Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004762.1 Hibiscus syriacus cultivar Beakdansim tig00010741_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: 47689
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:745 original size:17 final size:15
Alignment explanation
Indices: 684--757 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 15
674 AAAAATTGAC
684 TTTAAATAAT--A-T
1 TTTAAATAATAAATT
696 TTTAAATAATTAAATT
1 TTTAAATAA-TAAATT
*
712 TTATAAA-AAGTATATT
1 TT-TAAATAA-TAAATT
728 TTTATCAATAATAAA-T
1 TTTA--AATAATAAATT
744 TTTAAATAATAAAT
1 TTTAAATAATAAAT
758 AAAGAACAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
12 9 0.18
13 1 0.02
14 9 0.18
15 3 0.06
16 17 0.34
17 9 0.18
18 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (15 bp):
TTTAAATAATAAATT
Found at i:2802 original size:25 final size:23
Alignment explanation
Indices: 2770--2816 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
2760 AAAGAAAAAC
2770 CTTTTTTTAAAAAAATAATAATTA
1 CTTTTTTTAAAAAAATAA-AATTA
* *
2794 CTTTATTTTTAGAAAATAAAATT
1 CTTT-TTTTAAAAAAATAAAATT
2817 TATCTAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
CTTTTTTTAAAAAAATAAAATTA
Found at i:5534 original size:31 final size:31
Alignment explanation
Indices: 5493--5575 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
5483 ATTTAATTTG
*
5493 AATTTCTAAAATTTTGAAGGAGTC-AATTGA
1 AATTTTTAAAATTTTGAAGGAGTCAAATTGA
* *
5523 AATTTTTTAAAAATTT-AAGG-GTCAAAATTTA
1 AA-TTTTTAAAATTTTGAAGGAGTC-AAATTGA
*
5554 AATTTTTAAAATTTTGGAGGAG
1 AATTTTTAAAATTTTGAAGGAG
5576 CCATGACCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 3 0.07
30 18 0.42
31 21 0.49
32 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.40
Consensus pattern (31 bp):
AATTTTTAAAATTTTGAAGGAGTCAAATTGA
Found at i:7731 original size:14 final size:14
Alignment explanation
Indices: 7708--7745 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
7698 TCTCTCTCTC
*
7708 TCTCTATCTGCCTG
1 TCTCTGTCTGCCTG
7722 TCTCTGTCTGCCTG
1 TCTCTGTCTGCCTG
7736 TCTCTGTCTG
1 TCTCTGTCTG
7746 TCCCTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.03, C:0.34, G:0.18, T:0.45
Consensus pattern (14 bp):
TCTCTGTCTGCCTG
Found at i:7810 original size:15 final size:14
Alignment explanation
Indices: 7790--7821 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
7780 TCATTTTTTC
7790 TTTCATCTCTTTCAA
1 TTTCATCTCTTT-AA
7805 TTTCATCTCTTTAA
1 TTTCATCTCTTTAA
7819 TTT
1 TTT
7822 TTAGTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCATCTCTTTAA
Found at i:9962 original size:13 final size:13
Alignment explanation
Indices: 9944--9969 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9934 CGGATAAGAT
9944 CTATTTATATATA
1 CTATTTATATATA
9957 CTATTTATATATA
1 CTATTTATATATA
9970 TAAGTATATG
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
CTATTTATATATA
Found at i:19872 original size:14 final size:15
Alignment explanation
Indices: 19838--19878 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
19828 ATCCTATAGT
* *
19838 TTTTAATACTATCAC
1 TTTTAATTCTTTCAC
19853 TTTTAATTCTTTCA-
1 TTTTAATTCTTTCAC
19867 TTTTAATTCTTT
1 TTTTAATTCTTT
19879 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAATTCTTTCAC
Found at i:20183 original size:18 final size:18
Alignment explanation
Indices: 20157--20193 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20147 ATTAATTTAT
20157 TTTAATTATTTTTTAATA
1 TTTAATTATTTTTTAATA
*
20175 TTTATTTATTTTTTAATA
1 TTTAATTATTTTTTAATA
20193 T
1 T
20194 CGAAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTAATTATTTTTTAATA
Found at i:22294 original size:26 final size:27
Alignment explanation
Indices: 22260--22314 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
22250 TTTGCATTTG
*
22260 TACATTTTTACGTTTG-TATTTACATT
1 TACATTTTTACCTTTGATATTTACATT
22286 TACATTTTTACCTTTGCATATTTACATT
1 TACATTTTTACCTTTG-ATATTTACATT
22314 T
1 T
22315 GGCATCTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 15 0.58
28 11 0.42
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (27 bp):
TACATTTTTACCTTTGATATTTACATT
Found at i:22315 original size:14 final size:14
Alignment explanation
Indices: 22276--22329 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
22266 TTTACGTTTG
*
22276 TATTTACATTTACA
1 TATTTACATTTGCA
* *
22290 TTTTTACCTTTGCA
1 TATTTACATTTGCA
22304 TATTTACATTTGGCA
1 TATTTACATTT-GCA
* *
22319 TCTTTGCATTT
1 TATTTACATTT
22330 TTTATGTCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:24548 original size:2 final size:2
Alignment explanation
Indices: 24541--24592 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
24531 TTATCCTTTA
24541 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
24583 AT AT AT AT AT
1 AT AT AT AT AT
24593 CCTTTGTTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27596 original size:21 final size:21
Alignment explanation
Indices: 27570--27614 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27560 GATTTCTGGG
* *
27570 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27591 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27612 CAA
1 CAA
27615 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:29369 original size:23 final size:22
Alignment explanation
Indices: 29310--29376 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
29300 TATGGACATC
