Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002565.1 Hibiscus syriacus cultivar Beakdansim tig00005206_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: 54351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:525 original size:31 final size:31
Alignment explanation
Indices: 487--642 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
477 AAGGTCGAGG
487 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
518 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
549 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
580 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
611 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
642 G
1 G
643 GTCCTCGGGA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1487 original size:62 final size:62
Alignment explanation
Indices: 1417--1543 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
1407 CTGCATGTAG
*
1417 GGTGCTATTTTTTTGGCCTTATAAATGCGGCCTCCATTATACTATACAGAGTATGCATGGTT
1 GGTGCTATTTTTTTGGCCTTATAAATGCGACCTCCATTATACTATACAGAGTATGCATGGTT
1479 GGTGCTATTTTTTTGGCCTTATAAATGCGACCTCCATTATACTATACAGAGTATGCATGGTT
1 GGTGCTATTTTTTTGGCCTTATAAATGCGACCTCCATTATACTATACAGAGTATGCATGGTT
1541 GGT
1 GGT
1544 TGGAGAAAGC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (62 bp):
GGTGCTATTTTTTTGGCCTTATAAATGCGACCTCCATTATACTATACAGAGTATGCATGGTT
Found at i:2450 original size:17 final size:17
Alignment explanation
Indices: 2428--2466 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2418 TAGCACGGCT
*
2428 GGTTCGTTCACCGATCC
1 GGTTCGCTCACCGATCC
*
2445 GGTTCGCTGACCGATCC
1 GGTTCGCTCACCGATCC
*
2462 AGTTC
1 GGTTC
2467 TGAAAACCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.33, G:0.26, T:0.28
Consensus pattern (17 bp):
GGTTCGCTCACCGATCC
Found at i:5158 original size:19 final size:19
Alignment explanation
Indices: 5136--5172 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5126 ATTTAGTTGC
5136 CTAAATTATAGCCTAATTA
1 CTAAATTATAGCCTAATTA
5155 CTAAATTATAGCCTAATT
1 CTAAATTATAGCCTAATT
5173 GTTAGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (19 bp):
CTAAATTATAGCCTAATTA
Found at i:12884 original size:32 final size:32
Alignment explanation
Indices: 12834--12909 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
12824 CATTTTTCTA
12834 AAATGAAGTGATATATCACT-AAAATGTTTATG
1 AAATGAAGTGATATATCACTGAAAA-GTTTATG
* * *
12866 AAATTAAGTTATATATCACTGAAAAGTTTTTG
1 AAATGAAGTGATATATCACTGAAAAGTTTATG
* *
12898 AAGTAAAGTGAT
1 AAATGAAGTGAT
12910 TGGGCATTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (32 bp):
AAATGAAGTGATATATCACTGAAAAGTTTATG
Found at i:13006 original size:32 final size:32
Alignment explanation
Indices: 12969--13209 Score: 117
Period size: 32 Copynumber: 7.1 Consensus size: 32
12959 ATGATTTTTT
12969 TTTTCTAAAATGAAGTGATATATCACTGAAAA
1 TTTTCTAAAATGAAGTGATATATCACTGAAAA
* *
13001 TTTTCTAAAAAGAAGTTG-TATATCACTCAAAAA
1 TTTTCTAAAATGAAG-TGATATATCACT-GAAAA
* * * ** *
13034 GTTTCTGAAATGAAGTAAT-TGGGCTCTGAAAA
1 TTTTCTAAAATGAAGTGATAT-ATCACTGAAAA
* * * ** ** *
13066 GTTTCTATCATTGTGAATTAAATGGTATATGAGAAAAGAATA
1 TTTTCTA--A-----AATGAAGT-G-ATAT-ATCACTGAAAA
*
13108 TTTTTCTAAAATGACGTGATATATCACTGAAAA
1 TTT-TCTAAAATGAAGTGATATATCACTGAAAA
* * * *
13141 GTTTCTGAAATGAAATTATATATCACTGAAAA
1 TTTTCTAAAATGAAGTGATATATCACTGAAAA
* * *
13173 ATTTCTAAAATTAAGTGATATATCACTAAAAA
1 TTTTCTAAAATGAAGTGATATATCACTGAAAA
13205 GTTTT
1 -TTTT
13210 TTTCACTGAA
Statistics
Matches: 152, Mismatches: 41, Indels: 31
0.68 0.18 0.14
Matches are distributed among these distances:
32 86 0.57
33 33 0.22
34 5 0.03
35 1 0.01
36 5 0.03
39 6 0.04
41 3 0.02
42 9 0.06
43 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (32 bp):
TTTTCTAAAATGAAGTGATATATCACTGAAAA
Found at i:15553 original size:3 final size:3
Alignment explanation
Indices: 15539--15569 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
15529 TATTGGTAAA
15539 TCT TCAT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT
15570 CTTTGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:16188 original size:21 final size:21
Alignment explanation
