Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008965.1 Hibiscus syriacus cultivar Beakdansim tig00112306_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: 73592
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1233 original size:6 final size:6
Alignment explanation
Indices: 1222--1259 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1212 TTGTGGCGTG
1222 CAAAAA CAAAAA CAAAAA CAAAAA -AAAGAA -AAAAA CAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAA-AA CAAAAA CAA
1260 GGCTCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:20985 original size:11 final size:11
Alignment explanation
Indices: 20969--20993 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20959 TTTTTTTTTC
20969 AAAAAAACAAA
1 AAAAAAACAAA
20980 AAAAAAACAAA
1 AAAAAAACAAA
20991 AAA
1 AAA
20994 GGCAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:21000 original size:14 final size:14
Alignment explanation
Indices: 20972--21014 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
20962 TTTTTTCAAA
20972 AAAACAAAAAA---
1 AAAACAAAAAAGGC
20983 AAAACAAAAAAGGC
1 AAAACAAAAAAGGC
*
20997 AAAAAAAAAAAGGC
1 AAAACAAAAAAGGC
21011 AAAA
1 AAAA
21015 AAACAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.39
14 17 0.61
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAAGGC
Found at i:21006 original size:15 final size:15
Alignment explanation
Indices: 20981--21017 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
20971 AAAAACAAAA
20981 AAAAAACAAAAAAGGC
1 AAAAAA-AAAAAAGGC
20997 -AAAAAAAAAAAGGC
1 AAAAAAAAAAAAGGC
21011 AAAAAAA
1 AAAAAAA
21018 CAAGAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGGC
Found at i:21014 original size:34 final size:32
Alignment explanation
Indices: 20969--21036 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 32
20959 TTTTTTTTTC
*
20969 AAAAAAACAAAAAAAAAACAAAAAAGGCAAAA
1 AAAAAAACAAAAAAAAAACAAAAAAGCCAAAA
* * *
21001 AAAAAAAGGCAAAAAAACAAGAAAAGAGCCAAAA
1 AAAAAAA--CAAAAAAAAAACAAAAAAGCCAAAA
21035 AA
1 AA
21037 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 7 0.23
34 23 0.77
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAAAAAAAACAAAAAAGCCAAAA
Found at i:21015 original size:14 final size:14
Alignment explanation
Indices: 20982--21017 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
20972 AAAACAAAAA
20982 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
20997 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
21011 AAAAAAA
1 AAAAAAA
21018 CAAGAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:29426 original size:20 final size:20
Alignment explanation
Indices: 29401--29443 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
29391 TCTAAGAGTT
*
29401 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
29421 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
29441 CAT
1 CAT
29444 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:32364 original size:19 final size:19
Alignment explanation
Indices: 32311--32364 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
32301 CTGGTTAACG
* *
32311 GTCAACGGATCAAGTCAAA
1 GTCAACGGGTCAGGTCAAA
* *
32330 GTCAATGGG-CTGGGTCAAA
1 GTCAACGGGTC-AGGTCAAA
32349 GTCAACGGGTCAGGTC
1 GTCAACGGGTCAGGTC
32365 GGGTTGACTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.04
19 25 0.93
20 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.19
Consensus pattern (19 bp):
GTCAACGGGTCAGGTCAAA
Found at i:37427 original size:12 final size:11
Alignment explanation
Indices: 37404--37457 Score: 72
