Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 32
Found at i:3526924 original size:20 final size:19
Alignment explanation
Indices: 3526875--3526925 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 19
3526865 TCGGTAGCGC
*
3526875 TTTACCTGTTTTGTCATTT
1 TTTACCTGTTTTATCATTT
3526894 TTTAGACCTGTTTTATCATATT
1 TTT--ACCTGTTTTATCAT-TT
3526916 TTTACCTGTT
1 TTTACCTGTT
3526926 ATATTGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 7 0.25
21 13 0.46
22 5 0.18
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.59
Consensus pattern (19 bp):
TTTACCTGTTTTATCATTT
Found at i:3527449 original size:21 final size:22
Alignment explanation
Indices: 3527425--3527466 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3527415 GTAGCGCTTT
3527425 ACATGTTTTGTCAT-TTTTTAG
1 ACATGTTTTGTCATATTTTTAG
*
3527446 ACATGTTTTGTTATATTTTTA
1 ACATGTTTTGTCATATTTTTA
3527467 CCTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (22 bp):
ACATGTTTTGTCATATTTTTAG
Found at i:3535541 original size:94 final size:94
Alignment explanation
Indices: 3535375--3535554 Score: 243
Period size: 94 Copynumber: 1.9 Consensus size: 94
3535365 CTTACGATTA
* **
3535375 TAATCTAGATAAGTTCACACATGGTTAATTGATCCACATTAATTAATCAATAGATCGAAAATCAG
1 TAATCTAGATAAGCTCACACATAATTAATTGATCCACATTAATTAATCAATAGATCGAAAATCAG
* *
3535440 CGATTATACAACAATAATAATAATAATAC
66 CGATTATACAAAAAAAATAATAATAATAC
* ** * * *
3535469 TAATCTAGATAGGCTCACACATAATTAATTGATCCGGATTAGTTAATCAATATATCGGAAATCAG
1 TAATCTAGATAAGCTCACACATAATTAATTGATCCACATTAATTAATCAATAGATCGAAAATCAG
* *
3535534 TGGTTATACAAAAAAAATAAT
66 CGATTATACAAAAAAAATAAT
3535555 CTAGATAGGT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
94 73 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (94 bp):
TAATCTAGATAAGCTCACACATAATTAATTGATCCACATTAATTAATCAATAGATCGAAAATCAG
CGATTATACAAAAAAAATAATAATAATAC
Found at i:3540434 original size:16 final size:16
Alignment explanation
Indices: 3540413--3540471 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
3540403 AACTGGTATT
*
3540413 ACCCGACCTGTTTTCA
1 ACCCGACCTGTTTTTA
3540429 ACCCGACCTGTTTTTA
1 ACCCGACCTGTTTTTA
*
3540445 ACCTGACCTGTTTTTA
1 ACCCGACCTGTTTTTA
*
3540461 ACCTGACCTGT
1 ACCCGACCTGT
3540472 AAATGATCCG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.19, C:0.32, G:0.14, T:0.36
Consensus pattern (16 bp):
ACCCGACCTGTTTTTA
Found at i:3540784 original size:23 final size:24
Alignment explanation
Indices: 3540750--3540799 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
3540740 ATGAAAAGGA
3540750 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
3540774 AAATT-ATATAGTTTAATTTATTT
1 AAATTAATATAGTTTAATTTATAT
3540797 AAA
1 AAA
3540800 GAAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:3540992 original size:21 final size:21
Alignment explanation
Indices: 3540963--3541020 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
3540953 TCCATTTATA
**
3540963 TTAGGGTTTATGGTTTATTGT
1 TTAGGGTTTATGGTTTAAAGT
*
3540984 TTAGTGTTTATGGTTTAAAGT
1 TTAGGGTTTATGGTTTAAAGT
*
3541005 TTAGGGTTTAGGGTTT
1 TTAGGGTTTATGGTTT
3541021 CTATAAACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.53
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAAAGT
Found at i:3541020 original size:14 final size:14
Alignment explanation
Indices: 3540963--3541020 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
3540953 TCCATTTATA
*
3540963 TTAGGGTTTATGGT
1 TTAGGGTTTAGGGT
** *
3540977 TTATTGTTTAGTGT
1 TTAGGGTTTAGGGT
* **
3540991 TTATGGTTTAAAGT
1 TTAGGGTTTAGGGT
3541005 TTAGGGTTTAGGGT
1 TTAGGGTTTAGGGT
3541019 TT
1 TT
3541021 CTATAAACTA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.53
Consensus pattern (14 bp):
TTAGGGTTTAGGGT
Found at i:3541482 original size:7 final size:6
Alignment explanation
Indices: 3541470--3541540 Score: 52
Period size: 7 Copynumber: 10.3 Consensus size: 6
3541460 TTTACATTAG
*
3541470 GGTTTA TGGTTTA GTGTTTA GTGTTTAA AGTTTA GGGTTTA GGATTTAA
1 GGTTTA -GGTTTA G-GTTTA G-GTTT-A GGTTTA -GGTTTA GG-TTT-A
3541519 GGTTTA GGATTTAA GGTTTA GG
1 GGTTTA GG-TTT-A GGTTTA GG
3541541 ATTTCTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
6 10 0.18
7 38 0.69
8 7 0.13
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (6 bp):
GGTTTA
Found at i:3541488 original size:14 final size:13
Alignment explanation
Indices: 3541470--3541540 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
3541460 TTTACATTAG
*
3541470 GGTTTATGGTTTA
1 GGTTTAAGGTTTA
3541483 GTGTTT-AGTGTTTAA
1 G-GTTTAAG-GTTT-A
* *
3541498 AGTTTAGGGTTTA
1 GGTTTAAGGTTTA
3541511 GGATTTAAGGTTTA
1 GG-TTTAAGGTTTA
3541525 GGATTTAAGGTTTA
1 GG-TTTAAGGTTTA
3541539 GG
1 GG
3541541 ATTTCTATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.08
14 42 0.88
15 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
GGTTTAAGGTTTA
Found at i:3541490 original size:21 final size:20
Alignment explanation
Indices: 3541466--3541538 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
3541456 TCCATTTACA
*
3541466 TTAGGGTTTATGGTTTAGTGT
1 TTAGGGTTTAAGGTTTAG-GT
* *
3541487 TTAGTGTTTAAAGTTTAGGGT
1 TTAGGGTTTAAGGTTTA-GGT
*
3541508 TTAGGATTTAAGGTTTAGGAT
1 TTAGGGTTTAAGGTTTAGG-T
*
3541529 TTAAGGTTTA
1 TTAGGGTTTA
3541539 GGATTTCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.05
21 39 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (20 bp):
TTAGGGTTTAAGGTTTAGGT
Found at i:3541517 original size:28 final size:27
Alignment explanation
Indices: 3541471--3541544 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
3541461 TTACATTAGG
*
3541471 GTTTATGGTTTAGTG-TTT-AGTGTTTAAA
1 GTTTAAGGTTTAG-GATTTAAG-GTTT-AA
* *
3541499 GTTTAGGGTTTAGGATTTAAGGTTTAG
1 GTTTAAGGTTTAGGATTTAAGGTTTAA
3541526 GATTTAAGGTTTAGGATTT
1 G-TTTAAGGTTTAGGATTT
3541545 CTATAAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.08
28 35 0.88
29 2 0.05
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (27 bp):
GTTTAAGGTTTAGGATTTAAGGTTTAA
Found at i:3541541 original size:14 final size:14
Alignment explanation
Indices: 3541500--3541544 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
3541490 GTGTTTAAAG
*
3541500 TTTAGGGTTTAGGA
1 TTTAAGGTTTAGGA
3541514 TTTAAGGTTTAGGA
1 TTTAAGGTTTAGGA
3541528 TTTAAGGTTTAGGA
1 TTTAAGGTTTAGGA
3541542 TTT
1 TTT
3541545 CTATAAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TTTAAGGTTTAGGA
Found at i:3541584 original size:2 final size:2
Alignment explanation
Indices: 3541579--3541614 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3541569 TTTATATAGT
*
3541579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3541615 CATGGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3541894 original size:517 final size:535
Alignment explanation
Indices: 3541215--3543114 Score: 2462
Period size: 559 Copynumber: 3.5 Consensus size: 535
3541205 AATTGGGTCA
3541215 CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATA-TTT
1 CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTT
*
3541279 AGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
66 AGTTGCATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
3541344 AAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAA
131 AAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAA
3541409 TACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGGTT
196 TACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGGTT
3541474 TATGGTTTAGTGTTTA-GTGTTTAAAGTTTAGGGTTTAGGATTTAAGGTTTAGGATTTAAGGTTT
261 TATGGTTTAGTGTTTATG-GTTTAAAGTTTA--GTTTAGGATTTAAGGTTT-GGATTTAAGGTTT
*
3541538 AGGATTTCTATAAAACTATATACTTTATTACTTTATATAGTTAT-ATA-TAT-A-TATAT-A-T-
322 AGGGTTTCTATAAAACTATATACTTTATTACTTTATATAGTTATCATATTATAACTATATAAGTA
3541596 A-TA-TATATATATATT-TATACAT-GG-T-T-TATAC-ATAC------ATATTATATAAAATTA
387 ATTACTATATATATATTATATACATAGGTTATATATACTATACTATAATATATTATATAAAATTA
*
3541647 TTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
452 TTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGACTAATTAGGTGTTAAA
3541712 TAATTAGTATGTCACATTG
517 TAATTAGTATGTCACATTG
* *
3541731 CATATTATATGGTTCATAAATAGTGGTACATGACATATTAATTTCATTTGCATAATTAATATTTT
1 CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTT
* * *
3541796 AGTTACATGTTAAGTTAATTCACATTAATAGCCTATTTATTTTGTTGTTATGAATAAATAATAAT
66 AGTTGCATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
* *
3541861 AAAACCCAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAG
131 AAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAA
* * *
3541926 TACATAAACCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTTCATTTATATTAGGGTT
196 TACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGGTT
*
3541991 TATGGTTTAGTGTTTATGGTTT-AA----AGTTTAGGATTT-A----TGG-TTTAGGGTTTAGGG
261 TATGGTTTAGTGTTTATGGTTTAAAGTTTAGTTTAGGATTTAAGGTTTGGATTTAAGGTTTAGGG
*
3542045 TTTCTATAAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATAT
326 TTTCTATAAAACTATATACTTTATTACTTTATATAG-TTAT-CATA-----T-TAT-AACTATAT
* * *
3542110 AAGTAATTTACTTTATATATTTTATATATATAGGTTATATATACTATACATGGTTTATACATACA
382 AAGTAA-TTACTATATATATATTATATACATAGGTTATATATACTATAC------TATA-AT--A
3542175 TATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGAC
437 TATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGAC
*
3542240 TAATTATGTGTTAAATAATTAGTATGTCACATTG
502 TAATTAGGTGTTAAATAATTAGTATGTCACATTG
*
3542274 CATATTATATGGTTCATAAATAGTAGTACATGTTATATTAATTTCATTTGCATAATTAATATTTT
1 CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTT
*
3542339 AGTTGCATGTTAAGTTAATTCACATTAATAGCCCATTCATTTTGTTGTTATGAATAAGTAATAAT
66 AGTTGCATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
*