Indices: 16162--16235 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
16152 ATTTTCCATT
16162 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
16183 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
16203 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
16224 TCGCGTTGCGAT
1 TCGCGTTGCGAT
16236 TTTCTATTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:16199 original size:41 final size:41
Alignment explanation
Indices: 16142--16258 Score: 207
Period size: 41 Copynumber: 2.9 Consensus size: 41
16132 TATCGCAAAT
16142 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
16183 TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
16224 TCGCGTTGCGATTTTCTATTTTGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
16259 CTACAGTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:16292 original size:19 final size:19
Alignment explanation
Indices: 16268--16315 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
16258 TCTACAGTTG
16268 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
16287 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
16306 TCGTTGCGAT
1 TCGTTGCGAT
16316 AGTCTACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:16292 original size:82 final size:81
Alignment explanation
Indices: 16142--16296 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
16132 TATCGCAAAT
*
16142 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCAC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATT-AC
16207 GTTGCGATAGTTGAAAA
65 GTTGCGATAGTTGAAAA
* * * * *
16224 TCGCGTTGCGATTTTCTATTTTGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATT
16288 -CGTTGCGAT
63 ACGTTGCGAT
16297 TTTCCAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
82 46 0.72
83 15 0.23
84 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (81 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTACG
TTGCGATAGTTGAAAA
Found at i:16319 original size:60 final size:62
Alignment explanation
Indices: 16227--16358 Score: 178
Period size: 60 Copynumber: 2.1 Consensus size: 62
16217 TTGAAAATCG
* ** * *
16227 CGTTGCGATTTTCTATTTTGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT-TTTCCAAATT
1 CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATTGTCGTTGCGATATTTACAAATT
*
16288 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAATTGTTGTTGCGATAGTTTACAAATT
1 CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATTGTCGTTGCGATA-TTTACAAATT
*
16350 CATTGCGAT
1 CGTTGCGAT
16359 AGTCTACAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
60 29 0.47
61 16 0.26
62 17 0.27
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (62 bp):
CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATTGTCGTTGCGATATTTACAAATT
Found at i:16356 original size:43 final size:41
Alignment explanation
Indices: 16287--16391 Score: 147
Period size: 43 Copynumber: 2.5 Consensus size: 41
16277 TTTTCCAAAT
* *
16287 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAATTG
1 TCGTTGCGATTTTACAAATTCATTGCGATAGTCTACAATTG
* *
16328 TTGTTGCGATAGTTTACAAATTCATTGCGATAGTCTACAGTTG
1 TCGTTGCGAT--TTTACAAATTCATTGCGATAGTCTACAATTG
*
16371 TCGTTGCGATTTTCCAAATTC
1 TCGTTGCGATTTTACAAATTC
16392 GTTGTGATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 19 0.34
43 37 0.66
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (41 bp):
TCGTTGCGATTTTACAAATTCATTGCGATAGTCTACAATTG
Found at i:17517 original size:41 final size:41
Alignment explanation
Indices: 17470--17563 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
17460 TCTTTTTTTT
*
17470 ACTATCGCAACGAATTTGGAAA-ATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGAAAACATCGCAACGACAACT-TAG
*
17511 ACTATCGCAACGAATTTGAAAACTATCGCAACGACAACTTGG
1 ACTATCGCAACGAATTTGAAAAC-ATCGCAACGACAACTTAG
17553 ACTATCGCAAC
1 ACTATCGCAAC
17564 TCGAAATGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
41 21 0.43
42 13 0.27
43 15 0.31
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGAAAACATCGCAACGACAACTTAG
Found at i:17537 original size:21 final size:21
Alignment explanation
Indices: 17470--17544 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