Period size: 12 Copynumber: 4.6 Consensus size: 11
37394 ATGAGACTAC
37404 AAAAGAAAGAAG
1 AAAAG-AAGAAG
*
37416 AAAATGATGAAG
1 AAAA-GAAGAAG
37428 AAAAGAAGAAG
1 AAAAGAAGAAG
37439 AAGAAGAAGAAG
1 AA-AAGAAGAAG
37451 AAAAGAA
1 AAAAGAA
37458 AATGAGGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
11 13 0.34
12 24 0.63
13 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:37434 original size:20 final size:20
Alignment explanation
Indices: 37409--37462 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
37399 ACTACAAAAG
*
37409 AAAGAAGAAAATGATGAAGA
1 AAAGAAGAAAATGAAGAAGA
37429 AAAGAAGAAGAA-GAAGAAGA
1 AAAGAAGAA-AATGAAGAAGA
37449 AGAA-AAGAAAATGA
1 A-AAGAAGAAAATGA
37463 GGTAGGAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 24 0.80
21 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.06
Consensus pattern (20 bp):
AAAGAAGAAAATGAAGAAGA
Found at i:37436 original size:3 final size:3
Alignment explanation
Indices: 37410--37457 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
37400 CTACAAAAGA
*
37410 AAG AAG AA- AATG ATG AAG AA- AAG AAG AAG AAG AAG AAG AAG AA-
1 AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
37453 AAG AA
1 AAG AA
37458 AATGAGGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 32 0.82
4 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:37440 original size:23 final size:23
Alignment explanation
Indices: 37404--37457 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
37394 ATGAGACTAC
*
37404 AAAAGAAAGAAGAA-AATGATGAAG
1 AAAAG-AAGAAGAAGAA-GAAGAAG
37428 AAAAGAAGAAGAAGAAGAAGAAG
1 AAAAGAAGAAGAAGAAGAAGAAG
37451 AAAAGAA
1 AAAAGAA
37458 AATGAGGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (23 bp):
AAAAGAAGAAGAAGAAGAAGAAG
Found at i:39790 original size:16 final size:16
Alignment explanation
Indices: 39765--39799 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39755 GGTATTACCC
39765 GACCTATTTTTAACCT
1 GACCTATTTTTAACCT
*
39781 GACCTGTTTTTAACCT
1 GACCTATTTTTAACCT
39797 GAC
1 GAC
39800 ATGTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (16 bp):
GACCTATTTTTAACCT
Found at i:40536 original size:2 final size:2
Alignment explanation
Indices: 40477--40526 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
40467 TTATATAGTT
40477 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
40519 TA TA TA TA
1 TA TA TA TA
40527 AGTTTATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41002 original size:2 final size:2
Alignment explanation
Indices: 40997--41074 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
40987 TTATATAGTT
40997 TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
41038 TA T- 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
41075 ATGGTTTATA
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41547 original size:536 final size:532
Alignment explanation
Indices: 40468--42484 Score: 2421
Period size: 500 Copynumber: 3.8 Consensus size: 532
40458 TAATTTACTT
* *
40468 TATATAGTTTATATATATATATATATATATATATATATATATATATATATATATATATA-AGTTT
1 TATATA-TATATATATATATATATATATATATATATATATATATATATATATATATATATAGTAT
* *
40532 ATATAGGTTATACATACATATTATATAAAATTATTTAATAAATTTAAAAAAAAATTTAAATGTAA
65 ACAT-GGTTATACATACAT-TTATAT-AAATTATTTAA-AAA---AAATAAAAATTTAAATGTAA
40597 ATTATA-AAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
123 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
* * *
40661 CATAAATAGTAGTACATGTCATATTAATTTCATTTGTATAATTAGTATTTTAATTGCATGTTATG
188 CATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGG
* *
