Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006026.1 Hibiscus syriacus cultivar Beakdansim tig00014226_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: 79289
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2705 original size:13 final size:14
Alignment explanation
Indices: 2689--2750 Score: 87
Period size: 13 Copynumber: 4.7 Consensus size: 14
2679 GCGCAATGAG
2689 CGTCATAAATGC-T
1 CGTCATAAATGCGT
*
2702 CGTCATAAATACGT
1 CGTCATAAATGCGT
2716 -GTCATAAATGCGT
1 CGTCATAAATGCGT
2729 -GTCATAAATGCG-
1 CGTCATAAATGCGT
2741 CGTCATAAAT
1 CGTCATAAAT
2751 TTATGTCGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 44 0.98
14 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (14 bp):
CGTCATAAATGCGT
Found at i:3027 original size:23 final size:23
Alignment explanation
Indices: 3001--3048 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2991 GAATATGTTC
* *
3001 ATGAACACGTTTGTGAACATTAA
1 ATGAACACGTTCGTGAACAATAA
*
3024 ATGAACATGTTCGTGAACAATAA
1 ATGAACACGTTCGTGAACAATAA
3047 AT
1 AT
3049 AAACGAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (23 bp):
ATGAACACGTTCGTGAACAATAA
Found at i:3127 original size:11 final size:12
Alignment explanation
Indices: 3111--3140 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3101 AAAATTTAAG
3111 CGAACACGAAC-
1 CGAACACGAACA
3122 CGAACACGAACA
1 CGAACACGAACA
3134 CGAACAC
1 CGAACAC
3141 CTTCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.47, C:0.37, G:0.17, T:0.00
Consensus pattern (12 bp):
CGAACACGAACA
Found at i:3131 original size:6 final size:6
Alignment explanation
Indices: 3111--3140 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3101 AAAATTTAAG
3111 CGAACA CGAAC- CGAACA CGAACA CGAACA C
1 CGAACA CGAACA CGAACA CGAACA CGAACA C
3141 CTTCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.47, C:0.37, G:0.17, T:0.00
Consensus pattern (6 bp):
CGAACA
Found at i:3431 original size:5 final size:5
Alignment explanation
Indices: 3421--3445 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3411 AGCAAAACTT
3421 GACTC GACTC GACTC GACTC GACTC
1 GACTC GACTC GACTC GACTC GACTC
3446 AACTAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
GACTC
Found at i:5515 original size:22 final size:22
Alignment explanation
Indices: 5490--5536 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5480 CTCCCCCCTC
5490 CCCCCTCTC-CCTATCCATTTCT
1 CCCCCTCTCACC-ATCCATTTCT
* *
5512 CCCCCTTTCACCCTCCATTTCT
1 CCCCCTCTCACCATCCATTTCT
5534 CCC
1 CCC
5537 TCCCCCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.09, C:0.57, G:0.00, T:0.34
Consensus pattern (22 bp):
CCCCCTCTCACCATCCATTTCT
Found at i:5516 original size:24 final size:22
Alignment explanation
Indices: 5489--5541 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
5479 CCTCCCCCCT
*
5489 CCCCCCTCTCCCTATCCATTTCTC
1 CCCCCCTCACCC--TCCATTTCTC
**
5513 CCCCTTTCACCCTCCATTTCTC
1 CCCCCCTCACCCTCCATTTCTC
5535 CCTCCCC
1 CC-CCCC
5542 CTTTCCTCCC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
22 12 0.52
23 2 0.09
24 9 0.39
ACGTcount: A:0.08, C:0.60, G:0.00, T:0.32
Consensus pattern (22 bp):
CCCCCCTCACCCTCCATTTCTC
Found at i:5537 original size:12 final size:12
Alignment explanation
Indices: 5503--5539 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5493 CCTCTCCCTA
5503 TCCATTTCTCCC
1 TCCATTTCTCCC
