Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004183.1 Hibiscus syriacus cultivar Beakdansim tig00009150_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: 84469
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:821 original size:10 final size:11
Alignment explanation
Indices: 794--827 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
784 TCAAAAATAT
794 AAGTGCAAGTG
1 AAGTGCAAGTG
805 AAGTGCAAGT-
1 AAGTGCAAGTG
*
815 TAGTGCAAGTG
1 AAGTGCAAGTG
826 AA
1 AA
828 AGAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (11 bp):
AAGTGCAAGTG
Found at i:5772 original size:14 final size:14
Alignment explanation
Indices: 5753--5779 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5743 TAAGATACTA
5753 TTTCCATCACCATC
1 TTTCCATCACCATC
5767 TTTCCATCACCAT
1 TTTCCATCACCAT
5780 TCACGCACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:15536 original size:22 final size:22
Alignment explanation
Indices: 15484--15537 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
15474 CTAGAAATGC
* *
15484 ATGCATGGACGTAGGTTACAAT
1 ATGCATGGCCGAAGGTTACAAT
*
15506 ATGCATGGCCGAATGTTACAAT
1 ATGCATGGCCGAAGGTTACAAT
15528 ATGCATGGCC
1 ATGCATGGCC
15538 TCATGGTGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (22 bp):
ATGCATGGCCGAAGGTTACAAT
Found at i:17889 original size:35 final size:35
Alignment explanation
Indices: 17849--17925 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
17839 ATGATAATGG
*
17849 GATGGTGATTATATAGGCATGAAATAGAGATGAAA
1 GATGGTGATGATATAGGCATGAAATAGAGATGAAA
* * **
17884 GATGGTGATGATATAGGCGTGATATAGAGATGGGA
1 GATGGTGATGATATAGGCATGAAATAGAGATGAAA
17919 GATGGTG
1 GATGGTG
17926 TAGATAGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.36, T:0.26
Consensus pattern (35 bp):
GATGGTGATGATATAGGCATGAAATAGAGATGAAA
Found at i:26063 original size:13 final size:12
Alignment explanation
Indices: 26047--26095 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
26037 CTTTTTGAAC
26047 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
26060 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
*
26073 TTCTTATTTTTCTC
1 TTC-T-TTTTTCTT
26087 TTCTTTTTT
1 TTCTTTTTT
26096 GATTTTTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 8 0.25
13 13 0.41
14 8 0.25
15 3 0.09
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:26072 original size:19 final size:20
Alignment explanation
Indices: 26050--26113 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
26040 TTTGAACTTC
26050 TCTTTTTCTT-TTCTTT-TCT
1 TCTTTTTCTTATT-TTTCTCT
26069 TC-TTTTCTTATTTTTCTCT
1 TCTTTTTCTTATTTTTCTCT
* *
26088 TCTTTTT-TGATTTTTGTCT
1 TCTTTTTCTTATTTTTCTCT
26107 TCTTTTT
1 TCTTTTT
26114 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.25
19 26 0.65
20 4 0.10
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (20 bp):
TCTTTTTCTTATTTTTCTCT
Found at i:29481 original size:19 final size:19
Alignment explanation
Indices: 29448--29491 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
29438 TTGTAGGAGT
29448 CTTTTTCTTTCTCTTTTTG
1 CTTTTTCTTTCTCTTTTTG
*
29467 -TTTTTCTTATTTCTTTTTG
1 CTTTTTCTT-TCTCTTTTTG
29486 CTTTTT
1 CTTTTT
29492 GTTGTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (19 bp):
CTTTTTCTTTCTCTTTTTG
Found at i:29489 original size:26 final size:24
Alignment explanation
Indices: 29447--29494 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
29437 GTTGTAGGAG
29447 TCTTTTTCTTTCTCTTTTTGTTTT
1 TCTTTTTCTTTCTCTTTTTGTTTT
*
29471 TCTTATTTCTTTTTGCTTTTTGTT
1 TCTT-TTTCTTTCT-CTTTTTGTT
29495 GTTTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 9 0.43
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (24 bp):
TCTTTTTCTTTCTCTTTTTGTTTT
Found at i:29492 original size:7 final size:6
Alignment explanation
Indices: 29447--29491 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
29437 GTTGTAGGAG
* *
29447 TCTTTT TCTTTC TCTTTT TGTTTT TCTTATT TCTTTT TGCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT T-CTTTT T
29492 GTTGTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
