Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000673.1 Hibiscus syriacus cultivar Beakdansim tig00001307_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: 86809
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1859 original size:2 final size:2
Alignment explanation
Indices: 1847--1875 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1837 GTAAGCACAG
1847 GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1876 ATGGTGGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6035 original size:25 final size:25
Alignment explanation
Indices: 6005--6055 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5995 TCTTGAGCAG
*
6005 TAAAATCCTTTCTTAATATTTTCCA
1 TAAAATCCTTTCCTAATATTTTCCA
6030 TAAAATCCTTTCCTAATATTTTCCA
1 TAAAATCCTTTCCTAATATTTTCCA
6055 T
1 T
6056 CTATGCCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAAATCCTTTCCTAATATTTTCCA
Found at i:19138 original size:17 final size:17
Alignment explanation
Indices: 19118--19150 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19108 TATAAAGGAT
19118 TAAAAAA-ATATGTTATG
1 TAAAAAACATAT-TTATG
19135 TAAAAAACATATTTAT
1 TAAAAAACATATTTAT
19151 AAAATCGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (17 bp):
TAAAAAACATATTTATG
Found at i:30787 original size:29 final size:29
Alignment explanation
Indices: 30752--30833 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
30742 AAACTAAATT
*
30752 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
30781 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30810 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30834 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:35557 original size:29 final size:29
Alignment explanation
Indices: 35513--35603 Score: 137
Period size: 29 Copynumber: 3.0 Consensus size: 29
35503 CCCAAACCCA
*
35513 AATTAAATTGATGTCATTACTTACATCATTT
1 AATTAAA--GATGTCATTGCTTACATCATTT
35544 AATTAAAGATGTCATTGCTTACATCATTT
1 AATTAAAGATGTCATTGCTTACATCATTT
*
35573 AATTAATGATGTCATTGCTTACATCAATTT
1 AATTAAAGATGTCATTGCTTACATC-ATTT
35603 A
1 A
35604 GTTAGGTGAG
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
29 45 0.79
30 5 0.09
31 7 0.12
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (29 bp):
AATTAAAGATGTCATTGCTTACATCATTT
Found at i:36271 original size:18 final size:19
Alignment explanation
Indices: 36236--36272 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
36226 GTAGTAATTG
36236 AAATTATTAGCAATTATAT
1 AAATTATTAGCAATTATAT
36255 AAATT-TTAG-AA-TATAT
1 AAATTATTAGCAATTATAT
36271 AA
1 AA
36273 GTTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 4 0.22
19 5 0.28
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AAATTATTAGCAATTATAT
Found at i:37264 original size:21 final size:22
Alignment explanation
Indices: 37224--37264 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37214 GCTTGAATAT
*
37224 ATCTCTGTTTAGCTTGTTTCTG
1 ATCTCTGTTCAGCTTGTTTCTG
*
37246 ATCTTTGTTCAGC-TGTTTC
1 ATCTCTGTTCAGCTTGTTTC
37265 CAGAAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.10, C:0.20, G:0.17, T:0.54
Consensus pattern (22 bp):
ATCTCTGTTCAGCTTGTTTCTG
Found at i:44762 original size:2 final size:2
Alignment explanation
Indices: 44755--44785 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44745 TATATTTACA
44755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44786 AATTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45519 original size:2 final size:2
Alignment explanation
Indices: 45512--45539 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45502 AATAATTACA
45512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45540 TAATGGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45596 original size:2 final size:2
Alignment explanation
Indices: 45584--45613 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45574 AATTATATTT
*
45584 CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
45614 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:45618 original size:2 final size:2
Alignment explanation
Indices: 45613--45642 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45603 ACACACACAC
45613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45643 TAAATTGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57865 original size:19 final size:19
Alignment explanation
Indices: 57818--57865 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
57808 TATATGCATA
* *
57818 CATATATGTCCTTATCATT
1 CATATATCTTCTTATCATT
57837 CATATATCTTCTTATCATT
1 CATATATCTTCTTATCATT
57856 CATATATCTT
1 CATATATCTT
57866 ATCTCATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.02, T:0.50
Consensus pattern (19 bp):
CATATATCTTCTTATCATT
Found at i:58259 original size:23 final size:23
Alignment explanation
Indices: 58233--58296 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
58223 CAGCTCATAT
58233 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
58256 AATTACACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
58279 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
58297 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:58486 original size:103 final size:103
Alignment explanation
Indices: 58307--58529 Score: 428
Period size: 103 Copynumber: 2.2 Consensus size: 103
58297 TATAATAATG
