Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008811.1 Hibiscus syriacus cultivar Beakdansim tig00111969_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: 45480
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7332 original size:81 final size:81
Alignment explanation
Indices: 7193--7595 Score: 517
Period size: 81 Copynumber: 5.0 Consensus size: 81
7183 TATTTTAAAA
* *
7193 TAAAA-ATTAATTGCCTAGTTGTGCATT-GACAGAAAGATGTCAATCATGCCAGTTAGATGACAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTGGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
7256 GTCAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
7272 TAAAAGATTAATTGCCCAGTTGTGCATTGGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTGGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
7337 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * ** * *
7353 TTAAAA-ATTAATTACCTAGATATGTATTTTACATAAATGTGTCAATCATGCCAGTTAGATGAAA
1 -TAAAAGATTAATTGCCTAGTTGTGCATTGGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAA
7417 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * *
7434 TAAAAGATTAATTGCCTAGTAGTGCATTTGACAGAAAGATGTAAATCATGCCAGTTAGATGAGAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTGGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
7499 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
** * * **
7515 TAAAAGATTAATTGCCTAACTATGCATTTGG-CAGAAAGGTGTCAATAATGAAAGTTAGAGATGA
1 TAAAAGATTAATTGCCTAGTTGTGCA-TTGGACAGAAAGGTGTCAATCATGCCAGTT--AGATGA
*
7579 AAGGTTAAATGCCTTTG
63 AAGGTTAAATACCTTTG
7596 GCATGAAAGG
Statistics
Matches: 279, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
79 5 0.02
80 26 0.09
81 219 0.78
82 8 0.03
83 21 0.08
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGTTGTGCATTGGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:7667 original size:46 final size:46
Alignment explanation
Indices: 7595--7795 Score: 260
Period size: 46 Copynumber: 4.4 Consensus size: 46
7585 AAATGCCTTT
*
7595 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTACATTATA
* * * * * *
7641 GGCATAAAAGGATACCATAAAAGAAAATACATAACGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTACATTATA
*** *
7687 GGCATGAAAGGATGCCATAAATGAAAATGCATAACAACATATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTACATTATA
* * *
7733 GGCATGAAATGG-TGCCATAAATGAAAATGCTTAACGGTACATAATT
1 GGCATGAAA-GGATGCCATAAATGAAAATGCATAACGGTACATTATA
7779 GGCATGAAAGGATGCCA
1 GGCATGAAAGGATGCCA
7796 CCAACGAAAA
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
45 2 0.02
46 127 0.97
47 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTACATTATA
Found at i:7821 original size:92 final size:92
Alignment explanation
Indices: 7593--7822 Score: 273
Period size: 92 Copynumber: 2.5 Consensus size: 92
7583 TTAAATGCCT
* **
7593 TTGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATAAAAGGATACCA
1 TTGGCATGAAAGGATGCCATAAATGAAAATGCATAACGATATATTATAGGCATAAAAGGATACCA
* *
7658 TAAAAGAAAATACATAACGGTGCATTA
66 TAAAAGAAAATACATAACGGTACATAA
* * * * *
7685 TCGGCATGAAAGGATGCCATAAATGAAAATGCATAACAACATATTATAGGCATGAAATGG-TGCC
1 TTGGCATGAAAGGATGCCATAAATGAAAATGCATAACGATATATTATAGGCAT-AAAAGGATACC
* * *
7749 ATAAATGAAAATGCTTAACGGTACATAA
65 ATAAAAGAAAATACATAACGGTACATAA
** * * * *
7777 TTGGCATGAAAGGATGCCACCAACGAAAATACATAATGTTATATTA
1 TTGGCATGAAAGGATGCCATAAATGAAAATGCATAACGATATATTA
7823 ACGGGACACT
Statistics
Matches: 115, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
92 110 0.96
93 5 0.04
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (92 bp):
TTGGCATGAAAGGATGCCATAAATGAAAATGCATAACGATATATTATAGGCATAAAAGGATACCA