3542404 AAAACCAAAAAATAAGTCCATTTGCAATAGTTG-TAGTCCATTTACATTAGTTTACATAAGG-CC
131 AAAACCCAAAAATAAGTCCATTTGCAATAG-TGCTAGTCCATTTACATTAGTTTACAT-AGGCCC
*
3542467 AATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGCCCATTTACATTAGGG
194 AATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGG
*
3542532 TTTATGGTTTA-TGGTTTATGGTTTAAAGTTT-G---A-GATTTAGGGTTT--A--TAA--TTTA
259 TTTATGGTTTAGT-GTTTATGGTTTAAAGTTTAGTTTAGGATTTAAGGTTTGGATTTAAGGTTTA
*
3542585 GGGTTTCTAT-AAACTATATACTTTATTACTTTATATAGTTTATGCACAGTGTTTCTATAAACTA
323 GGGTTTCTATAAAACTATATACTTTATTACTTTATATAG-TTAT---CA---TAT-TAT-AACTA
* * *
3542649 TATAAGTATTTTACCTTATATAGTTTATATATATATAGGTTATATATATATAGTTTATATATACT
379 TATAAG-----TA----AT-TA----CTATATATATA---T-TATATACATAGGTTATATATACT
3542714 ATACTTGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATG
426 ATAC------TATA-AT--ATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATG
* * *
3542779 TAAATTATATAAAATATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTA
482 TAAATTATATAAAACATGACTAATTAGGTGTTAAATAATTAGTATGTCACATTG
* *
3542833 AATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTT
1 CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTT
* * * *
3542898 AGTTACATGTTAGGTTAATTCACATCAATAGCTCATTTATTTTGTTGTTATGAATAAGTAATAAT
66 AGTTGCATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
** *
3542963 AAAACTAAAAAATAAGTCCATTTGTAATAGTTG-TAGTCCATTTACATTAGTTTACATAGGCCCA
131 AAAACCCAAAAATAAGTCCATTTGCAATAG-TGCTAGTCCATTTACATTAGTTTACATAGGCCCA
* * * *
3543027 ATACATAAGTCAACTCTTTTATTTCAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGT
195 ATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGGT
*
3543092 TTATGATTTAAG-GTTTATGGTTT
260 TTATGGTTT-AGTGTTTATGGTTT
3543115 CTATAAAATT
Statistics
Matches: 1239, Mismatches: 63, Indels: 121
0.87 0.04 0.09
Matches are distributed among these distances:
503 47 0.04
504 6 0.00
505 1 0.00
506 3 0.00
509 1 0.00
510 11 0.01
512 1 0.00
513 3 0.00
515 1 0.00
516 66 0.05
517 210 0.17
518 2 0.00
519 1 0.00
521 2 0.00
522 10 0.01
523 6 0.00
524 2 0.00
525 1 0.00
526 1 0.00
527 5 0.00
528 4 0.00
542 50 0.04
543 376 0.30
544 10 0.01
545 2 0.00
547 4 0.00
548 1 0.00
550 1 0.00
551 3 0.00
555 8 0.01
558 4 0.00
559 395 0.32
560 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (535 bp):
CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTT
AGTTGCATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
AAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAA
TACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGGTT
TATGGTTTAGTGTTTATGGTTTAAAGTTTAGTTTAGGATTTAAGGTTTGGATTTAAGGTTTAGGG
TTTCTATAAAACTATATACTTTATTACTTTATATAGTTATCATATTATAACTATATAAGTAATTA
CTATATATATATTATATACATAGGTTATATATACTATACTATAATATATTATATAAAATTATTTA
ATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGACTAATTAGGTGTTAAATAAT
TAGTATGTCACATTG
Found at i:3541999 original size:7 final size:7
Alignment explanation
Indices: 3541987--3542047 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
3541977 TTTATATTAG
3541987 GGTTTAT
1 GGTTTAT
3541994 GGTTTA-
1 GGTTTAT
3542000 GTGTTTAT
1 G-GTTTAT
*
3542008 GGTTTAA
1 GGTTTAT
*
3542015 AGTTTA-
1 GGTTTAT
3542021 GGATTTAT
1 GG-TTTAT
*
3542029 GGTTTAG
1 GGTTTAT
*
3542036 GGTTTAG
1 GGTTTAT
3542043 GGTTT
1 GGTTT
3542048 CTATAAAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 2 0.04
7 41 0.89
8 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (7 bp):
GGTTTAT
Found at i:3542005 original size:14 final size:14
Alignment explanation
Indices: 3541983--3542047 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
3541973 TTCATTTATA
3541983 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
3541997 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
**
3542011 TTAAAGTTTA-GGAT
1 TTAGGGTTTATGG-T
* *
3542025 TTATGGTTTAGGGT
1 TTAGGGTTTATGGT
3542039 TTAGGGTTT
1 TTAGGGTTT
3542048 CTATAAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.05
14 39 0.91
15 2 0.05
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:3542011 original size:21 final size:20
Alignment explanation
Indices: 3541987--3542043 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
3541977 TTTATATTAG
*
3541987 GGTTTATGGTTTAGTGTTTAT
1 GGTTTAAGGTTTAG-GTTTAT
*
3542008 GGTTTAAAGTTTAGGATTTAT
1 GGTTTAAGGTTTAGG-TTTAT
*
3542029 GGTTTAGGGTTTAGG
1 GGTTTAAGGTTTAGG
3542044 GTTTCTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (20 bp):
GGTTTAAGGTTTAGGTTTAT
Found at i:3542454 original size:20 final size:20
Alignment explanation
Indices: 3542418--3542455 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3542408 CCAAAAAATA
*
3542418 AGTCCATTTGCAATAGTTGT
1 AGTCCATTTACAATAGTTGT
*
3542438 AGTCCATTTACATTAGTT
1 AGTCCATTTACAATAGTT
3542456 TACATAAGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
AGTCCATTTACAATAGTTGT
Found at i:3542542 original size:7 final size:7
Alignment explanation
Indices: 3542530--3542556 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3542520 TTTACATTAG
3542530 GGTTTAT
1 GGTTTAT
3542537 GGTTTAT
1 GGTTTAT
3542544 GGTTTAT
1 GGTTTAT
3542551 GGTTTA
1 GGTTTA
3542557 AAGTTTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (7 bp):
GGTTTAT
Found at i:3542685 original size:15 final size:15
Alignment explanation
Indices: 3542665--3542716 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
3542655 TATTTTACCT
3542665 TATATAGTTTATATA
1 TATATAGTTTATATA
*
3542680 TATATAGGTTATATA
1 TATATAGTTTATATA
3542695 TATATAGTTTATATA
1 TATATAGTTTATATA
3542710 TACTATA
1 TA-TATA
3542717 CTTGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:3542917 original size:559 final size:554
Alignment explanation
Indices: 3541542--3543114 Score: 2506
Period size: 543 Copynumber: 2.9 Consensus size: 554
3541532 AGGTTTAGGA
*
3541542 TTTCTATAAAACTATAT-ACT-TTATTACTTTATATAGTTATATATATATA-TATATATATATA-
1 TTTCTAT-AAACTATATAAGTATT-TTAC-TTATATAGTTATATATATATATTATATATATATAG
*
3541603 -TATATAT-TTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAA
63 TTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAA
3541666 TTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTG
128 TTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTG
* *
3541731 CATATTATATGGTTCATAAATAGTGGTACATGACATATTAATTTCATTTGCATAATTAATATTTT
193 CATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTT
* *
3541796 AGTTACATGTTAAGTTAATTCACATTAATAGCCTATTTATTTTGTTGTTATGAATAAATAATAAT
258 AGTTACATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAAT
* *
3541861 AAAACCCAAAAATAAGTCCATTTGCATTAG-TGCTAGTCCATTTACATTAGTTTACATAGGCCCA
323 AAAACCAAAAAATAAGTCCATTTGCAATAGTTG-TAGTCCATTTACATTAGTTTACATAGGCCCA
* * *
3541925 GTACATAAACCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTTCATTTATATTAGGGT
387 ATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGT
* **
3541990 TTATGGTTTAGTGTTTATGGTTTAAAGTTTAGGATTTATGGTTTAGGGTTTAGGGTTTCTATAAA
452 TTATGGTTTAG-GTTTATGGTTTAAAGTTTAGGATTTAGGGTTTAGAATTTAGGGTTTCTATAAA
* *
3542055 ACTATATATTTTATTACTTTATATAGTTTATGCATAGTG
516 ACTATATACTTTATTACTTTATATAGTTTATGCACAGTG
* *
3542094 TTTCTATAAACTATATAAGTA----A--T-T-TACTT-TATATAT-T-TTATATATATA-GGTTA
1 TTTCTATAAACTATATAAGTATTTTACTTATATAGTTATATATATATATTATATATATATAGTTA
3542147 TATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTA
66 TATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTA
* *
3542212 TTTAAATGTAAATTATATAAAACATGACTAATTATGTGTTAAATAATTAGTATGTCACATTGCAT
131 TTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCAT
*
3542277 ATTATATGGTTCATAAATAGTAGTACATGTTATATTAATTTCATTTGCATAATTAATATTTTAGT
196 ATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTTAGT
* *
3542342 TGCATGTTAAGTTAATTCACATTAATAGCCCATTCATTTTGTTGTTATGAATAAGTAATAATAAA
261 TACATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAA
3542407 ACCAAAAAATAAGTCCATTTGCAATAGTTGTAGTCCATTTACATTAGTTTACATAAGG-CCAATA
326 ACCAAAAAATAAGTCCATTTGCAATAGTTGTAGTCCATTTACATTAGTTTACAT-AGGCCCAATA
* *
3542471 CATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGCCCATTTACATTAGGGTTTA
390 CATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTA
*
3542536 TGGTTTATGGTTTATGGTTTAAAGTTT-GAGATTTAGGGTTTATAATTTAGGGTTTCTAT-AAAC
455 TGGTTTA-GGTTTATGGTTTAAAGTTTAG-GATTTAGGGTTTAGAATTTAGGGTTTCTATAAAAC
3542599 TATATACTTTATTACTTTATATAGTTTATGCACAGTG
518 TATATACTTTATTACTTTATATAGTTTATGCACAGTG
3542636 TTTCTATAAACTATATAAGTATTTTACCTTATATAGTTTATATATATATAGGTTATATATATATA
1 TTTCTATAAACTATATAAGTATTTTA-CTTATATAG-TTATATATATATA--TTATATATATATA
*
3542701 GTTTATATATACTATACTTGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAA
62 G-TTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAA
*
3542766 AATTATTTAAATGTAAATTATATAAAATATGATTAATTAGGTGTTAAATAATTAGTATGTCACAT
126 AATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACAT
** *
3542831 TAAATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATT
191 TGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATT
* * *
3542896 TTAGTTACATGTTAGGTTAATTCACATCAATAGCTCATTTATTTTGTTGTTATGAATAAGTAATA
256 TTAGTTACATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATA
* *
3542961 ATAAAACTAAAAAATAAGTCCATTTGTAATAGTTGTAGTCCATTTACATTAGTTTACATAGGCCC
321 ATAAAACCAAAAAATAAGTCCATTTGCAATAGTTGTAGTCCATTTACATTAGTTTACATAGGCCC
* * *
3543026 AATACATAAGTCAACTCTTTTATTTCAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGG
386 AATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGG
*
3543091 TTTATGATTTAAGGTTTATGGTTT
451 TTTATGGTTT-AGGTTTATGGTTT
3543115 CTATAAAATT
Statistics
Matches: 943, Mismatches: 49, Indels: 51
0.90 0.05 0.05
Matches are distributed among these distances:
541 11 0.01
542 75 0.08
543 414 0.44