*
5515 -CC-TTTCACCC
1 TCCATTTCTCCC
5525 TCCATTTCTCCC
1 TCCATTTCTCCC
5537 TCC
1 TCC
5540 CCCTTTCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.08, C:0.54, G:0.00, T:0.38
Consensus pattern (12 bp):
TCCATTTCTCCC
Found at i:5551 original size:37 final size:38
Alignment explanation
Indices: 5510--5590 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 38
5500 CTATCCATTT
*
5510 CTCCCCCTTTCACC-CTCCATTTCTCCCTCCCCCTTT-C
1 CTCCCCCTTTC-CCTCTCCATCTCTCCCTCCCCCTTTCC
*
5547 CTCCCCCTTTCCCTCTCCGTCTCTCCCTCCCCCTTTCC
1 CTCCCCCTTTCCCTCTCCATCTCTCCCTCCCCCTTTCC
5585 CTCCCC
1 CTCCCC
5591 TCTCCCCTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 2 0.05
37 31 0.77
38 7 0.17
ACGTcount: A:0.02, C:0.63, G:0.01, T:0.33
Consensus pattern (38 bp):
CTCCCCCTTTCCCTCTCCATCTCTCCCTCCCCCTTTCC
Found at i:5561 original size:12 final size:12
Alignment explanation
Indices: 5533--5590 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
5523 CCTCCATTTC
5533 TCCCTCCCCCTT
1 TCCCTCCCCCTT
5545 T-CCTCCCCCTT
1 TCCCTCCCCCTT
* *
5556 TCCCTCTCCGTCTC
1 TCCCTC-CC-CCTT
5570 TCCCTCCCCCTT
1 TCCCTCCCCCTT
5582 TCCCTCCCC
1 TCCCTCCCC
5591 TCTCCCCTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 11 0.28
12 16 0.41
13 4 0.10
14 8 0.21
ACGTcount: A:0.00, C:0.66, G:0.02, T:0.33
Consensus pattern (12 bp):
TCCCTCCCCCTT
Found at i:5582 original size:26 final size:24
Alignment explanation
Indices: 5533--5599 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 24
5523 CCTCCATTTC
**
5533 TCCCTCCCC-CTTTCCTCCCCCTT
1 TCCCTCCCCTCTCCCCTCCCCCTT
*
5556 TCCCTCTCCGTCTCTCCCTCCCCCTT
1 TCCCTC-CCCTCTC-CCCTCCCCCTT
5582 TCCCTCCCCTCTCCCCTC
1 TCCCTCCCCTCTCCCCTC
5600 TCTTTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 8 0.22
26 16 0.43
ACGTcount: A:0.00, C:0.66, G:0.01, T:0.33
Consensus pattern (24 bp):
TCCCTCCCCTCTCCCCTCCCCCTT
Found at i:7339 original size:22 final size:22
Alignment explanation
Indices: 7300--7341 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7290 AGTGCAAAAT
*
7300 TAAAATAACAGTAGCTAAATCA
1 TAAAATAACAATAGCTAAATCA
7322 TAAAATAACAAT-GACTAAAT
1 TAAAATAACAATAG-CTAAAT
7342 TAAAATGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (22 bp):
TAAAATAACAATAGCTAAATCA
Found at i:22710 original size:21 final size:21
Alignment explanation
Indices: 22686--22726 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22676 TAGTTAAATA
*
22686 TATATAATAATTAAATTATTT
1 TATAAAATAATTAAATTATTT
*
22707 TATAAAATATTTAAATTATT
1 TATAAAATAATTAAATTATT
22727 CATACTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAAAATAATTAAATTATTT
Found at i:23659 original size:28 final size:28
Alignment explanation
Indices: 23628--23706 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
23618 AATATTTTTT
*
23628 AATTTTATATTAATTATAAAATATTACA
1 AATTATATATTAATTATAAAATATTACA
* *
23656 AATTATA-ACATAA-TATATAAATATTATA
1 AATTATATA-TTAATTATA-AAATATTACA
* *
23684 AGTTATATATTAATTCTAAAATA
1 AATTATATATTAATTATAAAATA
23707 AATTATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
27 5 0.12
28 32 0.78
29 4 0.10
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (28 bp):
AATTATATATTAATTATAAAATATTACA
Found at i:24989 original size:22 final size:22
Alignment explanation
Indices: 24943--24989 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
24933 CAAATTATTA
