Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007211.1 Hibiscus syriacus cultivar Beakdansim tig00019060_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: 55718
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:7956 original size:59 final size:59
Alignment explanation
Indices: 7867--8006 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 59
7857 CGTTAAAAAA
* *
7867 TATT-AAAGTATAC-AAATGGTCCATCGACTATAA-GATAATT-TTTGTTGATTCCAC-CGAC
1 TATTAAAAGT-TACAAAATGATCCATCAACTATAATG--AATTATTTGTTGATT-CACTCGAC
*
7925 TATTAAAAGTTACAAAATGATCCCTCAACTATAATGAATTACTTTGTTGATTCACTCGAC
1 TATTAAAAGTTACAAAATGATCCATCAACTATAATGAATTA-TTTGTTGATTCACTCGAC
*
7985 TATTAAAAGTTAAAAAATGATC
1 TATTAAAAGTTACAAAATGATC
8007 ATTTGACTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
58 11 0.15
59 25 0.35
60 36 0.50
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (59 bp):
TATTAAAAGTTACAAAATGATCCATCAACTATAATGAATTATTTGTTGATTCACTCGAC
Found at i:8405 original size:60 final size:60
Alignment explanation
Indices: 8293--8405 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
8283 ATAGTCAAGT
* * * *
8293 GACCATTTTGTAACTTTTAATAGTCAAGTGACTCGACAAAGCAATTTACTATAGTTGAAA
1 GACCATTTTGTAACTTTTAATAGTAAAGTAACTCAACAAAGCAATATACTATAGTTGAAA
*
8353 GACCATTTTGTAACTTTTAATAGTTAAAG-AACTCAACAAAGCAATATCCTATA
1 GACCATTTTGTAACTTTTAATAG-TAAAGTAACTCAACAAAGCAATATACTATA
8406 ATTAGGGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 43 0.91
61 4 0.09
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTAAAGTAACTCAACAAAGCAATATACTATAGTTGAAA
Found at i:9775 original size:25 final size:26
Alignment explanation
Indices: 9734--9786 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
9724 TTTGGGTGAT
* *
9734 ATAGAAGCTTAATGATTAA-AGATTA
1 ATAGAAGCTTAAGGATTAAGAAATTA
9759 ATAGAAG-TTAAGGGATTAAGAAATTA
1 ATAGAAGCTTAA-GGATTAAGAAATTA
9785 AT
1 AT
9787 GGTGAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 13 0.54
26 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (26 bp):
ATAGAAGCTTAAGGATTAAGAAATTA
Found at i:10223 original size:20 final size:20
Alignment explanation
Indices: 10176--10244 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
10166 AGATGAACAT
*
10176 TATCGATACTGATTGAAGTA-G
1 TATCGATACTGA-TGTAG-AGG
*
10197 CATCGATACTGATGTAGAGG
1 TATCGATACTGATGTAGAGG
**
10217 TATCGATACCAATAGTA-AGG
1 TATCGATACTGAT-GTAGAGG
10237 TATCGATA
1 TATCGATA
10245 TTGTAATTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 26 0.63
21 14 0.34
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (20 bp):
TATCGATACTGATGTAGAGG
Found at i:11480 original size:23 final size:23
Alignment explanation
Indices: 11435--11481 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11425 GGTTCTATAC
* *
11435 GGTCTTTCGGGACAATTTCATGT
1 GGTCATTCGGGACAATCTCATGT
11458 GGTCATTCGGGACAAATCT-ATGT
1 GGTCATTCGGGAC-AATCTCATGT
11481 G
1 G
11482 ACATTTCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (23 bp):
GGTCATTCGGGACAATCTCATGT
Found at i:18857 original size:31 final size:31
Alignment explanation
Indices: 18806--18899 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
18796 CCCGAATGAC
* * *
