Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001089.1 Hibiscus syriacus cultivar Beakdansim tig00002150_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: 50819
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5767 original size:35 final size:33
Alignment explanation
Indices: 5728--5812 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
5718 GCATTTTGGT
5728 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
5763 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
5798 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
5813 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:11132 original size:29 final size:27
Alignment explanation
Indices: 11072--11167 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
11062 CTCCCTAAAT
*
11072 TTTTTTGGAATTTTTAGGAATTTAGGAG
1 TTTTTT-GAAATTTTAGGAATTTAGGAG
* **
11100 TTTTTTTAAATTTTATGGAATTTAAGGTT
1 TTTTTTGAAATTTTA-GGAATTT-AGGAG
** *
11129 TTTTTTGAAATTTTAATAATTTCATGAG
1 TTTTTTGAAATTTTAGGAATTT-AGGAG
11157 TTTTTTAGAAA
1 TTTTTT-GAAA
11168 ATAACTTTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
27 7 0.13
28 26 0.48
29 21 0.39
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (27 bp):
TTTTTTGAAATTTTAGGAATTTAGGAG
Found at i:18745 original size:18 final size:19
Alignment explanation
Indices: 18705--18758 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
18695 CCCTATATCG
* *
18705 ATCCCTATCTCTATCTC-T
1 ATCCCTATCTCGATCACGT
18723 ATCCCTATCTCGATCACGT
1 ATCCCTATCTCGATCACGT
* *
18742 -TCCCTGTCACGATCACG
1 ATCCCTATCTCGATCACG
18759 ATTGCGGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 30 0.97
19 1 0.03
ACGTcount: A:0.19, C:0.39, G:0.09, T:0.33
Consensus pattern (19 bp):
ATCCCTATCTCGATCACGT
Found at i:23238 original size:25 final size:25
Alignment explanation
Indices: 23209--23284 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
23199 GAAAAAAATT
23209 ACATTTTAGGTAGCACCCAATATTA
1 ACATTTTAGGTAGCACCCAATATTA
*
23234 ACATTTCT-GGTAG-A---AA-AATA
1 ACATTT-TAGGTAGCACCCAATATTA
* * *
23254 ATATTTTAGGTAGCGCCCACTATTA
1 ACATTTTAGGTAGCACCCAATATTA
23279 ACATTT
1 ACATTT
23285 CCGGTAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 1 0.03
20 13 0.34
21 2 0.05
24 2 0.05
25 19 0.50
26 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (25 bp):
ACATTTTAGGTAGCACCCAATATTA
Found at i:23311 original size:44 final size:45
Alignment explanation
Indices: 23202--23313 Score: 154
Period size: 45 Copynumber: 2.5 Consensus size: 45
23192 TTAAGTAGAA
* * *
23202 AAAAATTACATTTTAGGTAGCACCCAATATTAACATTTCTGGTAG
1 AAAAATAATATTTTAGGTAGCACCCAATATTAACATTTCCGGTAG
* *
23247 AAAAATAATATTTTAGGTAGCGCCCACTATTAACATTTCCGGTA-
1 AAAAATAATATTTTAGGTAGCACCCAATATTAACATTTCCGGTAG
* *
23291 AAAAATAATGTTTTATGTAGCAC
1 AAAAATAATATTTTAGGTAGCAC
23314 TTTACCGGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 20 0.34
45 39 0.66