* *
24943 TAAATTATTTAAAAATTAAAGT
1 TAAATTATTTAAAAATAAAAAT
24965 TAAATTATTT-AAAATAAAATAT
1 TAAATTATTTAAAAATAAAA-AT
24987 TAA
1 TAA
24990 TTCCATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATTATTTAAAAATAAAAAT
Found at i:26698 original size:35 final size:35
Alignment explanation
Indices: 26657--26729 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
26647 CCCCTTAGGG
26657 TGGTACTTCAGCTATGTGCATTGGGTAAGTCCTTA
1 TGGTACTTCAGCTATGTGCATTGGGTAAGTCCTTA
26692 TGGTACTTCAGCTATGTGCATTGGGTAAGTCCTTA
1 TGGTACTTCAGCTATGTGCATTGGGTAAGTCCTTA
26727 TGG
1 TGG
26730 GCATGAGGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (35 bp):
TGGTACTTCAGCTATGTGCATTGGGTAAGTCCTTA
Found at i:28461 original size:25 final size:25
Alignment explanation
Indices: 28433--28507 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
28423 GCACTTTTAA
28433 ACAACAATTTTAAAAGTTATTTTCT
1 ACAACAATTTTAAAAGTTATTTTCT
* * * *
28458 ACAATATTTTTAAAAGTTCTTTTTT
1 ACAACAATTTTAAAAGTTATTTTCT
* *
28483 ACAACACTTTTAAAAGGTACTTTTC
1 ACAACAATTTTAAAAGTTA-TTTTC
28508 AAAAGTCCCG
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 36 0.90
26 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (25 bp):
ACAACAATTTTAAAAGTTATTTTCT
Found at i:29754 original size:21 final size:21
Alignment explanation
Indices: 29724--29763 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29714 AAGTTAAAAA
*
29724 GAGTAAATA-CTAATTTAGCT
1 GAGTAAATACCAAATTTAGCT
29744 GAGTAGAATACCAAATTTAG
1 GAGTA-AATACCAAATTTAG
29764 TCATAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (21 bp):
GAGTAAATACCAAATTTAGCT
Found at i:36939 original size:9 final size:9
Alignment explanation
Indices: 36910--36997 Score: 68
Period size: 9 Copynumber: 9.3 Consensus size: 9
36900 GCTGCTGGAA
*
36910 ACCGGTTTA
1 ACCGGTTTG
*
36919 ATCGGTTCTG
1 ACCGGTT-TG
36929 ACCGGTTTG
1 ACCGGTTTG
*
36938 ACCGGTTTCA
1 ACCGGTTT-G
*
36948 ACCGGTTCG
1 ACCGGTTTG
*
36957 AACCAGTTTG
1 -ACCGGTTTG
* *
36967 ACCGATCTG
1 ACCGGTTTG
36976 AACCGGTTTG
1 -ACCGGTTTG
*
36986 ACCGGTCTG
1 ACCGGTTTG
36995 ACC
1 ACC
36998 CGACCCGACC
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
9 33 0.54
10 28 0.46
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:36943 original size:19 final size:20
Alignment explanation
Indices: 36921--36995 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 20
36911 CCGGTTTAAT
36921 CGGTTCTGACCGGTT-TG-AC
1 CGGTT-TGACCGGTTCTGAAC
*
36940 CGGTTTCAACCGGTTC-GAAC
1 CGGTTT-GACCGGTTCTGAAC
* *
36960 CAGTTTGACC-GATCTGAAC
1 CGGTTTGACCGGTTCTGAAC
36979 CGGTTTGACCGG-TCTGA
1 CGGTTTGACCGGTTCTGA
36996 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
18 4 0.09
19 34 0.74
20 8 0.17
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (20 bp):
CGGTTTGACCGGTTCTGAAC
Found at i:36965 original size:29 final size:28
Alignment explanation
Indices: 36910--36997 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
36900 GCTGCTGGAA
* *
36910 ACCGGTTTAATCGGTTCTGACCGGTTTG
1 ACCGGTTTAACCGGTTCTGACCAGTTTG
36938 ACCGGTTTCAACCGGTTC-GAACCAGTTTG
1 ACCGGTTT-AACCGGTTCTG-ACCAGTTTG
* * * *
36967 ACCGATCTGAACCGGTT-TGACCGGTCTG
1 ACCGGT-TTAACCGGTTCTGACCAGTTTG
36995 ACC
1 ACC
36998 CGACCCGACC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 19 0.38
29 30 0.60
30 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.28
