Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000033.1 Hibiscus syriacus cultivar Beakdansim tig00000054_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: 78353
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:5566 original size:13 final size:13
Alignment explanation
Indices: 5527--5568 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5517 AGAAAAATAT
*
5527 TAAATTATTTGTA
1 TAAAATATTTGTA
5540 TAAAA-A-TT-TA
1 TAAAATATTTGTA
5550 TAAAATATTTGTA
1 TAAAATATTTGTA
5563 TAAAAT
1 TAAAAT
5569 TTAGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.28
11 3 0.12
12 3 0.12
13 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
TAAAATATTTGTA
Found at i:5567 original size:22 final size:23
Alignment explanation
Indices: 5519--5576 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
5509 TAAGCCGTAG
* *
5519 AAAAATAT-TAAATTATTTGTAT
1 AAAAATTTATAAAATATTTGTAT
5541 AAAAATTTATAAAATATTTGTAT
1 AAAAATTTATAAAATATTTGTAT
*
5564 -AAAATTTAGAAAA
1 AAAAATTTATAAAA
5577 ATATATTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
AAAAATTTATAAAATATTTGTAT
Found at i:5577 original size:23 final size:23
Alignment explanation
Indices: 5532--5580 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5522 AATATTAAAT
*
5532 TATTTGTATAAAAATTTATAAAA
1 TATTTGTATAAAAATTTAAAAAA
5555 TATTTGTAT-AAAATTTAGAAAAA
1 TATTTGTATAAAAATTTA-AAAAA
5578 TAT
1 TAT
5581 ATTCCACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
TATTTGTATAAAAATTTAAAAAA
Found at i:6103 original size:31 final size:31
Alignment explanation
Indices: 6068--6127 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
6058 GTGTTCGCCC
* *
6068 TGCTTACTAATGTAATATGATCATGTATTGA
1 TGCTTACTAATGTAATAAGATAATGTATTGA
** *
6099 TGCTTGTTACTGTAATAAGATAATGTATT
1 TGCTTACTAATGTAATAAGATAATGTATT
6128 AGTTCTTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (31 bp):
TGCTTACTAATGTAATAAGATAATGTATTGA
Found at i:17836 original size:21 final size:21
Alignment explanation
Indices: 17810--17849 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17800 CCCCCTTTGA
*
17810 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
17831 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
17850 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:29950 original size:76 final size:76
Alignment explanation
Indices: 29824--29968 Score: 263
Period size: 76 Copynumber: 1.9 Consensus size: 76
29814 CGTGCATGCA
* *
29824 TCCAGCCTATTTAATGTTTATATGATTTGTATTTTTGTAGAAATAATTTTAAAAACTGTGCTCTT
1 TCCAGCCTATATAATGTTTATATGATTTGTATTTTTATAGAAATAATTTTAAAAACTGTGCTCTT
29889 AGCAGTATTAT
66 AGCAGTATTAT
*
29900 TCCAGCCTATATAATGTTTATATGATTTGTATTTTTATAGAAATAATTTTAAAAATTGTGCTCTT
1 TCCAGCCTATATAATGTTTATATGATTTGTATTTTTATAGAAATAATTTTAAAAACTGTGCTCTT
29965 AGCA
66 AGCA
29969 CTATAGCAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (76 bp):
TCCAGCCTATATAATGTTTATATGATTTGTATTTTTATAGAAATAATTTTAAAAACTGTGCTCTT
AGCAGTATTAT
