Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003996.1 Hibiscus syriacus cultivar Beakdansim tig00008706_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: 553326
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:444146 original size:32 final size:30
Alignment explanation
Indices: 444105--444209 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 30
444095 AATTTAATAT
444105 AAAAATATATATGTTACTCTTATTTTAAATTA
1 AAAAATATATAT-TTA-TCTTATTTTAAATTA
* * **
444137 AAAAATATATA-ATATTTTATTCTTATCTTA
1 AAAAATATATATTTATCTTATT-TTAAATTA
444167 CTAAAAATATATATTTTATTCTTA-TTTAAATTA
1 --AAAAATATATA-TTTA-TCTTATTTTAAATTA
444200 AAAAATATAT
1 AAAAATATAT
444210 TTATTATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
29 6 0.10
30 8 0.14
31 10 0.17
32 22 0.37
33 6 0.10
34 3 0.05
35 4 0.07
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.48
Consensus pattern (30 bp):
AAAAATATATATTTATCTTATTTTAAATTA
Found at i:444202 original size:30 final size:30
Alignment explanation
Indices: 444082--444239 Score: 128
Period size: 31 Copynumber: 5.1 Consensus size: 30
444072 ATATATATAA
*
444082 ATATTTTATTATTAATTT-AATATAAAAATAT
1 ATATTTTATTCTT-ATTTAAAT-TAAAAATAT
* *
444113 ATATGTTACTCTTATTTTAAATTAAAAAATATAT
1 ATATTTTATTCTTA-TTTAAATT--AAAA-ATAT
*
444147 AATATTTTATTCTTATCTT--ACTAAAAATAT
1 -ATATTTTATTCTTAT-TTAAATTAAAAATAT
444177 ATATTTTATTCTTATTTAAATTAAAAA-AT
1 ATATTTTATTCTTATTTAAATTAAAAATAT
* *
444206 ATA-TTTATTATTATATTAACTTTTAAAAATAT
1 ATATTTTATTCTTAT-TTAA--ATTAAAAATAT
444238 AT
1 AT
444240 TAAAATATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
28 12 0.11
29 24 0.23
30 12 0.11
31 25 0.24
32 7 0.07
33 6 0.06
34 5 0.05
35 14 0.13
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (30 bp):
ATATTTTATTCTTATTTAAATTAAAAATAT
Found at i:444240 original size:30 final size:28
Alignment explanation
Indices: 444168--444240 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
444158 CTTATCTTAC
*
444168 TAAAAATATATATTTTATTCTTATTTAAAT
1 TAAAAA-ATATA-TTTATTATTATTTAAAT
*
444198 TAAAAAATATATTTATTATTATATTAACTT
1 TAAAAAATATATTTATTATTAT-TTAA-AT
*
444228 TTAAAAATATATT
1 TAAAAAATATATT
444241 AAAATATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 10 0.26
29 9 0.24
30 19 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
TAAAAAATATATTTATTATTATTTAAAT
Found at i:444278 original size:34 final size:33
Alignment explanation
Indices: 444240--444317 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 33
444230 AAAAATATAT
*
444240 TAAAATATTATAAATTTTTTAAATAAAATAAGAG
1 TAAAATATTATAAATTTTAT-AATAAAATAAGAG
* * *
444274 TAAAATA-TAT--ATTTTATATTAAATTAATAG
1 TAAAATATTATAAATTTTATAATAAAATAAGAG
444304 TAAAATATT-TAAAT
1 TAAAATATTATAAAT
444318 ATATTTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 18 0.49
31 7 0.19
32 2 0.05
33 3 0.08
34 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (33 bp):
TAAAATATTATAAATTTTATAATAAAATAAGAG
Found at i:444427 original size:29 final size:29
Alignment explanation
Indices: 444387--444461 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
444377 ATATTTTTAC
* *
444387 ATTAAAA-TAAAATAAAATTTATTTAATAA
1 ATTAAAACAAAAATAAAA-ATATTTAATAA
*
444416 ATTAAGACAAAAATAAAAATATTTAATAA