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTCTGACCAGTTTG
Found at i:37021 original size:7 final size:7
Alignment explanation
Indices: 37009--37046 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
36999 GACCCGACCC
37009 GACCGTT
1 GACCGTT
37016 GACCGTT
1 GACCGTT
*
37023 GATCGTT
1 GACCGTT
37030 GACCGTT
1 GACCGTT
37037 GACCGTT
1 GACCGTT
37044 GAC
1 GAC
37047 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:44240 original size:19 final size:19
Alignment explanation
Indices: 44215--44311 Score: 117
Period size: 19 Copynumber: 5.1 Consensus size: 19
44205 ACCGGTTTTC
* *
44215 AACCGGTTCTGACCAGTTTG
1 AACCGGTT-TGACCGGTCTG
*
44235 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
*
44254 AACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
44273 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
44292 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
44311 A
1 A
44312 CCCGACCCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
18 2 0.03
19 58 0.85
20 8 0.12
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:44248 original size:29 final size:29
Alignment explanation
Indices: 44200--44313 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
44190 CTGGAAACCG
*
44200 GTTTAACCGGTTTTCAACCGGTTCTGACCA
1 GTTTGACCGG-TTTCAACCGGTTCTGACCA
44230 GTTTGACCGGTTTCAACCGGTTC-GAACCA
1 GTTTGACCGGTTTCAACCGGTTCTG-ACCA
* * *
44259 GTTTGACCGGTCTGAACCGGTT-TGACCG
1 GTTTGACCGGTTTCAACCGGTTCTGACCA
* *
44287 GTCTGAACCGGTTT-GACCGG-TCTGACC
1 GTTTG-ACCGGTTTCAACCGGTTCTGACC
44314 CGACCCAACC
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.01
28 18 0.25
29 45 0.62
30 9 0.12
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (29 bp):
GTTTGACCGGTTTCAACCGGTTCTGACCA
Found at i:44250 original size:10 final size:9
Alignment explanation
Indices: 44195--44307 Score: 73
Period size: 10 Copynumber: 11.8 Consensus size: 9
44185 GGCTGCTGGA
44195 AACCGGTTT
1 AACCGGTTT
44204 AACCGGTTTT
1 AACCGG-TTT
44214 CAACCGGTTCT
1 -AACCGGTT-T
* *
44225 GACCAGTTT
1 AACCGGTTT
*
44234 GACCGGTTT
1 AACCGGTTT
*
44243 CAACCGGTTCG
1 -AACCGGTT-T
*
44254 AACCAGTTT
1 AACCGGTTT
* *
44263 GACCGGTCTG
1 AACCGGT-TT
44273 AACCGGTTT
1 AACCGGTTT
* *
44282 GACCGGTCTG
1 AACCGGT-TT
44292 AACCGGTTT
1 AACCGGTTT
*
44301 GACCGGT
1 AACCGGT
44308 CTGACCCGAC
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
9 34 0.43
10 39 0.49
11 7 0.09
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:44312 original size:9 final size:9
Alignment explanation
Indices: 44262--44313 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
44252 CGAACCAGTT
44262 TGACCGGTC
1 TGACCGGTC
*
44271 TGAACCGGTT
1 TG-ACCGGTC
44281 TGACCGGTC
1 TGACCGGTC
*
44290 TGAACCGGTT
1 TG-ACCGGTC
44300 TGACCGGTC
1 TGACCGGTC
44309 TGACC
1 TGACC
44314 CGACCCAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 21 0.57
10 16 0.43
ACGTcount: A:0.15, C:0.29, G:0.31, T:0.25
Consensus pattern (9 bp):
TGACCGGTC
Found at i:44341 original size:27 final size:28
Alignment explanation
Indices: 44300--44368 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 28
44290 TGAACCGGTT
44300 TGACCGGTCTGACCCGACCCAACCCGACC-
1 TGACC-GT-TGACCCGACCCAACCCGACCG
*
44329 TGACCGTTGACCCGACCCGACCCGACCG
1 TGACCGTTGACCCGACCCAACCCGACCG
44357 TTGACCGTTGAC
1 -TGACCGTTGAC
