Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006100.1 Hibiscus syriacus cultivar Beakdansim tig00014457_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: 61461
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1061 original size:20 final size:22
Alignment explanation
Indices: 1036--1076 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1026 AGGACAGGGA
1036 GTATCGATACT-CCTT-TAATG
1 GTATCGATACTACCTTGTAATG
*
1056 GTATCGGTACTACCTTGTAAT
1 GTATCGATACTACCTTGTAAT
1077 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
GTATCGATACTACCTTGTAATG
Found at i:1682 original size:28 final size:29
Alignment explanation
Indices: 1637--1691 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1627 ATGTTTTTTT
* *
1637 TTCCAGTTTAGTGTATAA-CATTTATTCG
1 TTCCAATTTAGTGCATAATCATTTATTCG
*
1665 TTCCAATTTGGTGCATAATCATTTATT
1 TTCCAATTTAGTGCATAATCATTTATT
1692 ACTCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (29 bp):
TTCCAATTTAGTGCATAATCATTTATTCG
Found at i:3047 original size:30 final size:30
Alignment explanation
Indices: 3013--3115 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
3003 TCGTTCCCTG
3013 ACCGAACTAATTCGGTGACCGACTGAATTA
1 ACCGAACTAATTCGGTGACCGACTGAATTA
*
3043 ACCGAACTAATTCGGTGGCCGACTGAATTA
1 ACCGAACTAATTCGGTGACCGACTGAATTA
* *
3073 ACCGAATTAATTCGATGACCGACTGAATTA
1 ACCGAACTAATTCGGTGACCGACTGAATTA
* *
3103 ATCAAACTAATTC
1 ACCGAACTAATTC
3116 AATTCGATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (30 bp):
ACCGAACTAATTCGGTGACCGACTGAATTA
Found at i:16096 original size:7 final size:7
Alignment explanation
Indices: 16084--16109 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16074 TTTGTGACAC
16084 ATCATAA
1 ATCATAA
16091 ATCATAA
1 ATCATAA
16098 ATCATAA
1 ATCATAA
16105 ATCAT
1 ATCAT
16110 CAATTACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCATAA
Found at i:19537 original size:27 final size:27
Alignment explanation
Indices: 19496--19670 Score: 305
Period size: 27 Copynumber: 6.5 Consensus size: 27
19486 GAAAATTGCT
* *
19496 CTGAATCATTTAGAATATACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
*
19523 TTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
19550 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
19577 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
*
19604 CTGAATCATTCAGAATGTACTTCTATA
1 CTGAATCATTCAGAATGTACTTCTATG
*
19631 CTGAATCATTCAGATTGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
19658 CTGAATCATTCAG
1 CTGAATCATTCAG
19671 CGCTATTTTG
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 141 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTATG
Found at i:19751 original size:22 final size:22
Alignment explanation
Indices: 19725--19777 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
19715 GAAACAAACG
19725 CGCTGAATGTTAAACGATTCAA
1 CGCTGAATGTTAAACGATTCAA
19747 CGCTGAATGTTAAACGATTCAA
1 CGCTGAATGTTAAACGATTCAA
19769 CGCTGAATG
1 CGCTGAATG
19778 GTTCCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (22 bp):
CGCTGAATGTTAAACGATTCAA
Found at i:26052 original size:44 final size:47
Alignment explanation
Indices: 25986--26083 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 47
25976 TTATTTTCGT
25986 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
26033 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
26078 TTTTTG
1 TTTTTG
26084 TGGATAACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 28 0.58
45 11 0.23
46 4 0.08
47 5 0.10
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:35751 original size:18 final size:16
Alignment explanation
Indices: 35724--35855 Score: 69
Period size: 18 Copynumber: 7.9 Consensus size: 16
35714 AAGAAGAAAT
35724 AAAA-GAGAAAAAATGA
1 AAAATGAGAAAAAA-GA
35740 GAAAATGAGAAAAAAGA