1 ATTAAAACAAAAATAAAAATATTTAATAA
*
444445 TTTAAAACAAAAATAAA
1 ATTAAAACAAAAATAAA
444462 GTGATAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 31 0.77
30 9 0.22
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (29 bp):
ATTAAAACAAAAATAAAAATATTTAATAA
Found at i:446529 original size:17 final size:17
Alignment explanation
Indices: 446507--446550 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
446497 ACCGACCCGA
446507 AATAAAAAAAATTATTC
1 AATAAAAAAAATTATTC
* * *
446524 AATAAAAACAGTTATTT
1 AATAAAAAAAATTATTC
446541 AATTAAAAAA
1 AA-TAAAAAA
446551 TATATATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAAAAAAAATTATTC
Found at i:447066 original size:16 final size:15
Alignment explanation
Indices: 447041--447074 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
447031 ACAATTTAAA
447041 GTTGATTTTAATAAT
1 GTTGATTTTAATAAT
*
447056 GTTGAATTTTAATCAT
1 GTTG-ATTTTAATAAT
447072 GTT
1 GTT
447075 AATGAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (15 bp):
GTTGATTTTAATAAT
Found at i:456024 original size:2 final size:2
Alignment explanation
Indices: 456019--456057 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
456009 TGTTTGTGTG
456019 TA TA TA 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 TA TA TA T
456058 TCCTGGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:462416 original size:18 final size:18
Alignment explanation
Indices: 462376--462410 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
462366 ACTCCACGAC
462376 CTTTCTCTCTCCCTTTCT
1 CTTTCTCTCTCCCTTTCT
462394 CTTTCTC-CTCCACTTTC
1 CTTTCTCTCTCC-CTTTC
462411 CATTTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (18 bp):
CTTTCTCTCTCCCTTTCT
Found at i:463338 original size:7 final size:7
Alignment explanation
Indices: 463326--463368 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
463316 CCCTAATTTA
463326 TAAACCC
1 TAAACCC
463333 TAAACCC
1 TAAACCC
463340 TAAACCC
1 TAAACCC
463347 TAAACCC
1 TAAACCC
*
463354 TAAATCC
1 TAAACCC
463361 TAAACCC
1 TAAACCC
463368 T
1 T
463369 TAACAAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:465333 original size:16 final size:15
Alignment explanation
Indices: 465312--465407 Score: 88
Period size: 16 Copynumber: 6.1 Consensus size: 15
465302 AAGTTATATT
*
465312 ATAATAAATAAATAAA
1 ATAAT-AATAATTAAA
*
465328 ATAATAATAAGTAAAA
1 ATAATAATAA-TTAAA
* *
465344 ATATTAATTATTAAA
1 ATAATAATAATTAAA
465359 TATAATAAATAATTAAA
1 -ATAAT-AATAATTAAA
465376 AT-ATAATAATATATAA
1 ATAATAATAAT-TA-AA
465392 AT-ATAATAATTAAA
1 ATAATAATAATTAAA
465406 AT
1 AT
465408 GGAAATTTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.15
15 15 0.22
16 34 0.50
17 9 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (15 bp):
ATAATAATAATTAAA
Found at i:465376 original size:48 final size:47
Alignment explanation
Indices: 465311--465564 Score: 156
Period size: 52 Copynumber: 5.0 Consensus size: 47
465301 AAAGTTATAT
*
465311 TATAATAAATAAATAAAATAATAATAAGTA-A-AAATATTAATTATTAAA
1 TATAATAAATAAATAAAAT-ATAATAA-TATATAAATA-TAATAATTAAA
*
465359 TATAATAAATAATTAAAATATAATAATATATAAATATAATAATTAAA
1 TATAATAAATAAATAAAATATAATAATATATAAATATAATAATTAAA
* * * * * *
465406 -ATGGAAATTTAATAAAAAAGAATTATAATATATTTTGTAAATTTTGAAATAATGAAAAA