Found at i:34201 original size:342 final size:342
Alignment explanation
Indices: 33576--34265 Score: 1353
Period size: 342 Copynumber: 2.0 Consensus size: 342
33566 TGTTCCCTAA
33576 TGCATTAAAACATTTTGAGAAATTGAGGTGTACTTGTTTATTGGGAATTCTAGTGTTCACCTTGC
1 TGCATTAAAACATTTTGAGAAATTGAGGTGTACTTGTTTATTGGGAATTCTAGTGTTCACCTTGC
33641 AGAAAAGTAAAAAAAATCATTGACTGAAGTTTTCAAGTTGCTATATATGAATTTAAGTTTTTACT
66 AGAAAAGTAAAAAAAATCATTGACTGAAGTTTTCAAGTTGCTATATATGAATTTAAGTTTTTACT
* * *
33706 AGTACAAATACTTTTTTTTTTAGGTTTTTATTGATTTCATTGGTTTTGCTGGATGACTACTTCTG
131 ACTACAAATACATTTTTTTTTAGGTTTTTATTGATTCCATTGGTTTTGCTGGATGACTACTTCTG
33771 AATAAGCTAATTTGGTTTCTTCAACAAGGTTTTCATATCTCTAAATCTAATTCTTCTTGAAAAGA
196 AATAAGCTAATTTGGTTTCTTCAACAAGGTTTTCATATCTCTAAATCTAATTCTTCTTGAAAAGA
33836 TAGCAGTGGCCACCACATCTCTAGTTTTGTTGTAGCAATCTTTTCATTCTATAATATCTCTCCAT
261 TAGCAGTGGCCACCACATCTCTAGTTTTGTTGTAGCAATCTTTTCATTCTATAATATCTCTCCAT
33901 GCTTCAGAATGAATTTT
326 GCTTCAGAATGAATTTT
33918 TGCATTAAAACATTTTGAGAAATTGAGGTGTACTTGTTTATTGGGAATTCTAGTGTTCACCTTGC
1 TGCATTAAAACATTTTGAGAAATTGAGGTGTACTTGTTTATTGGGAATTCTAGTGTTCACCTTGC
33983 AGAAAAGTAAAAAAAATCATTGACTGAAGTTTTCAAGTTGCTATATATGAATTTAAGTTTTTACT
66 AGAAAAGTAAAAAAAATCATTGACTGAAGTTTTCAAGTTGCTATATATGAATTTAAGTTTTTACT
34048 ACTACAAATACATTTTTTTTTAGGTTTTTATTGATTCCATTGGTTTTGCTGGATGACTACTTCTG
131 ACTACAAATACATTTTTTTTTAGGTTTTTATTGATTCCATTGGTTTTGCTGGATGACTACTTCTG
34113 AATAAGCTAATTTGGTTTCTTCAACAAGGTTTTCATATCTCTAAATCTAATTCTTCTTGAAAAGA
196 AATAAGCTAATTTGGTTTCTTCAACAAGGTTTTCATATCTCTAAATCTAATTCTTCTTGAAAAGA
34178 TAGCAGTGGCCACCACATCTCTAGTTTTGTTGTAGCAATCTTTTCATTCTATAATATCTCTCCAT
261 TAGCAGTGGCCACCACATCTCTAGTTTTGTTGTAGCAATCTTTTCATTCTATAATATCTCTCCAT
34243 GCTTCAGAATGAATTTT
326 GCTTCAGAATGAATTTT
34260 TGCATT
1 TGCATT
34266 TTCTGCATTT
Statistics
Matches: 345, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
342 345 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (342 bp):
TGCATTAAAACATTTTGAGAAATTGAGGTGTACTTGTTTATTGGGAATTCTAGTGTTCACCTTGC
AGAAAAGTAAAAAAAATCATTGACTGAAGTTTTCAAGTTGCTATATATGAATTTAAGTTTTTACT
ACTACAAATACATTTTTTTTTAGGTTTTTATTGATTCCATTGGTTTTGCTGGATGACTACTTCTG
AATAAGCTAATTTGGTTTCTTCAACAAGGTTTTCATATCTCTAAATCTAATTCTTCTTGAAAAGA
TAGCAGTGGCCACCACATCTCTAGTTTTGTTGTAGCAATCTTTTCATTCTATAATATCTCTCCAT
GCTTCAGAATGAATTTT
Found at i:38332 original size:15 final size:15
Alignment explanation
Indices: 38312--38343 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38302 CAATGGACAC
*
38312 AAGTCATTTTGCTAT
1 AAGTCATTTAGCTAT
38327 AAGTCATTTAGCTAT
1 AAGTCATTTAGCTAT
38342 AA
1 AA
38344 CCCATGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
AAGTCATTTAGCTAT
Found at i:40121 original size:4 final size:4
Alignment explanation
Indices: 40112--40195 Score: 54
Period size: 4 Copynumber: 22.5 Consensus size: 4
40102 ACATAATTAT
* * * *
40112 TATA TATA TATA -ATA T-TA -ATA AATT TA-A TTTA AATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
