Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006059.1 Hibiscus syriacus cultivar Beakdansim tig00014333_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: 73315
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8993 original size:31 final size:31
Alignment explanation
Indices: 8958--9018 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
8948 TGTATCATTG
*
8958 TAAAATTTTAT-TTATATAA-ATTTTATATTTT
1 TAAAA-TTTATGTTAT-TAATATATTATATTTT
8989 TAAAATTTATGTTATTAATATATTATATTT
1 TAAAATTTATGTTATTAATATATTATATTT
9019 ATCTCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
TAAAATTTATGTTATTAATATATTATATTTT
Found at i:8994 original size:16 final size:15
Alignment explanation
Indices: 8958--9018 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
8948 TGTATCATTG
8958 TAAAATTT-TATTTAT
1 TAAAATTTATATTT-T
*
8973 ATAAATTTTATATTTT
1 -TAAAATTTATATTTT
* *
8989 TAAAATTTATGTTAT
1 TAAAATTTATATTTT
*
9004 TAATATATTATATTT
1 TAAAAT-TTATATTT
9019 ATCTCAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 17 0.47
16 14 0.39
17 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TAAAATTTATATTTT
Found at i:9442 original size:16 final size:15
Alignment explanation
Indices: 9421--9450 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9411 AGCGAGTGAA
9421 TAAATAAATGGTTTTT
1 TAAATAAAT-GTTTTT
9437 TAAATAAATGTTTT
1 TAAATAAATGTTTT
9451 GGAGTCGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAATAAATGTTTTT
Found at i:11773 original size:3 final size:3
Alignment explanation
Indices: 11765--11849 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
11755 AATGGGTATG
11765 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11812 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11850 GTGATGCGCA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13703 original size:60 final size:59
Alignment explanation
Indices: 13586--13704 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 59
13576 TTCGATTATA
* * * * *
13586 AGAGGTTATATTGTTGAGTTTCTCAACTATTAAATGTTACAAAATTATCCTCCGACTAT
1 AGAGGTTATATTATTGAGTTTCTCAACTATTAAAAGTTACAAAATGATCATACGACTAT
* * *
13645 AGAGCGTTATTTTATTGAGTCTTC-CGACTATTAAAAGTTACAAAATGATCATATGACTAT
1 AGAG-GTTATATTATTGAGT-TTCTCAACTATTAAAAGTTACAAAATGATCATACGACTAT
13705 TTATATGTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 4 0.08
60 43 0.86
61 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (59 bp):
AGAGGTTATATTATTGAGTTTCTCAACTATTAAAAGTTACAAAATGATCATACGACTAT
Found at i:14358 original size:2 final size:2
Alignment explanation
Indices: 14346--14396 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
14336 TTGGGGAGGG
* * *
14346 GA GA GA CA GA GA GA GA CA GA GA GA GA CA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
14388 GA GA GA GA G
1 GA GA GA GA G
14397 GGAGGTGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.06, G:0.45, T:0.00
Consensus pattern (2 bp):
GA
Found at i:14361 original size:10 final size:10
Alignment explanation
Indices: 14346--14396 Score: 84
Period size: 10 Copynumber: 5.1 Consensus size: 10
14336 TTGGGGAGGG
14346 GAGAGACAGA
1 GAGAGACAGA
14356 GAGAGACAGA
1 GAGAGACAGA
14366 GAGAGACAGA
1 GAGAGACAGA
*
14376 GAGAGAGAGA
1 GAGAGACAGA
*
14386 GAGAGAGAGA
1 GAGAGACAGA
14396 G
1 G
14397 GGAGGTGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.49, C:0.06, G:0.45, T:0.00
Consensus pattern (10 bp):
GAGAGACAGA
Found at i:17234 original size:23 final size:22
Alignment explanation
Indices: 17196--17258 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
17186 GATTGTATAA
*
17196 TTAATTTTTTTATTAAAA-TAGTG
1 TTAA-TTTTTT-TTAAAATTAATG
17219 TTCATATTTTTTTTAAAATTAATG
1 TT-A-ATTTTTTTTAAAATTAATG
17243 TTAATTTTATTTTAAA
1 TTAATTTT-TTTTAAA
17259 TATTTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 5 0.14
23 16 0.46
24 13 0.37
25 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.59
Consensus pattern (22 bp):
TTAATTTTTTTTAAAATTAATG
Found at i:23803 original size:21 final size:22
Alignment explanation
