Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006534.1 Hibiscus syriacus cultivar Beakdansim tig00015941_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: 56220
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:20709 original size:8 final size:8
Alignment explanation
Indices: 20694--20735 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
20684 AAATGAGAAG
20694 GAAA-GAA
1 GAAATGAA
20701 GAAATGAA
1 GAAATGAA
20709 GAAATGAA
1 GAAATGAA
20717 GAAATGAA
1 GAAATGAA
*
20725 GAAAAGAA
1 GAAATGAA
20733 GAA
1 GAA
20736 GATAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 4 0.12
8 29 0.88
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.07
Consensus pattern (8 bp):
GAAATGAA
Found at i:27466 original size:65 final size:65
Alignment explanation
Indices: 27379--27532 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 65
27369 ACTAGGAGTA
* * *
27379 CATCGGTACACT-AATTACATTCGATGTTTCAAACA-AGTC-AGTAGTGCATCGATGCATATCAT
1 CATCGGTACA-TAAAATGCATTCGATGTTTCAAA-ATAGTCAAG-AGTGCATCGATGCATAGCAT
27441 GTG
63 GTG
* * *
27444 CATCGGTACATAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTGTG
1 CATCGGTACATAAAATGCATTCGATGTTTCAAAATAGTCAAGAGTGCATCGATGCATAGCATGTG
* *
27509 CATCGATACACAAAATGCATTCGA
1 CATCGGTACATAAAATGCATTCGA
27533 AATGGGTGTG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
64 2 0.03
65 74 0.95
66 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (65 bp):
CATCGGTACATAAAATGCATTCGATGTTTCAAAATAGTCAAGAGTGCATCGATGCATAGCATGTG
Found at i:29715 original size:18 final size:18
Alignment explanation
Indices: 29684--29718 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29674 AGTTTTCATG
29684 AAAACAACATAATTGAAT
1 AAAACAACATAATTGAAT
29702 AAAA-AACATCAATTGAA
1 AAAACAACAT-AATTGAA
29719 ACAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAACAACATAATTGAAT
Found at i:30237 original size:23 final size:23
Alignment explanation
Indices: 30211--30280 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
30201 TGTATCGATG
30211 CACATTCAAGGGATGCATCGGTA
1 CACATTCAAGGGATGCATCGGTA
* * * * *
30234 CACACTCTA--G-TGTATCGATG
1 CACATTCAAGGGATGCATCGGTA
30254 CACATTCAAGGGATGCATCGGTA
1 CACATTCAAGGGATGCATCGGTA
30277 CACA
1 CACA
30281 CTCTAGTGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 1 0.03
23 18 0.53
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (23 bp):
CACATTCAAGGGATGCATCGGTA
Found at i:30257 original size:20 final size:20
Alignment explanation
Indices: 30234--30298 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
30224 TGCATCGGTA
30234 CACACTCTAGTGTATCGATG
1 CACACTCTAGTGTATCGATG
* * * * *
30254 CACATTCAAGGGATGCATCGGTA
1 CACACTCTA--G-TGTATCGATG
30277 CACACTCTAGTGTATCGATG
1 CACACTCTAGTGTATCGATG
30297 CA
1 CA
30299 TTATGCACAA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
20 16 0.50
21 1 0.03
22 1 0.03
23 14 0.44
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (20 bp):
CACACTCTAGTGTATCGATG
Found at i:30260 original size:43 final size:43
Alignment explanation
Indices: 30155--30298 Score: 200
Period size: 43 Copynumber: 3.3 Consensus size: 43
30145 TGCACAGTAG
* * ** * *
30155 AGTGCATCGATGCACATTCAAGGAATAAATTGGTGCAC-CTTCAT
1 AGTGTATCGATGCACATTCAAGGGATGCATCGGTACACAC-TC-T
*
30199 GGTGTATCGATGCACATTCAAGGGATGCATCGGTACACACTCT
1 AGTGTATCGATGCACATTCAAGGGATGCATCGGTACACACTCT
30242 AGTGTATCGATGCACATTCAAGGGATGCATCGGTACACACTCT
1 AGTGTATCGATGCACATTCAAGGGATGCATCGGTACACACTCT
30285 AGTGTATCGATGCA
1 AGTGTATCGATGCA
30299 TTATGCACAA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
43 57 0.63
44 33 0.36
45 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGGATGCATCGGTACACACTCT
Found at i:30701 original size:15 final size:15