6 21 0.64
7 12 0.36
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:32482 original size:29 final size:28
Alignment explanation
Indices: 32442--32502 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
32432 AAAAGACAAA
*
32442 AAAAGAAGAAG-AAAATTTCAGAAAATAAG
1 AAAAGAAGAAGAAAAAATTCA-AAAA-AAG
32471 AAAAG-AGAAAGAAAAAATTCAAAAAAAG
1 AAAAGAAG-AAGAAAAAATTCAAAAAAAG
32499 AAAA
1 AAAA
32503 AGTAAGCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.31
29 12 0.41
30 8 0.28
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (28 bp):
AAAAGAAGAAGAAAAAATTCAAAAAAAG
Found at i:32503 original size:29 final size:32
Alignment explanation
Indices: 32439--32504 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
32429 AAGAAAAGAC
*
32439 AAAAAAAGAAGAAGAAAATTTCAGAAAATAAG
1 AAAAAGAGAAGAAGAAAATTTCAGAAAATAAG
32471 -AAAAGAGAAAGAA-AAAA-TTCA-AAAA-AAG
1 AAAAAGAG-AAGAAGAAAATTTCAGAAAATAAG
32499 AAAAAG
1 AAAAAG
32505 TAAGCCAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 3 0.10
29 9 0.29
30 4 0.13
31 10 0.32
32 5 0.16
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.09
Consensus pattern (32 bp):
AAAAAGAGAAGAAGAAAATTTCAGAAAATAAG
Found at i:46832 original size:6 final size:6
Alignment explanation
Indices: 46821--46879 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
46811 GATGTATAAG
* *
46821 TCTTTT TC-TTT TCTTTT TATTTT TCTTCTT TCTTCTT TCTCTT T-TTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTT-TT TCTTTT TCTTTT
*
46869 T-TTTT GCTTTT
1 TCTTTT TCTTTT
46880 GTTGTTTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 13 0.29
6 20 0.44
7 12 0.27
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:54776 original size:40 final size:40
Alignment explanation
Indices: 54732--54809 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
54722 AAGGATGAGG
*
54732 ATACTTGGAAGTCTTGAGACCCAACTTTTACACCATGTGA
1 ATACTTGGAAGTCTTGAGACCCAACTTTTACAACATGTGA
54772 ATACTTGGAAGTCTTGAGACCCAACTTTTACAACATGT
1 ATACTTGGAAGTCTTGAGACCCAACTTTTACAACATGT
54810 CCTTTTGACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (40 bp):
ATACTTGGAAGTCTTGAGACCCAACTTTTACAACATGTGA
Found at i:55359 original size:28 final size:25
Alignment explanation
Indices: 55304--55359 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
55294 TTCTTTGCTT
**
55304 TTTCTTCTTTTGAGTGCTGGATTTC
1 TTTCTTCTTTTGAGTGCTCAATTTC
55329 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGC-TCAATTTC
55357 TTT
1 TTT
55360 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 6 0.23
28 9 0.35
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (25 bp):
TTTCTTCTTTTGAGTGCTCAATTTC
Found at i:58438 original size:19 final size:20
Alignment explanation
Indices: 58391--58441 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
58381 GAAACCCCTT
**
58391 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
58411 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
58430 TGAAGATACATG
1 TGAAAATACATG
58442 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:60778 original size:21 final size:22
Alignment explanation
Indices: 60748--60789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
60738 AATATGATTA
*
60748 ATAAAGGAAAATTAATGAAATG
1 ATAAAGGAAAATGAATGAAATG
*
60770 ATAAA-GAAAATGAGTGAAAT
1 ATAAAGGAAAATGAATGAAAT
60790 TAAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (22 bp):
ATAAAGGAAAATGAATGAAATG
Found at i:62617 original size:47 final size:44
Alignment explanation
Indices: 62548--62659 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 44
62538 CTTAATTTTT
* *
62548 TTCCATATGCTCGTAATCTTATTTTACCAAAATACCTACCATATAAA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACCTACCAT-T--A
* * * * *
62595 TTCCATAAGCTCTTAAGCTTATTTTATCAATATACTTGCCATTA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACCTACCATTA
62639 TT-CATAAGCTCGTAAGCTTAT
1 TTCCATAAGCTCGTAAGCTTAT
62660 ATGCATACTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
43 18 0.32
44 3 0.05
46 1 0.02
47 35 0.61