44369 TTTCTTTGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 19 0.51
28 2 0.05
29 16 0.43
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.14
Consensus pattern (28 bp):
TGACCGTTGACCCGACCCAACCCGACCG
Found at i:44346 original size:22 final size:22
Alignment explanation
Indices: 44315--44362 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
44305 GGTCTGACCC
*
44315 GACCCAACCCGACCTGACCGTT
1 GACCCAACCCGACCCGACCGTT
*
44337 GACCCGACCCGACCCGACCGTT
1 GACCCAACCCGACCCGACCGTT
44359 GACC
1 GACC
44363 GTTGACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (22 bp):
GACCCAACCCGACCCGACCGTT
Found at i:52282 original size:18 final size:18
Alignment explanation
Indices: 52259--52294 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52249 GCGAGAAATC
* *
52259 AAAAGAAATAGACAAAGT
1 AAAAGAAAAAGAAAAAGT
52277 AAAAGAAAAAGAAAAAGT
1 AAAAGAAAAAGAAAAAGT
52295 TGTAGTGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAGT
Found at i:57289 original size:7 final size:7
Alignment explanation
Indices: 57273--57380 Score: 87
Period size: 7 Copynumber: 15.0 Consensus size: 7
57263 TAAAAATAAT
57273 GAAAAAA
1 GAAAAAA
*
57280 GAAAAGA
1 GAAAAAA
57287 GAAAAAA
1 GAAAAAA
57294 GAAAAAA
1 GAAAAAA
57301 TGATAAAAA
1 -GA-AAAAA
* *
57310 -ATAAAG
1 GAAAAAA
*
57316 GAAAAAGG
1 GAAAAA-A
57324 GAAAAAA
1 GAAAAAA
*
57331 -AAGAAA
1 GAAAAAA
*
57337 GGAAAAA
1 GAAAAAA
57344 G-AAAAA
1 GAAAAAA
57350 GAAAAAAA
1 G-AAAAAA
57358 GAAAAAA
1 GAAAAAA
57365 GAATAAAA
1 GAA-AAAA
57373 GAATAAAA
1 GAA-AAAA
57381 AAGAGGGTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
6 14 0.17
7 38 0.45
8 27 0.32
9 5 0.06
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (7 bp):
GAAAAAA
Found at i:57299 original size:8 final size:8
Alignment explanation
Indices: 57281--57381 Score: 57
Period size: 8 Copynumber: 12.5 Consensus size: 8
57271 ATGAAAAAAG
57281 AAAAGAGAA
1 AAAAGA-AA
57290 AAAAGAAA
1 AAAAGAAA
* *
57298 AAATG-AT
1 AAAAGAAA
*
57305 AAAA-AAT
1 AAAAGAAA
*
57312 AAAGGAAA
1 AAAAGAAA
**
57320 AAGGGAAAA
1 AAAAG-AAA
57329 AAAAGAAA
1 AAAAGAAA
*
57337 GGAAAA-AGA
1 --AAAAGAAA
57346 AAAAGAAA
1 AAAAGAAA
57354 AAAAG-AA
1 AAAAGAAA
*
57361 AAAAGAAT
1 AAAAGAAA
57369 AAAAGAATA
1 AAAAGAA-A
57378 AAAA
1 AAAA
57382 AGAGGGTTCA
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
7 20 0.28
8 30 0.42
9 18 0.25
10 4 0.06
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (8 bp):
AAAAGAAA
Found at i:57328 original size:30 final size:29
Alignment explanation
Indices: 57265--57367 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 29
57255 ATGAAGAATA
57265 AAAATAATGAAAAAAGAAAAGAGAAAAAAG
1 AAAA-AATGAAAAAAGAAAAGAGAAAAAAG
*
57295 AAAAAATGATAAAAA-ATAAAG-GAAAAAGGG
1 AAAAAATGA-AAAAAGA-AAAGAGAAAAA-AG
*
57325 AAAAAA--AAGAAAGGAAAA-AG-AAAAAG
1 AAAAAATGAA-AAAAGAAAAGAGAAAAAAG
*
57351 AAAAAAAGAAAAAAGAA
1 AAAAAATGAAAAAAGAA
57368 TAAAAGAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
26 7 0.11
27 11 0.18
28 10 0.16
29 13 0.21
30 20 0.33
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (29 bp):
AAAAAATGAAAAAAGAAAAGAGAAAAAAG
Found at i:58533 original size:104 final size:104
Alignment explanation
Indices: 58312--58732 Score: 360
Period size: 104 Copynumber: 3.9 Consensus size: 104
58302 CAACTATGAT
* * * * * *
58312 CATCACAGAAGGAGGTGGACCAACATTTCCAAAAGAGTTCACAATGAGAAGAACTCGCCCCAAAA