Indices: 23779--23819 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
23769 TTTCCTCTGG
23779 TTTTATAAAAG-TTTTCTTTTC
1 TTTTATAAAAGTTTTTCTTTTC
* *
23800 TTTTTTCAAAGTTTTTCTTT
1 TTTTATAAAAGTTTTTCTTT
23820 GTTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTATAAAAGTTTTTCTTTTC
Found at i:24473 original size:17 final size:18
Alignment explanation
Indices: 24451--24494 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
24441 AATTTATTTA
*
24451 TTTATTTTA-TCTTATCT
1 TTTATTTTATTCTCATCT
*
24468 TTTATTTTATTCTCATTT
1 TTTATTTTATTCTCATCT
24486 TTTATTTTA
1 TTTATTTTA
24495 AAATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTTATTCTCATCT
Found at i:24490 original size:18 final size:17
Alignment explanation
Indices: 24446--24494 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
24436 TTTAAAATTT
*
24446 ATTTATTTATTTTATCTT
1 ATTT-TTTATTTTATCTC
*
24464 ATCTTTTATTTTATTCTC
1 ATTTTTTATTTTA-TCTC
24482 ATTTTTTATTTTA
1 ATTTTTTATTTTA
24495 AAATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTATTTTATCTC
Found at i:24650 original size:4 final size:4
Alignment explanation
Indices: 24641--24671 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
24631 ACTATCTCTC
24641 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
24672 TTGAGGAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:27601 original size:5 final size:5
Alignment explanation
Indices: 27591--27640 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
27581 TTTATTCCAT
* **
27591 TTTTA TTTTA TTTTA TTCTAA GCTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
27641 TCTTTGAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
5 36 0.95
6 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:27605 original size:37 final size:36
Alignment explanation
Indices: 27551--27640 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 36
27541 CAACCCATTT
* * *
27551 CATTTTATTTTTGTTTTATTTTTAGCATACTTTATTC
1 CATTTTA-TTTTATTTTATTCTAAGCATACTTTATTC
* * *
27588 CATTTTTATTTTATTTTATTCTAAGCTTATTTTATTT
1 CA-TTTTATTTTATTTTATTCTAAGCATACTTTATTC
*
27625 TATTTTATTTTATTTT
1 CATTTTATTTTATTTT
27641 TCTTTGAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
36 14 0.31
37 26 0.58
38 5 0.11
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.69
Consensus pattern (36 bp):
CATTTTATTTTATTTTATTCTAAGCATACTTTATTC
Found at i:27641 original size:21 final size:21
Alignment explanation
Indices: 27581--27640 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
27571 TTTAGCATAC
*
27581 TTTATTCCATTTTTATTTTAT
1 TTTATTCTATTTTTATTTTAT
***
27602 TTTATTCTAAGCTTATTTTAT
1 TTTATTCTATTTTTATTTTAT
*
27623 TTTATTTTA-TTTTATTTT
1 TTTATTCTATTTTTATTTT
27641 TCTTTGAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTATTCTATTTTTATTTTAT
Found at i:31406 original size:20 final size:21
Alignment explanation
Indices: 31376--31414 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
31366 AGTTTAAGAA
31376 TTATCTTTAGGAATTATCTCT
1 TTATCTTTAGGAATTATCTCT
31397 TTAT-TTTAGGAATTATCT
1 TTATCTTTAGGAATTATCT
31415 TTTCCTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TTATCTTTAGGAATTATCTCT
Found at i:31528 original size:21 final size:22
Alignment explanation
Indices: 31504--31544 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31494 TTTACTCTGG
31504 TTTTATAAAAG-TTTTCTTTCC
1 TTTTATAAAAGTTTTTCTTTCC
*
31525 TTTTTTAAAAGTTTTTCTTT
1 TTTTATAAAAGTTTTTCTTT
31545 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTATAAAAGTTTTTCTTTCC
Found at i:32197 original size:18 final size:18
Alignment explanation
Indices: 32174--32215 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
32164 AATTTATTTA
32174 TTTATTTTA-TCCTTATCT
1 TTTATTTTATTCC-TATCT
32192 TTTATTTTATTCCTATCT
1 TTTATTTTATTCCTATCT
32210 TTTATT
1 TTTATT
32216 CTAAAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTATTCCTATCT
Found at i:33274 original size:20 final size:20
Alignment explanation
Indices: 33237--33335 Score: 55
Period size: 20 Copynumber: 5.0 Consensus size: 20
33227 CGATCTCTAA
*