40156 TATA TATA TA-A TATT TATA TATT TA-A TTTA AATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
40196 CCCGGCCCGA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
3 12 0.20
4 47 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:40123 original size:6 final size:6
Alignment explanation
Indices: 40112--40195 Score: 54
Period size: 6 Copynumber: 15.0 Consensus size: 6
40102 ACATAATTAT
* * * *
40112 TATATA TATATA -ATAT- TA-ATA AATTTA -ATTTA AATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
40156 TATATA TATA-A TATTTA TATATT TA-ATT TAAATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA
40196 CCCGGCCCGA
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
4 2 0.03
5 20 0.32
6 41 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:40165 original size:42 final size:42
Alignment explanation
Indices: 40112--40195 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
40102 ACATAATTAT
40112 TATATATATATAATATTAATAAATTTAATTTAAATATATATA
1 TATATATATATAATATTAATAAATTTAATTTAAATATATATA
* *
40154 TATATATATATAATATTTATATATTTAATTTAAATATATATA
1 TATATATATATAATATTAATAAATTTAATTTAAATATATATA
40196 CCCGGCCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
TATATATATATAATATTAATAAATTTAATTTAAATATATATA
Found at i:60081 original size:27 final size:27
Alignment explanation
Indices: 60051--60114 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
60041 TTTACTGGCT
* *
60051 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAAAATATACTTCTGTG
*
60078 CTGAATCGTTCAAAATATACTTCTGTG
1 CTGAATCATTCAAAATATACTTCTGTG
60105 CTGAATCATT
1 CTGAATCATT
60115 TAACACTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAAAATATACTTCTGTG
Found at i:60209 original size:22 final size:22
Alignment explanation
Indices: 60181--60241 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
60171 GCGCTGAATG
*
60181 CTGAACGGTTCAACATTCAATA
1 CTGAACGATTCAACATTCAATA
60203 CTGAACGATTCAACATTCAATA
1 CTGAACGATTCAACATTCAATA
**
60225 CTGAATAATTCAACATT
1 CTGAACGATTCAACATT
60242 TAACGTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (22 bp):
CTGAACGATTCAACATTCAATA
Found at i:61121 original size:19 final size:20
Alignment explanation
Indices: 61081--61131 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
61071 TTCTTTTTAA
*
61081 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
61101 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
61120 CGTTGCGATTTT
1 CGTTGCGATTTT
61132 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:67452 original size:23 final size:23
Alignment explanation
Indices: 67420--67463 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
67410 TGTTCGTTAA
67420 TTCGCAAACATGTTCGTTTAGTG
1 TTCGCAAACATGTTCGTTTAGTG
*
67443 TTCGCGAACATGTTCGTTTAG
1 TTCGCAAACATGTTCGTTTAG
67464 AATAAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (23 bp):
TTCGCAAACATGTTCGTTTAGTG
Found at i:68868 original size:9 final size:9
Alignment explanation
