Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004860.1 Hibiscus syriacus cultivar Beakdansim tig00010966_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: 77708
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2602 original size:15 final size:15
Alignment explanation
Indices: 2579--2612 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2569 AATATTACGA
*
2579 ACTCTATAAATTAAT
1 ACTCGATAAATTAAT
2594 ACTCGATAAATTAAT
1 ACTCGATAAATTAAT
2609 ACTC
1 ACTC
2613 TCTCTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (15 bp):
ACTCGATAAATTAAT
Found at i:9927 original size:59 final size:59
Alignment explanation
Indices: 9785--9931 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 59
9775 ATCATAAAAT
* * * *
9785 ACGCTTTCGCGGGGTTCCGTTCGAGCTGCCACCACGGTGGAAAGGCATGGATCATGAGGC
1 ACGCCTTCGCGGGGTTCCGTCCGAGCTGACACCACGGTGGAAAGGCA-GGATCATGAAGC
* * * * * * *
9845 ACGCCTTTGAGGGGTTCTGTCCGAGCTGACGCCACGTTGGAAGGTGC-GGATCATGAAGT
1 ACGCCTTCGCGGGGTTCCGTCCGAGCTGACACCACGGTGGAAAG-GCAGGATCATGAAGC
* *
9904 GCGCCTTCGCGGGGTTCCATCCGAGCTG
1 ACGCCTTCGCGGGGTTCCGTCCGAGCTG
9932 GCAAACGGCG
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 33 0.47
60 35 0.50
61 2 0.03
ACGTcount: A:0.16, C:0.27, G:0.35, T:0.22
Consensus pattern (59 bp):
ACGCCTTCGCGGGGTTCCGTCCGAGCTGACACCACGGTGGAAAGGCAGGATCATGAAGC
Found at i:10192 original size:18 final size:18
Alignment explanation
Indices: 10144--10193 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
10134 AAGCTAAATT
*
10144 TTTTATTATATTATAATCA
1 TTTTATTATATT-TTATCA
*
10163 -TTTA--ATAGTTTATCA
1 TTTTATTATATTTTATCA
10178 TTTTATTATATTTTAT
1 TTTTATTATATTTTAT
10194 AATAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
15 5 0.20
16 8 0.32
18 12 0.48
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATTATATTTTATCA
Found at i:11961 original size:23 final size:23
Alignment explanation
Indices: 11903--11969 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
11893 AGTTGAGGGT
* *
11903 TTCTACGTGGTCCTTTGGGACAAA
1 TTCTACGTGGTCATTCGGGAC-AA
* *
11927 TTTTACGCGGTCATTCGGGACAA
1 TTCTACGTGGTCATTCGGGACAA
*
11950 TTCTATGTGGTCATTCGGGA
1 TTCTACGTGGTCATTCGGGA
11970 TAAATCTATG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCATTCGGGACAA
Found at i:11977 original size:23 final size:23
Alignment explanation
Indices: 11935--11982 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
11925 AATTTTACGC
*
11935 GGTCATTCGGGACAATTCTATGT
1 GGTCATTCGGGACAAATCTATGT
*
11958 GGTCATTCGGGATAAATCTATGT
1 GGTCATTCGGGACAAATCTATGT
11981 GG
1 GG
11983 CACTTCAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (23 bp):
GGTCATTCGGGACAAATCTATGT
Found at i:12051 original size:24 final size:24
Alignment explanation
Indices: 11974--12036 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
11964 TCGGGATAAA
*
11974 TCTATGTGGCACTTCAGTGCATAT
1 TCTACGTGGCACTTCAGTGCATAT
11998 TCTACGTGGCACTTCAGTGCATAT
1 TCTACGTGGCACTTCAGTGCATAT
12022 TCTACGTGGCACTTC
1 TCTACGTGGCACTTC
12037 GATACAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
TCTACGTGGCACTTCAGTGCATAT
Found at i:19980 original size:17 final size:19
Alignment explanation
Indices: 19939--19974 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19929 TTTCGTTTTG
*
19939 ATGTTTTTCTTTTTCTCTT
1 ATGTTTTTCTTTTGCTCTT
19958 ATGTTTTT-TTTTGCTCT
1 ATGTTTTTCTTTTGCTCT
19975 CTGTTTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.06, C:0.14, G:0.08, T:0.72
Consensus pattern (19 bp):
ATGTTTTTCTTTTGCTCTT
Found at i:21789 original size:24 final size:24
Alignment explanation
Indices: 21744--21799 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
21734 CGAACGGTTC
*
