Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009444.1 Hibiscus syriacus cultivar Beakdansim tig00113511_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: 58872
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Found at i:1636 original size:32 final size:31
Alignment explanation
Indices: 1580--1655 Score: 120
Period size: 32 Copynumber: 2.5 Consensus size: 31
1570 ATTTGGACTT
*
1580 AACTTCACGACG--GAATCACCCATGATTTG
1 AACTTCACGATGAAGAATCACCCATGATTTG
1609 AACTTCACGATGAAGAAGTCACCCATGATTTG
1 AACTTCACGATGAAGAA-TCACCCATGATTTG
1641 AACTTCACGATGAAG
1 AACTTCACGATGAAG
1656 GATATCGTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
29 11 0.26
31 3 0.07
32 29 0.67
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (31 bp):
AACTTCACGATGAAGAATCACCCATGATTTG
Found at i:2345 original size:35 final size:35
Alignment explanation
Indices: 2239--2345 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 35
2229 TTTATTTAAA
*
2239 AAAACATATAATATATAGTTTTTTAAAAACAATTTTG
1 AAAACATAT-ATATAT-GTTTTTTAAAAACGATTTTG
* ** *
2276 AAAACGTATATAATAT-AATTTTGAAAACGTATTTTG
1 AAAACATATAT-ATATGTTTTTTAAAAACG-ATTTTG
*
2312 -AAACATATATATATGGTTTTTTAAAAATGATTTT
1 AAAACATATATATAT-GTTTTTTAAAAACGATTTT
2346 TTTAGAAAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
34 4 0.07
35 23 0.41
36 17 0.30
37 12 0.21
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (35 bp):
AAAACATATATATATGTTTTTTAAAAACGATTTTG
Found at i:2379 original size:8 final size:7
Alignment explanation
Indices: 2360--2405 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 7
2350 GAAAACATAA
2360 TATATAT
1 TATATAT
2367 TATATACT
1 TATATA-T
2375 TATATACT
1 TATATA-T
2383 TATATAT
1 TATATAT
*
2390 TATATGT
1 TATATAT
2397 TCATATAT
1 T-ATATAT
2405 T
1 T
2406 TTCATTACCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
7 14 0.40
8 21 0.60
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:8643 original size:78 final size:78
Alignment explanation
Indices: 8560--8705 Score: 247
Period size: 78 Copynumber: 1.9 Consensus size: 78
8550 AAAATCGTGC
* *
8560 CCACCATATACACCGAAGTATATTACACATAAGGTCGTGCCCACAATATTCACCGAAGTGTATTA
1 CCACCATATACACCGAAGTATATTACACATAAGGCCGTGCCCACAATATACACCGAAGTGTATTA
8625 CACTAAGGTCGTA
66 CACTAAGGTCGTA
* * *
8638 CCACCATATTCACCGAAGTGTATTACACATAAGGCCGTGCCCACCATATACACCGAAGTGTATTA
1 CCACCATATACACCGAAGTATATTACACATAAGGCCGTGCCCACAATATACACCGAAGTGTATTA
8703 CAC
66 CAC
8706 ATAAAGTCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (78 bp):
CCACCATATACACCGAAGTATATTACACATAAGGCCGTGCCCACAATATACACCGAAGTGTATTA
CACTAAGGTCGTA
Found at i:8656 original size:38 final size:40
Alignment explanation
Indices: 8543--8730 Score: 263
Period size: 40 Copynumber: 4.8 Consensus size: 40
8533 ACCGTAGTGC
** *
8543 TACACATAAAATCGTGCCCACCATATACACCGAAGTATAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
8583 TACACATAAGGTCGTGCCCACAATATTCACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
8623 TACAC-TAAGGTCGT-ACCACCATATTCACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
8661 TACACATAAGGCCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
8701 TACACATAAAGTCATGCCCACCATGTACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
8731 TTAGTGTCCT
Statistics
Matches: 132, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
38 27 0.20
39 17 0.13
40 88 0.67
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:16251 original size:40 final size:40
Alignment explanation
Indices: 16046--16235 Score: 308
Period size: 40 Copynumber: 4.8 Consensus size: 40
16036 ACCGTAGTGC
* * *
16046 TACACATAAGATCGTTCCCATCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
16086 TACACATAAGGTTGTGCCCACTATATTCACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
16126 TACACATAAGGTCGTGCCCACCATATTCACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
16166 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
16206 TACACATAAGGTCGTTCCCACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
16236 TTAGTGTCCT
