Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004568.1 Hibiscus syriacus cultivar Beakdansim tig00010153_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: 57898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2164 original size:22 final size:22
Alignment explanation
Indices: 2135--2186 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2125 ACATGTATGT
2135 GAAGTTGGTTTGCAAGG-CAT-A
1 GAAGTTGGTTTGC-AGGCCATGA
2156 GTAAGTTGGTTTGCAGGCCATGA
1 G-AAGTTGGTTTGCAGGCCATGA
2179 GAAGTTGG
1 GAAGTTGG
2187 AATTCTTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.29
Consensus pattern (22 bp):
GAAGTTGGTTTGCAGGCCATGA
Found at i:2271 original size:41 final size:41
Alignment explanation
Indices: 2226--2327 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 41
2216 AGGCATGTAA
* *
2226 AAAGCATGGAGAT-TTCACCAGGCTATGTTGAAGACTCATGG
1 AAAGCATGAAG-TCTTCACCAGGCCATGTTGAAGACTCATGG
* *
2267 AAAGCATGAAGTCATCACCA-GCCATGTTGAAGACTCGTGG
1 AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
2307 AAAGCATGAAGTCTTCACCAG
1 AAAGCATGAAGTCTTCACCAG
2328 CTCACTATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 38 0.70
41 16 0.30
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (41 bp):
AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
Found at i:4555 original size:357 final size:358
Alignment explanation
Indices: 3435--4849 Score: 2120
Period size: 358 Copynumber: 4.0 Consensus size: 358
3425 GTATCTTTGG
3435 TTATTAATGGTTTTGACCCCGACAAATGGAACGATC-GTGGTGGTGTTCTTGACCGAGAAAGGTA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGA-CGGTGGTGGTGTTCTTGACCGAGAAAGGTA
* *
3499 ACATTTTGAATTATTTTTCTCTCAATTCTAAATCATTACGGTTTGGTTTTCCTTAAGTTATTTTT
65 ACATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTT
* *
3564 TGAATTTTTCACTTTAAAACATAATTACTCAAATAATATTATTTATAT-TTTAATACCAATATAT
130 TCAATTTTTCACTTTAAAA-ATAATTACTCAAATAATATTATTTATATATTTAATACCAATATAG
3628 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAA-TTTTAATCA-TTTAATAGTATAT
194 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATA--ATAT
*
3691 AATATTTTCCAATGTTAAAATAATATATTCAATTATATTATAATATATATG--ATTATA-TCTTA
257 AATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATATATATGATATTATATTCTTA
*
3753 TTTTAA-AATATAT--A--A-T--AAATTAATTAT-T
322 TTTTAACAATATATAAATTATTAAAAAATAATTATAT
* * *
3781 TTATTAATGGTTTTGACCTCGACAAATGGAACGACAGTAGT-GTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
3845 CATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGA-TTTCCTTAAGTTA-TTTTT
66 CATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTT
* *
3908 CAAATTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATA-
131 CAATTTTTCACTTTAAA-AATAATTACTC-AAATAATATTATTTATATATTTAATACCAATATAG
* *
3972 TATATTATTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATAT-A
194 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAA
4036 TATTTTCCAATGTTATAATAATATATT-AATTATATTAT-ATAATATATGATATTATATTCTTAT
259 TATTTTCCAATGTTATAATAATATATTCAATTATATTATAAT-ATATATGATATTATATTCTTAT
4099 TTTAACAATAATAATAAATTATTAAAAAAATTAATTATAT
323 TTTAACAAT-AT-ATAAATTATT-AAAAAA-TAATTATAT
4139 TTATTAACT-GTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGT-
1 TTATTAA-TGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTA
*
4202 ACAATTTTGAATTA-TTTTCTCTCGATTCTAAATCATTATGGTTTGATTTTCCTTAAGTTATTTT
65 AC-ATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTT
*
4266 TTGAATTTTTCACTTTAAATAATAATTACTC-AA-AATATTATTTATATATTTAATACCAATATA
129 TTCAATTTTTCACTTTAAA-AATAATTACTCAAATAATATTATTTATATATTTAATACCAATATA
4329 -T-TTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATA
193 GTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAAT-A-ATA
* *
4392 TAATATTTTCCAATGTTATAATAATATATTCAATTATATTGTAATAATATATGATATTGTATTCT
256 TAATATTTTCCAATGTTATAATAATATATTCAATTATATTATAAT-ATATATGATATTATATTCT
* *
4457 TATTTTAACAATATATAAACTCTTAAAAAATAATTATAT
320 TATTTTAACAATATATAAATTATTAAAAAATAATTATAT
4496 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
* * * * *
4561 CATTTTGAATTATTTTTCTCTAGAATCAAAATCATTATGGTGTGATTTTCCTTAAGTTATTTTTT