40726 TTAATTCTCATTAATAGTCCATTTATTTTGTTGTTATGAATAAG---TAATAAAACCCAAAAATA
253 TTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATA
* *
40788 AATCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGTCCACT
318 AGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACT
* * * *
40853 CCTTTATTACAA-ATATATGCAATAGTGCTAGCCCATTTATATTAGGGTTTGTGATTTAGAGTTT
383 CTTTTATTACAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTGTGATTTAGGGTTT
* * * * * * * ** * * *
40917 AGGGTTTCT-ATAAACTATATACTTTATAGTTTATGCTT-AGTGTTTCTATAAACTATATAAGTA
448 AGTGTTTATGTTAAAGTTTAAAATTTAGGGTTTAGGTTTAAG-ATTTCTATAAACTATATAAGTA
40980 ATTTACTTTATATAGTTTATATATA
512 ATTTACTTTATATAG--TAT-T-TA
*
41005 TATATATATATATATATATTATATATATATATATATTATATATATATATATATATATATATATAT
1 TATATATATATATATATA-TATATATATATATATA-TATATATATATATATATATATATATA-GT
* *
41070 ATATAATGGTTTATACATACATTTATATAAATTATTTAAAAAAATTAAAAATTTAAATGTAAATT
63 ATA-CATGG-TTATACATACATTTATATAAATTATTTAAAAAAAATAAAAATTTAAATGTAAATT
* *
41135 ATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTACATATTATATGGTTAAT
126 ATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT
*
41200 AAATAGTAGTATATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTA
191 AAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTA
41265 ATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGT
256 ATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGT
* * *
41330 TCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCTCAATACATAAG-CCACTCTT
321 CCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTT
**
41394 TTATTACAAATATATATGCATTAGTGCTAGTTTATTTATATTAGGGTTTGTGATTTAGGGTTTAG
386 TTATTAC-AATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTGTGATTTAGGGTTTAG
* ** *
41459 TGCTTAGTGTCTATGGTTTAAAATTTAGGGTTTAAGGTTTAAGGTTTCTATAAACTATATAAGTA
450 TGTTTA-TGT-TAAAGTTTAAAATTTAGGGTTT-AGGTTTAAGATTTCTATAAACTATATAAGTA
41524 ATTTACTTTATATAG--TTTA
512 ATTTACTTTATATAGTATTTA
* * * * ** *
41543 TATATATATATATACA-CTATA-CTATACATA-AT-TATGCATACATAT-TA-A-ATA-A--A-A
1 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAGTATA
* ** * *
41597 -AT-GTT-TA-AT--A---AT-T---TTA---AAAAATAAT--TTA----AATGTAAATTACAAA
66 CATGGTTATACATACATTTATATAAATTATTTAAAAAAAATAAAAATTTAAATGTAAATTATATA
*
41640 AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTACATAAATA
131 AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATA
41705 GTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCA
196 GTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCA
* * *
41770 CATTAATAGCCCATTGATTTTGTTGTTATGAATAAGTAATAATAAAACTCAAAAATAAGTCTATT
261 CATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATT
* * * * *
41835 TGAATTAGTGCTAGTCCATTTACATTAGTTTATATAGGCCCAATACATAAGCTCACTCTTTGATT
326 TGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATT
* * * *
41900 ACAA-ATATATGCATTAGTACTAGTCCATTTACATTAGGGTTTGTGATCTAGGGTTTAGGGTTTA
391 ACAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTGTGATTTAGGGTTTAGTGTTTA
*** * * ** *
41964 TGATTTAAAGTTTAGTGTTTAGGGTTTAGGGTTTATGATTTTTATAAACTATATACTTTA-TTAC
456 TG--TTAAAGTTTAAAATTTAGGGTTTA-GGTTTAAGATTTCTATAAACTATATAAGTAATTTAC
* **
42028 TTTATAGT-TTATGCA
518 TTTATA-TAGTATTTA
* * * * * * * *
42043 TAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATAGTTTATAT
1 TA-TATATATATATA-TATAT-A-T-ATATA-TATATATA-TATATATATATATATA-TATATAT
* *
42108 ATATTATACATGGTT-T--ATACATATATAT-AA--ATTT-----AAA-AAAAA-TTAAATGT-A
58 ATAGTATACATGGTTATACATACATTTATATAAATTATTTAAAAAAAATAAAAATTTAAATGTAA