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (45 bp):
AAAAATAATATTTTAGGTAGCACCCAATATTAACATTTCCGGTAG
Found at i:29270 original size:107 final size:105
Alignment explanation
Indices: 29123--29504 Score: 321
Period size: 105 Copynumber: 3.7 Consensus size: 105
29113 AGTCAATACT
* ** *
29123 ATTATCAATA-AAAATGCAATGAACTTGTTCGACACTGAAAATATATTTTGTGACAATCAATATT
1 ATTATCAATAGAAATTGTGATGAACTTGTTCGACACTGAAAATATATTTTGTGACAATCAAT-GT
29187 TATCACACTAAGTATACATTTAATGACCAAATGTTTGACAAA
65 TATCACACTAAGTAT-CATTTAATGACCAAATGTTTGACAAA
* * * * * *
29229 ATTTTCAATGGAAATTGTGATGAA-TTCGTTCGACGCTGAAAATATATTTTCTAACTATCAATGT
1 ATTATCAATAGAAATTGTGATGAACTT-GTTCGACACTGAAAATATATTTTGTGACAATCAATGT
* * ** * * **
29293 TGTCACACTAAATATTTTTTAGTGACCAAGTGTTTGACACT
65 TATCACACTAAGTATCATTTAATGACCAAATGTTTGACAAA
* * * * *
29334 ATTATCAATAGAAATTGTGATGAATTTTTTTC-A-ACTGATAATATATTTTGTGACCACCAATGT
1 ATTATCAATAGAAATTGTGATGAA-CTTGTTCGACACTGAAAATATATTTTGTGACAATCAATGT
* * * * * **
29397 TACCACACTAAGTAT-TTTTAGTGACCAAATATTCGACACT
65 TATCACACTAAGTATCATTTAATGACCAAATGTTTGACAAA
* * ** * * *
29437 ATTATCCATTA-AAATTGT-ATGAA-TTTTTTAACACTAAAAATATATTTTATGACCATCAATGT
1 ATTAT-CAATAGAAATTGTGATGAACTTGTTCGACACTGAAAATATATTTTGTGACAATCAATGT
*
29499 TGTCAC
65 TATCAC
29505 TAAGTAAATT
Statistics
Matches: 228, Mismatches: 41, Indels: 18
0.79 0.14 0.06
Matches are distributed among these distances:
100 5 0.02
101 1 0.00
102 35 0.15
103 34 0.15
104 40 0.18
105 43 0.19
106 27 0.12
107 43 0.19
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (105 bp):
ATTATCAATAGAAATTGTGATGAACTTGTTCGACACTGAAAATATATTTTGTGACAATCAATGTT
ATCACACTAAGTATCATTTAATGACCAAATGTTTGACAAA
Found at i:29453 original size:103 final size:102
Alignment explanation
Indices: 29120--29628 Score: 442
Period size: 103 Copynumber: 4.9 Consensus size: 102
29110 TCTAGTCAAT
* * * * * *
29120 ACTATTATCAATAAAAATGCAATGAACTTGTTCGACACTGAAAATATATTTTGTGACAATCAATA
1 ACTATTATCATTAAAATTG-TATGAATTTTTTC-ACACTGAAAATATATTTTGTGACCATCAAT-
* ** * * *
29185 TTTATCACACTAAGTATACATTTAATGACCAAATGTTTGAC
63 GTTATCACACTAAGTAT-TTTTTAGTGACCAAATATTCGAC
** * ** ** * * * *
29226 AAAATTTTCAATGGAAATTGTGATGAATTCGTTCGACGCTGAAAATATATTTTCTAACTATCAAT
1 ACTATTATC-ATTAAAATTGT-ATGAATTTTTTC-ACACTGAAAATATATTTTGTGACCATCAAT
* * * * *
29291 GTTGTCACACTAAATATTTTTTAGTGACCAAGTGTTTGAC
63 GTTATCACACTAAGTATTTTTTAGTGACCAAATATTCGAC
* * *
29331 ACTATTATCAATAGAAATTGTGATGAATTTTTTTCA-ACTGATAATATATTTTGTGACCACCAAT
1 ACTATTATCATTA-AAATTGT-ATGAA-TTTTTTCACACTGAAAATATATTTTGTGACCATCAAT
*
29395 GTTACCACACTAAGTA-TTTTTAGTGACCAAATATTCGAC
63 GTTATCACACTAAGTATTTTTTAGTGACCAAATATTCGAC
* * *
29434 ACTATTATCCATTAAAATTGTATGAATTTTTTAACACTAAAAATATATTTTATGACCATCAATGT
1 ACTATTAT-CATTAAAATTGTATGAATTTTTTCACACTGAAAATATATTTTGTGACCATCAATGT
*
29499 TGT--CACTAAGTAAATTTTTTAGTGACCAAATATTCGAC
65 TATCACACTAAGT--ATTTTTTAGTGACCAAATATTCGAC
* * * * *
29537 ACTATTAT--TCAAAATTGTATGAATTTTTTAACA-TCAAAAATATATTTTGTGACAATCAATAT
