Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005802.1 Hibiscus syriacus cultivar Beakdansim tig00013607_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: 66179
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:14641 original size:16 final size:17
Alignment explanation
Indices: 14591--14642 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
14581 AAAACAATTA
14591 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
14608 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
14623 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
14639 AATT
1 AATT
14643 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:15153 original size:30 final size:29
Alignment explanation
Indices: 15113--15174 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
15103 GTTAAAAGTT
*
15113 TTTTTTTTTTTTGTAATT-TTAGGTCCATTC
1 TTTTTATTTTTTG--ATTATTAGGTCCATTC
15143 TTTTTATTTTTTGATTAGTTAGGTCCATTC
1 TTTTTATTTTTTGATTA-TTAGGTCCATTC
15173 TT
1 TT
15175 AATCCATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 3 0.10
30 26 0.90
ACGTcount: A:0.15, C:0.10, G:0.11, T:0.65
Consensus pattern (29 bp):
TTTTTATTTTTTGATTATTAGGTCCATTC
Found at i:16664 original size:30 final size:30
Alignment explanation
Indices: 16630--16692 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
16620 GAATATTAAA
16630 GTTGTGGTGGGAACTCGGATGGGGCAAAGG
1 GTTGTGGTGGGAACTCGGATGGGGCAAAGG
16660 GTTGTGGTGGGAACTCGGATGGGGCAAAGG
1 GTTGTGGTGGGAACTCGGATGGGGCAAAGG
16690 GTT
1 GTT
16693 TTCGTTGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.10, G:0.49, T:0.22
Consensus pattern (30 bp):
GTTGTGGTGGGAACTCGGATGGGGCAAAGG
Found at i:22630 original size:15 final size:15
Alignment explanation
Indices: 22580--22631 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 15
22570 TCTGAAATAT
22580 TATTATTATTT-AAA
1 TATTATTATTTAAAA
22594 TATT-TT-TTGTAAAA
1 TATTATTATT-TAAAA
*
22608 GA--ATTATTTAAAA
1 TATTATTATTTAAAA
22621 TATTATTATTT
1 TATTATTATTT
22632 TTATTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
12 2 0.07
13 11 0.37
14 10 0.33
15 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
TATTATTATTTAAAA
Found at i:25068 original size:19 final size:20
Alignment explanation
Indices: 25019--25068 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
25009 TGTATATATT
25019 TATTTATTTGAGTATATAAA
1 TATTTATTTGAGTATATAAA
**
25039 -ATTTAAGTGAGT-TA-AATA
1 TATTTATTTGAGTATATAA-A
25057 TATTTATTTGAG
1 TATTTATTTGAG
25069 CTTATGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.08
18 3 0.12
19 19 0.79
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (20 bp):
TATTTATTTGAGTATATAAA
Found at i:25288 original size:28 final size:28
Alignment explanation
Indices: 25254--25308 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
25244 TTACTAAAAA
*
25254 AATATTAAAA-ATATTATTTCTTAATACT
1 AATATTAAAAGATATTA-ATCTTAATACT
25282 AATATTAAAATGATATTAATCTTAATA
1 AATATTAAAA-GATATTAATCTTAATA
25309 TTGGTTGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 10 0.42
29 8 0.33
30 6 0.25
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
AATATTAAAAGATATTAATCTTAATACT
Found at i:34682 original size:23 final size:23
Alignment explanation
Indices: 34651--34724 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
34641 TTTACGTTAA
*
34651 TTTATGTTCATTTATTGTGTTCG
1 TTTACGTTCATTTATTGTGTTCG
* *
34674 TTTACGTTCATTCATTTGTGTTCA
1 TTTACGTTCATTTA-TTGTGTTCG
**
34698 TTTACGTTTGTTTATTGTGTTCG
1 TTTACGTTCATTTATTGTGTTCG
34721 TTTA
1 TTTA
34725 TGTTTGTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 24 0.56
24 19 0.44
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (23 bp):
TTTACGTTCATTTATTGTGTTCG
Found at i:34767 original size:24 final size:23
Alignment explanation
Indices: 34650--34767 Score: 101
Period size: 24 Copynumber: 5.0 Consensus size: 23
34640 GTTTACGTTA
*
