Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002797.1 Hibiscus syriacus cultivar Beakdansim tig00005760_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: 85145
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:2446 original size:4 final size:4
Alignment explanation
Indices: 2439--2473 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2429 GGATCTCTCT
2439 CTCC CTCC CTCC CT-C CTCC CTCC CTCC CT-C CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC C
2474 CTCACTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (4 bp):
CTCC
Found at i:2459 original size:15 final size:15
Alignment explanation
Indices: 2439--2473 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2429 GGATCTCTCT
2439 CTCCCTCCCTCCCTC
1 CTCCCTCCCTCCCTC
2454 CTCCCTCCCTCCCTC
1 CTCCCTCCCTCCCTC
2469 CTCCC
1 CTCCC
2474 CTCACTAACA
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:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (15 bp):
CTCCCTCCCTCCCTC
Found at i:4561 original size:9 final size:9
Alignment explanation
Indices: 4540--4569 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
4530 TAAATAATTC
4540 ATTATATTAT
1 ATTATA-TAT
4550 ATTATATAT
1 ATTATATAT
4559 ATTATATAT
1 ATTATATAT
4568 AT
1 AT
4570 ATAATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATATAT
Found at i:12341 original size:2 final size:2
Alignment explanation
Indices: 12336--12378 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12326 ACACACACAC
12336 AT AT AT AT AT 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 AT AT AT AT AT
12378 A
1 A
12379 CACTGAAGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15484 original size:18 final size:18
Alignment explanation
Indices: 15450--15484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15440 TTTAAGATTT
*
15450 TATTCGATTTAAATATTA
1 TATTCGATTCAAATATTA
*
15468 TATTCGATTCAATTATT
1 TATTCGATTCAAATATT
15485 CTAATATCAC
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:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (18 bp):
TATTCGATTCAAATATTA
Found at i:15915 original size:21 final size:21
Alignment explanation
Indices: 15891--15930 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15881 TTTTCAAAGG
15891 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
15912 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
15931 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:15980 original size:19 final size:19
Alignment explanation
Indices: 15956--15994 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15946 TCGAATGCAT
15956 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
15975 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
15994 T
1 T
15995 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:16027 original size:64 final size:65
Alignment explanation
Indices: 15891--16055 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 65
15881 TTTTCAAAGG
*
15891 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGC
15954 ATTC
62 ATTC
* * * *
15958 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGTATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * **
16022 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCAC
16056 CAGGCTATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 53 0.61
65 15 0.17
66 3 0.03
67 14 0.16
68 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:16073 original size:64 final size:63
Alignment explanation
Indices: 15891--16100 Score: 190
Period size: 64 Copynumber: 3.2 Consensus size: 63
15881 TTTTCAAAGG
* ** ** *
15891 CATGCACCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 CATGCATCGATGCA-CAAT-CCATGCATCGATGCA-CGCTG-ATTTATTAAAACATCGAATGCAT
*
15956 TC
62 TT
* ** * *
15958 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGTATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTAAAACATCGAATGCATTT
* * *
16022 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TTCAAACATCGAATGCACT
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATTAAAACATCGAATGCATT
16085 T
63 T
*
16086 CATGCATCGTTGCAC
1 CATGCATCGATGCAC
16101 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.02
64 80 0.67
65 16 0.13
66 6 0.05
67 16 0.13
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTATTAAAACATCGAATGCATTT
Found at i:21891 original size:24 final size:22
Alignment explanation
Indices: 21863--21942 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
21853 CACTTAACAA
21863 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
21887 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
* *
21907 ATACACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
21931 TGCATCGATGCA
1 TGCATCGATGCA
21943 CAAGATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 12 0.26