42159 ATTATATAAAACATGATTAATTAGGTGTT-AATAATTAGTATGTCACATTGCATATTATATGGTT
123 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
42223 CATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGG
188 CATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGG
* *
42288 TTAATTCACATTAATAGCCAATTTATTTTGTTGTTATGAATATGTAATAATAAAACCCAAAAATA
253 TTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATA
* *
42353 AGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCTCAATACATTAGCCCACT
318 AGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACT
* * * *
42418 CTTTTATTACAAATATATATACATCAGTGCTAGTCCATTTATATTAGGGTTTATGGTTTAGGGTT
383 CTTTTATTAC-AATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTGTGATTTAGGGTT
42483 TA
447 TA
42485 AGGTTTTTAT
Statistics
Matches: 1294, Mismatches: 123, Indels: 135
0.83 0.08 0.09
Matches are distributed among these distances:
498 13 0.01
499 96 0.07
500 255 0.20
501 21 0.02
502 1 0.00
503 1 0.00
504 2 0.00
505 1 0.00
506 8 0.01
507 2 0.00
508 4 0.00
509 4 0.00
510 1 0.00
511 10 0.01
512 1 0.00
513 3 0.00
514 1 0.00
515 3 0.00
516 2 0.00
518 3 0.00
519 3 0.00
520 6 0.00
521 5 0.00
522 3 0.00
524 3 0.00
525 4 0.00
526 229 0.18
527 30 0.02
528 52 0.04
529 3 0.00
530 1 0.00
531 2 0.00
532 10 0.01
533 1 0.00
534 1 0.00
535 31 0.02
536 174 0.13
537 22 0.02
538 58 0.04
539 88 0.07
540 64 0.05
541 15 0.01
543 14 0.01
544 41 0.03
545 2 0.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (532 bp):
TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAGTATA
CATGGTTATACATACATTTATATAAATTATTTAAAAAAAATAAAAATTTAAATGTAAATTATATA
AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATA
GTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCA
CATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATT
TGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATT
ACAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTGTGATTTAGGGTTTAGTGTTTA
TGTTAAAGTTTAAAATTTAGGGTTTAGGTTTAAGATTTCTATAAACTATATAAGTAATTTACTTT
ATATAGTATTTA
Found at i:41960 original size:7 final size:7
Alignment explanation
Indices: 41948--41998 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
41938 GTTTGTGATC
41948 TAGGGTT
1 TAGGGTT
41955 TAGGGTT
1 TAGGGTT
* *
41962 TATGATT
1 TAGGGTT
**
41969 TAAAGTT
1 TAGGGTT
*
41976 TAGTGTT
1 TAGGGTT
41983 TAGGGTT
1 TAGGGTT
41990 TAGGGTT
1 TAGGGTT
41997 TA
1 TA
41999 TGATTTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:41997 original size:21 final size:21
Alignment explanation
Indices: 41933--41998 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
41923 TCCATTTACA
*
41933 TTAGGGTTT-GTGATCTAGGGT
1 TTAGGGTTTAG-GATTTAGGGT
* **
41954 TTAGGGTTTATGATTTAAAGT
1 TTAGGGTTTAGGATTTAGGGT
* *
41975 TTAGTGTTTAGGGTTTAGGGT
1 TTAGGGTTTAGGATTTAGGGT
41996 TTA
1 TTA
41999 TGATTTTTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.47
Consensus pattern (21 bp):
TTAGGGTTTAGGATTTAGGGT
Found at i:42099 original size:17 final size:17
Alignment explanation
Indices: 42077--42136 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
42067 TAATTTACTT
42077 TATATAGTTTATATATA
1 TATATAGTTTATATATA
42094 TATATAGTTTATATATA
1 TATATAGTTTATATATA
* *
42111 TTATACATGGTTTATACATA
1 -TAT--ATAGTTTATATATA
42131 TATATA
1 TATATA
42137 AATTTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 19 0.51
18 3 0.08
19 3 0.08
20 12 0.32
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:42115 original size:9 final size:9
Alignment explanation
Indices: 42075--42108 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42065 AGTAATTTAC
