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
518898 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
518918 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
518938 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
518958 AATCACAAC
1 AATCGCAAC
518967 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:519688 original size:24 final size:24
Alignment explanation
Indices: 519649--519695 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
519639 AAATTTGGTC
519649 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
519673 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
519696 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:519886 original size:12 final size:12
Alignment explanation
Indices: 519869--519893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
519859 ATATAATCCT
519869 GAAGAAGAAAAA
1 GAAGAAGAAAAA
519881 GAAGAAGAAAAA
1 GAAGAAGAAAAA
519893 G
1 G
519894 TCCCGAAGAA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:522192 original size:19 final size:19
Alignment explanation
Indices: 522170--522476 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
522160 CGGAAAATAC
*
522170 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
522189 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
522203 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
522223 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
522237 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522256 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
522275 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
522289 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522308 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
522327 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
522341 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
522360 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522379 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522398 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522417 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
522431 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522450 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
522469 AATCGCAA
1 AATCGCAA
522477 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:522285 original size:52 final size:52
Alignment explanation
Indices: 522198--522476 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
522188 AAATCCCAAC
522198 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
522251 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
522303 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
522355 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
522412 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
522464 ATGAAAATCGCAA
1 ATGAAAATCGCAA
522477 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:522321 original size:71 final size:71
Alignment explanation
Indices: 522237--522476 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
522227 GCAACGAGAG
*
522237 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
522302 AATGAA
66 AATGAA
* *
522308 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
522368 TGCGAAATGAA
61 TGCGAAATGAA
522379 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
522444 AATGAA
66 AATGAA
522450 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
522477 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:522477 original size:52 final size:55
Alignment explanation
Indices: 522170--522498 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
522160 CGGAAAATAC
* *
522170 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
522223 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
522275 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
522327 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
522379 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
522431 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
522483 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
522499 ATAAACGCAT
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:522552 original size:142 final size:142
Alignment explanation
Indices: 522170--522503 Score: 520
Period size: 142 Copynumber: 2.4 Consensus size: 142
522160 CGGAAAATAC
* * *
522170 AATCGCAACGCGAAATGAAAATCCCAACATGA-A-AATCGCAATGCGGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAAC--GACAGAATCGCAATGC-GAAATTAAAATCGCAATG
* *
522231 CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
63 CGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATC
522293 GCAATGCGAAATGAA
128 GCAATGCGAAATGAA
522308 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
522373 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
522438 ATGCGAAATGAA
131 ATGCGAAATGAA
* *
522450 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATATAAA
1 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAAT-TAAA
522504 CGCATTGCGA
Statistics
Matches: 181, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.09
138 37 0.20
139 2 0.01
141 1 0.01
142 119 0.66
143 4 0.02
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (142 bp):
AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
ATGCGAAATGAA
Found at i:522613 original size:19 final size:19
Alignment explanation
Indices: 522504--522605 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
522494 GAAATATAAA
522504 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
522523 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
522543 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
522559 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
522576 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
522595 CGCATTGCGAT
1 CGCATTGCGAT
522606 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:524724 original size:14 final size:14
Alignment explanation
Indices: 524705--524761 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
524695 GCGAAATTAA
*
524705 AATCGCAACGACAG
1 AATCGCAACGAAAG
524719 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
524736 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
524752 AATCGCAACG
1 AATCGCAACG
524762 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:524732 original size:33 final size:33
Alignment explanation
Indices: 524686--524778 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
524676 GCGAAACCAA
* *
524686 AATCGCAACGCGAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
524719 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
524752 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
524779 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:524743 original size:19 final size:19
Alignment explanation
Indices: 524649--524783 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
524639 TAGTTTACTT
* *
524649 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
524669 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
524688 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
524707 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
524721 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
524740 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
524754 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
524773 TCGCAATGCGA
1 TCGCAACGCGA
524784 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.10
17 11 0.11
19 47 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:524801 original size:19 final size:19
Alignment explanation
Indices: 524779--524906 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
524769 AAAATCGCAA
524779 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
524798 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
524812 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
524830 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
524844 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
524863 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
524882 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
524902 TGCGA
1 TGCGA
524907 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 20 0.23
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:524864 original size:33 final size:34
Alignment explanation
Indices: 524779--524869 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 34
524769 AAAATCGCAA
524779 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
524812 TGCGA-TTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
524844 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
524870 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:525109 original size:93 final size:93
Alignment explanation
Indices: 524950--525513 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
524940 TTGAATGGAT
524950 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525015 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
525043 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525108 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
525136 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525201 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
525229 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525293 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
525321 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525384 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
525412 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
525477 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
525505 AAATTTACT
1 AAATTTACT
525514 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 89 0.19
92 96 0.21
93 283 0.60
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:525453 original size:276 final size:279
Alignment explanation
Indices: 524950--525513 Score: 1098
Period size: 276 Copynumber: 2.0 Consensus size: 279
524940 TTGAATGGAT
524950 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525015 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
525080 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
525145 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
196 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
525210 GAATTGGCAGCAACCGAAC
261 GAATTGGCAGCAACCGAAC
525229 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
