Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001654.1 Hibiscus syriacus cultivar Beakdansim tig00003310_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: 43145
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4756 original size:12 final size:12
Alignment explanation
Indices: 4739--4764 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4729 TTGTTGTGCT
4739 TGCTCCTCGGGC
1 TGCTCCTCGGGC
4751 TGCTCCTCGGGC
1 TGCTCCTCGGGC
4763 TG
1 TG
4765 TTCAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.35, T:0.27
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:6481 original size:20 final size:21
Alignment explanation
Indices: 6428--6489 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
6418 GAATCCCCTG
6428 TGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGAATCGGTT-CCC-TCAA
*
6451 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGAATCGGTTCCCTCAA
* *
6471 TGGGGGTATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
6490 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCTCAA
Found at i:15217 original size:21 final size:21
Alignment explanation
Indices: 15158--15252 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
15148 TTGTGCTTAA
*
15158 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
15178 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
*
15200 TGCATCGATACACCTTGAAGG
1 TGCATCGATACACCTTGAATG
* *
15221 TGCACCGATGCACGCATTGAATG
1 TGCATCGATACAC-C-TTGAATG
*
15244 TGCACCGAT
1 TGCATCGAT
15253 GCACAAGGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.17
21 21 0.33
22 14 0.22
23 17 0.27
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:15246 original size:23 final size:21
Alignment explanation
Indices: 15177--15256 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
15167 ACACCTAACA
*
15177 GTGCATCGATGCATCCTTGAAT
1 GTGCACCGATGCA-CCTTGAAT
* * *
15199 GTGCATCGATACACCTTGAAG
1 GTGCACCGATGCACCTTGAAT
15220 GTGCACCGATGCACGCATTGAAT
1 GTGCACCGATGCAC-C-TTGAAT
15243 GTGCACCGATGCAC
1 GTGCACCGATGCAC
15257 AAGGTCATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
21 19 0.37
22 13 0.25
23 19 0.37
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (21 bp):
GTGCACCGATGCACCTTGAAT
Found at i:16817 original size:21 final size:21
Alignment explanation
Indices: 16775--16818 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
16765 ACTCCGGGAG
* *
16775 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
16796 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
16817 CT
1 CT
16819 TCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:18075 original size:64 final size:67
Alignment explanation
Indices: 17916--18076 Score: 222
Period size: 66 Copynumber: 2.5 Consensus size: 67
17906 GAATAAATTG
* * *
17916 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCATCGATGCACTGAGGGTTTTAATG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTCAGGCTTTTAATG
17980 AA
66 AA
* * * *
17982 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATTGATGCACTCTGGCTTTT-TTG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTCAGGCTTTTAATG
18045 -A
66 AA
*
18046 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
18077 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
64 31 0.36
65 2 0.02
66 51 0.59
67 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (67 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTCAGGCTTTTAATG
AA
Found at i:18076 original size:17 final size:19
Alignment explanation
Indices: 18048--18096 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
18038 TTTTTTGAAA
18048 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
18066 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
18085 CACCGATGCACT
1 CATCGATGCACT
18097 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:19053 original size:27 final size:26
Alignment explanation