Alignment explanation
Indices: 30681--30714 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30671 ATATCTTCTT
*
30681 TAATGACATGATCTC
1 TAATGAAATGATCTC
*
30696 TAATGAAATGATGTC
1 TAATGAAATGATCTC
30711 TAAT
1 TAAT
30715 TTCAATGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (15 bp):
TAATGAAATGATCTC
Found at i:33705 original size:30 final size:30
Alignment explanation
Indices: 33671--33731 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
33661 TATATTAAAA
33671 TTTGATTTTTGGTACCCAATTTCTTTTGGG
1 TTTGATTTTTGGTACCCAATTTCTTTTGGG
33701 TTTGATTTTTGGTACCCAATTTCTTTTGGG
1 TTTGATTTTTGGTACCCAATTTCTTTTGGG
33731 T
1 T
33732 CCATATTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.54
Consensus pattern (30 bp):
TTTGATTTTTGGTACCCAATTTCTTTTGGG
Found at i:34162 original size:22 final size:21
Alignment explanation
Indices: 34120--34159 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
34110 AAGACTATTT
34120 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
34141 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
34160 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:36164 original size:19 final size:19
Alignment explanation
Indices: 36140--36183 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
36130 CAAGCCAGGA
36140 GTGCATCGATGCATGGCAT
1 GTGCATCGATGCATGGCAT
36159 GTGCATCGATGCATGGCAT
1 GTGCATCGATGCATGGCAT
36178 GTGCAT
1 GTGCAT
36184 TGGTACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCAT
Found at i:36226 original size:84 final size:84
Alignment explanation
Indices: 36094--36250 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 84
36084 TACACTAGGA
* * *
36094 GTGCATCGGTACACTAATTACATTCGATGTTTCAAACAAGCCAGGAGTGCATCGATGCATGGCAT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAACAAGCCAAGAGTGCATCGATGCATGGCAT
36159 GTGCATCGATGCATGGCAT
66 GTGCATCGATGCATGGCAT
* ** *
36178 GTGCATTGGTACACAAAATACATTCGATGTTTCAAA-ATATTCAAGAGTGCATCGATGCATGGCT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAACA-AGCCAAGAGTGCATCGATGCATGGCA
*
36242 TGTTCATCG
65 TGTGCATCG
36251 GTACACAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.02
84 63 0.98
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (84 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAAACAAGCCAAGAGTGCATCGATGCATGGCAT
GTGCATCGATGCATGGCAT
Found at i:40836 original size:16 final size:17
Alignment explanation
Indices: 40815--40848 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40805 TTTTATTATT
*
40815 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
40831 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
40848 A
1 A
40849 AAATAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:41368 original size:17 final size:18
Alignment explanation
Indices: 41348--41381 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41338 AAATTTTATT
41348 TTATTATT-TATTTTAAA
1 TTATTATTATATTTTAAA
*
41365 TTATTTTTATATTTTAA
1 TTATTATTATATTTTAA
41382 TAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTATATTTTAAA
Found at i:47929 original size:19 final size:19
Alignment explanation
Indices: 47905--47964 Score: 97
Period size: 18 Copynumber: 3.3 Consensus size: 19
47895 CAACCGAGCA
*
47905 GGGGAGTGAAAGGGGAAAG
1 GGGGAGAGAAAGGGGAAAG
47924 GGGGAGAG-AAGGGGAAAG
1 GGGGAGAGAAAGGGGAAAG
47942 GGGGAGAGAAA-GGGAAAG
1 GGGGAGAGAAAGGGGAAAG
47960 GGGGA
1 GGGGA
47965 CACAGGAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 30 0.77
19 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (19 bp):
GGGGAGAGAAAGGGGAAAG
Found at i:50400 original size:6 final size:6
Alignment explanation
Indices: 50391--50431 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