525293 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
525358 TA-TA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
525421 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
196 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
525486 GAATTGGCAGCAACCGAAT
261 GAATTGGCAGCAACCGAAC
525505 AAATTTACT
1 AAATTTACT
525514 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
276 151 0.53
277 2 0.01
278 92 0.32
279 39 0.14
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
GAATTGGCAGCAACCGAAC
Found at i:527236 original size:14 final size:14
Alignment explanation
Indices: 527217--527306 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
527207 TTGAAATGAA
527217 AATCGCAACGAGAG
1 AATCGCAACGAGAG
527231 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
527248 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
527264 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
527283 AATCGCAACGAGAG
1 AATCGCAACGAGAG
527297 AATCGCAACG
1 AATCGCAACG
527307 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:527254 original size:33 final size:33
Alignment explanation
Indices: 527209--527323 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
527199 TCTTTTGGTT
527209 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
527242 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
527275 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
527308 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
527324 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:527255 original size:19 final size:18
Alignment explanation
Indices: 527216--527328 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
527206 GTTGAAATGA
527216 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
527231 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
527248 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
527264 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
527281 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
527297 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
527314 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
527329 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:527359 original size:14 final size:14
Alignment explanation
Indices: 527340--527394 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
527330 TTTGGTTTCG
527340 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
527354 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
527373 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
527387 CGTTGCGA
1 CGTTGCGA
527395 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:527372 original size:33 final size:33
Alignment explanation
Indices: 527324--527394 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
527314 AAAATCGCAA
**
527324 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
527357 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
527390 TGCGA
1 TGCGA
527395 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:527402 original size:33 final size:33
Alignment explanation
Indices: 527335--527416 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
527325 GCGATTTTGG
***
527335 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
527368 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
527401 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
527417 TCATTTATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:527556 original size:33 final size:33
Alignment explanation
Indices: 527514--527584 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
527504 AATACTAACT
*
527514 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
527547 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
527580 TGAAA
1 TGAAA
527585 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:527818 original size:22 final size:22
Alignment explanation
Indices: 527766--527820 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
527756 TGGTTGTGAG
**
527766 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
527788 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
527810 GGATTTCTTCG
1 GGATTTCTTCG
527821 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:527991 original size:20 final size:20
Alignment explanation
Indices: 527966--528158 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
527956 CTTTAAATAT
527966 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
527986 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
528008 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
528027 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
528047 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
528067 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
528087 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
528107 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
528127 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
528147 CGCGTTGCGATT
1 CGCGTTGCGATT
528159 ATTAAAAAAT
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:528153 original size:60 final size:60
Alignment explanation
Indices: 527966--528158 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