42075 TTTATATAG
1 TTTATATAG
42084 TTTATATA-
1 TTTATATAG
*
42092 TATATATAG
1 TTTATATAG
42101 TTTATATA
1 TTTATATA
42109 TATTATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTATATAG
Found at i:42480 original size:14 final size:14
Alignment explanation
Indices: 42461--42490 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42451 TCCATTTATA
*
42461 TTAGGGTTTATGGT
1 TTAGGGTTTAAGGT
42475 TTAGGGTTTAAGGT
1 TTAGGGTTTAAGGT
42489 TT
1 TT
42491 TTATAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (14 bp):
TTAGGGTTTAAGGT
Found at i:42534 original size:15 final size:15
Alignment explanation
Indices: 42516--42564 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
42506 TTTATTACTT
*
42516 TATATAATTTATATA
1 TATATAGTTTATATA
42531 TATATAGGTTATATATA
1 TATATA-GTT-TATATA
42548 TATATAGTTTATATA
1 TATATAGTTTATATA
42563 TA
1 TA
42565 CCATACATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 14 0.45
16 5 0.16
17 12 0.39
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:42793 original size:8 final size:8
Alignment explanation
Indices: 42782--43160 Score: 596
Period size: 8 Copynumber: 48.5 Consensus size: 8
42772 TAATATAAAT
42782 TACACGCA
1 TACACGCA
42790 TACACGCA
1 TACACGCA
42798 TACACGCA
1 TACACGCA
42806 TACACGCA
1 TACACGCA
42814 TACACGCA
1 TACACGCA
42822 TACACGCA
1 TACACGCA
42830 TACACGCA
1 TACACGCA
42838 TACACGCA
1 TACACGCA
42846 TACACGCA
1 TACACGCA
42854 TACACGCA
1 TACACGCA
42862 TACACGCA
1 TACACGCA
42870 TACACGCA
1 TACACGCA
*
42878 TACACCCA
1 TACACGCA
* *
42886 TTCACCCA
1 TACACGCA
42894 TACACGCA
1 TACACGCA
42902 TACACGCA
1 TACACGCA
42910 TACACGCA
1 TACACGCA
42918 TACACGCA
1 TACACGCA
42926 TACACGCA
1 TACACGCA
42934 TACACGCA
1 TACACGCA
42942 TACACGCA
1 TACACGCA
42950 TACACGCA
1 TACACGCA
42958 TACACGCA
1 TACACGCA
42966 TACACGCA
1 TACACGCA
42974 TACACGCA
1 TACACGCA
42982 TACACGCA
1 TACACGCA
*
42990 TTCAC-CA
1 TACACGCA
42997 TACACGCA
1 TACACGCA
43005 TACACGCA
1 TACACGCA
43013 TACACGCA
1 TACACGCA
43021 TACACGCA
1 TACACGCA
43029 TACACGCA
1 TACACGCA
43037 TACACGCA
1 TACACGCA
*
43045 TACACCCA
1 TACACGCA
43053 TACACGCA
1 TACACGCA
43061 TACA--C-
1 TACACGCA
43066 -ACACGCA
1 TACACGCA
43073 TACAC-C-
1 TACACGCA
* **
43079 CACATACA
1 TACACGCA
43087 TACACGCA
1 TACACGCA
43095 TACA--CA
1 TACACGCA
43101 TACACGCA
1 TACACGCA
43109 TACACGCA
1 TACACGCA
43117 TACACGCA
1 TACACGCA
43125 TACACGCA
1 TACACGCA
*
43133 TACACACA
1 TACACGCA
*
43141 TACACACA
1 TACACGCA
*
43149 TACACACA
1 TACACGCA
43157 TACA
1 TACA
43161 TACATACATA
Statistics
Matches: 348, Mismatches: 14, Indels: 18
0.92 0.04 0.05
Matches are distributed among these distances:
4 3 0.01
6 11 0.03
7 8 0.02
8 326 0.94
ACGTcount: A:0.39, C:0.39, G:0.10, T:0.13
Consensus pattern (8 bp):
TACACGCA
Found at i:43088 original size:14 final size:14
Alignment explanation
Indices: 43038--43105 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
43028 ATACACGCAT
*
43038 ACACGCATACACCC
1 ACACACATACACCC
*
43052 ATACACGCATACA--C
1 --ACACACATACACCC
*
43066 ACACGCATACACCC
1 ACACACATACACCC
* *
43080 ACATACATACACGC
1 ACACACATACACCC
*
43094 ATACACATACAC
1 ACACACATACAC
43106 GCATACACGC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.24
14 23 0.51
16 11 0.24
ACGTcount: A:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (14 bp):
ACACACATACACCC
Found at i:43091 original size:22 final size:21
Alignment explanation
Indices: 43043--43184 Score: 85
Period size: 22 Copynumber: 7.3 Consensus size: 21
43033 CGCATACACG
* *
43043 CATACACCCATACA-CGCATA