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:18086 original size:25 final size:22
Alignment explanation
Indices: 18058--18102 Score: 54
Period size: 25 Copynumber: 1.9 Consensus size: 22
18048 ATATAAAATG
18058 CATTGATCACTGATATTATATATTA
1 CATTGATCA-TGA-A-TATATATTA
*
18083 CATTTATCATGAATATATAT
1 CATTGATCATGAATATATAT
18103 GATGTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 3 0.16
25 8 0.42
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (22 bp):
CATTGATCATGAATATATATTA
Found at i:18793 original size:21 final size:21
Alignment explanation
Indices: 18755--18805 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
18745 AGAAATGCCT
18755 TCAAAGTATTAATATAGT-TAGTA
1 TCAAA-TA-TAATATAGTAT-GTA
*
18778 TCAAATATAATTTAGTATGTA
1 TCAAATATAATATAGTATGTA
18799 -CAAATAT
1 TCAAATAT
18806 TATGATACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 3 0.12
23 5 0.19
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (21 bp):
TCAAATATAATATAGTATGTA
Found at i:31106 original size:7 final size:7
Alignment explanation
Indices: 31094--31145 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
31084 ATGATAATAC
31094 ATTATTT
1 ATTATTT
31101 ATTA-TT
1 ATTATTT
31107 ATTTATTT
1 A-TTATTT
31115 A-T-TTT
1 ATTATTT
31120 ATTA-TT
1 ATTATTT
31126 ATTATTT
1 ATTATTT
31133 ATTATTT
1 ATTATTT
31140 ATTATT
1 ATTATT
31146 CTTTTTAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.10
6 11 0.28
7 22 0.55
8 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:31107 original size:3 final size:3
Alignment explanation
Indices: 31094--31145 Score: 52
Period size: 3 Copynumber: 16.0 Consensus size: 3
31084 ATGATAATAC
31094 ATT ATTT ATT ATT ATTT ATTT ATT -TT ATT ATT ATT ATTT ATT ATTT
1 ATT A-TT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT A-TT ATT A-TT
31140 ATT ATT
1 ATT ATT
31146 CTTTTTAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.05
3 26 0.59
4 16 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:34972 original size:10 final size:11
Alignment explanation
Indices: 34953--34985 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
34943 TTAATTATGT
34953 AGATTTTTTTA
1 AGATTTTTTTA
*
34964 ATATTTTTTTA
1 AGATTTTTTTA
34975 AGATTTTTTTA
1 AGATTTTTTTA
34986 CAGTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (11 bp):
AGATTTTTTTA
Found at i:50514 original size:11 final size:11
Alignment explanation
Indices: 50498--50530 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
50488 CGATAATGTC
50498 TCGCCGGAGCA
1 TCGCCGGAGCA
*
50509 TCGCCGGAGCG
1 TCGCCGGAGCA
50520 TCGCCGGAGCA
1 TCGCCGGAGCA
50531 CCACCGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.36, G:0.39, T:0.09
Consensus pattern (11 bp):
TCGCCGGAGCA
Found at i:51042 original size:104 final size:106
Alignment explanation
Indices: 50897--51109 Score: 369
Period size: 104 Copynumber: 2.0 Consensus size: 106
50887 GCGGCACTCC
*
50897 CACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGA
1 CACCAATGGCCCGGGGTTACCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGA
*
50962 GGCCACCCGCCT-GGACTGCCGATGGTGACCGAGGCTCCCG
66 GGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACG
51002 CACCAAT-GCCC-GGGTTACCGATGGTTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCG
1 CACCAATGGCCCGGGGTTACCGATGG-TGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCG
*
51065 AGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACG
65 AGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACG
51107 CAC
1 CAC
51110 AAGCGGCCTG
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
103 12 0.12
104 55 0.53
105 36 0.35
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (106 bp):
CACCAATGGCCCGGGGTTACCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGA
GGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACG
Found at i:51100 original size:33 final size:33
Alignment explanation
Indices: 50913--51101 Score: 188
Period size: 33 Copynumber: 5.6 Consensus size: 33
50903 TGGCCCGGGG