66 CATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTA-TTTTT
* *
4626 TCAA-TTTTCA-TTTTAAAGTAATTACTCAAAATAATA-TATTTATATA-TTAATACCAATATAG
130 TCAATTTTTCACTTTAAAAATAATTACTC-AAATAATATTATTTATATATTTAATACCAATATAG
*
4687 TATTTTAG---TATTTTAATAAATTAATTACTAAGATAT-ATTTTTAATCATTTTAATAATATAA
194 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAA
*
4748 TATTTTCCAATGTTATAAT-A-ATATTAAATTATATTATAATA-ATATGATATTATATTCTTATT
259 TATTTTCCAATGTTATAATAATATATTCAATTATATTATAATATATATGATATTATATTCTTATT
4810 TTAACAATATATAAATTATTAAAAAATAATTATAT
324 TTAACAATATATAAATTATTAAAAAATAATTATAT
4845 TTATT
1 TTATT
4850 TTTCAAAAAT
Statistics
Matches: 989, Mismatches: 38, Indels: 81
0.89 0.03 0.07
Matches are distributed among these distances:
341 2 0.00
342 18 0.02
343 57 0.06
344 80 0.08
345 102 0.10
346 47 0.05
347 2 0.00
348 2 0.00
349 58 0.06
350 2 0.00
351 18 0.02
352 2 0.00
353 26 0.03
354 1 0.00
355 18 0.02
356 95 0.10
357 139 0.14
358 145 0.15
359 100 0.10
360 42 0.04
361 33 0.03
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.45
Consensus pattern (358 bp):
TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
CATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTT
CAATTTTTCACTTTAAAAATAATTACTCAAATAATATTATTTATATATTTAATACCAATATAGTA
TTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAATA
TTTTCCAATGTTATAATAATATATTCAATTATATTATAATATATATGATATTATATTCTTATTTT
AACAATATATAAATTATTAAAAAATAATTATAT
Found at i:4784 original size:21 final size:21
Alignment explanation
Indices: 4760--4803 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4750 TTTTCCAATG
*
4760 TTATAATAATATTAAATTATA
1 TTATAATAATATGAAATTATA
*
4781 TTATAATAATATGATATTATA
1 TTATAATAATATGAAATTATA
4802 TT
1 TT
4804 CTTATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATAATAATATGAAATTATA
Found at i:4844 original size:23 final size:22
Alignment explanation
Indices: 4815--4880 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
4805 TTATTTTAAC
4815 AATATATAAATTATTAAAAAAT
1 AATATATAAATTATTAAAAAAT
** * *
4837 AATTATATTTATTTTTCAAAAAT
1 AA-TATATAAATTATTAAAAAAT
*
4860 AATACTATTAAATTATCAAAA
1 AATA-TA-TAAATTATTAAAA
4881 TATATTTAGT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
22 4 0.12
23 20 0.62
24 8 0.25
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATAAATTATTAAAAAAT
Found at i:5527 original size:21 final size:21
Alignment explanation
Indices: 5503--5547 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5493 GGATTCAAAT
5503 AATTT-AACATATAATAATTTA
1 AATTTGAACATATAAT-ATTTA
**
5524 AATTTGAATTTATAATATTTA
1 AATTTGAACATATAATATTTA
5545 AAT
1 AAT
5548 ATGTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTTGAACATATAATATTTA
Found at i:14539 original size:18 final size:18
Alignment explanation
Indices: 14516--14555 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14506 TCATTTACAA
14516 TTTTTGAATTTTTGTATT
1 TTTTTGAATTTTTGTATT
** *
14534 TTTTTGGCTTTTTTTATT
1 TTTTTGAATTTTTGTATT
14552 TTTT
1 TTTT
14556 CTGTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.78
Consensus pattern (18 bp):
TTTTTGAATTTTTGTATT
Found at i:28940 original size:12 final size:11
Alignment explanation
Indices: 28921--28954 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28911 TTATCATGTT
28921 TAAAAATAAAA
1 TAAAAATAAAA
*
28932 GTTAAAATAAAA
1 -TAAAAATAAAA
28944 TAAAAATAAAA
1 TAAAAATAAAA
28955 ACTTGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:28955 original size:24 final size:24
Alignment explanation
Indices: 28921--28973 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
28911 TTATCATGTT
* *
28921 TAAAAATAAAAGTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
28944 TAAAAATAAAAACTTGAAAAGAAAA
1 TAAAAAT-AAAACTTGAAAAGAAAA
*
28969 GAAAA
1 TAAAA
28974 GAAAGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 6 0.24
25 12 0.48
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:34725 original size:18 final size:18
Alignment explanation
Indices: 34677--34726 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
34667 CTTATTTTTA
*
34677 ATTTAAATAT-TTTTATT
1 ATTTTAATATCTTTTATT