1 ACTATTATCATTAAAATTGTATGAATTTTTTCACACT-GAAAATATATTTTGTGACCATCAATGT
*
29599 TGTCAC-C-AAGTATTTTTTTAGTGACCAAAT
65 TATCACACTAAGTA-TTTTTTAGTGACCAAAT
29629 GTTAGACAGT
Statistics
Matches: 337, Mismatches: 53, Indels: 33
0.80 0.13 0.08
Matches are distributed among these distances:
98 1 0.00
99 18 0.05
100 63 0.19
101 8 0.02
102 34 0.10
103 66 0.20
104 40 0.12
105 39 0.12
106 25 0.07
107 43 0.13
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (102 bp):
ACTATTATCATTAAAATTGTATGAATTTTTTCACACTGAAAATATATTTTGTGACCATCAATGTT
ATCACACTAAGTATTTTTTAGTGACCAAATATTCGAC
Found at i:29568 original size:100 final size:99
Alignment explanation
Indices: 29267--29628 Score: 376
Period size: 100 Copynumber: 3.6 Consensus size: 99
29257 TTCGACGCTG
* * * * * * *
29267 AAAATATATTTTCTAACTATCAATGTTGTCACACTAAAT-ATTTTTTAGTGACCAAGTGTTTGAC
1 AAAATATATTTTGTGACCATCAATGTTGT--CACTAAGTAATTTTTTAGTGACCAAATATTCGAC
* *
29331 ACTATTA-TCAATAGAAATTGTGATGAATTTTTT-TCAACTG
64 ACTATTATTC---A-AAATTGT-ATGAATTTTTTAAC-ACTA
* * **
29371 ATAATATATTTTGTGACCACCAATGTTACCACACTAAGT-A-TTTTTAGTGACCAAATATTCGAC
1 AAAATATATTTTGTGACCATCAATGTT--GTCACTAAGTAATTTTTTAGTGACCAAATATTCGAC
*
29434 ACTATTATCCATTAAAATTGTATGAATTTTTTAACACTA
64 ACTATTAT---TCAAAATTGTATGAATTTTTTAACACTA
*
29473 AAAATATATTTTATGACCATCAATGTTGTCACTAAGTAAATTTTTTAGTGACCAAATATTCGACA
1 AAAATATATTTTGTGACCATCAATGTTGTCACTAAGT-AATTTTTTAGTGACCAAATATTCGACA
29538 CTATTATTCAAAATTGTATGAATTTTTTAACA-TCA
65 CTATTATTCAAAATTGTATGAATTTTTTAACACT-A
* * * *
29573 AAAATATATTTTGTGACAATCAATATTGTCACCAAGTATTTTTTTAGTGACCAAAT
1 AAAATATATTTTGTGACCATCAATGTTGTCACTAAGTAATTTTTTAGTGACCAAAT
29629 GTTAGACAGT
Statistics
Matches: 222, Mismatches: 25, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
99 19 0.09
100 66 0.30
102 39 0.18
103 66 0.30
104 31 0.14
107 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (99 bp):
AAAATATATTTTGTGACCATCAATGTTGTCACTAAGTAATTTTTTAGTGACCAAATATTCGACAC
TATTATTCAAAATTGTATGAATTTTTTAACACTA
Found at i:36165 original size:12 final size:13
Alignment explanation
Indices: 36145--36190 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
36135 ATCATTATGT
*
36145 TTTTTCTTTTT-C
1 TTTTACTTTTTAC
36157 TTTTACTTTTTAC
1 TTTTACTTTTTAC
**
36170 TTTT-CTTTTTGT
1 TTTTACTTTTTAC
36182 TTTTACTTT
1 TTTTACTTT
36191 GAAACATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTACTTTTTAC
Found at i:36173 original size:18 final size:18
Alignment explanation
Indices: 36152--36190 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
36142 TGTTTTTTCT
36152 TTTTCTTTTACTTTTTAC
1 TTTTCTTTTACTTTTTAC
**
36170 TTTTCTTTTTGTTTTTAC
1 TTTTCTTTTACTTTTTAC
36188 TTT
1 TTT
36191 GAAACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTACTTTTTAC
Found at i:36317 original size:11 final size:11
Alignment explanation
Indices: 36283--36320 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
36273 TACCAGGTTA