1 -AAAATGAGAAAAAAGA
35757 AAAATGATGGAAAAAACG-
1 AAAATGA--GAAAAAA-GA
* *
35775 AAAAGGAAAAAAAGAAGAA
1 AAAATG-AGAAAA-AAG-A
35794 AAAATG-GAAAAGGGAAGA
1 AAAATGAGAAAA---AAGA
*
35812 AAAA--ATGAAAAATGA
1 AAAATGA-GAAAAAAGA
* *
35827 AAAAAGAGAAAAATGA
1 AAAATGAGAAAAAAGA
35843 AAAATGA-AAAAAA
1 AAAATGAGAAAAAA
35856 AAGAGAAATA
Statistics
Matches: 94, Mismatches: 7, Indels: 30
0.72 0.05 0.23
Matches are distributed among these distances:
15 12 0.13
16 22 0.23
17 16 0.17
18 33 0.35
19 11 0.12
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (16 bp):
AAAATGAGAAAAAAGA
Found at i:35760 original size:26 final size:25
Alignment explanation
Indices: 35724--35856 Score: 75
Period size: 26 Copynumber: 5.2 Consensus size: 25
35714 AAGAAGAAAT
35724 AAAAGAGAAAAAATGAGAAAATGAGAA
1 AAAAGA-AAAAAATGA-AAAATGAGAA
*
35751 AAAAGAAAAATGATGGAAAAA--ACGAA
1 AAAAGAAAAA-AAT-GAAAAATGA-GAA
35777 AAGGAA-AAAAAGAA-GAAAAAATG-GAA
1 AA--AAGAAAAA-AATG-AAAAATGAGAA
35803 AAGGGAAG-AAAAAATGAAAAAT--GAA
1 AA---AAGAAAAAAATGAAAAATGAGAA
* *
35828 AAAAGAGAAAAATGAAAAATGAAAA
1 AAAAGAAAAAAATGAAAAATGAGAA
35853 AAAA
1 AAAA
35857 AGAGAAATAG
Statistics
Matches: 87, Mismatches: 5, Indels: 30
0.71 0.04 0.25
Matches are distributed among these distances:
22 3 0.03
23 13 0.15
25 13 0.15
26 27 0.31
27 27 0.31
28 4 0.05
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (25 bp):
AAAAGAAAAAAATGAAAAATGAGAA
Found at i:35787 original size:34 final size:34
Alignment explanation
Indices: 35740--35804 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
35730 GAAAAAATGA
* **
35740 GAAAATGAGAAAAAAGAA-AAATGATGGAAAAAAC
1 GAAAAGGA-AAAAAAGAAGAAAAAATGGAAAAAAC
35774 GAAAAGGAAAAAAAGAAGAAAAAATGGAAAA
1 GAAAAGGAAAAAAAGAAGAAAAAATGGAAAA
35805 GGGAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.06
Consensus pattern (34 bp):
GAAAAGGAAAAAAAGAAGAAAAAATGGAAAAAAC
Found at i:35797 original size:19 final size:19
Alignment explanation
Indices: 35775--35823 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
35765 GGAAAAAACG
35775 AAAAGGAAAAAAAGAAGAA
1 AAAAGGAAAAAAAGAAGAA
**
35794 AAAATGG-AAAAGGGAAGAA
1 AAAA-GGAAAAAAAGAAGAA
*
35813 AAAATGAAAAA
1 AAAAGGAAAAA
35824 TGAAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 22 0.88
20 2 0.08
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (19 bp):
AAAAGGAAAAAAAGAAGAA
Found at i:35829 original size:6 final size:7
Alignment explanation
Indices: 35812--35853 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
35802 AAAGGGAAGA
35812 AAAAATG
1 AAAAATG
35819 AAAAATG
1 AAAAATG
*
35826 AAAAAAGAG
1 -AAAAA-TG
35835 AAAAATG
1 AAAAATG
35842 AAAAATG
1 AAAAATG
35849 AAAAA
1 AAAAA
35854 AAAAGAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 20 0.65
8 10 0.32
9 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:35842 original size:23 final size:22
Alignment explanation
Indices: 35720--35854 Score: 85
Period size: 25 Copynumber: 5.5 Consensus size: 22
35710 CTTGAAGAAG
*
35720 AAAT-AAAAGAGAAAAAATGAGA
1 AAATGAAAAAAGAAAAAATGA-A
35742 AAATGAGAAAAAAGAAAAATGATGGAAA
1 AAAT--GAAAAAAGAAAAA--AT-G-AA
* *
35770 AAACGAAAAGGAA-AAAAAGAAGAAA
1 AAATGAAAA--AAGAAAAA-ATG-AA
35795 AAATGGAAAAGGGAAGAAAAAATGAA
1 AAAT-GAAAA---AAGAAAAAATGAA
35821 AAATGAAAAAAGAGAAAAATGAA
1 AAATGAAAAAAGA-AAAAATGAA
35844 AAATGAAAAAA
1 AAATGAAAAAA
35855 AAAGAGAAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 25
0.76 0.04 0.20
Matches are distributed among these distances:
22 8 0.08
23 20 0.21
25 23 0.24
26 18 0.19
27 13 0.14
28 12 0.13
29 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (22 bp):
AAATGAAAAAAGAAAAAATGAA
Found at i:35846 original size:8 final size:8
Alignment explanation
Indices: 35730--35854 Score: 64
Period size: 8 Copynumber: 14.9 Consensus size: 8