50381 CGAAGAAGAC
50391 GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAA
1 GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAA
50432 CGGTGAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (6 bp):
GGTAAT
Found at i:52934 original size:26 final size:26
Alignment explanation
Indices: 52905--52954 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
52895 GCATCAAAGC
52905 AAGTACTATATAACATACGACTTAAG
1 AAGTACTATATAACATACGACTTAAG
52931 AAGTACTATATAACATACGACTTA
1 AAGTACTATATAACATACGACTTA
52955 TTTTAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (26 bp):
AAGTACTATATAACATACGACTTAAG
Found at i:54404 original size:3 final size:3
Alignment explanation
Indices: 54396--54462 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
54386 ATAAAGAAAT
54396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54444 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
54463 CTTATTCGAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55608 original size:11 final size:11
Alignment explanation
Indices: 55587--55624 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
55577 TTTTTTTTAA
55587 AAAAAT-AAAT
1 AAAAATGAAAT
*
55597 AAAAATGCAAT
1 AAAAATGAAAT
55608 AAAAATGAAAT
1 AAAAATGAAAT
55619 AAAAAT
1 AAAAAT
55625 ATAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (11 bp):
AAAAATGAAAT
Found at i:55630 original size:11 final size:10
Alignment explanation
Indices: 55587--55630 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
55577 TTTTTTTTAA
55587 AAAAATAAAT
1 AAAAATAAAT
*
55597 AAAAATGCAAT
1 AAAAAT-AAAT
55608 AAAAATGAAAT
1 AAAAAT-AAAT
55619 AAAAATATAAT
1 AAAAATA-AAT
55630 A
1 A
55631 TAAAGCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:55630 original size:22 final size:21
Alignment explanation
Indices: 55587--55630 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
55577 TTTTTTTTAA
*
55587 AAAAATAAATAAAAATGCAAT
1 AAAAATAAATAAAAATACAAT
*
55608 AAAAATGAAATAAAAATATAAT
1 AAAAAT-AAATAAAAATACAAT
55630 A
1 A
55631 TAAAGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAATAAATAAAAATACAAT
Found at i:56096 original size:211 final size:208
Alignment explanation
Indices: 55770--56181 Score: 698
Period size: 211 Copynumber: 2.0 Consensus size: 208
55760 ACAATTAATG
*
55770 AATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTAGTCAAGTTTGATTGTTAAACAG
1 AATAATTCATTTGATCCCTCAATTGTAATTAAAAATTTATTTAGTCAAGTTTGATTGTTAAACAG
* * *
55835 TCGTAGGTGTGGAAAGCTACATGAATCGAATGAAAATTCGATCCTACAAAGTCAATAACTTAAAA
66 TCGTAGGTGTGGAAAACTACAGGAATAGAATGAAAATTCGATCCTACAAAGTCAATAACTTAAAA
* * *
55900 TTGTCTAACTGTTGTCTAAATATAAACTCAATTGTACCATGAATAAACATTCGATCAAAGAGTTG
131 TTGTCTAACTGCTGTCTAAATATAAACTCAATTGTACCACGAATAAACATTCAATCAAAGAGTTG
55965 ATCTTTTCTGAAT
196 ATCTTTTCTGAAT
*
55978 AATAATTCATTTGATCTCTCAATTGTAATTAAAAATTTATTTTAGTCAAGTTTATGATTGTTAAA
1 AATAATTCATTTGATCCCTCAATTGTAATTAAAAATTTA-TTTAGTCAAG-TT-TGATTGTTAAA
* *
56043 CAGTCGTAGGTGTGGAAAACTATAGGAATAGAATGAAAATTCGATCGTACAAAGTCAATAACTTA
63 CAGTCGTAGGTGTGGAAAACTACAGGAATAGAATGAAAATTCGATCCTACAAAGTCAATAACTTA
*
56108 AAATTGTCTAACTGCTGTCTAAATATCAACTCAATTGTACCACGAATAAACATTCAATCAAAGAG
128 AAATTGTCTAACTGCTGTCTAAATATAAACTCAATTGTACCACGAATAAACATTCAATCAAAGAG
56173 TTGATCTTT
193 TTGATCTTT
56182 CTGCTCAATC
Statistics
Matches: 190, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
208 37 0.19
209 10 0.05
210 2 0.01
211 141 0.74
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (208 bp):
AATAATTCATTTGATCCCTCAATTGTAATTAAAAATTTATTTAGTCAAGTTTGATTGTTAAACAG
TCGTAGGTGTGGAAAACTACAGGAATAGAATGAAAATTCGATCCTACAAAGTCAATAACTTAAAA
TTGTCTAACTGCTGTCTAAATATAAACTCAATTGTACCACGAATAAACATTCAATCAAAGAGTTG
ATCTTTTCTGAAT
Done.