1 TAT---AA-TAAATAAATAA-AA-TATAATA-A-TATATAAA-TAT--AATAAT--TAAA
* *
465465 TTATATTATAATAAAT-AAATATAATAAAATAATAAATAATAATAATTATTAAA
1 -TATAATA-AATAAATAAAATATAATAATAT-ATAAAT-ATAAT-A--ATTAAA
* * *
465518 AATAATAAATAATTAAAATATAATAATATATAAATATAGTAATTAAA
1 TATAATAAATAAATAAAATATAATAATATATAAATATAATAATTAAA
465565 ATAGATATCT
Statistics
Matches: 160, Mismatches: 22, Indels: 49
0.69 0.10 0.21
Matches are distributed among these distances:
46 4 0.03
47 24 0.15
48 23 0.14
49 3 0.02
50 12 0.08
51 14 0.09
52 28 0.17
53 7 0.04
54 12 0.08
55 11 0.07
56 2 0.01
57 8 0.05
58 7 0.04
59 3 0.02
61 2 0.01
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (47 bp):
TATAATAAATAAATAAAATATAATAATATATAAATATAATAATTAAA
Found at i:465489 original size:13 final size:13
Alignment explanation
Indices: 465471--465543 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 13
465461 AAAATTATAT
465471 TATAATAAATAAA
1 TATAATAAATAAA
465484 TATAATAAAATAATA
1 TATAAT-AAATAA-A
* *
465499 AATAAT-AATAAT
1 TATAATAAATAAA
465511 TATTAA-AAAT-AA
1 TA-TAATAAATAAA
*
465523 TA-AATAATTAAAA
1 TATAATAAAT-AAA
465536 TATAATAA
1 TATAATAA
465544 TATATAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 4 0.09
13 21 0.45
14 11 0.23
15 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATAATAAATAAA
Found at i:465491 original size:16 final size:16
Alignment explanation
Indices: 465467--465560 Score: 80
Period size: 16 Copynumber: 5.6 Consensus size: 16
465457 ATGAAAAATT
*
465467 ATATTATAATAAATAA
1 ATATAATAATAAATAA
*
465483 ATATAATAAAATAATAA
1 ATATAATAATA-AATAA
* *
465500 ATAATAATAATTATTAA
1 AT-ATAATAATAAATAA
* *
465517 AAATAATAAATAATTAAA
1 ATATAAT-AATAAAT-AA
*
465535 ATATAATAATATATAA
1 ATATAATAATAAATAA
*
465551 ATATAGTAAT
1 ATATAATAAT
465561 TAAAATAGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
16 25 0.40
17 23 0.37
18 15 0.24
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (16 bp):
ATATAATAATAAATAA
Found at i:465510 original size:34 final size:34
Alignment explanation
Indices: 465467--465555 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
465457 ATGAAAAATT
*
465467 ATATTATAATAAATAAATATAATAAAATAA-T-AA
1 ATATAATAATAAATAAATATAAT-AAATAATTAAA
* * *
465500 ATAATAATAATTATTAAAAATAATAAATAATTAAA
1 AT-ATAATAATAAATAAATATAATAAATAATTAAA
*
465535 ATATAATAATATATAAATATA
1 ATATAATAATAAATAAATATA
465556 GTAATTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
33 8 0.18
34 33 0.73
35 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (34 bp):
ATATAATAATAAATAAATATAATAAATAATTAAA
Found at i:465563 original size:47 final size:47
Alignment explanation
Indices: 465472--465565 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
465462 AAATTATATT
* *
465472 ATAATAAATAAATATAATAAAATAATAAATAATAATAATTATTAAAA
1 ATAATAAATAAATAAAATAAAATAATAAATAATAATAATAATTAAAA
* * * *
465519 ATAATAAATAATTAAAATATAATAATATATAA-ATATAGTAATTAAAA
1 ATAATAAATAAATAAAATAAAATAATAAATAATA-ATAATAATTAAAA
465566 TAGATATCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (47 bp):
ATAATAAATAAATAAAATAAAATAATAAATAATAATAATAATTAAAA
Found at i:465610 original size:159 final size:160
Alignment explanation
Indices: 465300--465613 Score: 492
Period size: 159 Copynumber: 2.0 Consensus size: 160