33237 ATCGCAACA-CGATCTCCAGT
1 ATCGCAA-ATCGATTTCCAGT
33257 ATCGCAAATC-AGTTTCCAG-
1 ATCGCAAATCGA-TTTCCAGT
** ** *
33276 ATTCGCAACGCGATTTTGACT
1 A-TCGCAAATCGATTTCCAGT
*
33297 ATCGC-AATGCGATCTCCAGT
1 ATCGCAAAT-CGATTTCCAGT
33317 ATCGCAAATC-AGTTTCCAG
1 ATCGCAAATCGA-TTTCCAG
33336 ATTCGCAACA
Statistics
Matches: 58, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
19 5 0.09
20 48 0.83
21 5 0.09
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAAATCGATTTCCAGT
Found at i:33330 original size:60 final size:60
Alignment explanation
Indices: 33237--33368 Score: 237
Period size: 60 Copynumber: 2.2 Consensus size: 60
33227 CGATCTCTAA
** *
33237 ATCGCAACACGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACT
1 ATCGCAATGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACACGATTTTGACT
33297 ATCGCAATGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACACGATTTTGACT
1 ATCGCAATGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACACGATTTTGACT
33357 ATCGCAATGCGA
1 ATCGCAATGCGA
33369 ATATGTAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (60 bp):
ATCGCAATGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACACGATTTTGACT
Found at i:33402 original size:21 final size:21
Alignment explanation
Indices: 33376--33598 Score: 108
Period size: 21 Copynumber: 10.7 Consensus size: 21
33366 CGAATATGTA
33376 AATCGCAACGCGATAATACAG
1 AATCGCAACGCGATAATACAG
33397 AATCGCAACGCGATAATACAG
1 AATCGCAACGCGATAATACAG
*** ** * *
33418 AATCGCGTTGTTGCGATTTTAGAA
1 AATCGC---AACGCGATAATACAG
* **
33442 AATCGCAATGCGA-ATATGTA-
1 AATCGCAACGCGATA-ATACAG
* *
33462 AATCGTAACGCGAT--T-CTG
1 AATCGCAACGCGATAATACAG
* *
33480 ACTATCGCAATGCGATAATACAA
1 A--ATCGCAACGCGATAATACAG
*
33503 AATCGCAACGCGAT--T-CTG
1 AATCGCAACGCGATAATACAG
*
33521 ACTATCGCAACGCGATAATACAA
1 A--ATCGCAACGCGATAATACAG
*
33544 AATCGCAACGCGAT--T-CTG
1 AATCGCAACGCGATAATACAG
*
33562 ACTATCGCAACGCGATAATACAT
1 A--ATCGCAACGCGATAATACAG
*
33585 AATCGCAATGCGAT
1 AATCGCAACGCGAT
33599 TTTCCAAATT
Statistics
Matches: 150, Mismatches: 31, Indels: 42
0.67 0.14 0.19
Matches are distributed among these distances:
18 6 0.04
19 2 0.01
20 48 0.32
21 71 0.47
22 3 0.02
23 6 0.04
24 14 0.09
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAG
Found at i:33486 original size:20 final size:20
Alignment explanation
Indices: 33463--33577 Score: 108
Period size: 20 Copynumber: 5.7 Consensus size: 20
33453 GAATATGTAA
*
33463 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* ** *
33483 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
33504 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
** *
33524 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
33545 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
33565 ATCGCAACGCGAT
1 ATCGCAACGCGAT
33578 AATACATAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.05
20 39 0.53
21 27 0.36
22 4 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:33506 original size:41 final size:41
Alignment explanation
Indices: 33461--33599 Score: 242
Period size: 41 Copynumber: 3.4 Consensus size: 41
33451 GCGAATATGT
* *
33461 AAATCGTAACGCGATTCTGACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
33502 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
33543 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* *
33584 TAATCGCAATGCGATT
1 AAATCGCAACGCGATT
33600 TTCCAAATTT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:33993 original size:20 final size:20
Alignment explanation
Indices: 33968--34056 Score: 90
Period size: 20 Copynumber: 4.2 Consensus size: 20
33958 TTATTTTGGA
33968 TTTTTCACTATCGCAACACG
1 TTTTTCACTATCGCAACACG
33988 TTTTTCACTATCGCAACAACACG
1 TTTTTCACTATCG---CAACACG
*
34011 TTTTTCAAACTCTCGCAACAC-
1 TTTTTC--ACTATCGCAACACG
* * *
34032 ATTTTAACTATCGCAACACA
1 TTTTTCACTATCGCAACACG
34052 TTTTT
1 TTTTT
34057 TAAAATCGCG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 12 0.21
20 17 0.29
21 4 0.07
22 6 0.10
23 13 0.22
25 6 0.10
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (20 bp):