35720 AAATAAAAGA
35730 GAAAAAAT
1 GAAAAAAT
*
35738 GAGAAAAT
1 GAAAAAAT
*
35746 GAGAAAAAA
1 GA-AAAAAT
35755 GAAAAATGAT
1 GAAAAA--AT
*
35765 GGAAAAAAC
1 -GAAAAAAT
35774 GAAAAGGAA-
1 GAAAA--AAT
*
35783 -AAAAAGAA
1 GAAAAA-AT
35791 GAAAAAAT
1 GAAAAAAT
35799 GGAAAAGGGAA-
1 -GAAAA---AAT
35810 GAAAAAAT
1 GAAAAAAT
35818 G-AAAAAT
1 GAAAAAAT
35825 GAAAAAA-
1 GAAAAAAT
35832 GAGAAAAAT
1 GA-AAAAAT
35841 G-AAAAAT
1 GAAAAAAT
35848 GAAAAAA
1 GAAAAAA
35855 AAAGAGAAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 36
0.69 0.04 0.27
Matches are distributed among these distances:
6 1 0.01
7 19 0.20
8 39 0.42
9 18 0.19
10 8 0.09
11 6 0.06
12 2 0.02
ACGTcount: A:0.71, C:0.01, G:0.21, T:0.07
Consensus pattern (8 bp):
GAAAAAAT
Found at i:37089 original size:51 final size:51
Alignment explanation
Indices: 37030--37388 Score: 423
Period size: 51 Copynumber: 6.8 Consensus size: 51
37020 ACCCGTTTTA
* *
37030 TGAAGATTGAGTCCTATACTCTCCGAATGAATAGGGAGCGGACAAGTTCGT
1 TGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
37081 TGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
1 TGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
* * * *
37132 TGAAAATTGAGTCCTATACTCTCTGAAGGAATAGGGAACGGACAGGTTTGT
1 TGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
* * * * *
37183 TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTC-A
1 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAAGTTCGT
37238 TGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
1 TGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
* * ** *
37293 TGAAGATTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGT
1 TGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGT
* *
37345 TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCG
1 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCG
37389 AACCCGTTTT
Statistics
Matches: 269, Mismatches: 27, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
51 137 0.51
52 10 0.04
54 7 0.03
55 77 0.29
56 38 0.14
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
TGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT
Found at i:37377 original size:56 final size:56
Alignment explanation
Indices: 37038--37609 Score: 553
Period size: 55 Copynumber: 10.6 Consensus size: 56
37028 TATGAAGATT
* * * ** *
37038 GAGTCCTATACTCTCCGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* ** * *
37089 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAA-A--ATT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* * * *
37140 GAGTCCTATACTCTCTGAAGGAATAGGGAACGGA-CAGGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* * ** *
37195 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCC-ATTTCATGAAGATTGTTT
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* ** *
37250 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
*
37301 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* *
37357 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* * *
37413 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTTGTTGAAGATTGTTA
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* * * *
37469 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTT-ATGAAAATTGTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
* * * * * * *
37524 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTT-ATGAAGATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
*
37579 GAG-TCTTATACT-TCCTGAAGGAATACGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
37610 AGACTCGTCA
Statistics
Matches: 458, Mismatches: 46, Indels: 30
0.86 0.09 0.06
Matches are distributed among these distances:
50 3 0.01
51 122 0.27
52 13 0.03
54 6 0.01
55 164 0.36
56 148 0.32
57 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTGTTGAAGATTGTTC
Done.