544 7 0.01
545 1 0.00
546 1 0.00
548 1 0.00
549 1 0.00
550 1 0.00
551 11 0.01
552 11 0.01
553 7 0.01
554 1 0.00
557 11 0.01
558 4 0.00
559 385 0.41
560 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (554 bp):
TTTCTATAAACTATATAAGTATTTTACTTATATAGTTATATATATATATTATATATATATAGTTA
TATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTA
TTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCAT
ATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAATATTTTAGT
TACATGTTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAA
ACCAAAAAATAAGTCCATTTGCAATAGTTGTAGTCCATTTACATTAGTTTACATAGGCCCAATAC
ATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTAT
GGTTTAGGTTTATGGTTTAAAGTTTAGGATTTAGGGTTTAGAATTTAGGGTTTCTATAAAACTAT
ATACTTTATTACTTTATATAGTTTATGCACAGTG
Found at i:3543202 original size:2 final size:2
Alignment explanation
Indices: 3543197--3543255 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
3543187 TTATATAGTT
*
3543197 TA TA TA TA TA TA TA TA TA TC 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
3543239 TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
3543256 CATGGTTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3543372 original size:2 final size:2
Alignment explanation
Indices: 3543361--3543541 Score: 71
Period size: 2 Copynumber: 94.0 Consensus size: 2
3543351 ATAGTGTTTC
* *
3543361 TA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TT TA TA GA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3543400 CT- TA TA T- TA GT- TA TA CA TA CA TA TA TA TA TA CTA TA T- TA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
3543439 -A TA TA AA T- TA TA -A TT TA TA AA CTA TA TA T- TT TA AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * * * * *
3543477 TT TA TA CA TA TA TA GTT TA TA TA CA TA CA TA CA TA CA TA CA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3543520 CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3543542 GAAAATTAAA
Statistics
Matches: 127, Mismatches: 35, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
1 12 0.09
2 109 0.86
3 6 0.05
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3543495 original size:24 final size:25
Alignment explanation
Indices: 3543448--3543495 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3543438 AATATAAATT
*
3543448 ATAATTTATAAACTATATATTTTAA
1 ATAATTTATAAACTATATAGTTTAA
*
3543473 ATAATTTATACA-TATATAGTTTA
1 ATAATTTATAAACTATATAGTTTA
3543496 TATACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
ATAATTTATAAACTATATAGTTTAA
Found at i:3543760 original size:19 final size:20
Alignment explanation
Indices: 3543733--3543808 Score: 102
Period size: 19 Copynumber: 3.9 Consensus size: 20
3543723 ATCTCAATTC
*
3543733 TCAATTTCCCTCCAAATTTT
1 TCAATTTCCCTCTAAATTTT
* *
3543753 TCTA-TTCCCTCTAAGTTTT
1 TCAATTTCCCTCTAAATTTT
*
3543772 TCAATTTCCCTCTAAA-TTC
1 TCAATTTCCCTCTAAATTTT
3543791 TCAATTTCCCTCTAAATT
1 TCAATTTCCCTCTAAATT
3543809 CCCAAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 34 0.71
20 14 0.29
ACGTcount: A:0.24, C:0.29, G:0.01, T:0.46
Consensus pattern (20 bp):
TCAATTTCCCTCTAAATTTT
Found at i:3543939 original size:25 final size:24
Alignment explanation
Indices: 3543907--3543954 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3543897 TATACACTAT
3543907 ATTAATATAAATTATAGTTTATAA
1 ATTAATATAAATTATAGTTTATAA
***
3543931 ATTATATATTTTTTATAGTTTATA
1 ATTA-ATATAAATTATAGTTTATA
3543955 CCTATATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTAATATAAATTATAGTTTATAA
Found at i:3543964 original size:15 final size:15
Alignment explanation
Indices: 3543944--3543980 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
3543934 ATATATTTTT
*
3543944 TATAGTTTATACCTA
1 TATAGTTTATACATA
3543959 TATAG-TT-TACATA
1 TATAGTTTATACATA
3543972 TATAGTTTA
1 TATAGTTTA
3543981 GATATATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:3543997 original size:11 final size:13
Alignment explanation
Indices: 3543957--3543991 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3543947 AGTTTATACC
3543957 TATATAGTTTACA
1 TATATAGTTTACA
*
3543970 TATATAGTTTAGA
1 TATATAGTTTACA
3543983 TATATAGTT
1 TATATAGTT
3543992 AATATAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (13 bp):
TATATAGTTTACA
Found at i:3544034 original size:2 final size:2
Alignment explanation
Indices: 3544029--3544122 Score: 70
Period size: 2 Copynumber: 47.5 Consensus size: 2
3544019 TTATAATAAT
* * * *
3544029 TA TA TA -A TT TA TA -A TA TA AA TA TA GTT TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * *
3544071 TA TA CA AA CT- TA TA T- TA TA TT 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
3544112 TA TA TA TA TA T
1 TA TA TA TA TA T
3544123 TTCAATTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
1 4 0.06
2 66 0.92
3 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3544051 original size:18 final size:18
Alignment explanation
Indices: 3544007--3544065 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
3543997 AAACATAATT
*
3544007 TATATATATAACTTATAA
1 TATATATATAATTTATAA
3544025 TA-ATTATATAATTTATAA
1 TATA-TATATAATTTATAA
* *
3544043 TATAAATATAGTTTAT-A
1 TATATATATAATTTATAA
3544060 TATATA
1 TATATA
3544066 GTTTATATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.20
18 27 0.77
19 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TATATATATAATTTATAA
Found at i:3544072 original size:49 final size:53
Alignment explanation
Indices: 3543991--3544119 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 53
3543981 GATATATAGT
* *
3543991 TAATATAAACATAATTTATATATATAACTTATA-A-TAA-TTATA-TA-ATTTA
1 TAATATAAATAT-ATTTATATATATAACTTATATACAAACTTATATTATATTTA
**
3544040 TAATATAAATATAGTTTATATATATAGTTTATATACAAACTTATATTATATTTA
1 TAATATAAATATA-TTTATATATATAACTTATATACAAACTTATATTATATTTA
* *
3544094 TATATATATATATATATATATATATA
1 TA-ATATAAATATATTTATATATATA
3544120 TATTTCAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
48 1 0.01
49 28 0.42
50 1 0.01
51 2 0.03
52 5 0.07
53 2 0.03
54 18 0.27
55 10 0.15
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (53 bp):
TAATATAAATATATTTATATATATAACTTATATACAAACTTATATTATATTTA
Found at i:3548556 original size:123 final size:123
Alignment explanation
Indices: 3548337--3548586 Score: 437
Period size: 123 Copynumber: 2.0 Consensus size: 123
3548327 TTGGGTTTAG
3548337 GAACTGCTAGAGCTGGAAAATCAAATGGGGAATGTTAGCACTAGGCTAACCCAGGCAACTATTCG
1 GAACTGCTAGAGCTGGAAAATCAAATGGGGAATGTTAGCACTAGGCTAACCCAGGCAACTATTCG
* *
3548402 TGCCAATCTGTGGCGACGCAAATTTCAGCCCATCACAGCCGGTTGTACTGCCGAAACT
66 CGCCAATCTGTGGCGACGCAAATTTCAGCCCATCACAGCCGGTTCTACTGCCGAAACT
* * *
3548460 GAACTGTTGGAGCTGGAAAATCAAATGGGGAATGTTAGCACTGGGCTAACCCAGGCAACTATTCG
1 GAACTGCTAGAGCTGGAAAATCAAATGGGGAATGTTAGCACTAGGCTAACCCAGGCAACTATTCG
* *
3548525 CGCCAATCTGTGGCGACGTAAATTTTAGCCCATCACAGCCGGTTCTACTGCCGAAACT
66 CGCCAATCTGTGGCGACGCAAATTTCAGCCCATCACAGCCGGTTCTACTGCCGAAACT
3548583 GAAC
1 GAAC
3548587 AAGGTTGTAT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 120 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (123 bp):
GAACTGCTAGAGCTGGAAAATCAAATGGGGAATGTTAGCACTAGGCTAACCCAGGCAACTATTCG
CGCCAATCTGTGGCGACGCAAATTTCAGCCCATCACAGCCGGTTCTACTGCCGAAACT
Found at i:3551937 original size:137 final size:137
Alignment explanation
Indices: 3551682--3552744 Score: 1459
Period size: 137 Copynumber: 7.8 Consensus size: 137
3551672 CAACTGGTGT
* * *
3551682 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTTAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* * * * *
3551747 CCTTTGTGATGAAGACGTCTAGTTATCTGAGGATGACTCG-G-CTCCTACGTGATGAGGAGTTCT
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGA-T-GTGACTCCTTCGTGATGAGGAGTTCT
* ** *
3551810 GGTCAGTGG
129 GATTGGTAG
* *
3551819 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGACATCTTTAAAGATATTTGAGATAACACAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* * * *
3551884 CCTTCGTGATGAGGACGTCTGGTTATCTAAGAATGGTGATG-CTGCTTCATGATGAGGAGTTCTG
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG-TGACTCCTTCGTGATGAGGAGTTCTG
*
3551948 ATCGGT-G
130 ATTGGTAG
* * * *
3551955 AATGACATTGTTCCTTCATGATGAGGACATTTGGCCATCTTTCAAGATATTTGAGATAACATAGT
1 -ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGT
* ** *** *
3552020 TCCTTCGTGATGAGGACGACTGAATATCTAAGGATGACACGACTCCTTCATGATGAGGAGTTCTG
65 TCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTGACTCCTTCGTGATGAGGAGTTCTG
*
3552085 ATTGGTAT
130 ATTGGTAG
* * *
3552093 ATGACATTGTTCCTTCATGATGAGGACATATGGCCATCTTTGAAGATATTTGAGATAACACAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* * *
3552158 CCTTCGTGATGAGGACGTCTGGCTGTCTAAGGATGATGTGACTTCTTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTGACTCCTTCGTGATGAGGAGTTCTGA
3552223 TTGGTAG
131 TTGGTAG
* * ** *
3552230 ATGACATTATTCCTTTGTGATGAGGACATCTCCCCATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* * * * * *
3552295 CCTTCGTGATGATGATGTCTGGTTGTCTAAAGATGATGTGACTCATTCGTGATGTGGAGTTCTGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTGACTCCTTCGTGATGAGGAGTTCTGA
3552360 TTGGTAG
131 TTGGTAG
* * * *
3552367 ATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATCTTTTAAGATATTTTAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* * * * *
3552432 CATTCATGATGAGGATGTCTGGTTGTCTAAGGATGATGTGACTCCTTAGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTGACTCCTTCGTGATGAGGAGTTCTGA
3552497 TTGGTAG
131 TTGGTAG
* * *
3552504 ATGACATTGTTCCTTTGTAATGAGGACATCTGGCCATCTCTAAAGATATTTGAGATAACACAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* * *
3552569 CCTTCGTGATGAGGACGTCTGGTTGTCTAAGTATGATGTGACTCCTTCGTGATGAGGAGTTCTAA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTGACTCCTTCGTGATGAGGAGTTCTGA