TTTTTCACTATCGCAACACG
Found at i:34045 original size:19 final size:19
Alignment explanation
Indices: 33969--34055 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 19
33959 TATTTTGGAT
* *
33969 TTTTCACTATCGCAACACGT
1 TTTTAACTATCGCAACAC-A
*
33989 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
*
34009 CGTTTTTCAAACTCTCGCAACACA
1 ---TTTT--AACTATCGCAACACA
34033 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
34052 TTTT
1 TTTT
34056 TTAAAATCGC
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
19 18 0.32
20 16 0.28
21 6 0.11
23 4 0.07
24 3 0.05
25 10 0.18
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:39454 original size:23 final size:23
Alignment explanation
Indices: 39393--39503 Score: 140
Period size: 23 Copynumber: 4.9 Consensus size: 23
39383 CAGCTCGTAA
*
39393 TTTGCACCGAAGTGTCACATAA-
1 TTTGCACCGAAGTGCCACATAAG
39415 -TTGTC-CCGAA-TGACCACATAAG
1 TTTG-CACCGAAGTG-CCACATAAG
*
39437 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAAG
*
39460 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAAG
*
39483 TTTACACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
39504 TTTATCCCGA
Statistics
Matches: 80, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.03
21 15 0.19
22 2 0.03
23 59 0.74
24 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAAG
Found at i:40196 original size:20 final size:20
Alignment explanation
Indices: 40171--40270 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 20
40161 CTATCCCCTG
*
40171 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTAACA
*
40191 GTATCGATAC--CCATCTCAACTG
1 GTATCGATACTACC--CT-AAC-A
*
40213 GTATCGATACTACCCTCACA
1 GTATCGATACTACCCTAACA
* *
40233 GTATCGATAC-CCTCCTAAACGG
1 GTATCGATACTAC-CCT-AAC-A
40255 GTATCGATACTACCCT
1 GTATCGATACTACCCT
40271 TAGAAAATAC
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 25 0.40
21 6 0.10
22 25 0.40
23 1 0.02
24 2 0.03
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.27
Consensus pattern (20 bp):
GTATCGATACTACCCTAACA
Found at i:40219 original size:42 final size:42
Alignment explanation
Indices: 40168--40272 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
40158 ATACTATCCC
*
40168 CTGGTATCGATACTACCCTTACAGTATCGATACCCAT-CTCAA
1 CTGGTATCGATACTACCCTTACAGTATCGATACCC-TCCTAAA
*
40210 CTGGTATCGATACTACCCTCACAGTATCGATACCCTCCTAAA
1 CTGGTATCGATACTACCCTTACAGTATCGATACCCTCCTAAA
*
40252 CGGGTATCGATACTACCCTTA
1 CTGGTATCGATACTACCCTTA
40273 GAAAATACTC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 57 0.98
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (42 bp):
CTGGTATCGATACTACCCTTACAGTATCGATACCCTCCTAAA
Found at i:40230 original size:22 final size:20
Alignment explanation
Indices: 40151--40270 Score: 79
Period size: 22 Copynumber: 5.8 Consensus size: 20
40141 TCTTAATAAG
*
40151 GGTATCGATACTATCCC-C-T
1 GGTATCGATACTA-CCCTCAC
*
40170 GGTATCGATACTACCCTTAC
1 GGTATCGATACTACCCTCAC
*
40190 AGTATCGATAC--CCATCTCAAC
1 GGTATCGATACTACC--CTC-AC
40211 TGGTATCGATACTACCCTCAC
1 -GGTATCGATACTACCCTCAC
* * *
40232 AGTATCGATAC-CCTCCTAAAC
1 GGTATCGATACTAC-CCT-CAC
40253 GGGTATCGATACTACCCT
1 -GGTATCGATACTACCCT
40271 TAGAAAATAC
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.06
19 14 0.18
20 25 0.32
21 6 0.08
22 26 0.33
23 1 0.01
24 2 0.03
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.28
Consensus pattern (20 bp):
GGTATCGATACTACCCTCAC
Found at i:44201 original size:21 final size:21
Alignment explanation
Indices: 44175--44219 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
44165 GATTTCTGGG
*
44175 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
44196 CAAGGGGAATCGATACCCCTT
1 CAAGGGGAATCGATACCCATT
44217 CAA
1 CAA
44220 ACGAACAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:44826 original size:18 final size:18
Alignment explanation
Indices: 44803--44837 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
44793 CTAGGAGATT
44803 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
44821 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
