Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001370.1 Hibiscus syriacus cultivar Beakdansim tig00002682_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: 36665
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:564 original size:25 final size:25
Alignment explanation
Indices: 536--592 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
526 TTCATATTTC
536 AGATATT-T-CAGAGGATATCAAGTTT
1 AGATATTATACAGAGG--ATCAAGTTT
561 AGATATTGATACAGAGGATCAAGTTT
1 AGATATT-ATACAGAGGATCAAGTTT
587 AGATAT
1 AGATAT
593 CAGCCAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.24
26 15 0.52
27 1 0.03
28 6 0.21
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (25 bp):
AGATATTATACAGAGGATCAAGTTT
Found at i:11553 original size:3 final size:3
Alignment explanation
Indices: 11539--11579 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
11529 AAATATGTAA
*
11539 AAT AAT ATT AAT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
11580 GAACGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:11857 original size:38 final size:39
Alignment explanation
Indices: 11815--11898 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 39
11805 CACTCACCTT
*
11815 TATAATAAT-ACATATTTATAAACACAACTGTCTAAATA
1 TATAATAATAACACATTTATAAACACAACTGTCTAAATA
* *
11853 TATAATAATACACACATTTATAAACACAACTGTTTAAATC
1 TATAATAATA-ACACATTTATAAACACAACTGTCTAAATA
11893 TATAAT
1 TATAAT
11899 TGTTAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 9 0.22
40 32 0.78
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (39 bp):
TATAATAATAACACATTTATAAACACAACTGTCTAAATA
Found at i:12771 original size:15 final size:15
Alignment explanation
Indices: 12748--12781 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12738 GAAGAAATAG
12748 ACTACTATATTAACA
1 ACTACTATATTAACA
*
12763 ACTATTATATTAACA
1 ACTACTATATTAACA
12778 ACTA
1 ACTA
12782 GTTAATATAG
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:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (15 bp):
ACTACTATATTAACA
Found at i:13072 original size:72 final size:72
Alignment explanation
Indices: 12981--13116 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
12971 CAAGTTAATG
* * *
12981 GATTAAATTCCAATAATTAAACGAAAAGAAAAATGTTAAAGTATACAAACGGTCTTCGACTATAA
1 GATTAAATTCCAATAATTAAACCAAAAGAAAAAGGTTAAAGTATAAAAACGGTCTTCGACTATAA
13046 AGTGATA
66 AGTGATA
* * * * *
13053 GATTAAATTCCAATGATTAAACCAAAATAAAAAGGTTAAAGTATAAAAATGGTTTTTGACTATA
1 GATTAAATTCCAATAATTAAACCAAAAGAAAAAGGTTAAAGTATAAAAACGGTCTTCGACTATA
13117 GGGTGTTGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (72 bp):
GATTAAATTCCAATAATTAAACCAAAAGAAAAAGGTTAAAGTATAAAAACGGTCTTCGACTATAA
AGTGATA
Found at i:18866 original size:2 final size:2
Alignment explanation
Indices: 18859--18887 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18849 CTATTTTTAA
18859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18888 ATGTCTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20053 original size:2 final size:2
Alignment explanation
Indices: 20046--20075 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20036 TTAGCGACTT
20046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20076 AGCATTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22945 original size:3 final size:3
Alignment explanation
Indices: 22937--23043 Score: 160
Period size: 3 Copynumber: 35.7 Consensus size: 3
22927 TTAATATATT
* * *
22937 TAA TAA TAA TAG TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
22985 TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23033 TAA TAA TAA TA
1 TAA TAA TAA TA
23044 TGGATAAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:23489 original size:113 final size:113
Alignment explanation
Indices: 23291--24137 Score: 1560
Period size: 113 Copynumber: 7.5 Consensus size: 113
23281 TCTTGATGAG
23291 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * * * * * *
23354 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
23404 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
23469 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
23517 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
23582 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
23630 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
23695 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
23743 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCT
23807 GGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
65 GGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
23856 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
23921 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
23969 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
24034 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
24082 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-T-TCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