24 17 0.37
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:24466 original size:21 final size:21
Alignment explanation
Indices: 24442--24481 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
24432 TTTTCAAAGG
24442 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
24463 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
24482 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:24531 original size:19 final size:19
Alignment explanation
Indices: 24507--24545 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
24497 TCGAATGCAT
24507 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
24526 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
24545 T
1 T
24546 AATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:24571 original size:64 final size:64
Alignment explanation
Indices: 24442--24671 Score: 186
Period size: 64 Copynumber: 3.5 Consensus size: 64
24432 TTTTCAAAGG
* *
24442 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTCAAT--ATAAATTAAAACATCGAAAGC
24505 ATTC
61 ATTC
* *
24509 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTAAT-TTAATTAAAACATCGAAAGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-AATATAAATTAAAACATCGAAAGCATTC
* * ** ** * *
24573 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAGACTAT-TTTTCAAACATCGAATGCACT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCA-A-TATAAATTAAAACATCGAAAGCA-T
24636 T-
63 TC
* * *
24637 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
24672 AGGAGTCCAA
Statistics
Matches: 137, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 93 0.68
65 18 0.13
66 3 0.02
67 17 0.12
68 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCAATATAAATTAAAACATCGAAAGCATTC
Found at i:24651 original size:17 final size:19
Alignment explanation
Indices: 24623--24671 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
24613 ATTTTTCAAA
24623 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
24641 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
24660 CACCGATGCACT
1 CATCGATGCACT
24672 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:28897 original size:22 final size:22
Alignment explanation
Indices: 28867--28927 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
28857 GGGTTTACGC
*
28867 GGTCCTTCGGGACAAATACATA
1 GGTCTTTCGGGACAAATACATA
28889 GGTCTTTCGGGACAAATACATA
1 GGTCTTTCGGGACAAATACATA
*
28911 GGT-TCTTCGAGACAAAT
1 GGTCT-TTCGGGACAAAT
28928 TTCATATGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (22 bp):
GGTCTTTCGGGACAAATACATA
Found at i:31327 original size:15 final size:15
Alignment explanation
Indices: 31300--31347 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
31290 ATTCAAAATT
31300 AAACATCCAAAACAC
1 AAACATCCAAAACAC
31315 AAACAATCC-AAACAACC
1 AAAC-ATCCAAAAC-A-C
*
31332 AAATATCCAAAACAC
1 AAACATCCAAAACAC
31347 A
1 A
31348 CAAATTCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 10 0.36
16 10 0.36
17 8 0.29
ACGTcount: A:0.60, C:0.31, G:0.00, T:0.08
Consensus pattern (15 bp):
AAACATCCAAAACAC
Found at i:31351 original size:17 final size:17
Alignment explanation
Indices: 31304--31352 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
31294 AAAATTAAAC
31304 ATCCAAAACACA-AACA-
1 ATCCAAAACACACAA-AT
31320 ATCC-AAACA-ACCAAAT
1 ATCCAAAACACA-CAAAT
31336 ATCCAAAACACACAAAT
1 ATCCAAAACACACAAAT
31353 TCATCAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.04
15 6 0.21
16 10 0.36
17 10 0.36
18 1 0.04
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.10
Consensus pattern (17 bp):
ATCCAAAACACACAAAT
Found at i:33312 original size:21 final size:21
Alignment explanation
Indices: 33288--33355 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 21
33278 GTATGAACAA
33288 TATCGATACCTATTG-AAGGAG
1 TATCGATACCTA-TGCAAGGAG
* *
33309 TATCGATA-CTATGCTAGTAG
1 TATCGATACCTATGCAAGGAG
33329 TATCGATACCTA-GCAAGAGGAG
1 TATCGATACCTATGC-A-AGGAG
33351 TATCG
1 TATCG
33356 GTACTGGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.05
20 17 0.44
21 11 0.28
22 9 0.23
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (21 bp):
TATCGATACCTATGCAAGGAG
Found at i:43701 original size:3 final size:3
Alignment explanation
Indices: 43695--43719 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43685 CTGTCCTCTG
43695 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
43720 TTCTTCACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:45323 original size:20 final size:20
Alignment explanation
Indices: 45300--45359 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
45290 GAAGTGTTAG
45300 AAAGGATTAAGAACAAGTTT
1 AAAGGATTAAGAACAAGTTT
45320 AAAGGATTAAGAACAAGTTT
1 AAAGGATTAAGAACAAGTTT
45340 AAAGGATTAAGAACAAGTTT
1 AAAGGATTAAGAACAAGTTT