*
3552634 TTGGTAT
131 TTGGTAG
*
3552641 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
* *
3552706 TCTTCGTGATGAGGACGTCTGGCTATCTAAGGATGATGT
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGT
3552745 TGATGGACAC
Statistics
Matches: 826, Mismatches: 95, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
135 1 0.00
136 3 0.00
137 822 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACACAGTT
CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTGACTCCTTCGTGATGAGGAGTTCTGA
TTGGTAG
Found at i:3554209 original size:33 final size:30
Alignment explanation
Indices: 3554132--3554211 Score: 81
Period size: 33 Copynumber: 2.6 Consensus size: 30
3554122 TTCTGGTTAA
*
3554132 AATA-GACCTTCAAAATGTCCCAACATGAT
1 AATATGACCTTCAAAATCTCCCAACATGAT
* * *
3554161 GATGTGAGTCTTCAAAATCTCCCAATCATTGAT
1 AATATGA-CCTTCAAAATCTCCCAA-CA-TGAT
3554194 AATATGGACCTTCAAAAT
1 AATAT-GACCTTCAAAAT
3554212 ACCCTTCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
29 2 0.05
30 2 0.05
31 15 0.38
32 2 0.05
33 16 0.41
34 2 0.05
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (30 bp):
AATATGACCTTCAAAATCTCCCAACATGAT
Found at i:3555724 original size:7 final size:8
Alignment explanation
Indices: 3555705--3555732 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3555695 TTTTCTTTAT
3555705 TTTTTTGA
1 TTTTTTGA
3555713 TTTTTTGA
1 TTTTTTGA
3555721 TTTTTTGA
1 TTTTTTGA
3555729 TTTT
1 TTTT
3555733 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (8 bp):
TTTTTTGA
Found at i:3555742 original size:16 final size:17
Alignment explanation
Indices: 3555679--3555742 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
3555669 TTTTTTCTTC
**
3555679 TTTTCTT-TTCTTTTCT
1 TTTTCTTATTCTTTTGA
*
3555695 TTTTCTTTATTTTTTTGA
1 TTTTC-TTATTCTTTTGA
3555713 TTTT-TTGATT-TTTTGA
1 TTTTCTT-ATTCTTTTGA
3555729 TTTTCTT-TTCTTTT
1 TTTTCTTATTCTTTT
3555743 CTTTTTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.05
16 21 0.52
17 7 0.17
18 10 0.25
ACGTcount: A:0.06, C:0.09, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTCTTATTCTTTTGA
Found at i:3564309 original size:19 final size:19
Alignment explanation
Indices: 3564285--3564328 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3564275 TGTAAATTTA
*
3564285 AAAAAATCAAAAAAAATAT
1 AAAAAATCAAAAAAAATAC
* *
3564304 AAAAAATCAGAAAAATTAC
1 AAAAAATCAAAAAAAATAC
3564323 AAAAAA
1 AAAAAA
3564329 AATTAGTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAATCAAAAAAAATAC
Found at i:3565734 original size:12 final size:12
Alignment explanation
Indices: 3565717--3565741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3565707 TATTAAGAAC
3565717 AATAATAATTTT
1 AATAATAATTTT
3565729 AATAATAATTTT
1 AATAATAATTTT
3565741 A
1 A
3565742 TTAACTTGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATAATAATTTT
Found at i:3577149 original size:20 final size:20
Alignment explanation
Indices: 3577124--3577196 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3577114 TAATACAAAA
*
3577124 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
* *
3577144 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATACTGACTT
* *
3577164 TCGCAACGAGATTCTGACTA
1 TCGCAACGAGATACTGACTT
3577184 TCGCAACGAGATA
1 TCGCAACGAGATA
3577197 ATACAGAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:3577369 original size:12 final size:12
Alignment explanation
Indices: 3577350--3577383 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3577340 CTCTCCGGCG
3577350 ACATCCGTTCCT
1 ACATCCGTTCCT
*
3577362 ATATCCGTTCCT
1 ACATCCGTTCCT
3577374 ACATCC-TTCC
1 ACATCCGTTCC
3577384 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:3577965 original size:24 final size:24
Alignment explanation
Indices: 3577938--3577991 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3577928 GTATTTGAAA
*
3577938 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
3577962 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
3577986 TTTGAT
1 TTTGAT
3577992 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:3580485 original size:20 final size:20
Alignment explanation
Indices: 3580460--3580566 Score: 148
Period size: 20 Copynumber: 5.5 Consensus size: 20
3580450 CAACGGGGAA
* *
3580460 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAAAATGGCT
3580480 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
3580500 ATCGCAA--AGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
3580518 ATCGCAACACGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
3580538 ATCGCAACGC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGGCT
3580558 ATCGCAACG
1 ATCGCAACG
3580567 AGAGAATCGC
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
18 17 0.22
19 1 0.01
20 61 0.77
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:3580522 original size:38 final size:40
Alignment explanation
Indices: 3580460--3580566 Score: 148
Period size: 38 Copynumber: 2.7 Consensus size: 40
3580450 CAACGGGGAA
* *
3580460 ATCGCAACGC-GAATATGACTATCGCAACGCGAAAATGGCT
1 ATCGCAAAGCAGAA-ATGGCTATCGCAACGCGAAAATGGCT
*
3580500 ATCGCAAAG-A-AAATGGCTATCGCAACACGAAAATGGCT
1 ATCGCAAAGCAGAAATGGCTATCGCAACGCGAAAATGGCT
*
3580538 ATCGCAACGCAGAAATGGCTATCGCAACG
1 ATCGCAAAGCAGAAATGGCTATCGCAACG
3580567 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 32 0.54
39 3 0.05
40 24 0.41
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (40 bp):
ATCGCAAAGCAGAAATGGCTATCGCAACGCGAAAATGGCT
Found at i:3580608 original size:20 final size:20
Alignment explanation
Indices: 3580571--3580623 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3580561 GCAACGAGAG
3580571 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
3580590 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
3580610 AATCGCAATGCGAA
1 AATCGCAATGCGAA
3580624 TTTAGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:3580836 original size:14 final size:14
Alignment explanation
Indices: 3580817--3580853 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3580807 CATTAATTAA
3580817 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3580831 ACAAATCATCTTTT
1 ACAAATCAACATTT
3580845 ACAAATCAA
1 ACAAATCAA
3580854 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3580942 original size:40 final size:40
Alignment explanation
Indices: 3580891--3580978 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
3580881 CTTATTTCCT
*
3580891 CATCAATTATTGAATCAATGAATCAACTTTTGCACCCGTA
1 CATCCATTATTGAATCAATGAATCAACTTTTGCACCCGTA
3580931 CATCCATTATTGAATCAATGAATCAACTTTTGCACCCGTA
1 CATCCATTATTGAATCAATGAATCAACTTTTGCACCCGTA
3580971 CATCCATT
1 CATCCATT
3580979 TCACGCAGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (40 bp):
CATCCATTATTGAATCAATGAATCAACTTTTGCACCCGTA
Found at i:3582352 original size:41 final size:42
Alignment explanation
Indices: 3582307--3582385 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
3582297 CGATGACGGT
*
3582307 GGCCTCTTGAACG-GTGGGGGGGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGATAGG
*
3582348 GGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGATGA
1 GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGA
3582386 CAGGTGAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.19, C:0.15, G:0.43, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGATAGG
Found at i:3582354 original size:21 final size:21
Alignment explanation
Indices: 3582325--3582385 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
3582315 GAACGGTGGG
*
3582325 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
3582346 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
3582367 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
3582386 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:3582775 original size:20 final size:19
Alignment explanation
Indices: 3582752--3582819 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
3582742 GAAACTTAAA
3582752 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
3582772 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3582792 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3582811 ATCGCAACG
1 ATCGCAACG
3582820 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3582871 original size:14 final size:14
Alignment explanation
Indices: 3582808--3582864 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3582798 ATGCGAAATG
3582808 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3582822 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3582841 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3582855 AAAATCGCAA
1 AAAATCGCAA
3582865 TGCCAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3582882 original size:33 final size:33
Alignment explanation
Indices: 3582792--3582867 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
3582782 GGAAATGGCT
3582792 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3582825 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3582858 ATCGCAATGC
1 ATCGCAATGC
3582868 CAAACACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3582906 original size:20 final size:20
Alignment explanation
Indices: 3582878--3583034 Score: 72
Period size: 20 Copynumber: 8.6 Consensus size: 20
3582868 CAAACACAAA
*
3582878 TCGCATTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
3582898 TCGCGTTGCGA--TT--TTG
1 TCGCGTTGCGATTTTCATTT
3582914 T--CGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
* *
3582932 T-GCATTGCGA--TT--TTG
1 TCGCGTTGCGATTTTCATTT
3582947 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
* ***
3582964 TCGCATTGCGATAGCCATTT
1 TCGCGTTGCGATTTTCATTT