44838 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:44923 original size:21 final size:22
Alignment explanation
Indices: 44894--44937 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44884 GTTGTATGAT
44894 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
44915 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
44937 A
1 A
44938 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:45820 original size:149 final size:149
Alignment explanation
Indices: 45640--45943 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
45630 GAGTCGAGGG
45640 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
45705 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
45770 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
45789 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
45854 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
45919 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
45938 TCTACG
1 TCTACG
45944 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:45966 original size:23 final size:23
Alignment explanation
Indices: 45922--45966 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
45912 ATCATTATAT
*
45922 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
45945 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
45967 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:49597 original size:23 final size:23
Alignment explanation
Indices: 49548--49623 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
49538 TGTACTACAA
49548 TGCCACATAA-TTAT-CA-CGAA-
1 TGCCACATAAGTT-TGCACCGAAG
49568 TGACCACATAAGTTTGCACCGAAG
1 TG-CCACATAAGTTTGCACCGAAG
*
49592 TGCCACATAGGTTTGCACCGAAG
1 TGCCACATAAGTTTGCACCGAAG
49615 TGCCACATA
1 TGCCACATA
49624 TTTATCCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
20 2 0.04
21 9 0.18
22 4 0.08
23 33 0.66
24 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (23 bp):
TGCCACATAAGTTTGCACCGAAG
Found at i:50226 original size:19 final size:22
Alignment explanation
Indices: 50178--50229 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
50168 CTACCCCTAA
*
50178 GTACCGATACTTCCCTTCAAGG
1 GTACCGATACCTCCCTTCAAGG
*
50200 GTATCGATACCT-CC-TCAA-G
1 GTACCGATACCTCCCTTCAAGG
50219 GTACCGATACC
1 GTACCGATACC
50230 GAAATAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 2 0.07
22 10 0.37
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (22 bp):
GTACCGATACCTCCCTTCAAGG
Found at i:50340 original size:42 final size:42
Alignment explanation
Indices: 50264--50385 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
50254 CTTAATAAGG
** * *
50264 GTATCGATA-CCATC-CCCCTGGTATCGGTACTACCCTTATA
1 GTATCGATACCCATCTCAACTGGTATCGATACTACCCTTACA
* *
50304 GTATCGATACCCATCTCAACTGGTATCGATAGTACCCTCACA
1 GTATCGATACCCATCTCAACTGGTATCGATACTACCCTTACA
* *
50346 GTTTCAATACCC-TCCTCAACTGGTATCGATACTACCCTTA
1 GTATCGATACCCAT-CTCAACTGGTATCGATACTACCCTTA
50386 GAAAATACTC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 9 0.13
41 6 0.09
42 54 0.78
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (42 bp):
GTATCGATACCCATCTCAACTGGTATCGATACTACCCTTACA
Found at i:56359 original size:17 final size:17
Alignment explanation
Indices: 56298--56363 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
56288 GTTATCAAAC
*
56298 TATGACTCTT-ATTCAAA
1 TATGACT-TTAATTTAAA
***
56315 TATGATCTTTAATTTTTT
1 TATGA-CTTTAATTTAAA
* *
56333 TAAGATTTTAATTTAAA
1 TATGACTTTAATTTAAA
56350 TATGACTTTAATTT
1 TATGACTTTAATTT
56364 TATTTTTGTT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
17 27 0.75
18 9 0.25
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (17 bp):
TATGACTTTAATTTAAA
Found at i:62876 original size:12 final size:12
Alignment explanation
Indices: 62859--62887 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
62849 TTGGCAAATT
62859 TGATGCTAAAAG
1 TGATGCTAAAAG
62871 TGATGCTAAAAG
1 TGATGCTAAAAG
62883 TGATG
1 TGATG
62888 AAGGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (12 bp):
TGATGCTAAAAG
Done.