527956 CTTTAAATAT
**
527966 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
528027 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
528087 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
528147 CGCGTTGCGATT
1 CGCGTTGCGATT
528159 ATTAAAAAAT
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:528220 original size:42 final size:42
Alignment explanation
Indices: 528126--528220 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
528116 ATTTATGTGT
* * *
528126 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTATTAAAAAA
1 TCGCGTTGCGAATTTCATATTCGCATCGCGATTATTAAAAAA
** * *
528168 TCGCAATGCGAATTTC-TACTATCGCATCGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTCATA-T-TCGCATCGCGATTATTAAAAAA
528210 TCGCGTTGCGA
1 TCGCGTTGCGA
528221 TTTTGGAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
41 2 0.05
42 29 0.69
43 11 0.26
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (42 bp):
TCGCGTTGCGAATTTCATATTCGCATCGCGATTATTAAAAAA
Found at i:528240 original size:20 final size:20
Alignment explanation
Indices: 528215--528266 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
528205 AAGAATCGCG
*
528215 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
528235 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
528255 TTGCGATTCTGG
1 TTGCGATTCTGG
528267 GAATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:530021 original size:18 final size:18
Alignment explanation
Indices: 529998--530032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
529988 GGAGTAATTC
*
529998 TGGTATACAGCATGCCTT
1 TGGTATACAGCAGGCCTT
*
530016 TGGTATAGAGCAGGCCT
1 TGGTATACAGCAGGCCT
530033 ACAGAAAGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
TGGTATACAGCAGGCCTT
Found at i:531370 original size:35 final size:37
Alignment explanation
Indices: 531303--531390 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 37
531293 GTTTTGGCAC
531303 TTAAGCCCATAAGCTTAATTTCCTTTTTTTTTTACTAAGCT
1 TTAAGCCCATAAGCTTAATTTCC----TTTTTTACTAAGCT
531344 TTAAGCCCATAAGCTTAA-TTCC-TTTTTACTAAGCT
1 TTAAGCCCATAAGCTTAATTTCCTTTTTTACTAAGCT
531379 TTAAGCCCATAA
1 TTAAGCCCATAA
531391 TTGATTATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
35 25 0.53
40 4 0.09
41 18 0.38
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (37 bp):
TTAAGCCCATAAGCTTAATTTCCTTTTTTACTAAGCT
Found at i:539415 original size:21 final size:21
Alignment explanation
Indices: 539389--539433 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
539379 GATTTCTGGG
* *
539389 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
539410 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
539431 CAA
1 CAA
539434 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:540326 original size:31 final size:31
Alignment explanation
Indices: 540288--540441 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
540278 GGGTCGAGGG
540288 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
540319 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
540350 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
540381 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
540412 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
540442 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:543414 original size:21 final size:21
Alignment explanation
Indices: 543388--543432 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
543378 GATTTCTGGG
* *
543388 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
543409 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
543430 CAA
1 CAA
543433 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:544330 original size:31 final size:31
Alignment explanation
Indices: 544292--544445 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
544282 GGGTCGAGGG
544292 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
544323 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
544354 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
544385 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
544416 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
544446 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:555334 original size:2 final size:2
Alignment explanation
Indices: 555327--555369 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
555317 ACTAAATCAT
555327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
555369 T
1 T
555370 TTACCATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560058 original size:60 final size:60
Alignment explanation
Indices: 559930--560058 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 60
559920 ATAGTTGGGT
* * **
559930 GACCATTTTTTTAACTTTTAATAGTCAAATGACTCAACAAAGCAATATCATATAGTCAGAG
1 GACCA-TTTTATAACTTTTAATAGTCAAAGGACTCAACAAAGCAATATCATATAAACAGAG
* ** * * * * * *
559991 GATCATTTTATAACTTTTAATAGTCGGAGGACTCAACAAAGTAGTCTCCTATAAACGGGG
1 GACCATTTTATAACTTTTAATAGTCAAAGGACTCAACAAAGCAATATCATATAAACAGAG
560051 GACCATTT
1 GACCATTT
560059 ATGTACTTTA
Statistics
Matches: 54, Mismatches: 14, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
60 50 0.93
61 4 0.07