* * **
3582984 CCGCATTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTT
* * *
3583004 TCGCGTTGCGGTTTTAAGTT
1 TCGCGTTGCGATTTTCATTT
*
3583024 TCGTGTTGCGA
1 TCGCGTTGCGA
3583035 AAGTAAACTA
Statistics
Matches: 103, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
14 15 0.15
15 3 0.03
16 7 0.07
17 4 0.04
18 5 0.05
19 17 0.17
20 52 0.50
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:3582918 original size:14 final size:14
Alignment explanation
Indices: 3582901--3582959 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3582891 TTCATTTTCG
3582901 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3582915 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TT--TTGT
*
3582933 GCATTGCGATTTTGT
1 -CGTTGCGATTTTGT
3582948 CGTTGCGATTTT
1 CGTTGCGATTTT
3582960 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.53
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 7 0.19
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3582945 original size:33 final size:33
Alignment explanation
Indices: 3582883--3582975 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3582873 ACAAATCGCA
*
3582883 TTGCGATTTTCATTTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTT-GCATTGCGATTTTGTCG
3582917 TTGCGATTTTCATTTTGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTTGCATTGCGATTTTGTCG
*
3582950 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTTGCATTGCGAT
3582976 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 41 0.72
34 16 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTTGCATTGCGATTTTGTCG
Found at i:3583595 original size:18 final size:18
Alignment explanation
Indices: 3583572--3583619 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3583562 CGGGTCGATC
3583572 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
3583590 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
3583608 AGGTGATGGCTC
1 AGGTGATGGCTC
3583620 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:3584969 original size:20 final size:20
Alignment explanation
Indices: 3584946--3585015 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
3584936 TCTGAAACTT
3584946 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
3584966 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
3584986 ACTATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
3585005 AAAATCGCAAC
1 AAAATCGCAAC
3585016 GAAAAAATCG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 14 0.30
20 32 0.70
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3585696 original size:21 final size:22
Alignment explanation
Indices: 3585667--3585729 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 22
3585657 CGTTGCGAAA
3585667 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
*
3585689 GT-AGTATCGCGTTGCGA--TA
1 GTCAGTATCGCGTTGCGATTTT
*
3585708 GTCAGTATCGCATTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
3585730 CCAAATTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 14 0.40
21 15 0.43
22 3 0.09
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.38
Consensus pattern (22 bp):
GTCAGTATCGCGTTGCGATTTT
Found at i:3585726 original size:20 final size:20
Alignment explanation
Indices: 3585632--3585726 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
3585622 GATTCTGTAT
* *
3585632 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
3585652 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
3585672 TATCGCGTTGCGATTTTGT-AG
1 TATCGCGTTGCGA--TAGTCAG
3585693 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
3585713 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
3585727 TTTCCAAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.69
21 15 0.23
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:3585745 original size:41 final size:41
Alignment explanation
Indices: 3585653--3585747 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
3585643 GAAAGTCAGA
* * ** *
3585653 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAGT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
3585694 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAAT
*
3585736 -TCGCATTGCGAT
1 ATCGCGTTGCGAT
3585748 TTACTTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
Found at i:3585759 original size:20 final size:21
Alignment explanation
Indices: 3585715--3585766 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3585705 ATAGTCAGTA
*
3585715 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
3585736 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3585756 TCGCATTGCGA
1 TCGCATTGCGA
3585767 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3586536 original size:32 final size:34
Alignment explanation
Indices: 3586479--3586545 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
3586469 GGACAAAAGA
* * *
3586479 GAAACAAAGCTTTGAAAAAGTTAAGT-AAGAAAT
1 GAAACAAAACTTAGAAAAAGCTAAGTAAAGAAAT
3586512 GAAACAAAACTTAG-AAAAGCTAAGTGAAAGAAAT
1 GAAACAAAACTTAGAAAAAGCTAAGT-AAAGAAAT
3586546 AAGCTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 10 0.34
33 12 0.41
34 7 0.24
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (34 bp):
GAAACAAAACTTAGAAAAAGCTAAGTAAAGAAAT
Found at i:3593298 original size:21 final size:22
Alignment explanation
Indices: 3593226--3593322 Score: 92
Period size: 23 Copynumber: 4.5 Consensus size: 22
3593216 CGACGAGCGT
* *
3593226 ATCGATGCACA-AC-ATAGTGC
1 ATCGATGCACATTCAATGGTGC
*
3593246 ATCGATGCACAATCAATGCGTGC
1 ATCGATGCACATTCAATG-GTGC
* * *
3593269 ATCGGTGCACCTTC-ATGGTGA
1 ATCGATGCACATTCAATGGTGC
*
3593290 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACATTCAATGG-TGC
3593313 ATCGATGCAC
1 ATCGATGCAC
3593323 TAGGTAGTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 16 0.26
22 8 0.13
23 27 0.44
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (22 bp):
ATCGATGCACATTCAATGGTGC
Found at i:3597150 original size:22 final size:21
Alignment explanation
Indices: 3597108--3597147 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3597098 AAGACTATTT
3597108 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
3597129 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
3597148 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:3599151 original size:64 final size:63
Alignment explanation
Indices: 3599080--3599235 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 63
3599070 TACACTAGGG
*
3599080 TGTGCATCGGTGCACAAATTTGCTTCGATGTTTCAA-AAATAGT-C-GGGTGCATCGATGCATGA
1 TGTGCATCGGTGCACAAA-TTGCTTCGATGTTTCAATAAA-A-TCCAGAGTGCATCGATGCATGA
3599142 C
63 C
*** *
3599143 TTGTGCATCGGTGCACAGAATCAATTCGATGTTTTAATAAAATCCAGAGTGCATCGATGCATGAC
1 -TGTGCATCGGTGCACA-AATTGCTTCGATGTTTCAATAAAATCCAGAGTGCATCGATGCATGAC
*
3599208 TGTGCATCGGTGCATAAATTGCATTCGA
1 TGTGCATCGGTGCACAAATTGC-TTCGA
3599236 AATGGGTGAG
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
63 4 0.05
64 51 0.65
65 23 0.29
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
TGTGCATCGGTGCACAAATTGCTTCGATGTTTCAATAAAATCCAGAGTGCATCGATGCATGAC
Found at i:3604676 original size:13 final size:13
Alignment explanation
Indices: 3604658--3604682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3604648 GAGACTGAGG
3604658 CCGTGATTGCAGA
1 CCGTGATTGCAGA
3604671 CCGTGATTGCAG
1 CCGTGATTGCAG
3604683 CATTATTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (13 bp):
CCGTGATTGCAGA
Found at i:3605738 original size:24 final size:24
Alignment explanation
Indices: 3605706--3605756 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3605696 GCTGGTTACT
3605706 ACACCCAAGGTGGTTCCACAAAGC
1 ACACCCAAGGTGGTTCCACAAAGC
3605730 ACACCCAAGGTGGTTCCACAAAGC
1 ACACCCAAGGTGGTTCCACAAAGC
3605754 ACA
1 ACA
3605757 ATCTTACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.12
Consensus pattern (24 bp):
ACACCCAAGGTGGTTCCACAAAGC
Found at i:3619694 original size:29 final size:29
Alignment explanation
Indices: 3619662--3619718 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
3619652 ATATCATAAA
* *
3619662 TAAA-TACTTAAAGTATTTTATTTTTATAT
1 TAAAGTACCTAAAGTATTTT-TTTATATAT
3619691 TAAAGTACCTAAAGTATTTTTTTATATA
1 TAAAGTACCTAAAGTATTTTTTTATATA
3619719 AAATTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (29 bp):
TAAAGTACCTAAAGTATTTTTTTATATAT
Found at i:3619771 original size:27 final size:28
Alignment explanation
Indices: 3619740--3619797 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3619730 TAGAGTTATC
*
3619740 TTTTTGGTCAAAATAGAG-ACCTAAAGTA
1 TTTTAGGTCAAAATAG-GTACCTAAAGTA
* *
3619768 TTTTATGTCAAAATAGGTACCTAAATTA
1 TTTTAGGTCAAAATAGGTACCTAAAGTA
3619796 TT
1 TT
3619798 CAAACTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (28 bp):
TTTTAGGTCAAAATAGGTACCTAAAGTA
Found at i:3619951 original size:27 final size:29
Alignment explanation
Indices: 3619873--3619952 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
3619863 CTTAGATGAA
* * *
3619873 AAAATAAATATTTTAAGTACTTATTTTGAC
1 AAAA-AAATACTTTAAATACTTATTTTAAC
3619903 AAAAAAATTAACTTTAAATACTTATTTTAAC
1 AAAAAAA-T-ACTTTAAATACTTATTTTAAC
* *
3619934 -CAAAAATA-TTTAATTACTT
1 AAAAAAATACTTTAAATACTT
3619953 TAATATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 10 0.23
28 1 0.02
29 4 0.09
30 10 0.23
31 18 0.42
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (29 bp):
AAAAAAATACTTTAAATACTTATTTTAAC
Found at i:3623374 original size:5 final size:5
Alignment explanation
Indices: 3623361--3623399 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
3623351 ATTGAAAATA
*
3623361 ATATT ATATA ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
3623400 AGTTCGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:3628300 original size:13 final size:13