18806 CAATCCATATATTCCGAAGAACATAGTTAAA
1 CAATCCATATGTCCCAAAGAACATAGTTAAA
*
18837 CAGTCCATATGTCCCAAAGAACATA-TGTAAA
1 CAATCCATATGTCCCAAAGAACATAGT-TAAA
* * *
18868 CAATCCATATGTCCCGAAGAATATAGGTAAA
1 CAATCCATATGTCCCAAAGAACATAGTTAAA
18899 C
1 C
18900 CCTCGACCCT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 52 0.98
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (31 bp):
CAATCCATATGTCCCAAAGAACATAGTTAAA
Found at i:24721 original size:24 final size:23
Alignment explanation
Indices: 24677--24721 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
24667 CCTGTTAGGT
* *
24677 AAAGAAAAATACAAGTTTAATAC
1 AAAGAAAAATACAAATATAATAC
*
24700 AAAGTAAAATACTAAATATAAT
1 AAAGAAAAATAC-AAATATAAT
24722 CCTAACTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAGAAAAATACAAATATAATAC
Found at i:33491 original size:15 final size:15
Alignment explanation
Indices: 33473--33511 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
33463 AGAAGGGTGG
*
33473 TGTTCAGAAGGAGAA
1 TGTTCAAAAGGAGAA
33488 TGTTCAAAAGGAGAA
1 TGTTCAAAAGGAGAA
33503 TGTTCAAAA
1 TGTTCAAAA
33512 TTAAAATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.23
Consensus pattern (15 bp):
TGTTCAAAAGGAGAA
Found at i:38710 original size:18 final size:18
Alignment explanation
Indices: 38687--38723 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
38677 TGAAAATGCA
*
38687 TTTAATAGTTTGTGGGTC
1 TTTAATAGTTTGCGGGTC
38705 TTTAATAGTTTGCGGGTC
1 TTTAATAGTTTGCGGGTC
38723 T
1 T
38724 AACTATCTTC
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:0.08, G:0.27, T:0.49
Consensus pattern (18 bp):
TTTAATAGTTTGCGGGTC
Found at i:40316 original size:692 final size:693
Alignment explanation
Indices: 38985--40369 Score: 2664
Period size: 692 Copynumber: 2.0 Consensus size: 693
38975 TTAGCTACCT
*
38985 CATTTTATTGTGGAGTGATCACGCATGAGAATTCATGAATAATTCCTTTATCCTGAAAAAGGTTG
1 CATTTTATTGTGGAGTGATCACGCATGAAAATTCATGAATAATTCCTTTATCCTGAAAAAGGTTG
39050 AAAGAACTTGATTAGAAAAATCTTTTGTATTTCACAGCAAATTGTGTATGAATCATGTTAAAAAA
66 AAAGAACTTGATTAGAAAAATCTTTTGTATTTCACAGCAAATTGTGTATGAATCATGTTAAAAAA
39115 ATTAGGAAAGATATTGTTTTTTTATAGGAATGGTAGGCCTCATTAAAAGCCCCCTTCATGATTAA
131 ATTAGGAAAGATATTGTTTTTTTATAGGAATGGTAGGCCTCATTAAAAGCCCCCTTCATGATTAA
39180 TGGATCACAAGGTGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGCCTTATAATTCATTAATACC
196 TGGATCACAAGGTGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGCCTTATAATTCATTAATACC
39245 AGAAAGTTACATAATTCTTAAGAAACAAACATACAAGCTCCCTTTACAATAACCAACCCAAAGCC
261 AGAAAGTTACATAATTCTTAAGAAACAAACATACAAGCTCCCTTTACAATAACCAACCCAAAGCC
39310 TAAACGATAACCTAACCAAAACAGTGAAACTAGCCAATACCAGCCTTAGCTAAGTTGTCAGCCTC
326 TAAACGATAACCTAACCAAAACAGTGAAACTAGCCAATACCAGCCTTAGCTAAGTTGTCAGCCTC
39375 AACATTGGCTGACCTAGCAACCCATCTAATAATACCCTTAAAACCTCTTAACTTAGTAACAATGT
391 AACATTGGCTGACCTAGCAACCCATCTAATAATACCCTTAAAACCTCTTAACTTAGTAACAATGT
39440 CTTTCACAAAGTCTACGTAGACATAGGAACAACGATCATTGTTCTTGACCCAATCCACTGCTAGT
456 CTTTCACAAAGTCTACGTAGACATAGGAACAACGATCATTGTTCTTGACCCAATCCACTGCTAGT
*
39505 TTACTGTCAGATTCAACAATTAAACGTTCCTTAAACCGCTGCTGAATCGAAGCAAAGAAAGTTAA
521 TTACTGTCAGATTCAACAATTAAACGTTCCTTAAACCGCTGCTAAATCGAAGCAAAGAAAGTTAA
*