34650 ATTTATGTTCATTTATTGTGTTC
1 ATTTATGTTCGTTTATTGTGTTC
* * * *
34673 GTTTACGTTCATTCATTTGTGTTC
1 ATTTATGTTCGTTTA-TTGTGTTC
* *
34697 ATTTACGTTTGTTTATTGTGTTC
1 ATTTATGTTCGTTTATTGTGTTC
* * * **
34720 GTTTATGTTTGTTTACATCCGTTC
1 ATTTATGTTCGTTTA-TTGTGTTC
34744 ATTTATGTTCGTTTATTTGTGTTC
1 ATTTATGTTCGTTTA-TTGTGTTC
34768 GTGTATCATT
Statistics
Matches: 75, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
23 33 0.44
24 42 0.56
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (23 bp):
ATTTATGTTCGTTTATTGTGTTC
Found at i:36517 original size:34 final size:35
Alignment explanation
Indices: 36467--36532 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
36457 AAAGAGTGTA
*
36467 TATCTATTTATTATTTAAA-ATTTAAAAGATATTAT
1 TATCTATTTATAATTTAAATA-TTAAAAGATATTAT
*
36502 TATCTATTTA-AATTTATATATTAAAAGATAT
1 TATCTATTTATAATTTAAATATTAAAAGATAT
36533 ATGGTTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (35 bp):
TATCTATTTATAATTTAAATATTAAAAGATATTAT
Found at i:40074 original size:30 final size:27
Alignment explanation
Indices: 40017--40074 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
40007 CCCAAAACAT
**
40017 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
40044 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
40074 T
1 T
40075 TAATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:41070 original size:2 final size:2
Alignment explanation
Indices: 41065--41128 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
41055 TATTTTTTAA
41065 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
41107 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
41129 TTTATTATTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44356 original size:17 final size:18
Alignment explanation
Indices: 44324--44357 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44314 TATTTAAATA
44324 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
44342 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
44358 ACCTTAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:50825 original size:20 final size:21
Alignment explanation
Indices: 50800--50839 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
50790 TTTTGGTGCA
*
50800 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
50820 GAGGGAACCGATTCCCCCCT
1 GAGGGAACCGATTCCCCCCT
50840 GGGGTTCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:55855 original size:29 final size:28
Alignment explanation
Indices: 55801--55861 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
55791 ATATTTTTTT
* *
55801 ATTTTTTTTATTAAAATAATTATTTAAC
1 ATTTTTTTTATAAAAATAAGTATTTAAC
* *
55829 ATTTTATTTTATAAAAATAAGTGTTTAAT
1 ATTTT-TTTTATAAAAATAAGTATTTAAC
55858 ATTT
1 ATTT
55862 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (28 bp):
ATTTTTTTTATAAAAATAAGTATTTAAC
Found at i:58700 original size:46 final size:46
Alignment explanation
Indices: 58630--58720 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
58620 ATAAATAGAT
* *
58630 AATTCTCGATATCCTCTCCAAATTCACTCGAATCAATTAAAGAACC
1 AATTCTCGAGATCCTCTCCAAATTCACTCAAATCAATTAAAGAACC
* *
58676 AATTCTCGAGATCCTCTCCCAATTCACTCAAATCAATTGAAGAAC
1 AATTCTCGAGATCCTCTCCAAATTCACTCAAATCAATTAAAGAAC
58721 TAAGGATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.36, C:0.29, G:0.08, T:0.27
Consensus pattern (46 bp):
AATTCTCGAGATCCTCTCCAAATTCACTCAAATCAATTAAAGAACC
Found at i:64969 original size:19 final size:19
Alignment explanation
Indices: 64918--64969 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 19
64908 ACAACACAGC
64918 TTTTTAATAGAGCATGATAT
1 TTTTTAATAGA-CATGATAT
64938 TTTCTT-ATA-ACATGA-AT
1 TTT-TTAATAGACATGATAT
64955 TTTTTAATATGACAT
1 TTTTTAATA-GACAT
64970 TGTATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.07
17 8 0.29
18 5 0.18
19 5 0.18
20 6 0.21
21 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (19 bp):
TTTTTAATAGACATGATAT
Done.