Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009612.1 Hibiscus syriacus cultivar Beakdansim tig00116998_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: 49536
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3545 original size:20 final size:19
Alignment explanation
Indices: 3520--3601 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 19
3510 TTTTGGTGCA
*
3520 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCC-T
*
3540 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC--T
*
3561 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATACCCCCT
*
3582 -AGGGAAATCGATACCCCCT
1 GAGGG-AACCGATACCCCCT
3601 G
1 G
3602 GGGTTCTGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.06
19 13 0.25
20 16 0.31
21 3 0.06
22 1 0.02
23 16 0.31
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GAGGGAACCGATACCCCCT
Found at i:5826 original size:22 final size:23
Alignment explanation
Indices: 5774--5829 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
5764 TAACAAAAAG
*
5774 GGGGAGAAAGTGTTAAAGTTTTAAA
1 GGGGAGTAAGTGTTAAAG--TTAAA
*
5799 GAGGAGTAAGTGTTAAAG-TAAA
1 GGGGAGTAAGTGTTAAAGTTAAA
5821 GGGGAGTAA
1 GGGGAGTAA
5830 TTTTCAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.43
25 16 0.57
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.23
Consensus pattern (23 bp):
GGGGAGTAAGTGTTAAAGTTAAA
Found at i:12697 original size:19 final size:19
Alignment explanation
Indices: 12673--12742 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
12663 TTGGACCCTT
*
12673 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
*
12692 AGTGCATCGATGCA-TCA-
1 AGTGCATCGATGCACTAAG
12709 AGTGCATTCGATGCACTAAG
1 AGTGCA-TCGATGCACTAAG
12729 AGTGCATCGATGCA
1 AGTGCATCGATGCA
12743 TCAAGTGCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
17 6 0.13
18 10 0.22
19 23 0.51
20 6 0.13
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:12726 original size:37 final size:37
Alignment explanation
Indices: 12673--12758 Score: 156
Period size: 37 Copynumber: 2.4 Consensus size: 37
12663 TTGGACCCTT
*
12673 AGTGCA-TCGGTGCACTAAGAGTGCATCGATGCATCA
1 AGTGCATTCGATGCACTAAGAGTGCATCGATGCATCA
12709 AGTGCATTCGATGCACTAAGAGTGCATCGATGCATCA
1 AGTGCATTCGATGCACTAAGAGTGCATCGATGCATCA
12746 AGTGCATTCGATG
1 AGTGCATTCGATG
12759 TTTCAAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 6 0.12
37 42 0.88
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (37 bp):
AGTGCATTCGATGCACTAAGAGTGCATCGATGCATCA
Found at i:12764 original size:18 final size:17
Alignment explanation
Indices: 12673--12758 Score: 91
Period size: 19 Copynumber: 4.7 Consensus size: 17
12663 TTGGACCCTT
* *
12673 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
12691 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
*
12709 AGTGCATTCGATGCACTAA
1 AGTGCA-TCGATGCA-TCA
12728 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
12746 AGTGCATTCGATG
1 AGTGCA-TCGATG
12759 TTTCAAAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
17 12 0.20
18 18 0.31
19 23 0.39
20 6 0.10
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:12816 original size:28 final size:28
Alignment explanation
Indices: 12783--12872 Score: 171
Period size: 28 Copynumber: 3.2 Consensus size: 28
12773 GAGCGCATCG
12783 ATGCATGGCTGGTGCATCGATGCATCAA
1 ATGCATGGCTGGTGCATCGATGCATCAA
*
12811 ATGCATGGTTGGTGCATCGATGCATCAA
1 ATGCATGGCTGGTGCATCGATGCATCAA
12839 ATGCATGGCTGGTGCATCGATGCATCAA
1 ATGCATGGCTGGTGCATCGATGCATCAA
12867 ATGCAT
1 ATGCAT
12873 TCGATGTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (28 bp):
ATGCATGGCTGGTGCATCGATGCATCAA
Found at i:12920 original size:19 final size:19
Alignment explanation
Indices: 12896--12986 Score: 173
Period size: 19 Copynumber: 4.8 Consensus size: 19
12886 AAAATCCTCA
12896 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
*
12915 GTGCATCGATTCATGGTAT
1 GTGCATCGATGCATGGTAT
12934 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
12953 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
12972 GTGCATCGATGCATG
1 GTGCATCGATGCATG
12987 AAATGCATTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:20995 original size:32 final size:31
Alignment explanation