465290 TTTATGATCC
* * *
465300 AAAAGTTATATTATAATAAATAAATAAAATAATAATAAGTAAAAATATTAATTATTAAATATAAT
1 AAAAATTATATTATAATAAATAAATAAAATAATAATAAGTAAAAATAATAATTATTAAAAATAAT
*
465365 AAATAATTAAAATATAATAATATATAAATATAATAATTAAAATGGAAATTTAATAAAAAAGAATT
66 AAATAATTAAAATATAATAATATATAAATATAATAATTAAAATAGAAATTTAATAAAAAAGAATT
*
465430 ATAATATATTTTGTAAATTTTGAAATAATG
131 ATAATATATTTTGAAAATTTTGAAATAATG
*
465460 AAAAATTATATTATAATAAATAAATATAATAA-AATAA-TAAATAATAATAATTATTAAAAATAA
1 AAAAATTATATTATAATAAATAAATAAAATAATAATAAGTAAA-AATAATAATTATTAAAAATAA
* * *
465523 TAAATAATTAAAATATAATAATATATAAATATAGTAATTAAAATAGATATCTT-ATAAAAAATAA
65 TAAATAATTAAAATATAATAATATATAAATATAATAATTAAAATAGAAAT-TTAATAAAAAAGAA
465587 TTATAATATATTTT-AAAATTTTTGAAA
129 TTATAATATATTTTGAAAA-TTTTGAAA
465614 ATTGAATTTG
Statistics
Matches: 142, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
158 7 0.05
159 103 0.73
160 32 0.23
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (160 bp):
AAAAATTATATTATAATAAATAAATAAAATAATAATAAGTAAAAATAATAATTATTAAAAATAAT
AAATAATTAAAATATAATAATATATAAATATAATAATTAAAATAGAAATTTAATAAAAAAGAATT
ATAATATATTTTGAAAATTTTGAAATAATG
Found at i:476097 original size:2 final size:2
Alignment explanation
Indices: 476090--476121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
476080 TACCCATTTC
476090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
476122 TTATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:476126 original size:4 final size:4
Alignment explanation
Indices: 476119--476143 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
476109 TATATATATA
476119 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
476144 TATCTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:476243 original size:2 final size:2
Alignment explanation
Indices: 476236--476296 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
476226 TTAAAAGTGT
476236 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
476278 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
476297 TCAAATGAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:484455 original size:18 final size:18
Alignment explanation
Indices: 484434--484468 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
484424 CCCTTTCTTC
484434 CCCTTTTTCTTCCCCCTA
1 CCCTTTTTCTTCCCCCTA
484452 CCCTTTTTCTTCCCCCT
1 CCCTTTTTCTTCCCCCT
484469 TCTCACACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (18 bp):
CCCTTTTTCTTCCCCCTA
Found at i:485096 original size:3 final size:3
Alignment explanation
Indices: 485088--485124 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
485078 CACAAGGGTG
485088 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
485125 ATGTTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:486614 original size:195 final size:196
Alignment explanation
Indices: 486282--486673 Score: 750
Period size: 195 Copynumber: 2.0 Consensus size: 196
486272 TATGTTCTCC
*
486282 GTATCTTGTAACTTTACATTTTAATTGTTAATGAAAGTTTTGTTATTTGTATTTCGAGCCTCTGT
1 GTATCTTGTAACTTTACATTTTAATTGTTAATGAAAGTTTTGTTATTTGTATTTCGAGCCTATGT
486347 TTTTTTAATATTTTCATTTCAGTCACTAGTTTATGTTTTATGCTATATTTGCTGATATTCAAATC
66 TTTTTTAATATTTTCATTTCAGTCACTAGTTTATGTTTTATGCTATATTTGCTGATATTCAAATC