1 CATACACGCATACACCACATA
*
43063 CACACACGCATACACCCACATA
1 CATACACGCATACA-CCACATA
* **
43085 CATACACGCATACACATACACG
1 CATACACGCATACAC-CACATA
*
43107 CATACACGCAT--A-CAC--G
1 CATACACGCATACACCACATA
43123 CATACACGCATACA-CACATA
1 CATACACGCATACACCACATA
43143 C--ACA--CATACA-CACATA
1 CATACACGCATACACCACATA
** *
43159 CATACATACATACA-TACATA
1 CATACACGCATACACCACATA
43179 CATACA
1 CATACA
43185 TACATACATA
Statistics
Matches: 101, Mismatches: 10, Indels: 22
0.76 0.08 0.17
Matches are distributed among these distances:
16 25 0.25
18 12 0.12
20 31 0.31
21 1 0.01
22 32 0.32
ACGTcount: A:0.44, C:0.37, G:0.05, T:0.15
Consensus pattern (21 bp):
CATACACGCATACACCACATA
Found at i:43163 original size:4 final size:4
Alignment explanation
Indices: 43131--43194 Score: 101
Period size: 4 Copynumber: 16.0 Consensus size: 4
43121 CGCATACACG
* * *
43131 CATA CACA CATA CACA CATA CACA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43179 CATA CATA CATA CATA
1 CATA CATA CATA CATA
43195 TATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (4 bp):
CATA
Found at i:43453 original size:19 final size:20
Alignment explanation
Indices: 43413--43457 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
43403 AATTTTTCTA
* *
43413 TTCCCTCTAATTTTCTCAAT
1 TTCCCTCTAATATTCACAAT
43433 TTCCCTCTAA-ATTCACAAT
1 TTCCCTCTAATATTCACAAT
43452 TTCCCT
1 TTCCCT
43458 ATATTCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (20 bp):
TTCCCTCTAATATTCACAAT
Found at i:43575 original size:2 final size:2
Alignment explanation
Indices: 43568--43600 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43558 CACTTTGAAT
43568 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43601 TAATATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43950 original size:18 final size:18
Alignment explanation
Indices: 43927--43987 Score: 90
Period size: 18 Copynumber: 3.4 Consensus size: 18
43917 TCATATAAAC
43927 ATAATATATATATAGTTT
1 ATAATATATATATAGTTT
43945 ATAATA-ATTATATAGTTT
1 ATAATATA-TATATAGTTT
*
43963 ATAATATAAATATAGTTT
1 ATAATATATATATAGTTT
43981 AT-ATATA
1 ATAATATA
43988 ACTTATATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 6 0.15
18 33 0.82
19 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
ATAATATATATATAGTTT
Found at i:43994 original size:18 final size:17
Alignment explanation
Indices: 43937--44011 Score: 70
Period size: 18 Copynumber: 4.5 Consensus size: 17
43927 ATAATATATA
43937 TATAGTTTATA-ATAATT
1 TATAGTTTATATATAA-T
*
43954 ATATAGTTTATAATATAAA
1 -TATAGTTTAT-ATATAAT
43973 TATAGTTTATATATAACT
1 TATAGTTTATATATAA-T
43991 TATA--TTATATAT-AT
1 TATAGTTTATATATAAT
44005 TAT-GTTT
1 TATAGTTT
44012 TTTTCAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 8 0.16
17 6 0.12
18 24 0.48
19 1 0.02
20 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TATAGTTTATATATAAT
Found at i:44473 original size:208 final size:210
Alignment explanation
Indices: 44073--44573 Score: 620
Period size: 208 Copynumber: 2.4 Consensus size: 210
44063 CATTTTGCAT
* * * * * *
44073 TTATTTTGATTTCATCCTTTTGTGTTTTTTAATTTATTTCAATTTTAAGTCTT-TCATTTTTATA
1 TTATTTTGATTTGATCCTCTTGTGTTGTTTAATTTATTTAAATTTTAA-T-TTGT-AATTTCATA
* * * * ** * * ** *
44137 TGTATTCAATTTAGTTCTTAAATTTATATTTGCATCTTCATTTGACCTATTGTTAGTTGTTATTT
63 TTTGTTCAATTTAGTCCTCAAATTTATATTTGCATCTGAAATTGACCCATACTTAGTTCTTATTT
44202 ATATTTTCGTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTCTTTTTTTATATTAATTT
128 ATATTTTCGTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTCTTTTTTTATATTAATTT
44267 CAACCTCACAATTTAAAA
193 CAACCTCACAATTTAAAA
*
44285 TTATTTTGATTTGATCC-CTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTT
1 TTATTTTGATTTGATCCTCTTGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTT
44349 GTTCAATTTAGTCCTCCAAA-TTATATTTGCATCTGAAATTGACCCATACTTA-TTACTTATTTA
66 GTTCAATTTAGTCCT-CAAATTTATATTTGCATCTGAAATTGACCCATACTTAGTT-CTTATTTA
** * *
44412 -ATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC-TTTTTTGTATTAATTT
129 TATTTTCGTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGT-CTTTTTTTATATTAATTT
44475 CAACCTCACAATTTAAAA
193 CAACCTCACAATTTAAAA
**
44493 TTATTTCAATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTT
1 TTATTTTGATTTGAT--C-C-TC--T-TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTT
44558 CATATTTGTTC-ATTTA
59 CATATTTGTTCAATTTA
44574 ATTCTTACAT
Statistics
Matches: 252, Mismatches: 25, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
208 90 0.36
209 58 0.23
210 6 0.02
211 27 0.11
212 16 0.06
213 1 0.00
215 6 0.02
216 48 0.19
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (210 bp):
TTATTTTGATTTGATCCTCTTGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTT
GTTCAATTTAGTCCTCAAATTTATATTTGCATCTGAAATTGACCCATACTTAGTTCTTATTTATA
TTTTCGTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTCTTTTTTTATATTAATTTCAA
CCTCACAATTTAAAA
Found at i:45031 original size:59 final size:58
Alignment explanation
Indices: 44968--45149 Score: 151
Period size: 59 Copynumber: 3.1 Consensus size: 58
44958 CCAAGAGCCA
44968 ACCTGATATGAGTCGAATCATCAAATTTACCTGACTTGACTTGTATCCGATTTTACCCG
1 ACCTGATA-GAGTCGAATCATCAAATTTACCTGACTTGACTTGTATCCGATTTTACCCG
* * * * * * * **
45027 ACCTGACAG-GATCCGACTGAAACCTGAATGATTACCCGACTTGATTTG-A-CC-A--GGACCCG
1 ACCTGATAGAG-T-CGAAT--CATC-AAAT--TTACCTGACTTGACTTGTATCCGATTTTACCCG
* *
45086 ACCTGATAGAGTCAAAGCATCAAATTTACCTGACTTGACTTGTATCCGATTTTACCCG
1 ACCTGATAGAGTCGAATCATCAAATTTACCTGACTTGACTTGTATCCGATTTTACCCG
45144 ACCTGA
1 ACCTGA
45150 CAGGATCCGA
Statistics
Matches: 90, Mismatches: 20, Indels: 27
0.66 0.15 0.20
Matches are distributed among these distances:
53 15 0.17
54 1 0.01
55 5 0.06
56 3 0.03
57 1 0.01
58 15 0.17
59 25 0.28
60 1 0.01
61 3 0.03
62 5 0.06
63 1 0.01
64 15 0.17
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (58 bp):
ACCTGATAGAGTCGAATCATCAAATTTACCTGACTTGACTTGTATCCGATTTTACCCG
Found at i:45070 original size:64 final size:64
Alignment explanation
Indices: 44994--45182 Score: 188
Period size: 64 Copynumber: 3.1 Consensus size: 64
44984 ATCATCAAAT
*
44994 TTACCTGACTTGACTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGA
1 TTACCCGACTTGACTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGA
* ** * * * *
45058 TTACCCGACTTGATTTG-A-CC-A--GGACCCGACCTGATA-GAGT-C-A---AAGCATCAA--A
1 TTACCCGACTTGACTTGTATCCGATTTTACCCGACCTGACAGGA-TCCGACTGAAACCTGAATGA
*
45110 TTTACCTGACTTGACTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGA
1 -TTACCCGACTTGACTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGA
45175 TTACCCGA
1 TTACCCGA
45183 TTTTACATCC
Statistics
Matches: 93, Mismatches: 17, Indels: 30
0.66 0.12 0.21
Matches are distributed among these distances:
52 1 0.01
53 15 0.16
54 7 0.08
55 2 0.02
56 1 0.01
57 1 0.01
58 16 0.17
59 16 0.17
60 1 0.01
61 1 0.01
62 2 0.02
63 7 0.08
64 22 0.24
65 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (64 bp):
TTACCCGACTTGACTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGA
Found at i:45122 original size:117 final size:118
Alignment explanation