24138 ACCTTGCAAT
Statistics
Matches: 721, Mismatches: 9, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
111 12 0.02
112 5 0.01
113 700 0.97
114 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:24876 original size:52 final size:52
Alignment explanation
Indices: 24805--24945 Score: 282
Period size: 52 Copynumber: 2.7 Consensus size: 52
24795 ATTCTGTCCA
24805 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
24857 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
24909 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
24946 TGGCAAATTC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (52 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
Found at i:25039 original size:182 final size:182
Alignment explanation
Indices: 24726--25139 Score: 801
Period size: 182 Copynumber: 2.3 Consensus size: 182
24716 CACTTCTTCG
* *
24726 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATG
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATATTCTAAATTCAATG
24791 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
66 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
24856 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
131 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
24908 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATATTCTAAATTCAATG
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATATTCTAAATTCAATG
24973 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
66 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
25038 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
131 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
25090 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCATATTCAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
25140 TTGTTCCAGT
Statistics
Matches: 229, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 229 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (182 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATATTCTAAATTCAATG
CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:25058 original size:52 final size:52
Alignment explanation
Indices: 24987--25127 Score: 282
Period size: 52 Copynumber: 2.7 Consensus size: 52
24977 ATTCTGTCCA
24987 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
25039 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
25091 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
25128 TGGCATATTC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (52 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
Found at i:26317 original size:17 final size:15
Alignment explanation
Indices: 26290--26368 Score: 88
Period size: 16 Copynumber: 5.0 Consensus size: 15
26280 TTTCTTTTTC
*
26290 TTCTCTTTTTTTCATT
1 TTCTTTTTTTTTC-TT
26306 TTCTATTTTTTTTCTT
1 TTCT-TTTTTTTTCTT
26322 TTCTTTTTTCTTTTCTT
1 TTC-TTTTT-TTTTCTT
*
26339 TTC-TTTCTTTTCTTT
1 TTCTTTTTTTTTC-TT
26354 TTCTTTTTTTTTCTT
1 TTCTTTTTTTTTCTT
26369 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
14 5 0.09
15 10 0.18
16 21 0.38
17 19 0.35
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTTTTTTTTCTT
Found at i:26325 original size:5 final size:5
Alignment explanation
Indices: 26280--26368 Score: 76
Period size: 5 Copynumber: 17.2 Consensus size: 5
26270 CTTGACCCCC
* *
26280 TTTCT TTT-T CTTCT CTTT-T TTTCAT TTTCT ATTTTT TTTCT TTTCTTT
1 TTTCT TTTCT TTTCT -TTTCT TTTC-T TTTCT -TTTCT TTTCT TTTC--T
*
26328 TTTCT TTTCT TTTC- TTTCT TTTCTT TTTCT TTTTT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT T
26369 CAAGCATAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
4 10 0.14
5 38 0.55
6 16 0.23
7 5 0.07
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:26328 original size:14 final size:14
Alignment explanation
Indices: 26279--26355 Score: 79
Period size: 14 Copynumber: 5.4 Consensus size: 14
26269 CCTTGACCCC
*
26279 CTTTCTTTTTCTTCT
1 CTTT-TTTTTCTTTT
26294 C-TTTTTTTCATTTT
1 CTTTTTTTTC-TTTT
26308 CTATTTTTTTTCTTTT
1 C--TTTTTTTTCTTTT
26324 C--TTTTTTCTTTT
1 CTTTTTTTTCTTTT
*
26336 CTTTTCTTTCTTTT
1 CTTTTTTTTCTTTT
26350 CTTTTT
1 CTTTTT
26356 CTTTTTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
12 12 0.23
13 6 0.11
14 21 0.40
15 1 0.02
16 5 0.09
17 8 0.15
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTTCTTTT
Found at i:26340 original size:42 final size:42
Alignment explanation
Indices: 26280--26368 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
26270 CTTGACCCCC
26280 TTTC-TTTTTCTTCTCTTTT-TTTCATTTTCTATTTT-TTTTCT
1 TTTCTTTTTTCTTCTCTTTTCTTTC-TTTTCT-TTTTCTTTTCT
* *
26321 TTTCTTTTTTCTTTTCTTTTCTTTCTTTTCTTTTTCTTTTTT
1 TTTCTTTTTTCTTCTCTTTTCTTTCTTTTCTTTTTCTTTTCT
26363 TTTCTT
1 TTTCTT
26369 CAAGCATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 8 0.19
42 31 0.72
43 4 0.09
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (42 bp):
TTTCTTTTTTCTTCTCTTTTCTTTCTTTTCTTTTTCTTTTCT
Done.