45360 GAAGAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAGGATTAAGAACAAGTTT
Found at i:45665 original size:20 final size:20
Alignment explanation
Indices: 45636--45691 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
45626 TATTGGTTGA
*
45636 ATAA-GTATCGATACTGATG
1 ATAAGGTATCGATACTGAGG
**
45655 -TGAAGGTATCGATACCAAGG
1 AT-AAGGTATCGATACTGAGG
45675 ATAAGGTATCGATACTG
1 ATAAGGTATCGATACTG
45692 TAAGTAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 2 0.07
20 25 0.86
21 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (20 bp):
ATAAGGTATCGATACTGAGG
Found at i:46526 original size:23 final size:23
Alignment explanation
Indices: 46489--46571 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
46479 GTCGAGGGTT
46489 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* * *
46512 CTATGTCGTCCTTCGGGACAAAC
1 CTATGTGGTCATTCGGGACAAAA
*
46535 CTATGTGGTCATTCGAGAC-AAA
1 CTATGTGGTCATTCGGGACAAAA
46557 -TATGTGG-CACTTCGG
1 CTATGTGGTCA-TTCGG
46572 TGCAAATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 2 0.04
23 36 0.71
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:46562 original size:21 final size:22
Alignment explanation
Indices: 46489--46584 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 22
46479 GTCGAGGGTT
46489 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGAC-AAA
* *
46512 CTATGTCGTCCTTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
*
46534 CCTATGTGGTCATTCGAGACAAA
1 -CTATGTGGTCATTCGGGACAAA
46557 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTCA-TTCGG-GACAAA
*
46578 TTATGTG
1 CTATGTG
46585 AGCTGTGGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.03
21 15 0.24
22 10 0.16
23 36 0.57
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:50172 original size:30 final size:30
Alignment explanation
Indices: 50133--50225 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
50123 AAATGGATTT
* * * *
50133 AGTTAAGTGATCAAATTATAAGA-TTTTAAA
1 AGTTTAGTGACCAAAGTATAA-ACTTTAAAA
50163 AGTTTAGTGACCAAAGTATAAACTTTAAAA
1 AGTTTAGTGACCAAAGTATAAACTTTAAAA
* * * *
50193 AGTTTAGGGACCAAAATGT-AATTTTAAAA
1 AGTTTAGTGACCAAAGTATAAACTTTAAAA
50222 AGTT
1 AGTT
50226 ACAAATTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 14 0.26
30 40 0.74
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTAAAA
Found at i:50218 original size:29 final size:30
Alignment explanation
Indices: 50144--50225 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
50134 GTTAAGTGAT
* *
50144 CAAATTATAAGATTTT-AAAAGTTTAGTGAC
1 CAAAATATAA-ATTTTAAAAAGTTTAGGGAC
* *
50174 CAAAGTATAAACTTTAAAAAGTTTAGGGAC
1 CAAAATATAAATTTTAAAAAGTTTAGGGAC
*
50204 CAAAATGT-AATTTTAAAAAGTT
1 CAAAATATAAATTTTAAAAAGTT
50226 ACAAATTGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (30 bp):
CAAAATATAAATTTTAAAAAGTTTAGGGAC
Found at i:50336 original size:16 final size:16
Alignment explanation
Indices: 50315--50346 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
50305 AATTCCATGT
50315 TTAGTTTGGATTGTTG
1 TTAGTTTGGATTGTTG
50331 TTAGTTTGGATTGTTG
1 TTAGTTTGGATTGTTG
50347 GATTAAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.56
Consensus pattern (16 bp):
TTAGTTTGGATTGTTG
Found at i:53418 original size:20 final size:20
Alignment explanation
Indices: 53389--53428 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53379 GTAAGGAGTT
53389 GAGTTCGGCATAAATCACCA
1 GAGTTCGGCATAAATCACCA
*
53409 GAGTTTGGCATAAATCACCA
1 GAGTTCGGCATAAATCACCA
53429 AGGAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAGTTCGGCATAAATCACCA
Found at i:59906 original size:20 final size:20
Alignment explanation
Indices: 59881--59920 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
59871 GTAAGGAGTT
59881 GAGTTTGGCATAAATCACCA
1 GAGTTTGGCATAAATCACCA
59901 GAGTTTGGCATAAATCACCA
1 GAGTTTGGCATAAATCACCA
59921 AGGAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGTTTGGCATAAATCACCA
Found at i:67162 original size:23 final size:23
Alignment explanation
Indices: 67125--67200 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
67115 GTCGAGGGTT
67125 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* * *
67148 CTATGTCGTCATTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
*
67171 CTCTGTGGTCCTTCGGGAC-AAA
1 CTATGTGGTCCTTCGGGACAAAA
67193 -TATGTGGT
1 CTATGTGGT
67201 ACTTTGGTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
21 7 0.16
22 2 0.04
23 36 0.80
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:68134 original size:16 final size:17
Alignment explanation
Indices: 68104--68138 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
68094 TTAGTGAGGC
*
68104 AACATAATAAGATAAAT
1 AACATAATAAAATAAAT
68121 AACAT-ATAAAATAAAT
1 AACATAATAAAATAAAT
68137 AA
1 AA