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCAAAGGACTCAACAAAGCAATATCATATAAACAGAG
Found at i:562869 original size:18 final size:19
Alignment explanation
Indices: 562825--562871 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
562815 TTAATTTCCG
562825 ATCGAAT-ATCTAAAAAAA
1 ATCGAATAATCTAAAAAAA
562843 ATCGAATAAT-TAAAAAAA
1 ATCGAATAATCTAAAAAAA
562861 ATCGAATAATC
1 ATCGAATAATC
562872 GAATTGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (19 bp):
ATCGAATAATCTAAAAAAA
Found at i:564906 original size:60 final size:59
Alignment explanation
Indices: 564800--564948 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 59
564790 TCAAAAGTGT
* * * *
564800 GGACCAATTTAGAAAGAGGGTCATAGTTTAGGGATGAAATCAAAATACTCAAAAGA-TTAA
1 GGACCAATTTAGAATGAGAGTTATAGTTT-GGGATGAAATCAAAATA-TCAAAAAATTTAA
** * ** *
564860 GGATTAATTTAGAATGAGAGTTATAGTTTGTGGATTAAATTGAAATATTAAAAAATTTAA
1 GGACCAATTTAGAATGAGAGTTATAGTTTG-GGATGAAATCAAAATATCAAAAAATTTAA
*
564920 GGACCAATTTA-AATGA-AGTTTATAATTTG
1 GGACCAATTTAGAATGAGAG-TTATAGTTTG
564949 AGGGTGTATG
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.03
59 21 0.29
60 50 0.68
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (59 bp):
GGACCAATTTAGAATGAGAGTTATAGTTTGGGATGAAATCAAAATATCAAAAAATTTAA
Found at i:565359 original size:19 final size:18
Alignment explanation
Indices: 565319--565362 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
565309 ATTGTTTTTC
*
565319 TTTTATTTTTTTAAATAA
1 TTTTATTTTTATAAATAA
565337 TTTTATTTTTATAACAT-A
1 TTTTATTTTTATAA-ATAA
565355 TTTT-TTTT
1 TTTTATTTT
565363 GTCTCTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTTTTATAAATAA
Found at i:574849 original size:11 final size:11
Alignment explanation
Indices: 574835--574902 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
574825 TTTATTAAAT
574835 TTAATATATAA
1 TTAATATATAA
*
574846 TTAAAATATAA
1 TTAATATATAA
* *
574857 TAAACATATAA
1 TTAATATATAA
574868 -T-ATATATAA
1 TTAATATATAA
* *
574877 ATAAAATATAA
1 TTAATATATAA
574888 -TAGATATATAA
1 TTA-ATATATAA
574899 TTAA
1 TTAA
574903 AAATAAAGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
9 7 0.15
10 3 0.07
11 34 0.74
12 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (11 bp):
TTAATATATAA
Found at i:574857 original size:18 final size:17
Alignment explanation
Indices: 574831--574889 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
574821 GATTTTTATT
*
574831 AAATTTAATATATAATTA
1 AAATATAATATA-AATTA
574849 AAATATAATA-AACA-TA
1 AAATATAATATAA-ATTA
*
574865 TAATAT-ATATAAA-TA
1 AAATATAATATAAATTA
574880 AAATATAATA
1 AAATATAATA
574890 GATATATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 11 0.31
16 13 0.37
17 2 0.06
18 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATATAAATTA
Found at i:574876 original size:20 final size:19
Alignment explanation
Indices: 574851--574895 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
574841 TATAATTAAA
*
574851 ATATAATAAACATATAATAT
1 ATATAATAAA-ATATAATAG
574871 ATATAAATAAAATATAATAG
1 ATAT-AATAAAATATAATAG
574891 ATATA
1 ATATA
574896 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.70
21 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATAATAAAATATAATAG
Found at i:574876 original size:31 final size:31
Alignment explanation
Indices: 574838--574899 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
574828 ATTAAATTTA
*
574838 ATATATAATTAAAATATAATAAACATATAAT
1 ATATATAAATAAAATATAATAAACATATAAT
* *
574869 ATATATAAATAAAATATAATAGATATATAAT
1 ATATATAAATAAAATATAATAAACATATAAT
574900 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (31 bp):
ATATATAAATAAAATATAATAAACATATAAT
Found at i:574897 original size:22 final size:20
Alignment explanation
Indices: 574851--574908 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
574841 TATAATTAAA
574851 ATAT-AATAAACATATAATAT
1 ATATAAATAAA-ATATAATAT
574871 ATATAAATAAAATATAATAGAT
1 ATATAAATAAAATATAAT--AT
*
574893 ATATAATTAAAA-ATAA
1 ATATAAATAAAATATAA
574909 AGCCGGTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 11 0.32
21 10 0.29
22 13 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATAAATAAAATATAATAT
Found at i:575810 original size:39 final size:39
Alignment explanation
Indices: 575756--575953 Score: 317
Period size: 39 Copynumber: 5.1 Consensus size: 39
575746 GTCACTAAAC
* * *
575756 CTGAGGGAGTGGTTAATGTTGCAA-TCAATTCTTCAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACT-GATTCTTCAAAAT
*
575795 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTACAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
* *
575834 CTGAGGGAGAGGTTAATGTTGCAACTGATTCTACAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
575873 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
*
575912 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAGT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
575951 CTG
1 CTG
575954 CTGTTATTGA
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 149 0.99
40 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (39 bp):
CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
Found at i:580212 original size:2 final size:2
Alignment explanation
Indices: 580207--580234 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