Alignment explanation
Indices: 3628282--3628307 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3628272 GGAGTTGCAC
3628282 ACGGACTAAAATT
1 ACGGACTAAAATT
3628295 ACGGACTAAAATT
1 ACGGACTAAAATT
3628308 TCAATTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ACGGACTAAAATT
Found at i:3632799 original size:32 final size:32
Alignment explanation
Indices: 3632774--3632844 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
3632764 AATTTAGCGA
3632774 AACCGAAAGCAACATGAACCGAAATTAACCCG
1 AACCGAAAGCAACATGAACCGAAATTAACCCG
* * **
3632806 AACTGAAAGTAACATGAACCGAAAGCAACCCG
1 AACCGAAAGCAACATGAACCGAAATTAACCCG
3632838 AACCGAA
1 AACCGAA
3632845 TTTAACCCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (32 bp):
AACCGAAAGCAACATGAACCGAAATTAACCCG
Found at i:3632852 original size:16 final size:16
Alignment explanation
Indices: 3632774--3632844 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
3632764 AATTTAGCGA
* **
3632774 AACCGAAAGCAACATG
1 AACCGAAAGTAACCCG
*
3632790 AACCGAAATTAACCCG
1 AACCGAAAGTAACCCG
* **
3632806 AACTGAAAGTAACATG
1 AACCGAAAGTAACCCG
*
3632822 AACCGAAAGCAACCCG
1 AACCGAAAGTAACCCG
3632838 AACCGAA
1 AACCGAA
3632845 TTTAACCCAG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (16 bp):
AACCGAAAGTAACCCG
Found at i:3632862 original size:48 final size:48
Alignment explanation
Indices: 3632774--3632876 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 48
3632764 AATTTAGCGA
* *
3632774 AACCGAAAGCAACATGAACCGAAATTAACCCGAACTGAAAGTAA-CATG
1 AACCGAAAGCAACACGAACCGAAATTAACCCGAACTGAAAGAAATC-TG
* * *
3632822 AACCGAAAGCAACCCGAACCGAATTTAACCCAGATC-GAAAGAAATCTG
1 AACCGAAAGCAACACGAACCGAAATTAACCC-GAACTGAAAGAAATCTG
3632870 AACCGAA
1 AACCGAA
3632877 TTTTAATTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 44 0.92
49 4 0.08
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.12
Consensus pattern (48 bp):
AACCGAAAGCAACACGAACCGAAATTAACCCGAACTGAAAGAAATCTG
Found at i:3635765 original size:18 final size:18
Alignment explanation
Indices: 3635742--3635776 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3635732 TTGTTAAAAA
*
3635742 TATTTTTAAATACTTTTT
1 TATTTTTAAATAATTTTT
*
3635760 TATTTTTTAATAATTTT
1 TATTTTTAAATAATTTT
3635777 GATGTAAAAT
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:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTTAAATAATTTTT
Found at i:3638375 original size:65 final size:65
Alignment explanation
Indices: 3638271--3638412 Score: 266
Period size: 65 Copynumber: 2.2 Consensus size: 65
3638261 ACATCAATGA
3638271 GTATCGATACTCGGGACCTAGTATCGATACTCGGGGACTTGATCAGATTCTAGTAAGCTATTTTG
1 GTATCGATACTCGGGACCTAGTATCGATACTCGGGGACTTGATCAGATTCTAGTAAGCTATTTTG
*
3638336 GTATCGATACTCGGGACCTAGTATCGATACTCGGGGACTTGATCAGATTCTAGTAATCTATTTTG
1 GTATCGATACTCGGGACCTAGTATCGATACTCGGGGACTTGATCAGATTCTAGTAAGCTATTTTG
*
3638401 ATATCGATACTC
1 GTATCGATACTC
3638413 ATGAAAGTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 75 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (65 bp):
GTATCGATACTCGGGACCTAGTATCGATACTCGGGGACTTGATCAGATTCTAGTAAGCTATTTTG
Found at i:3638425 original size:18 final size:21
Alignment explanation
Indices: 3638402--3638450 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3638392 TCTATTTTGA
3638402 TATCGATACTC-AT-G-AAAG
1 TATCGATACTCGATGGTAAAG
*
3638420 TATCGATAC-CGATGGTAGAG
1 TATCGATACTCGATGGTAAAG
3638440 TATCGATACTC
1 TATCGATACTC
3638451 CCAATAGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 1 0.04
20 12 0.46
21 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (21 bp):
TATCGATACTCGATGGTAAAG
Found at i:3645566 original size:15 final size:16
Alignment explanation
Indices: 3645546--3645575 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3645536 TAAAATATTC
3645546 AATTTTAATT-AATAT
1 AATTTTAATTGAATAT
3645561 AATTTTAATTGAATA
1 AATTTTAATTGAATA
3645576 AATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTTTAATTGAATAT
Found at i:3654003 original size:19 final size:19
Alignment explanation
Indices: 3653979--3654015 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3653969 ATGACCAACA
*
3653979 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
3653998 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
3654016 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3654064 original size:20 final size:20
Alignment explanation
Indices: 3654041--3654153 Score: 122
Period size: 20 Copynumber: 5.6 Consensus size: 20
3654031 GTTTCCAGAT
*
3654041 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
3654061 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
3654081 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
3654101 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
3654122 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
3654142 TCGCAACGCGAT
1 TCGCAACGCGAT
3654154 AATACAAATC
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.04
20 55 0.72
21 16 0.21
22 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:3654133 original size:41 final size:41
Alignment explanation
Indices: 3654041--3654167 Score: 188
Period size: 41 Copynumber: 3.1 Consensus size: 41
3654031 GTTTCCAGAT
* * **
3654041 TCGCAACGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT-AA
3654081 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
3654122 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACA-AA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
3654162 TCGCAA
1 TCGCAA
3654168 TACGATTTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 36 0.44
41 40 0.49
42 5 0.06
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
Found at i:3654164 original size:20 final size:21
Alignment explanation
Indices: 3654078--3654167 Score: 89
Period size: 20 Copynumber: 4.4 Consensus size: 21
3654068 GCGAATATGT
**
3654078 AAATCGCAACGCGATTCTGAC
1 AAATCGCAACGCGATAATGAC
*
3654099 -TATCGCAACGCGATAAT-AC
1 AAATCGCAACGCGATAATGAC
**
3654118 ATAATCGCAACGCGATTCTGAC
1 A-AATCGCAACGCGATAATGAC
*
3654140 -TATCGCAACGCGATAAT-AC
1 AAATCGCAACGCGATAATGAC
3654159 AAATCGCAA
1 AAATCGCAA
3654168 TACGATTTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.07
20 35 0.64
21 14 0.25
22 2 0.04
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (21 bp):
AAATCGCAACGCGATAATGAC
Found at i:3654342 original size:22 final size:22
Alignment explanation
Indices: 3654317--3654367 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3654307 CTACGGCGAC
3654317 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
3654339 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
3654361 ATCCGTC
1 ATCCGTC
3654368 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:3654503 original size:25 final size:25
Alignment explanation
Indices: 3654473--3654527 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
3654463 TTATTATTAG
3654473 GTTTTTCATATTGAAATTGATAATAA
1 GTTTTTCATA-TGAAATTGATAATAA
*
3654499 GTTTTTCATATGAAATTGATGATAA
1 GTTTTTCATATGAAATTGATAATAA
3654524 GTTT
1 GTTT
3654528 ACTGGTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.47
Consensus pattern (25 bp):
GTTTTTCATATGAAATTGATAATAA
Found at i:3654771 original size:20 final size:20
Alignment explanation
Indices: 3654746--3654789 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3654736 AAAATCGCAA
3654746 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
3654766 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
3654786 CGAT
1 CGAT
3654790 TTTAAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:3656728 original size:20 final size:19
Alignment explanation
Indices: 3656670--3656738 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
3656660 CGAAACTTAA
3656670 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
3656690 ATCGTAATGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
3656710 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
3656730 ATCGCAACG
1 ATCGCAACG
3656739 GGATAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3656929 original size:20 final size:20
Alignment explanation
Indices: 3656866--3656930 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
3656856 CGATTATCCT
**
3656866 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
*
3656886 GTTGTGAT-GTCATTTTC-C
1 GTTGCGATAGTCATTTTCGC
3656904 -TTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
3656923 GTTGCGAT
1 GTTGCGAT
3656931 TTGAGTTTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 6 0.16
18 10 0.26
19 8 0.21
20 14 0.37
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:3656959 original size:20 final size:19
Alignment explanation
Indices: 3656917--3656959 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3656907 CGATAGTCAT
*
3656917 TTTCGCGTTGCGATTTGAG
1 TTTCGCGTTGCGATTTAAG
*
3656936 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGA-TTTAAG
3656956 TTTC
1 TTTC
3656960 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTAAG
Found at i:3658014 original size:19 final size:19
Alignment explanation
Indices: 3657990--3658077 Score: 95
Period size: 19 Copynumber: 4.5 Consensus size: 19
3657980 TCTACAGTTG
*
3657990 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
3658009 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
3658028 TTGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
3658049 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
3658069 TCGTTGCGA
1 TCGTTGCGA
3658078 AAATTCGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
19 36 0.65
20 5 0.09
21 5 0.09
22 9 0.16
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:3658891 original size:21 final size:21