58307 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGCCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGCCT
58372 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
* *
58410 TCCCGAAGGACCACATATCACTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGCCT
58475 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
58513 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
58530 GACCCTCGAC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.25
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGCCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:59365 original size:19 final size:19
Alignment explanation
Indices: 59341--59391 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
59331 TATTACTGGG
59341 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
59360 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
59379 ATGCATCGATGCA
1 ATGCATCGATGCA
59392 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGCCTT
Found at i:59493 original size:64 final size:64
Alignment explanation
Indices: 59360--59520 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
59350 TGCATGCCTT
* * * * *
59360 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCCTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTCCATATTAAAGAG
* *
59424 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATT-TATTTTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCCATATTAAAGAG
**
59487 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
59521 CTTCAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 80 0.94
65 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCCATATTAAAGAG
Found at i:64024 original size:23 final size:23
Alignment explanation
Indices: 63994--64057 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
63984 CAGCTCATAT
* *
63994 AATTGCACTGAAGTGTCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
64017 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
64040 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
64058 TAAAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:64247 original size:103 final size:101
Alignment explanation
Indices: 64068--64288 Score: 388
Period size: 103 Copynumber: 2.2 Consensus size: 101
64058 TAAAATAATG
* *
64068 TCCCGAAGAACCACATATCACTCCTTAAGAATCATATACATATACTATGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
*
64133 CGCCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATAC--ATATA
*
64171 TCCCGAAGGACCACATATCACTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
64236 CACCAGACTTCACACATGTTCCAAAGAATACATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATA
64272 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
64289 GACCCTCGAC
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 22 0.19
103 92 0.81
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (101 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATA
Found at i:65227 original size:64 final size:63
Alignment explanation
Indices: 65030--65254 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 63
65020 TAATGAAGGT
* * * * * * *
65030 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTTATT-TTAATGGG
* * ** *
65094 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCCTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTT-TATTTTAATGGG
**
65158 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTTATTTTAATGGG
* *
65221 AGTGCATCGATGCAATA-TCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACT-TATGCATCGATGCAC
65255 CTTCAAACAA
Statistics
Matches: 134, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
63 4 0.03
64 126 0.94
65 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTTATTTTAATGGG
Found at i:71799 original size:21 final size:22
Alignment explanation
Indices: 71756--71799 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
71746 TATATAATAA
* **
71756 TTTAATAAATTTAATAATTATT
1 TTTAATAAATTTAAAAACGATT
71778 TTTAA-AAATTTAAAAACGATT
1 TTTAATAAATTTAAAAACGATT
71799 T
1 T
71800 CTTTAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAATAAATTTAAAAACGATT
Found at i:79183 original size:10 final size:11
Alignment explanation
Indices: 79144--79208 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
79134 TTTAATTTGT
*
79144 TATATAGAATA
1 TATATATAATA
*
79155 TATTAATATAAAA
1 TA-T-ATATAATA
79168 TA-ATTATAATA
1 TATA-TATAATA
79179 TATTATATAATA
1 TA-TATATAATA
79191 TATATAT-ATA
1 TATATATAATA
79201 TATATATA
1 TATATATA
79209 TCTCTCAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
10 11 0.24
11 15 0.33
12 10 0.22
13 9 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TATATATAATA
Found at i:79187 original size:2 final size:2
Alignment explanation
Indices: 79172--79209 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
79162 ATAAAATAAT
79172 TA TA -A TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79210 CTCTCAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83394 original size:4 final size:4
Alignment explanation
Indices: 83385--83414 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
83375 TTAATTTCAC
*
83385 TAGA TAGA TAGA TAGA TAGA TAGA CAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
83415 AAAGTTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.23, T:0.23
Consensus pattern (4 bp):
TAGA
Done.