486412 TGGCCCAGGAATTTATGCATG-TTTTATTTTGGTCACAGCTTCATATTTGGTTTAATTACTATTT
131 TGGCCCAGGAATTTATGCATGTTTTTATTTTGGTCACAGCTTCATATTTGGTTTAATTACTATTT
486476 G
196 G
486477 GTATCTTGTAACTTTACATTTTAATTGTTAATGAAAGTTTTGTTATTTGTATTTCGAGCCTATGT
1 GTATCTTGTAACTTTACATTTTAATTGTTAATGAAAGTTTTGTTATTTGTATTTCGAGCCTATGT
*
486542 TTTTTTAATATTTTCATTTCAGTCACTAGTTTATGTTTTATGTTATATTTGCTGATATTCAAATC
66 TTTTTTAATATTTTCATTTCAGTCACTAGTTTATGTTTTATGCTATATTTGCTGATATTCAAATC
*
486607 TGGCCCAGGAATTTATGCATGTTTTTATTTTGGTCACAGCTTCATATTTGGTTTAATTATTATTT
131 TGGCCCAGGAATTTATGCATGTTTTTATTTTGGTCACAGCTTCATATTTGGTTTAATTACTATTT
486672 G
196 G
486673 G
1 G
486674 CATTTTATGT
Statistics
Matches: 193, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
195 149 0.77
196 44 0.23
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (196 bp):
GTATCTTGTAACTTTACATTTTAATTGTTAATGAAAGTTTTGTTATTTGTATTTCGAGCCTATGT
TTTTTTAATATTTTCATTTCAGTCACTAGTTTATGTTTTATGCTATATTTGCTGATATTCAAATC
TGGCCCAGGAATTTATGCATGTTTTTATTTTGGTCACAGCTTCATATTTGGTTTAATTACTATTT
G
Found at i:486864 original size:30 final size:30
Alignment explanation
Indices: 486816--486926 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
486806 TACCTTCCTG
* *
486816 TTTTAGCTATTTTAGTCCTTTAAGTTTCCTA
1 TTTTAGATATTTTAGTCCTTTAACTTT-CTA
*
486847 TTTT-GATATTTTTGTCCTTTAACTTTCTA
1 TTTTAGATATTTTAGTCCTTTAACTTTCTA
* * *
486876 TTTTAGCTATTTTA-TCCCTTCAA-ATT-TA
1 TTTTAGATATTTTAGT-CCTTTAACTTTCTA
*
486904 TTATTA-TTATTTTAGTCCTTTAA
1 TT-TTAGATATTTTAGTCCTTTAA
486927 ATGTCTGTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
28 17 0.25
29 14 0.21
30 32 0.48
31 4 0.06
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (30 bp):
TTTTAGATATTTTAGTCCTTTAACTTTCTA
Found at i:486995 original size:30 final size:30
Alignment explanation
Indices: 486961--487036 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
486951 CCCGTTTGTA
* ** *
486961 CTATTTTGGTCCTTTGAGTTTATGTTTTTG
1 CTATTTTGGTCCTTTAAGTTTATGTTAATC
*
486991 CTATTTTGGTCC-TCAAGTTTATGTTAATC
1 CTATTTTGGTCCTTTAAGTTTATGTTAATC
*
487020 CTATTTTGATCCTTTAA
1 CTATTTTGGTCCTTTAA
487037 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.54
Consensus pattern (30 bp):
CTATTTTGGTCCTTTAAGTTTATGTTAATC
Found at i:491428 original size:36 final size:35
Alignment explanation
Indices: 491381--491457 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 35
491371 TCGAGCCGAG
491381 TATATA-TATTTAAATTAAATATATAAATAATATA
1 TATATATTATTTAAATTAAATATATAAATAATATA
* * *
491415 TATATATTAATTTAAATTAAATTTATTAATATTATA
1 TATATATT-ATTTAAATTAAATATATAAATAATATA
491451 TATATAT
1 TATATAT
491458 AATAATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 6 0.16
35 1 0.03
36 31 0.82
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TATATATTATTTAAATTAAATATATAAATAATATA
Found at i:491465 original size:32 final size:32
Alignment explanation
Indices: 491381--491476 Score: 85
Period size: 36 Copynumber: 3.0 Consensus size: 32
491371 TCGAGCCGAG
* * * *
491381 TATATATAT-TTA-AATTAAATATATAAATAA
1 TATATATATATAATAATTAAATTTATTAATAT
491411 TATATATATATTAATTTAAATTAAATTTATTAATAT
1 TATATATATA-TAA--T-AATTAAATTTATTAATAT
491447 TATATATATATAATAATT--ATTT-TTAATAT
1 TATATATATATAATAATTAAATTTATTAATAT
491476 T
1 T