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (44 bp):
TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACCTACCATTA
Found at i:62808 original size:40 final size:40
Alignment explanation
Indices: 62743--62826 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
62733 ATAGGAGTCA
* * * * *
62743 AATATTGCACCGAAGTGCTGTGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
* *
62783 AATAATGCACCGTAGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
62823 AATA
1 AATA
62827 CACCGTAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
Found at i:64134 original size:29 final size:29
Alignment explanation
Indices: 64077--64142 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
64067 AGGTTCTTCA
* * *
64077 TCAATTTTCCAAAATTTACGAATTTATCC
1 TCAATTTTCCAAAACTTACGAAATGATCC
64106 TCAACTTTTCC-AAACTTACGAAATGATCC
1 TCAA-TTTTCCAAAACTTACGAAATGATCC
*
64135 CCAATTTT
1 TCAATTTT
64143 TATGAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.12
29 22 0.69
30 6 0.19
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
TCAATTTTCCAAAACTTACGAAATGATCC
Found at i:67377 original size:8 final size:8
Alignment explanation
Indices: 67364--67393 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
67354 ATTTCATATG
67364 CAAATTTC
1 CAAATTTC
67372 CAAATTTC
1 CAAATTTC
67380 CAAATTTC
1 CAAATTTC
67388 CAAATT
1 CAAATT
67394 ATCTATCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (8 bp):
CAAATTTC
Found at i:69563 original size:43 final size:46
Alignment explanation
Indices: 69452--69563 Score: 149
Period size: 47 Copynumber: 2.5 Consensus size: 46
69442 CTTACTTTTT
*
69452 TTCCATATGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTT-AA
* * **
69499 TTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTGTCA-TT-A
1 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAA
69543 TT-CATAAGCTCGTAAGCTTAT
1 TTCCATAAGCTCGTAAGCTTAT
69564 ATGCATACTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 19 0.32
44 3 0.05
46 2 0.03
47 36 0.60
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (46 bp):
TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAA
Found at i:71007 original size:29 final size:30
Alignment explanation
Indices: 70954--71017 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
70944 TCTTCATCAA
* * *
70954 TTTTCCAAAATTTACGAATTTATCCCCAAC
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
* *
70984 TTTTCC-AAACTTACGAAATGATCCCTAAT
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
71013 TTTTC
1 TTTTC
71018 TGAGGCTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCCAAC
Found at i:72383 original size:90 final size:90
Alignment explanation
Indices: 72277--72440 Score: 292
Period size: 90 Copynumber: 1.8 Consensus size: 90
72267 ATTTAATTTC
* * *
72277 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGGTAACTT
72342 GGATATAAAAAGATTATTAAATTAT
66 GGATATAAAAAGATTATTAAATTAT
72367 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGGTAACTT
*
72432 GGCTATAAA
66 GGATATAAA
72441 TAGGCGCCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGGTAACTT
GGATATAAAAAGATTATTAAATTAT
Found at i:73331 original size:17 final size:19
Alignment explanation
Indices: 73308--73354 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
73298 GTGCTGAAAC
*
73308 AAAAGAAACAAA-AAAAAG
1 AAAAGAAAAAAACAAAAAG
73326 -AAAGAAGAAAAACAAAAAG
1 AAAAGAA-AAAAACAAAAAG
73345 AAAAGAAAAA
1 AAAAGAAAAA
73355 GACTCCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 9 0.36
20 6 0.24
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAACAAAAAG
Found at i:73336 original size:13 final size:12
Alignment explanation
Indices: 73308--73356 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
73298 GTGCTGAAAC
*
73308 AAAAGAAACAAAA
1 AAAAGAAA-AAGA
73321 AAAAGAAAGAAGA
1 AAAAGAAA-AAGA
*
73334 AAAACAAAAAG-
1 AAAAGAAAAAGA
73345 AAAAGAAAAAGA
1 AAAAGAAAAAGA
73357 CTCCTACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 10 0.32
12 3 0.10
13 18 0.58
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Done.