Indices: 20934--20995 Score: 72
Period size: 32 Copynumber: 1.9 Consensus size: 31
20924 GTTCGTTTGG
*
20934 TTATAGAAAATATTTTCCATTTCTGTTTTTAT
1 TTATAGAAAATATTTT-CATTTCTATTTTTAT
*
20966 TTATAGAAAATTATTTT-ATTTTTCATTTTT
1 TTATAGAAAA-TATTTTCATTTCT-ATTTTT
20996 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 5 0.19
32 15 0.58
33 6 0.23
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (31 bp):
TTATAGAAAATATTTTCATTTCTATTTTTAT
Found at i:22371 original size:33 final size:33
Alignment explanation
Indices: 22334--22404 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
22324 AAGAAAAAGT
*
22334 TAATATTTTAGGTCGCG-ACTTATATTAGCCTTA
1 TAATATTTTAGGTCGCGCA-TTATACTAGCCTTA
*
22367 TAATATTTTAGGTCGTGCATTATACTAGCCTTA
1 TAATATTTTAGGTCGCGCATTATACTAGCCTTA
22400 TAATA
1 TAATA
22405 AGTGATTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TAATATTTTAGGTCGCGCATTATACTAGCCTTA
Found at i:24975 original size:16 final size:18
Alignment explanation
Indices: 24943--24978 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
24933 AAGAGAGAGA
24943 AAAAGAAAAGTAGAAAAT
1 AAAAGAAAAGTAGAAAAT
24961 AAAAG-AAAG-AGAAAAT
1 AAAAGAAAAGTAGAAAAT
24977 AA
1 AA
24979 CCTCAGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAGTAGAAAAT
Found at i:25121 original size:20 final size:20
Alignment explanation
Indices: 25098--25142 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
25088 TTTCAATTTT
25098 GCAACGCGAATCTGTAAATC
1 GCAACGCGAATCTGTAAATC
* *
25118 GCAAGGCGAATTTGTAAATC
1 GCAACGCGAATCTGTAAATC
25138 GCAAC
1 GCAAC
25143 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
GCAACGCGAATCTGTAAATC
Found at i:25159 original size:20 final size:19
Alignment explanation
Indices: 25136--25195 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
25126 AATTTGTAAA
*
25136 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
25156 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
*
25176 TCACAACGCGAAAGTCAAAT
1 TCGCAACGCG-AAGTCAAAT
25196 GTTTTTACGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 33 0.92
21 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:25704 original size:20 final size:19
Alignment explanation
Indices: 25669--25722 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
25659 AAATCACAAC
25669 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
25688 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
25708 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
25723 ATAAACTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:27825 original size:42 final size:42
Alignment explanation
Indices: 27778--27878 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
27768 GATGCACCTA
* * *
27778 TCATCATTCAAGAGGTGCCTCCTATCATTCAAGGGGCCCCTC
1 TCATCATTCAAGAGGTCCCTCCCATCATTCAAGAGGCCCCTC
* * * *
27820 TCATCA-TCGAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGTCCCTCCCATCATTCAAGAGGCCCCTC
*
27862 TCATCGTTCAAGAGGTC
1 TCATCATTCAAGAGGTC
27879 TTTCCCGCCG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAGGTCCCTCCCATCATTCAAGAGGCCCCTC
Found at i:27866 original size:21 final size:21
Alignment explanation
Indices: 27778--27876 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
27768 GATGCACCTA
* **
27778 TCATCATTCAAGAGGTGCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
27799 -CTATCATTCAAGGGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
27820 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* *
27841 CCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
27862 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
27877 TCTTTCCCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:29523 original size:20 final size:20
Alignment explanation
Indices: 29500--29542 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
29490 GATTTTCGGT
29500 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
29520 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCGCG
29540 TTG
1 TTG
29543 ATCGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:29772 original size:39 final size:39
Alignment explanation
Indices: 29718--29804 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
29708 TCAAGTTGTA