491477 TATCAGGGCG
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
29 8 0.14
30 13 0.23
32 6 0.11
33 1 0.02
35 3 0.05
36 25 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATATATATAATAATTAAATTTATTAATAT
Found at i:498875 original size:17 final size:17
Alignment explanation
Indices: 498853--498887 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
498843 TTTGTCCCAT
498853 ATATTTTTCTATTTTAA
1 ATATTTTTCTATTTTAA
498870 ATATTTTTCTATTTTAA
1 ATATTTTTCTATTTTAA
498887 A
1 A
498888 CTAGTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTTTCTATTTTAA
Found at i:499395 original size:59 final size:60
Alignment explanation
Indices: 499304--499447 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 60
499294 AACATAATGA
* * * * *
499304 ATAGTCGAGTGACCA-TTTGTAACTTTTAATAGT-AAGGGACCCAACAAAGCAATCTCCT
1 ATAGTCGAGGGACTATTTTGTAACTTTTAATAGTCAAGGAACCCAACAAAACAATATCCT
* * * * *
499362 ATAGTCGAGGGACTATTTTGTAACTTTTGATAGTCAATGAACTCAATAAAACAATATCTT
1 ATAGTCGAGGGACTATTTTGTAACTTTTAATAGTCAAGGAACCCAACAAAACAATATCCT
*
499422 ATAGTCAAGGGA-TATTTGTGT-ACTTT
1 ATAGTCGAGGGACTATTT-TGTAACTTT
499448 ACCCTAAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 13 0.18
59 27 0.38
60 32 0.44
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (60 bp):
ATAGTCGAGGGACTATTTTGTAACTTTTAATAGTCAAGGAACCCAACAAAACAATATCCT
Found at i:504461 original size:11 final size:12
Alignment explanation
Indices: 504446--504487 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
504436 CACAATTTGA
504446 TATTTTAAATA-
1 TATTTTAAATAT
*
504457 TATTTAAAATTTAT
1 TATTTTAAA--TAT
504471 TATTTTAAATAT
1 TATTTTAAATAT
504483 TATTT
1 TATTT
504488 ACTACTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 2 0.08
14 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTAAATAT
Found at i:524356 original size:33 final size:32
Alignment explanation
Indices: 524278--524356 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
524268 AGACCTAAAA
524278 ATCACACTTAAAAAACTCAACCCGACCCGAAT
1 ATCACACTTAAAAAACTCAACCCGACCCGAAT
524310 ATCACACTTAAAAAACTCAACCCGACCCGAAT
1 ATCACACTTAAAAAACTCAACCCGACCCGAAT
524342 ATCACACTTAAAAAA
1 ATCACACTTAAAAAA
524357 ACCCGACCCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.47, C:0.32, G:0.05, T:0.16
Consensus pattern (32 bp):
ATCACACTTAAAAAACTCAACCCGACCCGAAT
Found at i:524366 original size:33 final size:32
Alignment explanation
Indices: 524278--524372 Score: 145
Period size: 32 Copynumber: 2.9 Consensus size: 32
524268 AGACCTAAAA
*
524278 ATCACACTTAAAAAACTCAACCCGACCCGAAT
1 ATCACACTTAAAAAACCCAACCCGACCCGAAT
*
524310 ATCACACTTAAAAAACTCAACCCGACCCGAAT
1 ATCACACTTAAAAAACCCAACCCGACCCGAAT
*
524342 ATCACACTTAAAAAAACCCGACCCGAACCCG
1 ATCACACTT-AAAAAACCCAACCCG-ACCCG
524373 GGATTTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 41 0.69
33 13 0.22
34 5 0.08
ACGTcount: A:0.43, C:0.36, G:0.07, T:0.14
Consensus pattern (32 bp):
ATCACACTTAAAAAACCCAACCCGACCCGAAT
Found at i:524411 original size:33 final size:33
Alignment explanation
Indices: 524374--524505 Score: 122
Period size: 33 Copynumber: 3.9 Consensus size: 33
524364 CCGAACCCGG
* *
524374 GATTTTTTTTAAAAAAAAATCCGACCTGATTCT
1 GATTTTTTTTTAAAAAAAATCCGACCTGATCCT
* * * *