Indices: 19023--19074 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19013 AGCACCTATG
19023 GTGCAAATGATTCACAAGGCACTAAAT
1 GTGCAAATGATTCAC-AGGCACTAAAT
* * *
19050 GTGCAATTTATTCACAGGCAGTAAA
1 GTGCAAATGATTCACAGGCACTAAA
19075 ACTGCATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (26 bp):
GTGCAAATGATTCACAGGCACTAAAT
Found at i:30283 original size:13 final size:13
Alignment explanation
Indices: 30265--30313 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
30255 ACCCGACCCG
30265 ACCCGACCCGTTT
1 ACCCGACCCGTTT
30278 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* * * *
30291 ATCCAACCAGTTG
1 ACCCGACCCGTTT
30304 ACCCGACCCG
1 ACCCGACCCG
30314 ACCCGTTGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:30326 original size:8 final size:8
Alignment explanation
Indices: 30313--30369 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
30303 GACCCGACCC
30313 GACCCGTT
1 GACCCGTT
30321 GACCC---
1 GACCCGTT
*
30326 GACCCATT
1 GACCCGTT
30334 GA-CCGTT
1 GACCCGTT
30341 GACCCGTT
1 GACCCGTT
30349 GA-CCGTT
1 GACCCGTT
30356 GACCGGCGTT
1 GACC--CGTT
30366 GACC
1 GACC
30370 TTTGTTGACC
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
5 5 0.12
7 13 0.32
8 15 0.37
10 8 0.20
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:30335 original size:13 final size:13
Alignment explanation
Indices: 30308--30337 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30298 CAGTTGACCC
*
30308 GACCCGACCCGTT
1 GACCCGACCCATT
30321 GACCCGACCCATT
1 GACCCGACCCATT
30334 GACC
1 GACC
30338 GTTGACCCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:30350 original size:15 final size:15
Alignment explanation
Indices: 30313--30369 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
30303 GACCCGACCC
*
30313 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
30326 GACCCATTGACCGTT
1 GACCCGTTGACCGTT
30341 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
30356 GACCGGCGTTGACC
1 GACC--CGTTGACC
30370 TTTGTTGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:35294 original size:13 final size:13
Alignment explanation
Indices: 35276--35324 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
35266 ACCCGACCCG
35276 ACCCGACCCGTTT
1 ACCCGACCCGTTT
35289 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* * * *
35302 ATCCAACCAGTTG
1 ACCCGACCCGTTT
35315 ACCCGACCCG
1 ACCCGACCCG
35325 ACCCGTTGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:35337 original size:8 final size:8
Alignment explanation
Indices: 35324--35380 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
35314 GACCCGACCC
35324 GACCCGTT
1 GACCCGTT
35332 GACCC---
1 GACCCGTT
*
35337 GACCCATT
1 GACCCGTT
35345 GA-CCGTT
1 GACCCGTT
35352 GACCCGTT
1 GACCCGTT
35360 GA-CCGTT
1 GACCCGTT
35367 GACCGGCGTT
1 GACC--CGTT
35377 GACC
1 GACC
35381 TTTGTTGACC
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
5 5 0.12
7 13 0.32
8 15 0.37
10 8 0.20
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:35346 original size:13 final size:13
Alignment explanation
Indices: 35319--35348 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35309 CAGTTGACCC
*
35319 GACCCGACCCGTT
1 GACCCGACCCATT
35332 GACCCGACCCATT
1 GACCCGACCCATT
35345 GACC
1 GACC
35349 GTTGACCCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:35361 original size:15 final size:15
Alignment explanation
Indices: 35324--35380 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
35314 GACCCGACCC
*
35324 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
35337 GACCCATTGACCGTT
1 GACCCGTTGACCGTT
35352 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
35367 GACCGGCGTTGACC
1 GACC--CGTTGACC
35381 TTTGTTGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:42218 original size:14 final size:15
Alignment explanation
Indices: 42199--42231 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
42189 TTTCAGATTT
