Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002767.1 Hibiscus syriacus cultivar Beakdansim tig00005704_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: 66289
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12739 original size:2 final size:2
Alignment explanation
Indices: 12732--12759 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12722 AAACATATCT
12732 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
12760 CATTGTTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13685 original size:90 final size:89
Alignment explanation
Indices: 13540--13705 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 89
13530 CTTTTATAGC
*
13540 CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTATTTAATT
1 CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
* *
13605 GGAATTTAATAATACTCTTATATT
66 GAAATTAAATAATACTCTTATATT
13629 CAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1 CAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
13694 TGAAATTAAATA
65 TGAAATTAAATA
13706 TTCAGGATTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 24 0.33
90 49 0.67
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
GAAATTAAATAATACTCTTATATT
Found at i:14889 original size:20 final size:20
Alignment explanation
Indices: 14864--14905 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14854 TTGGCTTGCT
*
14864 TTCTTTT-TTAATTTTTTCTC
1 TTCTTTTCTGAATTTTTT-TC
14884 TTCTTTTCTGAATTTTTTTC
1 TTCTTTTCTGAATTTTTTTC
14904 TT
1 TT
14906 TTTGTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTTCTGAATTTTTTTC
Found at i:18737 original size:28 final size:28
Alignment explanation
Indices: 18692--18753 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
18682 CAGAATTGTT
18692 CAAAATAACCAAAATTACCCTCAAGCTC
1 CAAAATAACCAAAATTACCCTCAAGCTC
* * * *
18720 CAAAATAATCGAATTTACCCTCGAGCTC
1 CAAAATAACCAAAATTACCCTCAAGCTC
*
18748 CGAAAT
1 CAAAAT
18754 GAATTAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (28 bp):
CAAAATAACCAAAATTACCCTCAAGCTC
Found at i:19608 original size:40 final size:40
Alignment explanation
Indices: 19559--19652 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
19549 ATATTAAGCC
* * *
19559 TTTGTTATGGATACTCAGT-CTACACTATAGAGACTAGTTT
1 TTTGGTATGGAGACT-AGTCCTACACTATAGAGACCAGTTT
****
19599 TTTGGTATGGAGACTAGTCCTTTGGTATAGAGACCAGTTT
1 TTTGGTATGGAGACTAGTCCTACACTATAGAGACCAGTTT
*
19639 TTTGGTATAGAGAC
1 TTTGGTATGGAGAC
19653 CAGTAGTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
39 3 0.07
40 42 0.93
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (40 bp):
TTTGGTATGGAGACTAGTCCTACACTATAGAGACCAGTTT
Found at i:19613 original size:20 final size:20
Alignment explanation
Indices: 19584--19652 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
19574 CAGTCTACAC
19584 TATAGAGACTAGTTTTTTGG
1 TATAGAGACTAGTTTTTTGG
* **
19604 TATGGAGACTAGTCCTTTGG
1 TATAGAGACTAGTTTTTTGG
*
19624 TATAGAGACCAGTTTTTTGG
1 TATAGAGACTAGTTTTTTGG
19644 TATAGAGAC
1 TATAGAGAC
19653 CAGTAGTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (20 bp):
TATAGAGACTAGTTTTTTGG
Found at i:30155 original size:11 final size:11
Alignment explanation
Indices: 30139--30173 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30129 GCTTTTAAGA
30139 TAACTTAAGCT
1 TAACTTAAGCT
30150 TAACTTAAGCT
1 TAACTTAAGCT
**
30161 TTCCTTAAGCT
1 TAACTTAAGCT
30172 TA
1 TA
30174 GTTATCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (11 bp):
TAACTTAAGCT
Found at i:39744 original size:19 final size:20
Alignment explanation
Indices: 39720--39757 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39710 CAAAATAGCC
39720 CAATTTC-ACATTATAACAT
1 CAATTTCAACATTATAACAT
*
39739 CAATTTCAACATTCTAACA
1 CAATTTCAACATTATAACA
39758 CTAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (20 bp):
CAATTTCAACATTATAACAT
Found at i:49872 original size:22 final size:22
Alignment explanation
Indices: 49837--49918 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
49827 TTCTCTTCCA
*
49837 CAGTGCTATGGCACTTTTGTAT
1 CAGTGCTAAGGCACTTTTGTAT
* *
49859 CAGTGCGAATGCACTTTTGTAT