*
29310 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
29332 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
29354 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
29377 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:32474 original size:21 final size:21
Alignment explanation
Indices: 32448--32492 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32438 GATTTCTGGG
* *
32448 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
32469 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
32490 CAA
1 CAA
32493 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:34245 original size:23 final size:22
Alignment explanation
Indices: 34186--34252 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
34176 TATGGACATC
*
34186 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
34208 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
34230 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
34253 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:35469 original size:115 final size:115
Alignment explanation
Indices: 35203--35431 Score: 345
Period size: 115 Copynumber: 2.0 Consensus size: 115
35193 GTTCCACGTT
* * *
35203 CTCATAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
35268 ATTTGGTATGAAACCACAGAACCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTATGAAACCACAGAACCAATCATTGGAATTAAAAGATGAATCTG
* *
35318 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
35383 GTTTGGTA-GGAACCATAGAACCAATCATTGGAATTAAAAGATGAA-CTG
66 ATTTGGTATGAAACCACAGAACCAATCATTGGAATTAAAAGATGAATCTG
35431 C
1 C
35432 ATGATCGTCT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 3 0.03
114 33 0.31
115 71 0.66
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (115 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAAACCACAGAACCAATCATTGGAATTAAAAGATGAATCTG
Found at i:37758 original size:22 final size:22
Alignment explanation
Indices: 37732--37810 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
37722 ACACCTACAT
37732 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
37754 TCTTCAAAGATGATAGATT-TCC
1 TCTTCAAAGATGATAGATTCT-C
* * *
37776 TTTTTAAAGATG-TCATATTCTC
1 TCTTCAAAGATGAT-AGATTCTC
*
37798 TTTTCAAAGATGA
1 TCTTCAAAGATGA
37811 AAGCTTTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 46 0.94
23 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:38412 original size:114 final size:114
Alignment explanation
Indices: 38212--38665 Score: 718
Period size: 114 Copynumber: 4.0 Consensus size: 114
38202 TAGGAAAAAG
* * *
38212 TCAAATTCATCACTCGATGGATCAGCATTGCCAGGTAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTCGATGGATCAACATTGCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTG
*
38277 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
38326 TCAAATCCATCACTCGATGGATCAACATTACCAGGTAGAAAGTTCATAATGAGAAGAACTCATCT
1 TCAAATCCATCACTCGATGGATCAACATTGCCAGGTAG-AAGTTCATAATGAGAAGAACTCATCT
*
38391 GAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
38440 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTG-AGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTCGATGGATCAACATTGCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTG
38504 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
38553 TTC-AATTCATCACTCGATGGATCAACATTGCCAGGTAGAAGGTCATAATGAGAAGAACTCATTT
1 -TCAAATCCATCACTCGATGGATCAACATTGCCAGGTAGAAGTTCATAATGAGAAGAACTCATCT
*
38617 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
38666 ATGACTCTAT
Statistics
Matches: 313, Mismatches: 23, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
112 29 0.09
113 116 0.37
114 138 0.44
115 30 0.10
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (114 bp):
TCAAATCCATCACTCGATGGATCAACATTGCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:40290 original size:17 final size:18
Alignment explanation
Indices: 40258--40298 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40248 AATTTCTTTC
40258 ATTTTAATTATTATTATT
1 ATTTTAATTATTATTATT
*
40276 ATTTTTATT-TTATTATT
1 ATTTTAATTATTATTATT
40293 ACTTTT
1 A-TTTT
40299 GATATATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTAATTATTATTATT
Found at i:40576 original size:18 final size:18
Alignment explanation
Indices: 40550--40586 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40540 ATTAATTTAT
40550 TTTAATTATTTTTTAATA
1 TTTAATTATTTTTTAATA
*
40568 TTTATTTATTTTTTAATA
1 TTTAATTATTTTTTAATA
40586 T
1 T
40587 CGAAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTAATTATTTTTTAATA
Found at i:46321 original size:20 final size:20
Alignment explanation
Indices: 46296--46333 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46286 CCGTTAGACA
46296 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
*
46316 GGGGGGAATCTGTACCCC
1 GGGGGGAATCGGTACCCC
46334 TGGCAATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.29, G:0.39, T:0.16
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:46343 original size:16 final size:16
Alignment explanation
Indices: 46322--46359 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
46312 CCCTGGGGGG
46322 AATCTGTACCCCTGGC
1 AATCTGTACCCCTGGC
46338 AATCTGTACCCCTGGC
1 AATCTGTACCCCTGGC
46354 AATCTG
1 AATCTG
46360 ATTTTTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.26
Consensus pattern (16 bp):
AATCTGTACCCCTGGC
Done.