68139 ATTTTGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (17 bp):
AACATAATAAAATAAAT
Found at i:71358 original size:30 final size:31
Alignment explanation
Indices: 71290--71385 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 31
71280 GAAGGACCTA
* ** *
71290 TCCAGAGGTCACAAAG-ACCCCGGT-AACTA
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * * * *
71319 TCCAGAGGTCATAAAGAACTTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
71349 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
71380 TCCATA
1 TCCATA
71386 TGTTCCTTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.28
30 28 0.52
31 11 0.20
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:71382 original size:31 final size:31
Alignment explanation
Indices: 71344--71438 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
71334 GAACTTCGGC
* *
71344 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
71375 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
** *
71406 TTCTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
71437 AA
1 AA
71439 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 47 0.94
32 3 0.06
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:72709 original size:64 final size:64
Alignment explanation
Indices: 72557--72713 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
72547 CAATAAGGGT
* * ** *
72557 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
* * * *
72621 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATG-TTCTATTATTAAAG
72682 AG
63 AG
72684 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
72714 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
63 3 0.04
64 62 0.82
65 11 0.14
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
Found at i:73651 original size:29 final size:30
Alignment explanation
Indices: 73618--73687 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
73608 TTAACGTCTT
* * *
73618 AGTGATCAAATTGTTATTAATCGT-ATGGA
1 AGTGACCAAATTGTTATTAATCATAATGCA
73647 AGTGACCAAATTGTTATTAATCATAATGCA
1 AGTGACCAAATTGTTATTAATCATAATGCA
73677 AGTGACCAAAT
1 AGTGACCAAAT
73688 CAAAATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (30 bp):
AGTGACCAAATTGTTATTAATCATAATGCA
Found at i:73856 original size:12 final size:12
Alignment explanation
Indices: 73839--73864 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
73829 ATTAATTTGC
73839 ACAGACGATTTT
1 ACAGACGATTTT
73851 ACAGACGATTTT
1 ACAGACGATTTT
73863 AC
1 AC
73865 CTAAAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (12 bp):
ACAGACGATTTT
Found at i:76146 original size:17 final size:17
Alignment explanation
Indices: 76124--76157 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
76114 GGATGTGCCT
76124 TTCGAAAGCTCTTTTGG
1 TTCGAAAGCTCTTTTGG
76141 TTCGAAAGCTCTTTTGG
1 TTCGAAAGCTCTTTTGG
76158 GGGAACACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (17 bp):
TTCGAAAGCTCTTTTGG
Found at i:79922 original size:20 final size:21
Alignment explanation
Indices: 79873--79923 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
79863 TATGAATCAA
79873 TCATTCAAATATATTAATTAT
1 TCATTCAAATATATTAATTAT
*
79894 TCTTTCAAATATATTAATTAT
1 TCATTCAAATATATTAATTAT
79915 T-ATTCAAAT
1 TCATTCAAAT
79924 TTAAAAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
TCATTCAAATATATTAATTAT
Found at i:80113 original size:18 final size:18
Alignment explanation
Indices: 80090--80127 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
80080 TTACATTTTA
80090 TAAACATTTAACAAAA-AT
1 TAAACATTTAA-AAAACAT
80108 TAAACATTTAAAAAACAT
1 TAAACATTTAAAAAACAT
80126 TA
1 TA
80128 CATAATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAACATTTAAAAAACAT
Found at i:80536 original size:21 final size:21
Alignment explanation
Indices: 80505--80577 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
80495 GGTGTCATAA
*
80505 AACCCTACGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
80526 AACCTTGCGGGCTAGGTATGT
1 AACCCTGCGGGCTAGGAATGT
* *
80547 ACCCCTGTGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
80568 AACCCTGCGG
1 AACCCTGCGG
80578 TGGTGGCATA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.22
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:80617 original size:42 final size:42
Alignment explanation
Indices: 80570--80658 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
80560 AGGAATGTAA
* * *
80570 CCCTGCGGTGGTGGCATATGAATTGTTGGACTGGGCATATAC
1 CCCTGCGGAGGTGGCATATGAACTGGTGGACTGGGCATATAC
* * *
80612 CCCTGCGGAGGTGGCATTTGAACTGGTGGGCTGGGCATGTAC
1 CCCTGCGGAGGTGGCATATGAACTGGTGGACTGGGCATATAC
80654 CCCTG
1 CCCTG
80659 TGGGTTCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.16, C:0.22, G:0.36, T:0.26
Consensus pattern (42 bp):
CCCTGCGGAGGTGGCATATGAACTGGTGGACTGGGCATATAC
Done.