17460 TCTTTTTTTT
*
17470 ACTATCGCAACGAATTTGGAA
1 ACTATCGCAACGAATTTGAAA
** * *
17491 A--ATCGCAACGACAACTGTAG
1 ACTATCGCAACGA-ATTTGAAA
17511 ACTATCGCAACGAATTTGAAA
1 ACTATCGCAACGAATTTGAAA
17532 ACTATCGCAACGA
1 ACTATCGCAACGA
17545 CAACTTGGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 10 0.23
20 5 0.12
21 18 0.42
22 10 0.23
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGAATTTGAAA
Found at i:17556 original size:21 final size:19
Alignment explanation
Indices: 17470--17563 Score: 71
Period size: 21 Copynumber: 4.6 Consensus size: 19
17460 TCTTTTTTTT
*
17470 ACTATCGCAACGAATTTGG
1 ACTATCGCAACGAACTTGG
** *
17489 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACG--AACT-TGG
* *
17511 ACTATCGCAACGAATTTGAAA
1 ACTATCGCAACGAACTTG--G
17532 ACTATCGCAACGACAACTTGG
1 ACTATCGCAACG--AACTTGG
17553 ACTATCGCAAC
1 ACTATCGCAAC
17564 TCGAAATGGA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
19 11 0.19
20 3 0.05
21 26 0.46
22 12 0.21
23 5 0.09
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (19 bp):
ACTATCGCAACGAACTTGG
Found at i:17579 original size:20 final size:20
Alignment explanation
Indices: 17556--17607 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
17546 AACTTGGACT
* *
17556 ATCGCAACTCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
17576 ATCGTAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
17596 ATCGTAACGCGA
1 ATCGCAACGCGA
17608 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:23282 original size:37 final size:36
Alignment explanation
Indices: 23241--23314 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
23231 GTTGAAAAAT
*
23241 ATTTATAT-ATTTTCTTTAAAAAATTAAAATTCATAAA
1 ATTTATATAATTTT-TTTAAAAAATTAAAAAT-ATAAA
*
23278 ATTTATATAATTTTTTTACAAAATTAAAAATATAAA
1 ATTTATATAATTTTTTTAAAAAATTAAAAATATAAA
23314 A
1 A
23315 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.18
37 23 0.68
38 5 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTATATAATTTTTTTAAAAAATTAAAAATATAAA
Found at i:24229 original size:20 final size:20
Alignment explanation
Indices: 24204--24241 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24194 ACAACATTCT
24204 CTGGTAATCTTACATTTCCA
1 CTGGTAATCTTACATTTCCA
*
24224 CTGGTAATCTTATATTTC
1 CTGGTAATCTTACATTTC
24242 GTAAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTTCCA
Found at i:35338 original size:64 final size:65
Alignment explanation
Indices: 35268--35447 Score: 238
Period size: 65 Copynumber: 2.8 Consensus size: 65
35258 TGGAACACTT
* * * *
35268 AGTGCATCGGTGCACT-AAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCT
1 AGTGCATCGATGCA-TGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCT
35331 A
65 A
* * * *
35332 AGTGCATCGATGCATGGTGTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
** *
35397 AGTGCATCGATGCATGGAGAATGCATCGATGCATAAACTGCATTCGATGTT
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTT
35448 CAATTTATTC
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
63 1 0.01
64 49 0.49
65 51 0.50
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
Found at i:35487 original size:65 final size:66
Alignment explanation
Indices: 35288--35495 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 66
35278 TGCACTAAGT
* *
35288 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAA--TAAGCCTAAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAATTTAAACCTAAGTGCATCGATGCATGGAT
*
35350 GT
65 GA
* * *
35352 GTGCATCGATGCATAAAATGCAATCGATGTTTTC-ATTAAAACCTGAGTGCATCGATGCATGGA-
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAATTTAAACCTAAGTGCATCGATGCATGGAT
35415 GA
65 GA
* * ** * * *
35417 ATGCATCGATGCATAAACTGCATTCGATG-TTCAATTTATTCATTAGTGCATCAATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATTTAAACCTAAGTGCATCGATGCATGGA-T
35481 G-
65 GA
*
35482 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
35496 TCCTTTGAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
63 4 0.03
64 55 0.45
65 61 0.50
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (66 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATTTAAACCTAAGTGCATCGATGCATGGATG
A
Done.