580197 ACACACACAA
580207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
580235 TTGTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:589135 original size:16 final size:16
Alignment explanation
Indices: 589114--589152 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
589104 ATTAATAATT
*
589114 ATTAATTTATCGATAA
1 ATTAATATATCGATAA
**
589130 ATTAATATATCTTTAA
1 ATTAATATATCGATAA
589146 ATTAATA
1 ATTAATA
589153 AATTTTTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (16 bp):
ATTAATATATCGATAA
Found at i:589160 original size:16 final size:16
Alignment explanation
Indices: 589127--589160 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
589117 AATTTATCGA
*
589127 TAAATTAATATATCTT
1 TAAATTAATAAATCTT
*
589143 TAAATTAATAAATTTT
1 TAAATTAATAAATCTT
589159 TA
1 TA
589161 GTGTAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTAATAAATCTT
Found at i:589778 original size:8 final size:9
Alignment explanation
Indices: 589757--589789 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
589747 ATTAATTAAA
589757 TTTAAAATT
1 TTTAAAATT
589766 TTTAAAA-T
1 TTTAAAATT
589774 TTTAAAATT
1 TTTAAAATT
589783 TTTAAAA
1 TTTAAAA
589790 ATAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:589779 original size:17 final size:17
Alignment explanation
Indices: 589757--589789 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
589747 ATTAATTAAA
589757 TTTAAAATTTTTAAAAT
1 TTTAAAATTTTTAAAAT
589774 TTTAAAATTTTTAAAA
1 TTTAAAATTTTTAAAA
589790 ATAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAAATTTTTAAAAT
Found at i:589803 original size:9 final size:9
Alignment explanation
Indices: 589756--589804 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
589746 TATTAATTAA
589756 ATTTAAAAT
1 ATTTAAAAT
*
589765 TTTTAAAAT
1 ATTTAAAAT
589774 -TTTAAAAT
1 ATTTAAAAT
*
589782 TTTTAAAA-
1 ATTTAAAAT
589790 A--TAAAAT
1 ATTTAAAAT
589797 ATTTAAAA
1 ATTTAAAA
589805 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.15
7 1 0.03
8 8 0.24
9 20 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:589809 original size:14 final size:15
Alignment explanation
Indices: 589776--589810 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
589766 TTTAAAATTT
*
589776 TAAAATTTTTAAAAA
1 TAAAATATTTAAAAA
589791 TAAAATATTTAAAAA
1 TAAAATATTTAAAAA
589806 -AAAAT
1 TAAAAT
589811 TAAAAATACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATATTTAAAAA
Found at i:593209 original size:22 final size:21
Alignment explanation
Indices: 593176--593216 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
593166 AACTGAAACC
593176 GGTTTTTTCGGTTC-GGTTCG
1 GGTTTTTTCGGTTCAGGTTCG
593196 GGTTTTTTAACGGTTCAGGTT
1 GGTTTTTT--CGGTTCAGGTT
593217 TTTCGGTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.07, C:0.12, G:0.32, T:0.49
Consensus pattern (21 bp):
GGTTTTTTCGGTTCAGGTTCG
Found at i:593380 original size:27 final size:28
Alignment explanation
Indices: 593350--593421 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 28
593340 AACCGAATTA
*
593350 AAAAAACGAAGCC-TTTAAA-CCGAACCG
1 AAAAAACGAA-CCGTTTAAAGCCAAACCG
*
593377 -AAAACCGAACCGTTTAAAGCCAAACCG
1 AAAAAACGAACCGTTTAAAGCCAAACCG
*
593404 AACCAAACCGAACCGTTT
1 AA--AAAACGAACCGTTT
593422 TACTCAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 14 0.37
27 7 0.18
28 1 0.03
30 14 0.37
ACGTcount: A:0.44, C:0.29, G:0.14, T:0.12
Consensus pattern (28 bp):
AAAAAACGAACCGTTTAAAGCCAAACCG
Found at i:594137 original size:97 final size:93
Alignment explanation
Indices: 593992--594182 Score: 346
Period size: 97 Copynumber: 2.0 Consensus size: 93
593982 TTTTGAATAA
593992 ATATTATCTTATAATCATCTCAAAACATAAAAAATAATATAGGACAGGTAGAACCGATTTTCTTT
1 ATATTATCTTATAATCATCTCAAAACATAAAAAATAATATAGGACAGGTAGAACCGATTTTCTTT
594057 CGGTTATTGAGAATGAAGCGATTAAGGT
66 CGGTTATTGAGAATGAAGCGATTAAGGT
594085 ATATTATCTTATAATCATCTCAAATTATCCATAAAAAATAATATAGGACAGGTAGAACCGATTTT
1 ATATTATCTTATAATCATCTCAAA--A--CATAAAAAATAATATAGGACAGGTAGAACCGATTTT
594150 CTTTCGGTTATTGAGAATGAAGCGATTAAGGT
62 CTTTCGGTTATTGAGAATGAAGCGATTAAGGT
594182 A
1 A
594183 ATACTTTATC
Statistics
Matches: 94, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
93 24 0.26
95 1 0.01
97 69 0.73
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (93 bp):
ATATTATCTTATAATCATCTCAAAACATAAAAAATAATATAGGACAGGTAGAACCGATTTTCTTT
CGGTTATTGAGAATGAAGCGATTAAGGT
Found at i:594323 original size:31 final size:31
Alignment explanation
Indices: 594288--594358 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
594278 GAATAAATAT
* *
594288 AATTTGATCCTCGAACTTTTGAGAAATTGCA
1 AATTTGATCCTCAAAATTTTGAGAAATTGCA
594319 AATTTGATCCTCAAAATTTTGAGAAATTGCA
1 AATTTGATCCTCAAAATTTTGAGAAATTGCA
*
594350 AATTGGATC
1 AATTTGATC
594359 ATAAATGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (31 bp):
AATTTGATCCTCAAAATTTTGAGAAATTGCA
Found at i:597233 original size:2 final size:2
Alignment explanation
Indices: 597228--597265 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
597218 TATTTTTTAA
597228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
597266 ATTTCTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.