Indices: 44942--45182 Score: 430
Period size: 117 Copynumber: 2.1 Consensus size: 118
44932 CCTGAAAATG
* * *
44942 ACCCGACTTGATTTGACCAAGAGCCAACCTGATATGAGTCGAATCATCAAATTTACCTGACTTGA
1 ACCCGACTTGATTTGACCAAGACCCAACCTGATATGAGTCAAAGCATCAAATTTACCTGACTTGA
45007 CTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGATT
66 CTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGATT
* *
45060 ACCCGACTTGATTTGACCAGGACCCGACCTGATA-GAGTCAAAGCATCAAATTTACCTGACTTGA
1 ACCCGACTTGATTTGACCAAGACCCAACCTGATATGAGTCAAAGCATCAAATTTACCTGACTTGA
45124 CTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGATT
66 CTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGATT
45177 ACCCGA
1 ACCCGA
45183 TTTTACATCC
Statistics
Matches: 118, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 87 0.74
118 31 0.26
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (118 bp):
ACCCGACTTGATTTGACCAAGACCCAACCTGATATGAGTCAAAGCATCAAATTTACCTGACTTGA
CTTGTATCCGATTTTACCCGACCTGACAGGATCCGACTGAAACCTGAATGATT
Found at i:57298 original size:14 final size:14
Alignment explanation
Indices: 57256--57298 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
57246 ACGGTCAACG
57256 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
* *
57270 ATCAGGTCGGGTCA
1 GTCGGGTCGGGTCA
57284 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
57298 G
1 G
57299 ACCGGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:57305 original size:9 final size:9
Alignment explanation
Indices: 57293--57362 Score: 68
Period size: 9 Copynumber: 7.3 Consensus size: 9
57283 AGTCGGGTCG
*
57293 GGTCAGACC
1 GGTCAAACC
*
57302 GGTCAAATC
1 GGTCAAACC
57311 GGTCGAAACC
1 GGTC-AAACC
57321 GGTCAAACC
1 GGTCAAACC
57330 GGTCAGAACC
1 GGTCA-AACC
* *
57340 GGTTGAAAACT
1 GG-T-CAAACC
57351 GGTCAAACC
1 GGTCAAACC
57360 GGT
1 GGT
57363 TTCCAGCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 28 0.56
10 15 0.30
11 6 0.12
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:57312 original size:19 final size:18
Alignment explanation
Indices: 57293--57342 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
57283 AGTCGGGTCG
57293 GGTCAGACCGGTCAAATC
1 GGTCAGACCGGTCAAATC
* *
57311 GGTCGAAACCGGTCAAACC
1 GGTC-AGACCGGTCAAATC
57330 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
57343 TGAAAACTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAATC
Found at i:57361 original size:20 final size:21
Alignment explanation
Indices: 57325--57363 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57315 GAAACCGGTC
57325 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
57346 AAACTGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
57364 TCCAGCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:63643 original size:10 final size:9
Alignment explanation
Indices: 63613--63662 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
63603 AGTCAGGTTG
*
63613 GGTCAGACC
1 GGTCAAACC
63622 GGTCAAACC
1 GGTCAAACC
*
63631 GGTTCATACC
1 GG-TCAAACC
63641 GGTCAAACC
1 GGTCAAACC
63650 GGTCAGAACC
1 GGTCA-AACC
63660 GGT
1 GGT
63663 TGAAAATCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:63660 original size:19 final size:18
Alignment explanation
Indices: 63613--63662 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
63603 AGTCAGGTTG
63613 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
*
63631 GGTTCATACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
63650 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
63663 TGAAAATCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Done.