Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001188.1 Hibiscus syriacus cultivar Beakdansim tig00002357_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: 65765
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:731 original size:17 final size:17
Alignment explanation
Indices: 709--743 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
699 GGCCCCCATA
709 ACATAGTAAAACTGAAC
1 ACATAGTAAAACTGAAC
726 ACATAGTAAAACTGAAC
1 ACATAGTAAAACTGAAC
743 A
1 A
744 TATGGACAAT
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:0.54, C:0.17, G:0.11, T:0.17
Consensus pattern (17 bp):
ACATAGTAAAACTGAAC
Found at i:8275 original size:20 final size:20
Alignment explanation
Indices: 8250--8304 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
8240 TTGGGGCCTG
8250 ATGGTATCGATACTATGCTC
1 ATGGTATCGATACTATGCTC
*
8270 ATGGTATCGATGCTATGCTC
1 ATGGTATCGATACTATGCTC
8290 ATGGTATCGATACTA
1 ATGGTATCGATACTA
8305 CTATGCAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
ATGGTATCGATACTATGCTC
Found at i:16137 original size:18 final size:19
Alignment explanation
Indices: 16116--16155 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
16106 TGTTTTAACC
16116 CTTAATAATATATAA-ATA
1 CTTAATAATATATAACATA
*
16134 CTTAATAGTATATAACATA
1 CTTAATAATATATAACATA
16153 CTT
1 CTT
16156 CTAAGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (19 bp):
CTTAATAATATATAACATA
Found at i:16456 original size:13 final size:13
Alignment explanation
Indices: 16409--16459 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
16399 TGCTTTTAGG
* *
16409 TTAAAAATGTAAA
1 TTAAAAATTTATA
*
16422 TTTAAAAAATTATA
1 -TTAAAAATTTATA
16436 TTAAAAATTTATA
1 TTAAAAATTTATA
16449 TTAAAAATTTA
1 TTAAAAATTTA
16460 AGAATATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
TTAAAAATTTATA
Found at i:16936 original size:35 final size:35
Alignment explanation
Indices: 16885--16952 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
16875 ACTGCATTTG
* * *
16885 TATTTAAAATTTTAACATATCTGTAATAATTAACT
1 TATTTAAAATTCTAACAAATCTATAATAATTAACT
16920 TATTTAAAATTCTAACAAATCTATAATAATTAA
1 TATTTAAAATTCTAACAAATCTATAATAATTAA
16953 GTAACTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (35 bp):
TATTTAAAATTCTAACAAATCTATAATAATTAACT
Found at i:21468 original size:38 final size:37
Alignment explanation
Indices: 21391--21473 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 37
21381 AAAAATCATG
* *
21391 AAATATTAAAGAATAAATAATAGTGAAAATGAAAGAA
1 AAATATTAAACAATAAATAATAGTGAAAATGAAAAAA
21428 AAATATTAAACAATTAAA-AATAGTAGAAAAT-ATAAAAA
1 AAATATTAAACAA-TAAATAATAGT-GAAAATGA-AAAAA
*
21466 AAAAATTA
1 AAATATTA
21474 TAAAAATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 19 0.47
38 21 0.52
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.23
Consensus pattern (37 bp):
AAATATTAAACAATAAATAATAGTGAAAATGAAAAAA
Found at i:21470 original size:40 final size:37
Alignment explanation
Indices: 21391--21473 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
21381 AAAAATCATG
* * *
21391 AAATATTAAAGAATAAATAATAGTGAAAATGAAAGAA
1 AAATATTAAACAATAAATAATAGTGAAAATAAAAAAA
21428 AAATATTAAACAATTAAA-AATAGTAGAAAATATAAAAAA
1 AAATATTAAACAA-TAAATAATAGT-GAAAATA-AAAAAA
21467 AAA-ATTA
1 AAATATTA
21474 TAAAAATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 18 0.45
38 14 0.35
39 8 0.20
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.23
Consensus pattern (37 bp):
AAATATTAAACAATAAATAATAGTGAAAATAAAAAAA
Found at i:22552 original size:32 final size:35
Alignment explanation
Indices: 22482--22558 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
22472 ATTTAATTTT
**
22482 ATAATATTTTTATATTTAATATATTAAATATCTTA
1 ATAATATTTTTATATTTAATATATTAAATATCAAA
* *
22517 ATAATTTTTTTATATTT-ATATTTTAAAT-T-AAA
1 ATAATATTTTTATATTTAATATATTAAATATCAAA
22549 ATAATATTTT
1 ATAATATTTT
22559 AATTTTTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 10 0.27
33 1 0.03
34 10 0.27
35 16 0.43
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (35 bp):
ATAATATTTTTATATTTAATATATTAAATATCAAA
Found at i:24852 original size:46 final size:47
Alignment explanation
Indices: 24777--24898 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 47
24767 AAGCTCTTCC
* *** * **
24777 TAAAATATTATTTTTTTTCTACTGGAAATGATAATATTGGTCGTTACA
1 TAAAATGTTA-TTTTTTTCTACCAAAAATGATAATATTGGACACTACA
* *
24825 TAAAATGTTA-TTTTTTCTACCAAAAATGTTAATATTGGACACTACC
1 TAAAATGTTATTTTTTTCTACCAAAAATGATAATATTGGACACTACA
*
24871 TAAAATGTTATTTTTTTCTACCGAAAAT
1 TAAAATGTTATTTTTTTCTACCAAAAAT
24899 TAGATAATGA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
46 38 0.60
47 16 0.25
48 9 0.14
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (47 bp):
TAAAATGTTATTTTTTTCTACCAAAAATGATAATATTGGACACTACA
Found at i:28704 original size:2 final size:2
Alignment explanation
Indices: 28697--28759 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
28687 CAAAATATTG
28697 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
28739 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
28760 GAGAGAGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28764 original size:2 final size:2
Alignment explanation
Indices: 28759--28783 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28749 ATATATATAT
28759 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
28784 TAACGTACGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32798 original size:20 final size:20
Alignment explanation
Indices: 32762--32801 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
32752 TGTTTGAATC
*
32762 AAATTAATTAGATATTATTT
1 AAATTAATTAGAAATTATTT
32782 AAATTAATT-GTAAATTATTT
1 AAATTAATTAG-AAATTATTT
32802 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTT
Found at i:43176 original size:16 final size:16
Alignment explanation
Indices: 43151--43192 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
43141 TGAAATATTA
43151 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
43167 GCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTG
43183 GCAAAGTTGA
1 GCAAAGTTGA
43193 CATCTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (16 bp):
GCAAAGTTGAAAGTTG
Found at i:58801 original size:24 final size:20
Alignment explanation
Indices: 58748--58805 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
58738 TCCCCTTTGA
*
58748 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
58768 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
58791 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
58806 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:61812 original size:12 final size:12
Alignment explanation
Indices: 61791--61841 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
61781 ACCTGAAAAG
*
61791 ACAAGGAAAATA
1 ACAAGTAAAATA
61803 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
*
61816 TACAA-AAAAATGA
1 -ACAAGTAAAAT-A
61829 ACAAGTAAAATA
1 ACAAGTAAAATA
61841 A
1 A
61842 AAATGCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Done.