1 CAGTGCTAAGGCACTTTTGTAT
* *
49881 CTGTGCTAAGGCACTTTGGTAT
1 CAGTGCTAAGGCACTTTTGTAT
*
49903 TAGTGCTAAGGCACTT
1 CAGTGCTAAGGCACTT
49919 CCATGATTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (22 bp):
CAGTGCTAAGGCACTTTTGTAT
Found at i:53596 original size:42 final size:42
Alignment explanation
Indices: 53534--53661 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
53524 GCTTACACAC
* *
53534 AAAAATT-CTACTCGAATTATCATTTGATCATAAAATTCCCA
1 AAAAATTGCTTCTCGAATTATCATTTGACCATAAAATTCCCA
* * *
53575 AAAAATTGCTTCTCAAATTATCATTTCACCATAAAATT-CAA
1 AAAAATTGCTTCTCGAATTATCATTTGACCATAAAATTCCCA
*
53616 AAAAACTTGCTTCCCGAATTATCATTTGACCATAAAAGTTCCCA
1 AAAAA-TTGCTTCTCGAATTATCATTTGACCATAAAA-TTCCCA
53660 AA
1 AA
53662 GAAGGTGGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 14 0.19
42 54 0.73
43 2 0.03
44 4 0.05
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.32
Consensus pattern (42 bp):
AAAAATTGCTTCTCGAATTATCATTTGACCATAAAATTCCCA
Found at i:54234 original size:49 final size:49
Alignment explanation
Indices: 54162--54260 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
54152 AAGAAGGCAC
54162 TCACTTTGTTGCATATCATGTGAATAGAGATGATCACGGGTGAGATATG
1 TCACTTTGTTGCATATCATGTGAATAGAGATGATCACGGGTGAGATATG
54211 TCACTTTGTTGCATATCATGTGAATAGAGATGATCACGGGTGAGATATG
1 TCACTTTGTTGCATATCATGTGAATAGAGATGATCACGGGTGAGATATG
54260 T
1 T
54261 TTTTGACTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.33
Consensus pattern (49 bp):
TCACTTTGTTGCATATCATGTGAATAGAGATGATCACGGGTGAGATATG
Found at i:59738 original size:32 final size:32
Alignment explanation
Indices: 59697--59817 Score: 181
Period size: 32 Copynumber: 3.8 Consensus size: 32
59687 ACTGACTCTC
*
59697 TTATGCATTATCTGAATTCAATACTAACTTTG
1 TTATGCATTATCTGAATGCAATACTAACTTTG
*
59729 TTATGCATTATCTGAATGCAATACTAGCTTTG
1 TTATGCATTATCTGAATGCAATACTAACTTTG
*
59761 TTATGCATTATCTGAATGCAATACTAACTCTG
1 TTATGCATTATCTGAATGCAATACTAACTTTG
* *
59793 CTATGCATTAT-TAGAATGCCATACT
1 TTATGCATTATCT-GAATGCAATACT
59818 GATTCTACTA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 1 0.01
32 81 0.99
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (32 bp):
TTATGCATTATCTGAATGCAATACTAACTTTG
Found at i:59829 original size:32 final size:32
Alignment explanation
Indices: 59698--59831 Score: 144
Period size: 32 Copynumber: 4.2 Consensus size: 32
59688 CTGACTCTCT
* * **
59698 TATGCATTATCTGAATTCAATACTAACTTTGT
1 TATGCATTATCTGAATGCAATACTAACTCTAC
* * **
59730 TATGCATTATCTGAATGCAATACTAGCTTTGT
1 TATGCATTATCTGAATGCAATACTAACTCTAC
*
59762 TATGCATTATCTGAATGCAATACTAACTCTGC
1 TATGCATTATCTGAATGCAATACTAACTCTAC
* * *
59794 TATGCATTAT-TAGAATGCCATACTGATTCTAC
1 TATGCATTATCT-GAATGCAATACTAACTCTAC
59826 TATGCA
1 TATGCA
59832 ACACATAAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 1 0.01
32 91 0.99
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (32 bp):
TATGCATTATCTGAATGCAATACTAACTCTAC
Found at i:59830 original size:64 final size:64
Alignment explanation
Indices: 59698--59831 Score: 173
Period size: 64 Copynumber: 2.1 Consensus size: 64
59688 CTGACTCTCT
* * * * **
59698 TATGCATTATCTGAATTCAATACTAACTTTGTTATGCATTATCTGAATGCAATACTAGCTTTGT
1 TATGCATTATCTGAATGCAATACTAACTCTGCTATGCATTATCTGAATGCAATACTAGATTTAC
*
59762 TATGCATTATCTGAATGCAATACTAACTCTGCTATGCATTAT-TAGAATGCCATACT-GATTCTA
1 TATGCATTATCTGAATGCAATACTAACTCTGCTATGCATTATCT-GAATGCAATACTAGATT-TA
59825 C
64 C
59826 TATGCA
1 TATGCA
59832 ACACATAAGC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
63 4 0.07
64 57 0.93
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (64 bp):
TATGCATTATCTGAATGCAATACTAACTCTGCTATGCATTATCTGAATGCAATACTAGATTTAC
Found at i:61025 original size:21 final size:21
Alignment explanation
Indices: 61001--61054 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
60991 CCTAATTTTA
61001 CCAGTATCGATATTATTTATC
1 CCAGTATCGATATTATTTATC
*
61022 CCAGTATCGATATTGTTTATC
1 CCAGTATCGATATTATTTATC
*
61043 CTAGTATCGATA
1 CCAGTATCGATA
61055 CTCGAACCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (21 bp):
CCAGTATCGATATTATTTATC
Done.