39570 ACCCTTTTTAATTGCCATAAGCTCTATCAAAATAGGAGGACCTGGACTAGCAGCCTCTTGGAAAG
586 ACCCTTTTTAATTGCCATAAGCTCTATCAAAATAGGAGGACCTGGACCAGCAGCCTCTTGGAAAG
39635 AACCCACCACCGAGCCATCCTCAACTCTTAGAATGCCCCCAAC
651 AACCCACCACCGAGCCATCCTCAACTCTTAGAATGCCCCCAAC
* *
39678 CATTTTATTGTGGAGTGATCACGCATGAAAATTCATGAATAGTTCCTTTATCTTGAAAAAGGTTG
1 CATTTTATTGTGGAGTGATCACGCATGAAAATTCATGAATAATTCCTTTATCCTGAAAAAGGTTG
39743 AAAGAACTTGATTAGAAAAATCTTTTGTATTTCACAGCAAATTGTGTATGAATCATGTTAAAAAA
66 AAAGAACTTGATTAGAAAAATCTTTTGTATTTCACAGCAAATTGTGTATGAATCATGTTAAAAAA
39808 ATTAGGAAAGATATTGTTTTTTTATAGGAATGGTAGGCCTCATTAAAAG-CCCCTTCATGATTAA
131 ATTAGGAAAGATATTGTTTTTTTATAGGAATGGTAGGCCTCATTAAAAGCCCCCTTCATGATTAA
**
39872 TGGATCACAAGGTGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGTTTTATAATTCATTAATACC
196 TGGATCACAAGGTGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGCCTTATAATTCATTAATACC
* *
39937 CGAAAGTTACATAATTCTTAAGAAACAAACATACAAGCTCCCTTTACAATAACCAACCCAAAGCT
261 AGAAAGTTACATAATTCTTAAGAAACAAACATACAAGCTCCCTTTACAATAACCAACCCAAAGCC
40002 TAAACGATAACCTAACCAAAACAGTGAAACTAGCCAATACCAGCCTTAGCTAAGTTGTCAGCCTC
326 TAAACGATAACCTAACCAAAACAGTGAAACTAGCCAATACCAGCCTTAGCTAAGTTGTCAGCCTC
*
40067 AACATTGGCTGACCTAGCAACCCATCTAATAATACCCTTCAAACCTCTTAACTTAGTAACAATGT
391 AACATTGGCTGACCTAGCAACCCATCTAATAATACCCTTAAAACCTCTTAACTTAGTAACAATGT
40132 CTTTCACAAAGTCTACGTAGACATAGGAACAACGATCATTGTTCTTGACCCAATCCACTGCTAGT
456 CTTTCACAAAGTCTACGTAGACATAGGAACAACGATCATTGTTCTTGACCCAATCCACTGCTAGT
*
40197 TTACTGTCAGATTCAACAATTAAACGTTCCTTAAACCGCTGCTAAATCGAAGCAAAGAGAGTTAA
521 TTACTGTCAGATTCAACAATTAAACGTTCCTTAAACCGCTGCTAAATCGAAGCAAAGAAAGTTAA
40262 ACCCTTTTTAATTGCCATAAGCTCTATCAAAATAGGAGGACCTGGACCAGCAGCCTCTTGGAAAG
586 ACCCTTTTTAATTGCCATAAGCTCTATCAAAATAGGAGGACCTGGACCAGCAGCCTCTTGGAAAG
40327 AACCCACCACCGAGCCATCCTCAACTCTTAGAATGCCCCCAAC
651 AACCCACCACCGAGCCATCCTCAACTCTTAGAATGCCCCCAAC
40370 ACCACTTTTC
Statistics
Matches: 681, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
692 505 0.74
693 176 0.26
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (693 bp):
CATTTTATTGTGGAGTGATCACGCATGAAAATTCATGAATAATTCCTTTATCCTGAAAAAGGTTG
AAAGAACTTGATTAGAAAAATCTTTTGTATTTCACAGCAAATTGTGTATGAATCATGTTAAAAAA
ATTAGGAAAGATATTGTTTTTTTATAGGAATGGTAGGCCTCATTAAAAGCCCCCTTCATGATTAA
TGGATCACAAGGTGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGCCTTATAATTCATTAATACC
AGAAAGTTACATAATTCTTAAGAAACAAACATACAAGCTCCCTTTACAATAACCAACCCAAAGCC
TAAACGATAACCTAACCAAAACAGTGAAACTAGCCAATACCAGCCTTAGCTAAGTTGTCAGCCTC
AACATTGGCTGACCTAGCAACCCATCTAATAATACCCTTAAAACCTCTTAACTTAGTAACAATGT
CTTTCACAAAGTCTACGTAGACATAGGAACAACGATCATTGTTCTTGACCCAATCCACTGCTAGT
TTACTGTCAGATTCAACAATTAAACGTTCCTTAAACCGCTGCTAAATCGAAGCAAAGAAAGTTAA
ACCCTTTTTAATTGCCATAAGCTCTATCAAAATAGGAGGACCTGGACCAGCAGCCTCTTGGAAAG
AACCCACCACCGAGCCATCCTCAACTCTTAGAATGCCCCCAAC
Found at i:55646 original size:21 final size:21
Alignment explanation
Indices: 55622--55664 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
55612 CACTTTTAAC
55622 ATTTGTTCTC-TTAATTTATTT
1 ATTT-TTCTCTTTAATTTATTT
55643 ATTTTTCTCTTTAATTTATTT
1 ATTTTTCTCTTTAATTTATTT
55664 A
1 A
55665 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTCTCTTTAATTTATTT
Done.