**
34694 -TATTTAATCGCTTTTATT
1 AT-TTTAATATCTTTTATT
34712 ATTTTAATATCTTTT
1 ATTTTAATATCTTTT
34727 TATCAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.04
17 5 0.20
18 18 0.72
19 1 0.04
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTAATATCTTTTATT
Found at i:38189 original size:19 final size:19
Alignment explanation
Indices: 38165--38205 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
38155 AGTTTCCACG
38165 CCACCCGCTCCTCTCTACT
1 CCACCCGCTCCTCTCTACT
38184 CCACCCGCTCCTCTCTACT
1 CCACCCGCTCCTCTCTACT
38203 CCA
1 CCA
38206 TGACGGTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.59, G:0.05, T:0.24
Consensus pattern (19 bp):
CCACCCGCTCCTCTCTACT
Found at i:39138 original size:12 final size:12
Alignment explanation
Indices: 39121--39154 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
39111 CTTGCCTTGA
39121 ATTTTTAGCCAT
1 ATTTTTAGCCAT
39133 ATTTTTAGCCAT
1 ATTTTTAGCCAT
39145 ATTTTTAGCC
1 ATTTTTAGCC
39155 TTTTCCCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (12 bp):
ATTTTTAGCCAT
Found at i:43634 original size:5 final size:6
Alignment explanation
Indices: 43621--43647 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43611 TTTAATTTAA
43621 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
43648 GCAGGAACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:50451 original size:22 final size:22
Alignment explanation
Indices: 50423--50465 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
50413 AGTTTTATTA
50423 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTT-CTTTTC
*
50445 AAGTTTTTTCCTTTTTCTTTT
1 AAGTTTTCTCCTTTTTCTTTT
50466 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTCTTTTC
Found at i:52246 original size:25 final size:25
Alignment explanation
Indices: 52218--52299 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
52208 TTTGTATAGT
52218 TTAA-TTTTTTATTGTATTGTTTAAA
1 TTAAGTTTTTTATT-TATTGTTTAAA
* ***
52243 TTAAGTTTAGTTTGTTTTATT-TTTTTT
1 TTAAGTTT--TTT-ATTTATTGTTTAAA
*
52270 TTAATTTTTTTACTTTATTGTTTAAA
1 TTAAGTTTTTTA-TTTATTGTTTAAA
52296 TTAA
1 TTAA
52300 TTTATATTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 11
0.68 0.15 0.18
Matches are distributed among these distances:
25 13 0.31
26 10 0.24
27 10 0.24
28 7 0.17
29 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.67
Consensus pattern (25 bp):
TTAAGTTTTTTATTTATTGTTTAAA
Found at i:52294 original size:21 final size:21
Alignment explanation
Indices: 52247--52294 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
52237 TTTAAATTAA
* *
52247 GTTTAGTTTGTTTTATTTTTT
1 GTTTAATTTGTTTTATTTATT
*
52268 TTTTAATTT-TTTTACTTTATT
1 GTTTAATTTGTTTTA-TTTATT
52289 GTTTAA
1 GTTTAA
52295 ATTAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (21 bp):
GTTTAATTTGTTTTATTTATT
Found at i:52317 original size:11 final size:10
Alignment explanation
Indices: 52295--52335 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
52285 TATTGTTTAA
*
52295 ATTAATTTAT
1 ATTAAATTAT
52305 ATTAAACTTAT
1 ATTAAA-TTAT
52316 ATTAAATTAT
1 ATTAAATTAT
*
52326 ATTAAGTTAT
1 ATTAAATTAT
52336 TGTTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
ATTAAATTAT
Found at i:54597 original size:31 final size:31
Alignment explanation
Indices: 54562--54633 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
54552 TAGTAGAAAC
*
54562 AATATTTACAAAC-ACTCGTTCAAATAAAAAT
1 AATATTTACAAACAAC-CATTCAAATAAAAAT
*
54593 AATATTTACAAACAACCATTCAAATATAAAT
1 AATATTTACAAACAACCATTCAAATAAAAAT
**
54624 AGGATTTACA
1 AATATTTACA
54634 TTATAGAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.29
Consensus pattern (31 bp):
AATATTTACAAACAACCATTCAAATAAAAAT
Found at i:54727 original size:27 final size:27
Alignment explanation
Indices: 54697--54762 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
54687 GAGTTTACTA
* * **
54697 ACATTAATTCAAATGTAGATATTTATC
1 ACATTCATTCAAATATAGATATCCATC
*
54724 ACATTCATTAAAATATAGATATCCATC
1 ACATTCATTCAAATATAGATATCCATC
54751 AC-TTCATTCAAA
1 ACATTCATTCAAA
54763 AAAATATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (27 bp):
ACATTCATTCAAATATAGATATCCATC
Done.