* * *
50913 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
50945 TTGCCGATGGTGACCGAGGCCACCCGCCT-GGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
* * *
50977 CTGCCGATGGTGACCGAGGCTC-CCGCACCAATGCCCGGG
1 TTGCCGATGGTGACCGAGGC-CACC-CGCC--TG---GGA
* * * *
51016 TTACCGATGGTTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGG-TGACCGAGGCCACCCGCCTGGGA
51049 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
51082 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
51102 TCACGCACAA
Statistics
Matches: 129, Mismatches: 16, Indels: 23
0.77 0.10 0.14
Matches are distributed among these distances:
32 47 0.36
33 56 0.43
35 1 0.01
36 2 0.02
38 3 0.02
39 13 0.10
40 7 0.05
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:51260 original size:167 final size:169
Alignment explanation
Indices: 50996--51571 Score: 984
Period size: 167 Copynumber: 3.4 Consensus size: 169
50986 GTGACCGAGG
* *
50996 CTCCCGCACCAAT-GCCCGGGTTACCGATGGTTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCGGGGTTGCCGATGG-TGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* * *
51060 GACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACA-AGCGGCCTGATGG
65 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
*
51124 TGACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCA
130 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
51164 CTCCCGCACCAATGGCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTG-CGATGGTG
1 CTCCCGCACCAATGGCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
51228 ACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGGT
66 ACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGGT
* *
51293 GACCGAGGCT-CCGCACCAAAGCTCGGTACTGTGCGGCA
131 GACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
51331 CTCCCGCACCAATGGCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
1 CTCCCGCACCAATGGCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
* *
51396 ACCGAGGCCACCCG-CTTGGATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCTGATGGT
66 ACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGGT
51460 GACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 GACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
**
51499 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTGCCGATGGT
1 CTCCCGCACCAATGG-CCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
51564 GA-CGAGGC
65 GACCGAGGC
51572 ACGCACACGT
Statistics
Matches: 389, Mismatches: 14, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
167 197 0.51
168 128 0.33
169 64 0.16
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (169 bp):
CTCCCGCACCAATGGCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
ACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGGT
GACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
Found at i:51262 original size:33 final size:33
Alignment explanation
Indices: 51185--51268 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 33
51175 ATGGCCGGGG
* * *
51185 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
*
51217 TTG-CGATGGTGACCGAGGCCACCCGCCTTGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
51249 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
51269 TCACGCACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 13 0.28
32 17 0.37
33 16 0.35
ACGTcount: A:0.15, C:0.29, G:0.36, T:0.20
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:51434 original size:32 final size:33
Alignment explanation
Indices: 51355--51435 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 33
51345 GCCGGGGTTG
* * *
51355 CCGATGGTGACCGA-GACACCCGTCTGGGTTTG
1 CCGATGGTGACCGAGGCCACCCGTCTGGGATTA
*
51387 CCGATGGTGACCGAGGCCACCCG-CTTGGATTA
1 CCGATGGTGACCGAGGCCACCCGTCTGGGATTA
51419 CCGATGGTGACCGAGGC
1 CCGATGGTGACCGAGGC
51436 GCACGCACAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 37 0.84
33 7 0.16
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.19
Consensus pattern (33 bp):
CCGATGGTGACCGAGGCCACCCGTCTGGGATTA
Done.