1 CATCACAGAAGGAAGTGGATCAATATTTCCAAAATAGTTCATAATGAGAAGAACTCG-CCCAAAG
* *
58377 GAAAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATC
65 GAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATC
* *
58417 CATCACAGAAGGATGTGGATCAATATTTCCAAAATAGTTCATAATAAGAAGAACTCGCCCAAAGG
1 CATCACAGAAGGAAGTGGATCAATATTTCCAAAATAGTTCATAATGAGAAGAACTCGCCCAAAGG
* *
58482 AGAAAGTTCATAATGAGAAGAACTTATTCTTTTCAAATG
66 AGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATC
* * * * * *
58521 CATCACAAAAGGAAATGAATC-ATCATTTCCAATGAAGT-GTTCATAATGATAAGAACTCATCCG
1 CATCACAGAAGGAAGTGGATCAAT-ATTTCCAA--AA-TAGTTCATAATGAGAAGAACTC-GCCC
* *
58584 AAGAGGGAGAAGTAGTTCATAATGAGAAGAACTTGTTTGACCTTTTGCTCAAAAC
61 AA-A-GGAGAA--AGTTCATAATGAGAAGAACTT-ATT--CC--TT--TCAAATC
* * * * * * * * * *
58639 CATCATAGAAGGAGGTGGCTCAACATTTTCGATTGAATGGTTCACAATGAGAAGAACTTGTCCTA
1 CATCACAGAAGGAAGTGGATCAATA-TTTCCA--AAATAGTTCATAATGAGAAGAACTCG-CCCA
*
58704 AAGGAGAAAGTTCATACTGAGAAGAACTT
62 AAGGAGAAAGTTCATAATGAGAAGAACTT
58733 GTTCAATCGT
Statistics
Matches: 256, Mismatches: 38, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
103 2 0.01
104 67 0.26
105 51 0.20
106 20 0.08
107 5 0.02
108 1 0.00
109 6 0.02
111 21 0.08
112 2 0.01
114 1 0.00
115 20 0.08
116 2 0.01
117 6 0.02
118 23 0.09
119 29 0.11
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (104 bp):
CATCACAGAAGGAAGTGGATCAATATTTCCAAAATAGTTCATAATGAGAAGAACTCGCCCAAAGG
AGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATC
Found at i:58979 original size:165 final size:159
Alignment explanation
Indices: 58627--59022 Score: 429
Period size: 165 Copynumber: 2.4 Consensus size: 159
58617 TGTTTGACCT
* * * * * * *
58627 TTTGCTCAAAACCATCATAGAAGGAGGTGGCTCAACATTTTCGATTGAATGGTTCACAATGAGAA
1 TTTGTTCAAATCCATCATAGAAGGAGGTGGATCAATA-TTTCCATGGAATGGTTCATAATGAGAA
* * * *
58692 GAACTTGTCCTAAAGGAGAAAGTTCATACTGAGAAGAACTTGTTCAATCGTTTTGCTCGATTCTA
65 GAACTCGTCCAAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCAACCGTTTTGCTCGATTCTA
* * *
58757 CCACAAAAGGAGGTAAATCAACATCAACAC
130 CCAAAAAAGAAGATAAATCAACATCAACAC
* *
58787 TTTGTTCAAATCCATCATA-ACAGGAGGTTGATCAATATTTCTACTGGAATGGTTCATAATGAGA
1 TTTGTTCAAATCCATCATAGA-AGGAGGTGGATCAATATTTCCA-TGGAATGGTTCATAATGAGA
* * *
58851 ATAACTCGTCCGAACAAGGAGTATAAGTTCATAATGAGAAGAACTTGTTCAACCATTTTTGCTTG
64 AGAACTCGTCC-AA-AAGGAG-A-AAGTTCATAATGAGAAGAACTTGTTCAACC-GTTTTGCTCG
* * * *
58916 ATTCTATCAAAAAAGAAGATAGATCAACATCAGCAT
124 ATTCTACCAAAAAAGAAGATAAATCAACATCAACAC
* * * *
58952 TTTGTTCGATTCCATCGTAGAAGGAGGTGGATC-GTCATTTCCAATGGAA-GAGTTCATAATGAG
1 TTTGTTCAAATCCATCATAGAAGGAGGTGGATCAAT-ATTTCC-ATGGAATG-GTTCATAATGAG
59015 AAGAACTC
63 AAGAACTC
59023 ATCTGAAGAG
Statistics
Matches: 196, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
159 6 0.03
160 57 0.29
161 1 0.01
162 6 0.03
163 1 0.01
164 30 0.15
165 93 0.47
166 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (159 bp):
TTTGTTCAAATCCATCATAGAAGGAGGTGGATCAATATTTCCATGGAATGGTTCATAATGAGAAG
AACTCGTCCAAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCAACCGTTTTGCTCGATTCTAC
CAAAAAAGAAGATAAATCAACATCAACAC
Found at i:66613 original size:14 final size:14
Alignment explanation
Indices: 66594--66628 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
66584 TAACCAATAC
66594 CTTAAATCCTAAAA
1 CTTAAATCCTAAAA
*
66608 CTTAAACCCTAAAA