524407 GATTTTTTTTTATAAAAAACCCGACCCGACTCGAACCC
1 GATTTTTTTTTAAAAAAAATCCGA--C--CT-GATCCT
* **
524445 GATTTTTTTTTAATAAAAATCCGACCCAATCCT
1 GATTTTTTTTTAAAAAAAATCCGACCTGATCCT
*
524478 GA-TTTTTTTTAAAAAAAATTCGACCTGA
1 GATTTTTTTTTAAAAAAAATCCGACCTGA
524506 ATACCAAAAG
Statistics
Matches: 77, Mismatches: 17, Indels: 11
0.73 0.16 0.10
Matches are distributed among these distances:
32 22 0.29
33 26 0.34
34 1 0.01
35 1 0.01
36 1 0.01
37 2 0.03
38 24 0.31
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (33 bp):
GATTTTTTTTTAAAAAAAATCCGACCTGATCCT
Found at i:524480 original size:71 final size:71
Alignment explanation
Indices: 524357--524495 Score: 190
Period size: 71 Copynumber: 1.9 Consensus size: 71
524347 ACTTAAAAAA
** * *
524357 ACCCGACCCGAACCCGGGATTTTTTTTAAAAAAAAATCCGACCTGATTCTGATTTTTTTTTATAA
1 ACCCGACCCGAACCC-GGATTTTTTTTAAAAAAAAATCCGACCCAATCCTGA-TTTTTTTTAAAA
524422 AAAACCCG
64 AAAACCCG
* * *
524430 ACCCGACTCGAACCC-GATTTTTTTTTAATAAAAATCCGACCCAATCCTGATTTTTTTTAAAAAA
1 ACCCGACCCGAACCCGGATTTTTTTTAAAAAAAAATCCGACCCAATCCTGATTTTTTTTAAAAAA
524494 AA
66 AA
524496 TTCGACCTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 15 0.25
71 30 0.51
73 14 0.24
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (71 bp):
ACCCGACCCGAACCCGGATTTTTTTTAAAAAAAAATCCGACCCAATCCTGATTTTTTTTAAAAAA
AACCCG
Found at i:526607 original size:2 final size:2
Alignment explanation
Indices: 526600--526624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
526590 AATAAAATTG
526600 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
526625 ATTGATAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:527652 original size:10 final size:9
Alignment explanation
Indices: 527633--527657 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
527623 ACCTGGTTAG
527633 TTTTTATTT
1 TTTTTATTT
527642 TTTTTATTT
1 TTTTTATTT
527651 TTTTTAT
1 TTTTTAT
527658 ATATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:528341 original size:38 final size:32
Alignment explanation
Indices: 528269--528329 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
528259 TCAAATTACA
*
528269 TAGTCCAACATCCAAACTTAATTAAAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
528301 TAGTCCAACATCCAAACATAATTAAAAAA
1 TAGTCCAACATCCAAACATAATTAAAAAA
528330 ATGTCATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.25
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATTAAAAAATGT
Found at i:528502 original size:68 final size:68
Alignment explanation
Indices: 528414--528620 Score: 351
Period size: 68 Copynumber: 3.0 Consensus size: 68
528404 ATTTTAGAAA
* *
528414 AAATAATAATAGAGTGACCAAAACAAAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
528479 CCT
66 CCT
* * * *
528482 AAATAATAATCGAGTAACCAAAACATAAATTAGATAATATATAAGTGAACAAATAGATAGTTTGC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
528547 CCT
66 CCT
*
528550 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATATGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
528615 CCT
66 CCT
528618 AAA
1 AAA
528621 AAACCTCTAA
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 128 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:528597 original size:31 final size:31
Alignment explanation