21744 AGCGGTTCTGACCAGTTCACTAGT
1 AGCGGTTCTGACCAGTTCACTAAT
* *
21768 AGCGGTTCTGGCC-GATTTACTAAT
1 AGCGGTTCTGACCAG-TTCACTAAT
*
21792 AGCAGTTC
1 AGCGGTTC
21800 AACCGGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (24 bp):
AGCGGTTCTGACCAGTTCACTAAT
Found at i:22012 original size:30 final size:30
Alignment explanation
Indices: 21976--22055 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
21966 AATTAGTAAG
**
21976 TATTTTAAAATTAAAATTAAACAAAAATCT
1 TATTTTATTATTAAAATTAAACAAAAATCT
*
22006 TATTTTATTATTAAAATTAAATAAAAATCT
1 TATTTTATTATTAAAATTAAACAAAAATCT
22036 TATTTTATTATTAAAATTAA
1 TATTTTATTATTAAAATTAA
22056 TTAGTTCATC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
TATTTTATTATTAAAATTAAACAAAAATCT
Found at i:26128 original size:23 final size:21
Alignment explanation
Indices: 26094--26136 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
26084 ATATAAAAAA
26094 TTATTTTTTATTAAATATTTTT
1 TTATTTTTTATTAAAT-TTTTT
*
26116 TTATATTTTTATTTAATTTTT
1 TTAT-TTTTTATTAAATTTTT
26137 AAAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTTTTATTAAATTTTTT
Found at i:32729 original size:19 final size:20
Alignment explanation
Indices: 32695--32735 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
32685 TGGGTGAGGG
32695 TAGGACTCAGTGTTTTGAAAA
1 TAGGACTCA-TGTTTTGAAAA
32716 TAGGACTC-TGTTTTGAAAA
1 TAGGACTCATGTTTTGAAAA
32735 T
1 T
32736 CGAACTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
21 8 0.40
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (20 bp):
TAGGACTCATGTTTTGAAAA
Found at i:32981 original size:27 final size:27
Alignment explanation
Indices: 32943--33004 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
32933 ACAAGCCGAG
*
32943 TCGAACTCGAGTATTATTGAGCTCGAC
1 TCGAACTCGAGTATTACTGAGCTCGAC
32970 TCGAACTCGAGTATTACTGAGCTCGAC
1 TCGAACTCGAGTATTACTGAGCTCGAC
*
32997 TCAAACTC
1 TCGAACTC
33005 AAAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (27 bp):
TCGAACTCGAGTATTACTGAGCTCGAC
Found at i:39794 original size:20 final size:21
Alignment explanation
Indices: 39770--39815 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39760 TTTATATATT
39770 ATATTTAATATT-TTAAAAAA
1 ATATTTAATATTATTAAAAAA
* *
39790 TTATTTTATATTATTAAAAAA
1 ATATTTAATATTATTAAAAAA
39811 ATATT
1 ATATT
39816 ACTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTTAATATTATTAAAAAA
Found at i:47981 original size:15 final size:15
Alignment explanation
Indices: 47961--47996 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
47951 ATTATTTATC
*
47961 ATATTTATTAATTTA
1 ATATTTAATAATTTA
47976 ATATTTAATAATTTA
1 ATATTTAATAATTTA
*
47991 CTATTT
1 ATATTT
47997 CTCCTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTAATAATTTA
Found at i:48021 original size:23 final size:23
Alignment explanation
Indices: 47992--48040 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
47982 AATAATTTAC
47992 TATTTCTCCT-TTTTTATTAA-ATT
1 TATTTCT-CTATTTTT-TTAATATT
48015 TATTTCTCTATTTTTTTAATATT
1 TATTTCTCTATTTTTTTAATATT
48038 TAT
1 TAT
48041 ATGATAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTCTCTATTTTTTTAATATT
Found at i:50264 original size:25 final size:24
Alignment explanation
Indices: 50229--50282 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
50219 CATATAAAAT
*
50229 ATATAAGAAAATCATATAACAT-TTC
1 ATATAAGAAAAT-ACAT-ACATATTC
*
50254 ATATAATAAAATACATACATATTC
1 ATATAAGAAAATACATACATATTC
50278 ATATA
1 ATATA
50283 CAATCATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 11 0.42
25 11 0.42
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (24 bp):
ATATAAGAAAATACATACATATTC
Found at i:50657 original size:21 final size:21
Alignment explanation