TAAAAGAAAATACATAACGGTACATAA
Found at i:13126 original size:81 final size:81
Alignment explanation
Indices: 12987--13225 Score: 345
Period size: 81 Copynumber: 3.0 Consensus size: 81
12977 TGTTTTAAAA
* * * *
12987 TAAAAGATTAATTGCCTAGTTATGCATTTGACAGAAAGGTGTTAATCATTCCAGTTAGATGAAAA
1 TAAAAGATTAATTGACTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAA
13052 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
13068 TAATAGATTAATTGTCTAGTTGTGCATTGGACAGAAAGGTGTCAGTCATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGACTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAA
13133 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
13149 TAAAAGATTAATTGACTAGCTGTGCATTTGACAGAAATGTGTCAATCATGCTAGTTAGATG-AAA
1 TAAAAGATTAATTGACTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAA
*
13213 GTTTAAATGCCTT
66 G-TTAAATACCTT
13226 CAGCATGAAA
Statistics
Matches: 140, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 3 0.02
81 137 0.98
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGACTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAA
GTTAAATACCTTTGAG
Found at i:13294 original size:46 final size:45
Alignment explanation
Indices: 13228--13443 Score: 272
Period size: 46 Copynumber: 4.7 Consensus size: 45
13218 AATGCCTTCA
* * *
13228 GCATGAAAGGATGCGATAAATGAACATGCATAATGGTGCATTATAA
1 GCATGAAAGGATGC-ATAAATGAAAATGCATAACGGTGCATTATAG
*
13274 GCATGAAAGGATGCAATAAATGAAAATGCATAACGGTGCATTATCG
1 GCATGAAAGGATGC-ATAAATGAAAATGCATAACGGTGCATTATAG
* * *
13320 GCATGAAAGGATTTCATAAATGAAAATGCATAACGATACATTATAG
1 GCATGAAAGGA-TGCATAAATGAAAATGCATAACGGTGCATTATAG
* *
13366 GCATGAAAGGATGTCATAAATGAAAATGC-TAACGGTGCATAATTG
1 GCATGAAAGGATG-CATAAATGAAAATGCATAACGGTGCATTATAG
** *
13411 GCATGAAAGGATGCGACCAATGAAAATACATAA
1 GCATGAAAGGATGC-ATAAATGAAAATGCATAA
13444 TGGTATATTA
Statistics
Matches: 149, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.01
45 37 0.25
46 109 0.73
47 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (45 bp):
GCATGAAAGGATGCATAAATGAAAATGCATAACGGTGCATTATAG
Found at i:18040 original size:13 final size:13
Alignment explanation
Indices: 18019--18082 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
18009 AATGACGCTC
18019 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
18032 AATGTGCGTCATG
1 AATGCGCGTCATA
* *
18045 AATGTGAGTCATA
1 AATGCGCGTCATA
* *
18058 AATGCGTGTCATC
1 AATGCGCGTCATA
18071 AATGCGCGTCAT
1 AATGCGCGTCAT
18083 CTAAGATTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:18043 original size:85 final size:85
Alignment explanation
Indices: 17885--18043 Score: 187
Period size: 85 Copynumber: 1.9 Consensus size: 85
17875 CAATCACAAT
* * * * * *
17885 ACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTGAGTCATACAT
1 ACACAAATATGTGTCATCTTATTTAATGACGTGGGCTTCAATGACACGCAATGCGAGTCATAAAT
*
17950 GCGTGTCATAAATTTATGAC
66 GCGCGTCATAAATTTATGAC
* * *
17970 ACACAAATATGTGTCATCTTCATTT-ATGACAG-GGGCTTCAATGACGCTCAATGCGCGTCATAA
1 ACACAAATATGTGTCATCTT-ATTTAATGAC-GTGGGCTTCAATGACACGCAATGCGAGTCATAA
*
18033 ATGTGCGTCAT
64 ATGCGCGTCAT
18044 GAATGTGAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
85 57 0.93
86 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (85 bp):
ACACAAATATGTGTCATCTTATTTAATGACGTGGGCTTCAATGACACGCAATGCGAGTCATAAAT
GCGCGTCATAAATTTATGAC
Found at i:18048 original size:26 final size:26
Alignment explanation
Indices: 18017--18082 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
18007 TCAATGACGC
*
18017 TCAATGCGCGTCATAAATGTGCGTCA
1 TCAATGCGCGTCATAAATGCGCGTCA
* * * *