Indices: 528416--528602 Score: 99
Period size: 31 Copynumber: 5.6 Consensus size: 31
528406 TTTAGAAAAA
*
528416 ATAATA-ATAGAGTGACCAAAACAAAAATTAG
1 ATAATATATA-AGTGACCAAAACATAAATTAG
** ** *
528447 ATAATATATAAGTGACCAAATAGGTAGTTTACC
1 ATAATATATAAGTGACCAAA-ACATAAATTA-G
* * *
528480 CTAAATAATAATCGAGTAACCAAAACATAAATTAG
1 AT-AAT-AT-AT-AAGTGACCAAAACATAAATTAG
* * * *
528515 ATAATATATAAGTGAACAAATAGAT-AGTTTG
1 ATAATATATAAGTGACCAAA-ACATAAATTAG
* *
528546 CCCTAAATAATAATCGAGTGACCAAAACATAAATTAG
1 --AT-AAT-AT-AT-AAGTGACCAAAACATAAATTAG
528583 ATAATATATAAGTGACCAAA
1 ATAATATATAAGTGACCAAA
528603 TATGTAGTTT
Statistics
Matches: 112, Mismatches: 29, Indels: 30
0.65 0.17 0.18
Matches are distributed among these distances:
31 38 0.34
32 15 0.13
33 6 0.05
34 12 0.11
35 6 0.05
36 13 0.12
37 22 0.20
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (31 bp):
ATAATATATAAGTGACCAAAACATAAATTAG
Found at i:533482 original size:13 final size:13
Alignment explanation
Indices: 533464--533489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
533454 TGCAAATTCT
533464 GGCAAAGAAAGGA
1 GGCAAAGAAAGGA
533477 GGCAAAGAAAGGA
1 GGCAAAGAAAGGA
533490 TTGTTGAAAG
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:0.54, C:0.08, G:0.38, T:0.00
Consensus pattern (13 bp):
GGCAAAGAAAGGA
Found at i:538603 original size:22 final size:23
Alignment explanation
Indices: 538578--538620 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
538568 TTATAAATTT
538578 ATAAA-AATTAAAATGATTTTTA
1 ATAAATAATTAAAATGATTTTTA
**
538600 ATAAATTTTTAAAATGATTTT
1 ATAAATAATTAAAATGATTTT
538621 CGCCACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
ATAAATAATTAAAATGATTTTTA
Found at i:540981 original size:12 final size:12
Alignment explanation
Indices: 540972--541016 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
540962 TATTTTTCTT
540972 TATTTTTTTCAA
1 TATTTTTTTCAA
540984 TA-TTTTTTCAA
1 TATTTTTTTCAA
540995 TATTTTTTTCAA
1 TATTTTTTTCAA
541007 TATTTATTTT
1 TATTT-TTTT
541017 GTTTGATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.35
12 16 0.52
13 4 0.13
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTTTTTCAA
Found at i:540989 original size:11 final size:11
Alignment explanation
Indices: 540975--541011 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
540965 TTTTCTTTAT
540975 TTTTTTCAATA
1 TTTTTTCAATA
540986 TTTTTTCAATA
1 TTTTTTCAATA
540997 TTTTTTTCAATA
1 -TTTTTTCAATA
541009 TTT
1 TTT
541012 ATTTTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTCAATA
Found at i:543719 original size:15 final size:15
Alignment explanation
Indices: 543699--543729 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
543689 GGATATAAAT
543699 ATATGTCAAACATGA
1 ATATGTCAAACATGA
*
543714 ATATGTCATACATGA
1 ATATGTCAAACATGA
543729 A
1 A
543730 CTTTCATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
ATATGTCAAACATGA
Found at i:551058 original size:15 final size:15
Alignment explanation
Indices: 551035--551065 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
551025 TATGATCAAG
551035 TGTCAAATACAAGTA
1 TGTCAAATACAAGTA
*
551050 TGTCTAATACAAGTA
1 TGTCAAATACAAGTA
551065 T
1 T
551066 ATATATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
TGTCAAATACAAGTA
Done.