Indices: 50608--50671 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
50598 CATATGAAAT
*
50608 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
50629 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
50651 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
50672 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:50971 original size:14 final size:15
Alignment explanation
Indices: 50944--50972 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50934 ATATCATATA
50944 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
50959 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
50973 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:56501 original size:16 final size:16
Alignment explanation
Indices: 56480--56512 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56470 GTTAACTAAC
56480 TATAAATGTATGTTGA
1 TATAAATGTATGTTGA
56496 TATAAATGTATGTTGA
1 TATAAATGTATGTTGA
56512 T
1 T
56513 GACGTAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TATAAATGTATGTTGA
Found at i:59710 original size:37 final size:37
Alignment explanation
Indices: 59660--59734 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
59650 CTCAAAGAAC
59660 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
1 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
59697 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
1 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
59734 T
1 T
59735 CTTGTCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (37 bp):
TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
Found at i:63488 original size:26 final size:27
Alignment explanation
Indices: 63439--63495 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
63429 AAATACCCTT
* *
63439 AATCGAATTGTTTTTAACTGTTAATTG
1 AATCGAATTGTTTTTAACTATTAACTG
* *
63466 AATCG-ATTTTTTTTAAGTATTAACTG
1 AATCGAATTGTTTTTAACTATTAACTG
63492 AATC
1 AATC
63496 AAATAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (27 bp):
AATCGAATTGTTTTTAACTATTAACTG
Found at i:63592 original size:21 final size:23
Alignment explanation
Indices: 63568--63612 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
63558 TTAATATTTT
*
63568 TTAA-TTAAAAAATAGTT-TAAA
1 TTAATTTAAAAAATAATTATAAA
*
63589 TTAATTTAAATAATAATTATAAA
1 TTAATTTAAAAAATAATTATAAA
63612 T
1 T
63613 AATATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TTAATTTAAAAAATAATTATAAA
Found at i:63648 original size:35 final size:34
Alignment explanation
Indices: 63569--63649 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 34
63559 TAATATTTTT
*
63569 TAATTAAAA-AATAGTTTAAATTAATTTAAATAA
1 TAATTAAAATAATAGTTTAAATTAATTCAAATAA
* * *
63602 TAATTATAAATAATA-TATTAATTTGATTCAAATAT
1 TAATTA-AAATAATAGT-TTAAATTAATTCAAATAA
63637 TATATTAAAATAA
1 TA-ATTAAAATAA
63650 GATTTGTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 6 0.15
34 4 0.10
35 26 0.65
36 4 0.10
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (34 bp):
TAATTAAAATAATAGTTTAAATTAATTCAAATAA
Found at i:66569 original size:18 final size:17
Alignment explanation
Indices: 66537--66570 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
66527 TCACCCGGTT
66537 CGGTTTGAACGGTTCAA
1 CGGTTTGAACGGTTCAA
*
66554 CGGTTCTGATCGGTTCA
1 CGGTT-TGAACGGTTCA
66571 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAA
Found at i:73937 original size:21 final size:20
Alignment explanation
Indices: 73909--73947 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
73899 CATTGCAGGA
*
73909 ATTTATGGCTTCGACAAAAG
1 ATTTATGGCTTCAACAAAAG
*
73929 ATTTCATGGTTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
73948 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAAG
Done.