Alignment explanation
Indices: 3658860--3658932 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
3658850 AATTTGGAAA
3658860 ATCAC-ACGCGATTTTCAACT
1 ATCACAACGCGATTTTCAACT
** ** *
3658880 ATCACAACGCGAAATGGAA-A
1 ATCACAACGCGATTTTCAACT
*
3658900 ATCGCAACGCGATTTTCAACT
1 ATCACAACGCGATTTTCAACT
* *
3658921 ATCGCAAAGCGA
1 ATCACAACGCGA
3658933 AATGCAACGC
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (21 bp):
ATCACAACGCGATTTTCAACT
Found at i:3658916 original size:41 final size:40
Alignment explanation
Indices: 3658854--3658936 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 40
3658844 GCAACGAATT
*
3658854 TGGAAAATCACACGCGATTTTCAACTATCACAACGCGAAA
1 TGGAAAATCACACGCGATTTTCAACTATCACAAAGCGAAA
* *
3658894 TGGAAAATCGCAACGCGATTTTCAACTATCGCAAAGCGAAA
1 TGGAAAATCAC-ACGCGATTTTCAACTATCACAAAGCGAAA
3658935 TG
1 TG
3658937 CAACGCGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
TGGAAAATCACACGCGATTTTCAACTATCACAAAGCGAAA
Found at i:3658940 original size:21 final size:21
Alignment explanation
Indices: 3658875--3658940 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3658865 ACGCGATTTT
*
3658875 CAACTATCACAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
3658896 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
3658916 CAACTATCGCAAAGCGAAATG
1 CAACTATCGCAACGCGAAATG
3658937 CAAC
1 CAAC
3658941 GCGAATTTGT
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:3659866 original size:14 final size:14
Alignment explanation
Indices: 3659847--3659908 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
3659837 TTTCTTGTTT
3659847 AATTGATTTGTAAA
1 AATTGATTTGTAAA
3659861 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
3659875 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
3659890 TATTGATGTGTAAA
1 AATTGATTTGTAAA
3659904 TAATT
1 -AATT
3659909 CCTATTTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3659881 original size:28 final size:29
Alignment explanation
Indices: 3659849--3659903 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3659839 TCTTGTTTAA
*
3659849 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
3659877 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
3659904 TAATTCCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:3660103 original size:20 final size:20
Alignment explanation
Indices: 3660078--3660396 Score: 368
Period size: 20 Copynumber: 16.9 Consensus size: 20
3660068 GCAATTTTCT
* *
3660078 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
3660098 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
3660118 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
3660138 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
3660158 CGTTGCGAT--T----TTTA
1 CGTTGCGATAGTCAAATTCG
*
3660172 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
3660192 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3660212 -TTTGCGATAGTCAAATT--
1 CGTTGCGATAGTCAAATTCG
* *
3660229 C---GCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
3660246 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
3660266 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
3660286 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
3660306 CGTTGCGAT--T----TTTA
1 CGTTGCGATAGTCAAATTCG
*
3660320 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
3660340 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3660360 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
3660380 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
3660397 GAATGTCTAA
Statistics
Matches: 257, Mismatches: 24, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
14 22 0.09
15 13 0.05
16 2 0.01
17 1 0.00
18 2 0.01
19 16 0.06
20 201 0.78
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3660176 original size:74 final size:74
Alignment explanation
Indices: 3660098--3660388 Score: 424
Period size: 74 Copynumber: 3.9 Consensus size: 74
3660088 GTCAAATACC
3660098 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
3660163 CGATTTTTA
66 CGATTTTTA
* * * * *
3660172 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG-TTTGCGATAGTCAAATTCGCGATA
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG-TT
** ***
3660236 GTC-AAATACC
65 G-CGATTTTTA
3660246 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
3660311 CGATTTTTA
66 CGATTTTTA
* * * *
3660320 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
3660385 CGAT
66 CGAT
3660389 AGTCAAATGA
Statistics
Matches: 189, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
73 21 0.11
74 147 0.78
75 21 0.11
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (74 bp):
CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CGATTTTTA
Found at i:3660199 original size:54 final size:54
Alignment explanation
Indices: 3660113--3660389 Score: 272
Period size: 54 Copynumber: 5.0 Consensus size: 54
3660103 CGATAATCAA
3660113 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
* * * *
3660167 TTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG-TTTGCGAT
1 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
* ** * * * *
3660220 AGTCAAATTCGCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGT
1 ATTCACGTT-GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCG--A-T
* ** * ** *
3660278 CAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTACGTT-GCGATAGTC-AT
1 ---ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG-TTG-CGAT
* *
3660335 ATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
3660389 A
1 A
3660390 GTCAAATGAA
Statistics
Matches: 176, Mismatches: 35, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
53 12 0.07
54 115 0.65
55 8 0.05
57 2 0.01
58 2 0.01
59 2 0.01
60 29 0.16
61 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (54 bp):
ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
Found at i:3660199 original size:94 final size:93
Alignment explanation
Indices: 3660038--3660396 Score: 332
Period size: 94 Copynumber: 3.8 Consensus size: 93
3660028 CGCGAAAGTT
* * * * *
3660038 AATTCGCGTTGCGATAGTCTAATACGCTTTGCAATTTTCT-CGTTGCGATAGTCAAATACCCGTT
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTT-TACGTTGCGATAGTCAAATTCGCGTT
*
3660102 GCGATAATCAAATTCACGTTGCGATAGTCA
65 GCGATAGTCAAATTC-CGTTGCGATAGTCA
* *
3660132 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTACGTTGCGATAGTCATATTCGCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTTACGTTGCGATAGTCAAATTCGCGTTG
3660197 CGATAGTCAAATT-CGTTTGCGATAGTCA
66 CGATAGTCAAATTCCG-TTGCGATAGTCA
* *
3660225 AATT--C---GCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTC
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGAT--T----TTTACGTTGCGATAGTCAAATTC
3660285 GCGTTGCGATAGTCAAATTCGCGTTGCGAT--T--
60 GCGTTGCGATAGTCAAATTC-CGTTGCGATAGTCA
** * * *
3660316 --TTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATT-CGTGTTGCGATAGTCAAATT
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGAT--T---TTTAC--GTTGCGATAGTCAAATT
3660378 CGCGTTGCGATAGTCAAAT
59 CGCGTTGCGATAGTCAAAT
3660397 GAATGTCTAA
Statistics
Matches: 229, Mismatches: 19, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
88 23 0.10
89 2 0.01
90 1 0.00
91 2 0.01
92 3 0.01
93 21 0.09
94 168 0.73
95 7 0.03
96 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (93 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTTACGTTGCGATAGTCAAATTCGCGTTG
CGATAGTCAAATTCCGTTGCGATAGTCA
Found at i:3660235 original size:15 final size:16
Alignment explanation
Indices: 3660195--3660242 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 16
3660185 ATATTCGCGT
3660195 TGCGATAGTCAAATTC
1 TGCGATAGTCAAATTC
3660211 GTTTGCGATAGTCAAATTC
1 ---TGCGATAGTCAAATTC
3660230 -GCGATAGTCAAAT
1 TGCGATAGTCAAAT
3660243 ACCCGTTGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.45
19 16 0.55
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (16 bp):
TGCGATAGTCAAATTC
Found at i:3660307 original size:148 final size:149
Alignment explanation
Indices: 3660082--3660381 Score: 593
Period size: 148 Copynumber: 2.0 Consensus size: 149
3660072 TTTTCTCGTT
3660082 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
3660147 AGTCAAATTCGCGTTGCGATTTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG
66 AGTCAAATTCGCGTTGCGATTTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG
3660212 T-TTGCGATAGTCAAATTC
131 TGTTGCGATAGTCAAATTC
3660230 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
3660295 AGTCAAATTCGCGTTGCGATTTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG
66 AGTCAAATTCGCGTTGCGATTTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG
3660360 TGTTGCGATAGTCAAATTC
131 TGTTGCGATAGTCAAATTC
3660379 GCG
1 GCG
3660382 TTGCGATAGT
Statistics
Matches: 151, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 131 0.87
149 20 0.13
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (149 bp):
GCGATAGTCAAATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
AGTCAAATTCGCGTTGCGATTTTTACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCG
TGTTGCGATAGTCAAATTC
Found at i:3663762 original size:20 final size:20
Alignment explanation
Indices: 3663732--3663861 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
3663722 GAAATTCAGT
*
3663732 GTTGTGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
3663752 GCTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
3663772 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
3663793 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
3663813 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
3663834 GTTGCGATAGTTAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