29718 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
29757 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
29796 GATTTTGAT
1 GATTTTGAT
29805 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:30139 original size:18 final size:18
Alignment explanation
Indices: 30116--30152 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30106 CGAAATTTAT
30116 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
30134 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
30152 A
1 A
30153 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:30607 original size:20 final size:20
Alignment explanation
Indices: 30577--30627 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
30567 CAAATAATGT
* *
30577 ACAACATGAAAGTTAAATTC
1 ACAACACGAAAGTCAAATTC
* *
30597 GCAACGCGAAAGTCAAATTC
1 ACAACACGAAAGTCAAATTC
30617 ACAACACGAAA
1 ACAACACGAAA
30628 TAAGCGTTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.14, T:0.16
Consensus pattern (20 bp):
ACAACACGAAAGTCAAATTC
Found at i:31053 original size:18 final size:18
Alignment explanation
Indices: 31030--31066 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31020 AAGCCGGTTG
*
31030 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
31048 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
31066 T
1 T
31067 CTTTTGCTTG
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:0.16, C:0.03, G:0.24, T:0.57
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:33127 original size:3 final size:3
Alignment explanation
Indices: 33119--33143 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33109 TCTTCGGGGA
33119 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
33144 AGGGTTATAT
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:33345 original size:24 final size:24
Alignment explanation
Indices: 33318--33371 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
33308 CCATCACATC
*
33318 ATCAAAATCCGAGTATTCCCCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* * *
33342 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
33366 ATCAAA
1 ATCAAA
33372 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:34107 original size:14 final size:15
Alignment explanation
Indices: 34071--34108 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
34061 TAAATCATTG
34071 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
34086 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
34101 AAAAATTA
1 AAAAATTA
34109 GAGATAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:34293 original size:19 final size:19
Alignment explanation
Indices: 34265--34301 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34255 ACTAAAACTT
*
34265 GTTGCGAATTTGAAATTCA
1 GTTGCAAATTTGAAATTCA
34284 GTTGCAAATTTGAAATTC
1 GTTGCAAATTTGAAATTC
34302 CGCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (19 bp):
GTTGCAAATTTGAAATTCA
Found at i:42310 original size:23 final size:23
Alignment explanation
Indices: 42274--42323 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
42264 CTGAATGATT
*
42274 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
42297 CAGTGTTGAATGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
42320 CAGT
1 CAGT
42324 TCATTCTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAGCAAAA
Found at i:42341 original size:27 final size:24
Alignment explanation
Indices: 42274--42341 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
42264 CTGAATGATT
*
42274 CAGTG-CTGACTGATTCAGCAAAA
1 CAGTGTCTGAATGATTCAGCAAAA
42297 CAGTGT-TGAATGATTCAGCAAAA
1 CAGTGTCTGAATGATTCAGCAAAA
*
42320 CAGTTCATTCTGAATGATTCAG
1 CAG-T--GTCTGAATGATTCAG
42342 AGCCAGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 24 0.63
24 1 0.03
26 1 0.03
27 12 0.32
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (24 bp):
CAGTGTCTGAATGATTCAGCAAAA
Found at i:46319 original size:17 final size:17
Alignment explanation
Indices: 46286--46319 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46276 TATTTGAATG
*
46286 GACTCGACTCGAGTTCT
1 GACTCGACTCGAATTCT
*
46303 GACTCGACTTGAATTCT
1 GACTCGACTCGAATTCT
46320 TAACTAGCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (17 bp):
GACTCGACTCGAATTCT
Done.