*
36283 AGTCAGTTCCA
1 AGTCAGTTCCG
36294 AGTCAGTTCCG
1 AGTCAGTTCCG
*
36305 AGTCAGTTTCG
1 AGTCAGTTCCG
36316 AGTCA
1 AGTCA
36321 TATCCCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (11 bp):
AGTCAGTTCCG
Found at i:37743 original size:11 final size:10
Alignment explanation
Indices: 37727--37777 Score: 61
Period size: 11 Copynumber: 5.0 Consensus size: 10
37717 TAGGTCCTTA
37727 TATTTTATGTT
1 TATTTTAT-TT
37738 TATTTTATTT
1 TATTTTATTT
37748 TATTTTATGTT
1 TATTTTAT-TT
37759 GT-TTTTATTT
1 -TATTTTATTT
37769 T-TTTTATTT
1 TATTTTATTT
37778 GATATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.24
10 12 0.32
11 16 0.42
12 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (10 bp):
TATTTTATTT
Found at i:37746 original size:5 final size:5
Alignment explanation
Indices: 37727--37777 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
37717 TAGGTCCTTA
37727 TATTT TATGTT TATTT TATTT TATTT TATGTT GT-TTT TATTT T-TTT
1 TATTT TAT-TT TATTT TATTT TATTT TAT-TT -TATTT TATTT TATTT
37773 TATTT
1 TATTT
37778 GATATTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.12
5 27 0.66
6 8 0.20
7 1 0.02
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:37746 original size:16 final size:15
Alignment explanation
Indices: 37727--37777 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
37717 TAGGTCCTTA
37727 TATTTTATGTTTATTT
1 TATTTTAT-TTTATTT
37743 TATTTTATTTTATGTT
1 TATTTTATTTTAT-TT
37759 GT-TTTTATTTT-TTT
1 -TATTTTATTTTATTT
37773 TATTT
1 TATTT
37778 GATATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 19 0.59
17 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (15 bp):
TATTTTATTTTATTT
Found at i:37753 original size:21 final size:21
Alignment explanation
Indices: 37727--37775 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
37717 TAGGTCCTTA
37727 TATTTTATGTT-TATTTTATTT
1 TATTTTATGTTGT-TTTTATTT
37748 TATTTTATGTTGTTTTTATTT
1 TATTTTATGTTGTTTTTATTT
37769 T-TTTTAT
1 TATTTTAT
37776 TTGATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.22
21 20 0.74
22 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (21 bp):
TATTTTATGTTGTTTTTATTT
Found at i:39207 original size:20 final size:20
Alignment explanation
Indices: 39182--39224 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
39172 TTTCTTATTT
39182 AAATTAAAATTAATTTTT-TA
1 AAATT-AAATTAATTTTTGTA
*
39202 AAATTAAATTTATTTTTGTA
1 AAATTAAATTAATTTTTGTA
39222 AAA
1 AAA
39225 AATAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTAAATTAATTTTTGTA
Found at i:45703 original size:22 final size:23
Alignment explanation
Indices: 45672--45718 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
45662 TAATCGCGAG
45672 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* * *
45694 TTTAGCAGATATGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
45717 TT
1 TT
45719 GTTTAGGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Done.