Indices: 68854--68881 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
68844 TTAATATCCT
68854 TGTGCCAGA
1 TGTGCCAGA
68863 TGTGCCAGA
1 TGTGCCAGA
68872 TGTGCCAGA
1 TGTGCCAGA
68881 T
1 T
68882 TTATGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.25
Consensus pattern (9 bp):
TGTGCCAGA
Found at i:68970 original size:25 final size:25
Alignment explanation
Indices: 68915--68975 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
68905 ACAAGTATAG
68915 GGGCATAAAATTATTATCTCGCCCA
1 GGGCATAAAATTATTATCTCGCCCA
** *
68940 TAGCATAAAATTATTATCTCGCTCA
1 GGGCATAAAATTATTATCTCGCCCA
68965 GGGCATTAAAA
1 GGGCA-TAAAA
68976 CTCATTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (25 bp):
GGGCATAAAATTATTATCTCGCCCA
Found at i:77472 original size:48 final size:48
Alignment explanation
Indices: 77416--77517 Score: 188
Period size: 48 Copynumber: 2.1 Consensus size: 48
77406 CATATTCTTA
77416 TTGTATTCTTTTATCTTAC-TTTTTTTTCTCCTTTTAACCTTTTAATTT
1 TTGTATTCTTTTATCTTACTTTTTTTTTCTCCTTTTAACCTTTTAA-TT
77464 TTGTATTCTTTTATCTTACTTTTTTTTTCTCCTTTTAACCTTTTAATT
1 TTGTATTCTTTTATCTTACTTTTTTTTTCTCCTTTTAACCTTTTAATT
77512 TTGTAT
1 TTGTAT
77518 ATTTAAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 27 0.51
49 26 0.49
ACGTcount: A:0.15, C:0.16, G:0.03, T:0.67
Consensus pattern (48 bp):
TTGTATTCTTTTATCTTACTTTTTTTTTCTCCTTTTAACCTTTTAATT
Found at i:77488 original size:24 final size:24
Alignment explanation
Indices: 77416--77489 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
77406 CATATTCTTA
77416 TTGTATTCTTTTATCTTACTTTTT
1 TTGTATTCTTTTATCTTACTTTTT
* * *
77440 TT-TCTCCTTTTAACCTT--TTAATTT
1 TTGTATTCTTTT-ATCTTACTT--TTT
77464 TTGTATTCTTTTATCTTACTTTTT
1 TTGTATTCTTTTATCTTACTTTTT
77488 TT
1 TT
77490 TTCTCCTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 20 0.53
25 7 0.18
26 2 0.05
ACGTcount: A:0.14, C:0.15, G:0.03, T:0.69
Consensus pattern (24 bp):
TTGTATTCTTTTATCTTACTTTTT
Found at i:77498 original size:24 final size:24
Alignment explanation
Indices: 77423--77500 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
77413 TTATTGTATT
77423 CTTTTATCTTAC-TTTTTTTTCTC
1 CTTTTATCTTACTTTTTTTTTCTC
* * * *
77446 CTTTTAACCTT--TTAATTTTTGTATT
1 CTTTT-ATCTTACTT--TTTTTTTCTC
77471 CTTTTATCTTACTTTTTTTTTCTC
1 CTTTTATCTTACTTTTTTTTTCTC
77495 CTTTTA
1 CTTTTA
77501 ACCTTTTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
23 6 0.15
24 21 0.51
25 12 0.29
26 2 0.05
ACGTcount: A:0.13, C:0.18, G:0.01, T:0.68
Consensus pattern (24 bp):
CTTTTATCTTACTTTTTTTTTCTC
Found at i:77622 original size:22 final size:22
Alignment explanation
Indices: 77596--77644 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
77586 GTCTATATCC
*
77596 TTATAACACATTTT-TTATGTTA
1 TTATAACACATTTTCTTA-ATTA
*
77618 TTATAATACATTTTCTTAATTA
1 TTATAACACATTTTCTTAATTA
77640 TTATA
1 TTATA
77645 GTATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATAACACATTTTCTTAATTA
Done.