18043 TGAATGTGAGTCATAAATGCGTGTCA
1 TCAATGCGCGTCATAAATGCGCGTCA
18069 TCAATGCGCGTCAT
1 TCAATGCGCGTCAT
18083 CTAAGATTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (26 bp):
TCAATGCGCGTCATAAATGCGCGTCA
Found at i:22786 original size:60 final size:59
Alignment explanation
Indices: 22625--22786 Score: 138
Period size: 59 Copynumber: 2.7 Consensus size: 59
22615 CAAAGGGCAT
* * * *
22625 AGGTGCCAACCTAAGGGAGCACCTT-GGGTCCATAAGGTCTTA-CCACAGCCGAAGCAT
1 AGGTGCCACCCTAAGGGGGTACCTTAGGGTCCATAAGGTCTTACCCACAGCCGAAGCAG
* * * * *
22682 AGGTGCC-CACCTAAGGGGAGTGCCCTCA-TGCCCATAAGGACTTACCCA-ATGCAC-ATAGCAG
1 AGGTGCCAC-CCTAAGGGG-GT-ACCTTAGGGTCCATAAGGTCTTACCCACA-GC-CGA-AGCAG
*
22743 AGGTGCCACCCTAAGGGGGTACCTTAGGGTCCATAAAGTCTTAC
1 AGGTGCCACCCTAAGGGGGTACCTTAGGGTCCATAAGGTCTTAC
22787 TAGACCCATT
Statistics
Matches: 80, Mismatches: 15, Indels: 17
0.71 0.13 0.15
Matches are distributed among these distances:
57 15 0.19
58 1 0.01
59 21 0.26
60 21 0.26
61 21 0.26
62 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (59 bp):
AGGTGCCACCCTAAGGGGGTACCTTAGGGTCCATAAGGTCTTACCCACAGCCGAAGCAG
Found at i:25227 original size:8 final size:8
Alignment explanation
Indices: 25216--25244 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
25206 CCAAAAAAGC
25216 CAAAATTT
1 CAAAATTT
25224 CAAAATTT
1 CAAAATTT
25232 CAAAATTT
1 CAAAATTT
25240 CAAAA
1 CAAAA
25245 AATTGCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (8 bp):
CAAAATTT
Found at i:34941 original size:35 final size:35
Alignment explanation
Indices: 34898--34967 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
34888 TCCTTAGGTC
*
34898 TATAAGGAATTAGCA-TTTCAATCGATCTAAACCTA
1 TATAAGGAATTACCAGTTT-AATCGATCTAAACCTA
* *
34933 TATAAGGAATTACCAGTTTGATCGATCTGAACCTA
1 TATAAGGAATTACCAGTTTAATCGATCTAAACCTA
34968 AAGAAACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (35 bp):
TATAAGGAATTACCAGTTTAATCGATCTAAACCTA
Found at i:35562 original size:14 final size:15
Alignment explanation
Indices: 35527--35563 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
35517 AGTTATTGAC
35527 CTTAAATTAAATGAA
1 CTTAAATTAAATGAA
*
35542 CTT-AATTAAAT-TA
1 CTTAAATTAAATGAA
35555 CTTAAATTA
1 CTTAAATTA
35564 TATATGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 13 0.65
15 3 0.15
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (15 bp):
CTTAAATTAAATGAA
Found at i:38563 original size:20 final size:20
Alignment explanation
Indices: 38525--38563 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38515 CAGAGGGTAC
*
38525 CGATTCCCCCCATGACGTAT
1 CGATTCCCCCCATCACGTAT
* *
38545 CGATTCCCCTCATCTCGTA
1 CGATTCCCCCCATCACGTA
38564 ACGGTCGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.41, G:0.13, T:0.28
Consensus pattern (20 bp):
CGATTCCCCCCATCACGTAT
Found at i:44709 original size:22 final size:23
Alignment explanation
Indices: 44651--44715 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
44641 TAGTGCATGA
*
44651 GGAATCGATGCCCCC-TTGAAGG
1 GGAATCGATTCCCCCTTTGAAGG
* *
44673 GGAA-CTGATT-TCCCTTTG-ATG
1 GGAATC-GATTCCCCCTTTGAAGG
44694 GGAATCGATTCCCCCTTT-AAGG
1 GGAATCGATTCCCCCTTTGAAGG
44716 AATCGACACC
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGAATCGATTCCCCCTTTGAAGG
Found at i:45199 original size:13 final size:13
Alignment explanation
Indices: 45181--45213 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
45171 CGTATATTGA
45181 TTTCAAACCTT-GT
1 TTTCAAA-CTTAGT
45194 TTTCAAACTTAGT
1 TTTCAAACTTAGT
45207 TTTCAAA
1 TTTCAAA
45214 ATTGCCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTCAAACTTAGT
Done.