42199 TTTTCCTTTCTTT-C
1 TTTTCCTTTCTTTCC
*
42213 TTTTCCTTTTTTTCC
1 TTTTCCTTTCTTTCC
42228 TTTT
1 TTTT
42232 TTTTCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCCTTTCTTTCC
Found at i:42752 original size:10 final size:10
Alignment explanation
Indices: 42731--42767 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
42721 TTTCGGATTT
42731 TTTCTTTT-C
1 TTTCTTTTCC
42740 TTTCTTTTCC
1 TTTCTTTTCC
42750 TTT-TTTTCC
1 TTTCTTTTCC
*
42759 TTTTTTTTC
1 TTTCTTTTC
42768 TTCAAACGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTTTCC
Found at i:43112 original size:532 final size:526
Alignment explanation
Indices: 42105--43145 Score: 1976
Period size: 532 Copynumber: 2.0 Consensus size: 526
42095 AGTTCAAGCC
42105 ACAAATTGACAAAGTAAACAAATTCGAAGAAGTGTAATCAAACAATCGATTTTTTCTGATTTCTT
1 ACAAATTGACAAAGTAAACAAATTCGAAGAAGTGTAATCAAACAATCGATTTTTTCTGATTTCTT
42170 TTTGATTTTCCTTGTTGTTTTTCAGATTTTTTTCCTTTCTTTCTTTTCCTTTTTTTCCTTTTTTT
66 TTTGATTTTCCTTGTTGTTTTTCAGATTTTTTTCCTTTCTTTCTTTTCCTTTTTTTCCTTTTTTT
42235 TCTTCAAACGCTTTGTTCGATCCAGATTTTTTTTCGATTTTTTTTCAACTGCTTCATCTTTCTTC
131 TCTTCAAACGCTTTGTTCGATCCAGATTTTTTTTCGATTTTTTTTCAACTGCTTCATCTTTCTTC
42300 TCTTAATTTTTCGTTCATGGAGTAAATCTATCTCATGTCTCGACAATGGTAACAAGCAAGGGAAA
196 TCTTAATTTTTCGTTCATGGAGTAAATCTATCTCATGTCTCGACAATGGTAACAAGCAAGGGAAA
42365 AATAAAAATTGAAAGGCTTCGGGTTTTGTAATGTGGTAAAAATAAAGAAAAGGGTAAAGGCTCAA
261 AATAAAAATTGAAAGGCTTCGGGTTTTGTAATGTGGTAAAAATAAAGAAAAGGGTAAAGGCTCAA
42430 AGTGGGTTCATTATGGGATATAAATAAATGATAGAAAATTTGGGTAGAGAAGTGATTTAATCCCA
326 AGTGGGTTCATTATGGGATATAAATAAATGATAGAAAATTTGGGTAGAGAAGTGATTTAATCCCA
42495 AGTGTCATAATCATTTTAAAGCATCAAGTTTCAACATGTGGTCTCGATATGCATTTAATCACAAG
391 AGTGTCATAATCATTTTAAAGCATCAAGTTTCAACATGTGGTCTCGATATGCATTTAATCACAAG
42560 TTTTAGAATGTCAAAATTAATCCGAAACACTCAATCAAACAAATGAGCAAGAATAAGAAGATATG
456 TTTTAGAATGTCAAAATTAATCCGAAAC-C-CAATCAAA-AAATGAGCAAGAATAAGAAGATATG
42625 CTCGTTTAG
518 CTCGTTTAG
42634 ACAAATTTGACAAAGTAAACAAATTCGAAGAAGTGTAATCAAACAATCGATTTTTTCTTGATTTC
1 ACAAA-TTGACAAAGTAAACAAATTCGAAGAAGTGTAATCAAACAATCGATTTTTTC-TGATTTC
* *
42699 TTTTTTGATTTTCCTTGTTGTTTTTCGGA-TTTTTTCTTTTCTTTCTTTTCCTTTTTTTCCTTTT
64 -TTTTTGATTTTCCTTGTTGTTTTTCAGATTTTTTTCCTTTCTTTCTTTTCCTTTTTTTCCTTTT
* *
42763 TTTTCTTCAAACGCTTTGTTCGATCCAGATTTTTTTTTTGATTTTTTTTCAACTGCTTCCTCTTT
128 TTTTCTTCAAACGCTTTGTTCGATCCAGA-TTTTTTTTCGATTTTTTTTCAACTGCTTCATCTTT
42828 CTTCTCTTAATTTTTCGTTCATGGAGTAAATCTATCTCATGTCTCGACAATGGTAACAAGCAAGG
192 CTTCTCTTAATTTTTCGTTCATGGAGTAAATCTATCTCATGTCTCGACAATGGTAACAAGCAAGG
42893 GAAAAATAAAAATTGAAAGGCTTCGGGTTTTGTAATGTGGTAAAAATAAAGAAAAGGGTAAAGGC
257 GAAAAATAAAAATTGAAAGGCTTCGGGTTTTGTAATGTGGTAAAAATAAAGAAAAGGGTAAAGGC
42958 TCAAAGTGGGTTCATTATGGGATATAAATAAATGATAGAAAATTTGGGTAGAGAAGTGATTTAAT
322 TCAAAGTGGGTTCATTATGGGATATAAATAAATGATAGAAAATTTGGGTAGAGAAGTGATTTAAT
43023 CCCAAGTGTCATAATCATTTTAAAGCATCAAGTTTCAACATGTGGTCTCGATATGCATTTAATCA
387 CCCAAGTGTCATAATCATTTTAAAGCATCAAGTTTCAACATGTGGTCTCGATATGCATTTAATCA
43088 CAAGTTTTAGAATGTCAAAATTAATCCGAAACCCAATCAAAAAATGAGCAAGAATAAG
452 CAAGTTTTAGAATGTCAAAATTAATCCGAAACCCAATCAAAAAATGAGCAAGAATAAG
Statistics
Matches: 504, Mismatches: 4, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
529 22 0.04
530 59 0.12
531 71 0.14
532 352 0.70
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (526 bp):
ACAAATTGACAAAGTAAACAAATTCGAAGAAGTGTAATCAAACAATCGATTTTTTCTGATTTCTT
TTTGATTTTCCTTGTTGTTTTTCAGATTTTTTTCCTTTCTTTCTTTTCCTTTTTTTCCTTTTTTT
TCTTCAAACGCTTTGTTCGATCCAGATTTTTTTTCGATTTTTTTTCAACTGCTTCATCTTTCTTC
TCTTAATTTTTCGTTCATGGAGTAAATCTATCTCATGTCTCGACAATGGTAACAAGCAAGGGAAA
AATAAAAATTGAAAGGCTTCGGGTTTTGTAATGTGGTAAAAATAAAGAAAAGGGTAAAGGCTCAA
AGTGGGTTCATTATGGGATATAAATAAATGATAGAAAATTTGGGTAGAGAAGTGATTTAATCCCA
AGTGTCATAATCATTTTAAAGCATCAAGTTTCAACATGTGGTCTCGATATGCATTTAATCACAAG
TTTTAGAATGTCAAAATTAATCCGAAACCCAATCAAAAAATGAGCAAGAATAAGAAGATATGCTC
GTTTAG
Done.