1 CTTAAATCCTAAAA
*
66622 CTAAAAT
1 CTTAAAT
66629 ATTAAGCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
CTTAAATCCTAAAA
Found at i:66810 original size:22 final size:23
Alignment explanation
Indices: 66767--66811 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
66757 AAATATTCTC
*
66767 TCTTTATACCCTAAACCCTAAAA
1 TCTTTATACCCTAAACCATAAAA
*
66790 TCTTTA-ACCCTATACCATAAAA
1 TCTTTATACCCTAAACCATAAAA
66812 CTTATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (23 bp):
TCTTTATACCCTAAACCATAAAA
Found at i:69312 original size:15 final size:15
Alignment explanation
Indices: 69294--69328 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
69284 CGCAACACGT
69294 GCCGCTATAACAAGC
1 GCCGCTATAACAAGC
69309 GCCGCTATAACAAGC
1 GCCGCTATAACAAGC
69324 GCCGC
1 GCCGC
69329 AATTGTTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.37, G:0.23, T:0.11
Consensus pattern (15 bp):
GCCGCTATAACAAGC
Found at i:69561 original size:43 final size:43
Alignment explanation
Indices: 69379--69561 Score: 215
Period size: 43 Copynumber: 4.3 Consensus size: 43
69369 TTGAGACATA
* * *
69379 TAGCGACGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATT
1 TAGCGACATTTTTCTTTACAAACGCCGCTATTGACTGTGTATT
* ** * *
69422 TAGATG-CGGTTGTCTTTATAAACGCCGCTATTGACTGTGTATT
1 TAG-CGACATTTTTCTTTACAAACGCCGCTATTGACTGTGTATT
* ** *
69465 TAACGACATTTTTCTTTACAAACGCATCTATTGATTGTGTATT
1 TAGCGACATTTTTCTTTACAAACGCCGCTATTGACTGTGTATT
* *
69508 TAGCGGCATTTTTCTTTACAAACGCCGCTATTAACTGTGTATT
1 TAGCGACATTTTTCTTTACAAACGCCGCTATTGACTGTGTATT
*
69551 TAGTGACATTT
1 TAGCGACATTT
69562 ATAATTAAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 117 0.98
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (43 bp):
TAGCGACATTTTTCTTTACAAACGCCGCTATTGACTGTGTATT
Found at i:72544 original size:41 final size:41
Alignment explanation
Indices: 72396--72534 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 41
72386 AATATTTTGT
** * *
72396 TGCCACTAAAGTACGTGCATTTAGCGGCGTTTGTGCTTAAAA
1 TGCCACTAAAGTACAAGCATTTAGCGGCGTTTGT-ATAAAAA
* *
72438 CGCCACTAAAGTAAAAGCATTTAGCGGCGTTTGTATAAAAAA
1 TGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTAT-AAAAA
** * *
72480 TGCCGTTAAAATACAAGCATTTAGCGACGTTTGTATAAAAA
1 TGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTATAAAAA
72521 TGCCACTAAAGTAC
1 TGCCACTAAAGTAC
72535 GAGTCTTTAG
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 17 0.21
42 64 0.79
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (41 bp):
TGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTATAAAAA
Found at i:72567 original size:23 final size:23
Alignment explanation
Indices: 72537--72581 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
72527 TAAAGTACGA
72537 GTCTTTAGTAGTATTTTTATATC
1 GTCTTTAGTAGTATTTTTATATC
72560 GTCTTTAGTAGTATTTTTATAT
1 GTCTTTAGTAGTATTTTTATAT
72582 AAACGCCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.13, T:0.58
Consensus pattern (23 bp):
GTCTTTAGTAGTATTTTTATATC
Found at i:79270 original size:13 final size:13
Alignment explanation
Indices: 79252--79280 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
79242 ACTCACATGG
79252 TATGCCTCACTAT
1 TATGCCTCACTAT
79265 TATGCCTCACTAT
1 TATGCCTCACTAT
79278 TAT
1 TAT
79281 ACCTTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (13 bp):
TATGCCTCACTAT
Done.