3663854 GTTACGAT
1 GTTGCGAT
3663862 TTACATATTC
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.04
20 54 0.59
21 30 0.33
22 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:3663792 original size:41 final size:41
Alignment explanation
Indices: 3663747--3663862 Score: 205
Period size: 41 Copynumber: 2.8 Consensus size: 41
3663737 GATAGTCAGA
*
3663747 ATCGCGCTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
3663788 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
* *
3663829 ATCGCGTTGCGATAGTTAGAATCGCGTTACGATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
3663863 TACATATTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:3663793 original size:21 final size:21
Alignment explanation
Indices: 3663767--3663841 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
3663757 GATAGTCAGA
3663767 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
3663788 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
3663808 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
3663829 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
3663842 AGTTAGAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.04
20 15 0.32
21 28 0.60
22 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:3663853 original size:61 final size:61
Alignment explanation
Indices: 3663732--3663861 Score: 149
Period size: 61 Copynumber: 2.1 Consensus size: 61
3663722 GAAATTCAGT
* **
3663732 GTTGTGATAGTCAGAATCGCGCTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGCTGCGATAGTCAGAATCGCGTTGCGATTATGTAGAATCGC
* **
3663793 GTTGCGATAGTCAGAATCGCGTTGCGATTATGT-ATTATCGCGTTGCGA-TA-GTTAGAATCGC
1 GTTGCGATAGTCAGAATCGCGCTGCGA-TA-GTCAGAATCGCGTTGCGATTATG-TAGAATCGC
*
3663854 GTTACGAT
1 GTTGCGAT
3663862 TTACATATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 1 0.02
61 41 0.69
62 15 0.25
63 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (61 bp):
GTTGCGATAGTCAGAATCGCGCTGCGATAGTCAGAATCGCGTTGCGATTATGTAGAATCGC
Found at i:3663894 original size:21 final size:20
Alignment explanation
Indices: 3663848--3663902 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
3663838 CGATAGTTAG
* *
3663848 AATCGCGTTACGATTTACAT
1 AATCGCATTACGATTTACAA
* *
3663868 ATTCGCATTGCGATTTTACAA
1 AATCGCATTACGA-TTTACAA
*
3663889 AATCGCAATACGAT
1 AATCGCATTACGAT
3663903 AGTCAAAATC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (20 bp):
AATCGCATTACGATTTACAA
Found at i:3663959 original size:20 final size:19
Alignment explanation
Indices: 3663936--3663981 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3663926 GGAAACTGAT
* *
3663936 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
3663956 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
3663975 TTGCGAT
1 TTGCGAT
3663982 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:3663971 original size:19 final size:19
Alignment explanation
Indices: 3663947--3663983 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3663937 TGCGATACTG
*
3663947 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
3663966 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
3663984 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:3671933 original size:13 final size:13
Alignment explanation
Indices: 3671915--3671951 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
3671905 TTTTAAGAAG
3671915 GGTGAAGAAGCAA
1 GGTGAAGAAGCAA
3671928 GGTGAAGAAGCAA
1 GGTGAAGAAGCAA
3671941 GGTGAATGAAG
1 GGTGAA-GAAG
3671952 GAAAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.43, C:0.05, G:0.41, T:0.11
Consensus pattern (13 bp):
GGTGAAGAAGCAA
Found at i:3674438 original size:24 final size:24
Alignment explanation
Indices: 3674406--3674454 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3674396 TGTAATGAGG
*
3674406 TAAGGAGGAGGTAGGAAAGTAGGC
1 TAAGGAGGAGATAGGAAAGTAGGC
3674430 TAAGGAGGAGATAGGAAAGTAGGC
1 TAAGGAGGAGATAGGAAAGTAGGC
3674454 T
1 T
3674455 GCCTCTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (24 bp):
TAAGGAGGAGATAGGAAAGTAGGC
Found at i:3678414 original size:30 final size:30
Alignment explanation
Indices: 3678380--3678450 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
3678370 GGTAGACCAC
3678380 ATTTTCAAATTGTTTCTTTTAATTTTATAT
1 ATTTTCAAATTGTTTCTTTTAATTTTATAT
3678410 ATTTTCAAATTGTTTCTTTTAATTTTATAT
1 ATTTTCAAATTGTTTCTTTTAATTTTATAT
3678440 ATTTTCAAATT
1 ATTTTCAAATT
3678451 TTAGTTAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (30 bp):
ATTTTCAAATTGTTTCTTTTAATTTTATAT
Found at i:3679354 original size:31 final size:32
Alignment explanation
Indices: 3679293--3679364 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
3679283 CGGGGCCATG
* *
3679293 GGGCCTACCTGAGAACACATCTTAGGGCCGCA
1 GGGCCTACCCGAGAACACATCTCAGGGCCGCA
**
3679325 GGGCCTACCCGAGAA-TGATCTCAGGGCCGCA
1 GGGCCTACCCGAGAACACATCTCAGGGCCGCA
*
3679356 GAGCCTACC
1 GGGCCTACC
3679365 TAAGAGTCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.14
Consensus pattern (32 bp):
GGGCCTACCCGAGAACACATCTCAGGGCCGCA
Found at i:3680287 original size:17 final size:17
Alignment explanation
Indices: 3680265--3680339 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
3680255 CACAATCAAC
*
3680265 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
3680282 GGTCAACATTCGGGTCG
1 GGTCAACAGTCGGGTCG
3680299 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
3680316 GGTCAACAGTCGGGTCA
1 GGTCAACAGTCGGGTCG
3680333 GGTCAAC
1 GGTCAAC
3680340 CCGGTTCAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3680375 original size:20 final size:19
Alignment explanation
Indices: 3680333--3680384 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
3680323 AGTCGGGTCA
* *
3680333 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
3680352 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
*
3680372 GGTCAAACAGGTT
1 GGTCAAACCGGTT
3680385 TTCCAGCAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:3686050 original size:32 final size:30
Alignment explanation
Indices: 3686014--3686089 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
3686004 GGGGCCGTGG
*
3686014 GGCCTACCTAAGAACACATCTTAGGGCCGCAA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGC-A
** **
3686046 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCGCA
3686076 GAGCCTACCTAAGA
1 G-GCCTACCTAAGA
3686090 GTCACATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.06
31 22 0.61
32 12 0.33
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3686974 original size:7 final size:7
Alignment explanation
Indices: 3686959--3687002 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
3686949 GTCAAAGAAA
3686959 GTCAACG
1 GTCAACG
*
3686966 GTAAACG
1 GTCAACG
*
3686973 GTC-ACA
1 GTCAACG
3686979 GTCAACG
1 GTCAACG
3686986 GTCAACG
1 GTCAACG
3686993 GTCAACG
1 GTCAACG
3687000 GTC
1 GTC
3687003 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3686983 original size:20 final size:20
Alignment explanation
Indices: 3686958--3686996 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3686948 GGTCAAAGAA
3686958 AGTCAACGGTAAACGGTCAC
1 AGTCAACGGTAAACGGTCAC
*
3686978 AGTCAACGGTCAACGGTCA
1 AGTCAACGGTAAACGGTCA
3686997 ACGGTCGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (20 bp):
AGTCAACGGTAAACGGTCAC
Found at i:3687014 original size:17 final size:17
Alignment explanation
Indices: 3686992--3687065 Score: 121
Period size: 17 Copynumber: 4.4 Consensus size: 17
3686982 AACGGTCAAC
*
3686992 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
* *
3687009 GGTCAACATTCGGGTTG
1 GGTCAACAGTCGGGTCG
3687026 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3687043 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3687060 GGTCAA
1 GGTCAA
3687066 TCCGGTTCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.18, C:0.22, G:0.41, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3688850 original size:14 final size:14
Alignment explanation
Indices: 3688831--3688857 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3688821 TTTAAATTGA
3688831 TAGAATTTATTTAT
1 TAGAATTTATTTAT
3688845 TAGAATTTATTTA
1 TAGAATTTATTTA
3688858 AATAATTTTT
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:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
TAGAATTTATTTAT
Found at i:3693761 original size:9 final size:8
Alignment explanation
Indices: 3693658--3693762 Score: 50
Period size: 8 Copynumber: 12.1 Consensus size: 8
3693648 TATAAATATG
*
3693658 AAAATAAT
1 AAAAAAAT
*
3693666 AAATAAAAC
1 AAA-AAAAT
3693675 AAAAAAAT
1 AAAAAAAT
* **
3693683 AACAAAGG
1 AAAAAAAT
3693691 AAAAATAAT
1 AAAAA-AAT
3693700 AAAATAAAT
1 AAAA-AAAT
3693709 GAAAATAAA-
1 -AAAA-AAAT
3693718 AAACCAAAAT
1 AAA--AAAAT
3693728 AAATAAAAT
1 AAA-AAAAT
***
3693737 GGTAAAAT
1 AAAAAAAT
3693745 AAAAAAAT
1 AAAAAAAT
3693753 AAGAAAAAT
1 AA-AAAAAT
3693762 A
1 A
3693763 TGATGATAAT
Statistics
Matches: 73, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
8 31 0.42
9 29 0.40
10 13 0.18
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3693774 original size:3 final size:3
Alignment explanation
Indices: 3693768--3693881 Score: 144
Period size: 3 Copynumber: 38.3 Consensus size: 3
3693758 AAATATGATG
* ** * *
3693768 ATA ATA ATA ATA ATA ATA ACT- ATA ATA ATA AGA A-A CCA AAA CAGA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA -ATA
3693813 ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3693860 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
3693882 ATGAAAAAAT
Statistics
Matches: 100, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.04
3 93 0.93
4 3 0.03
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Done.