Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002733.1 Hibiscus syriacus cultivar Beakdansim tig00005637_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: 82851
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2537 original size:2 final size:2
Alignment explanation
Indices: 2530--2616 Score: 138
Period size: 2 Copynumber: 43.5 Consensus size: 2
2520 ACATTTATTC
2530 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * *
2572 TT TG TT TG TG TG TG TG TG TT TG TG TT TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2614 TG T
1 TG T
2617 TTAGGCTACA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:11563 original size:29 final size:28
Alignment explanation
Indices: 11492--11563 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
11482 TAACCCTAAT
*
11492 ATCTTACACGTGTAAGAATTGTACAGCAC
1 ATCTT-CACGTGTAAGAATTGCACAGCAC
*
11521 ATCTTCTACATGTAAGAATTGCACAGCAC
1 ATCTTC-ACGTGTAAGAATTGCACAGCAC
*
11550 ACTTTTCACGTGTA
1 A-TCTTCACGTGTA
11564 CAAAGTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 32 0.86
30 4 0.11
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (28 bp):
ATCTTCACGTGTAAGAATTGCACAGCAC
Found at i:14328 original size:24 final size:24
Alignment explanation
Indices: 14301--14352 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
14291 GTTGAATAAG
14301 ATAAAATATTCAATAACGTGTTGA
1 ATAAAATATTCAATAACGTGTTGA
* *
14325 ATAAAATATTCAATGATGTGTTGA
1 ATAAAATATTCAATAACGTGTTGA
14349 ATAA
1 ATAA
14353 TATTATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (24 bp):
ATAAAATATTCAATAACGTGTTGA
Found at i:14377 original size:10 final size:10
Alignment explanation
Indices: 14357--14389 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
14347 GAATAATATT
14357 ATAAGATAAA
1 ATAAGATAAA
14367 ATCAA-ATAAA
1 AT-AAGATAAA
14377 ATAAGATAAA
1 ATAAGATAAA
14387 ATA
1 ATA
14390 TTCAACAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.10
10 17 0.81
11 2 0.10
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (10 bp):
ATAAGATAAA
Found at i:25677 original size:24 final size:24
Alignment explanation
Indices: 25633--25682 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
25623 ATAAAGAACC
*
25633 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
25657 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
25681 AA
1 AA
25683 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:35947 original size:24 final size:24
Alignment explanation
Indices: 35903--35952 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35893 ATAAAGAACC
*
35903 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
35927 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
35951 AA
1 AA
35953 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:44423 original size:12 final size:12
Alignment explanation
Indices: 44384--44423 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
44374 ATTTTCTTCT
44384 TATTTTATTT--
1 TATTTTATTTAC
44394 TATTTTATTTATC
1 TATTTTATTTA-C
44407 T-TTTTATTTAC
1 TATTTTATTTAC
44418 TATTTT
1 TATTTT
44424 TACCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.38
11 2 0.08
12 13 0.50
13 1 0.04
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (12 bp):
TATTTTATTTAC
Found at i:48345 original size:69 final size:69
Alignment explanation
Indices: 48251--48400 Score: 246
Period size: 69 Copynumber: 2.2 Consensus size: 69
48241 AATGGTCAAA
* *
48251 TGAGAAAGAGAGGGAAGGAACGTCTTTGCCGGTATGGACTGAAGCTTCGGACAGTTGAAGATATG
1 TGAGAAAGAGAGAGAAGGAACGTCTTTGCCGGTATGGACAGAAGCTTCGGACAGTTGAAGATATG
48316 CAAC
66 CAAC
* * *
48320 TGAGAAAGAGAGAGAAGGAATGTCTTTGCCGGTATGGACAGAAGCTTCGGACAGTTGTAGATATT
1 TGAGAAAGAGAGAGAAGGAACGTCTTTGCCGGTATGGACAGAAGCTTCGGACAGTTGAAGATATG
48385 CAAC
66 CAAC
*
48389 TCAGAAAGAGAG
1 TGAGAAAGAGAG
48401 GTGGTGTTGA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (69 bp):
TGAGAAAGAGAGAGAAGGAACGTCTTTGCCGGTATGGACAGAAGCTTCGGACAGTTGAAGATATG
CAAC
Found at i:49292 original size:18 final size:17
Alignment explanation
Indices: 49265--49303 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
49255 ATCGTTGTTT
49265 TAAT-AAATTTTAGTTAA
1 TAATAAAATTTTA-TTAA
49282 TAATAAAATTTTATTAA
1 TAATAAAATTTTATTAA
49299 -AATAA
1 TAATAA
49304 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATAAAATTTTATTAA
Found at i:51331 original size:9 final size:9
Alignment explanation
Indices: 51319--51360 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
51309 ATATGAAGTG
51319 AGTGAAATT
1 AGTGAAATT
51328 AGTGAAA-T
1 AGTGAAATT
* *
51336 A-TGAAGTG
1 AGTGAAATT
51344 AGTGAAATT
1 AGTGAAATT
51353 AGTGAAAT
1 AGTGAAAT
51361 ATTTGTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
7 4 0.15
8 3 0.11
9 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AGTGAAATT
Found at i:51339 original size:25 final size:25
Alignment explanation
Indices: 51305--51362 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
51295 GAAGTTGAAA
51305 TGAAATATGAAGTGAGTGAAATTAG
1 TGAAATATGAAGTGAGTGAAATTAG
51330 TGAAATATGAAGTGAGTGAAATTAG
1 TGAAATATGAAGTGAGTGAAATTAG
51355 TGAAATAT
1 TGAAATAT
51363 TTGTTTCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (25 bp):
TGAAATATGAAGTGAGTGAAATTAG
Found at i:52154 original size:21 final size:21
Alignment explanation
Indices: 52109--52175 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
52099 GGGTTAAAAC
* * *
52109 CTTTCGATGAAAGGACATAAC
1 CTTTCGATAAAAGGACTTAAT
* *
52130 CTTTCGATTAAAGGACTTATT
1 CTTTCGATAAAAGGACTTAAT
* *
52151 CTTTTGATAAAAGGATTTAAT
1 CTTTCGATAAAAGGACTTAAT
52172 CTTT
1 CTTT
52176 TCATGAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (21 bp):
CTTTCGATAAAAGGACTTAAT
Found at i:57548 original size:69 final size:68
Alignment explanation
Indices: 57457--57610 Score: 236
Period size: 69 Copynumber: 2.2 Consensus size: 68
57447 TGTACAAACG
*
57457 AGAAAGAGATGGGAGGAACGTCTTTTCCGGCATGGACTGAAGCTTCGGACAGTAGTTGATACTCA
1 AGAAAGAGA-GGGAGGAACGTCTTTTCCGGCATGGACTGAAGCTTCGGACAGTAGTTGATACCCA
* *
57522 ATTC
65 AATA
* *
57526 AGAAAGAGAGGGAAGGAGCGTCTTTTCCGGTATGGACTGAAGCTTCGGACAGTAGTTGATACCCA
1 AGAAAGAGAGGG-AGGAACGTCTTTTCCGGCATGGACTGAAGCTTCGGACAGTAGTTGATACCCA
57591 AATA
65 AATA
57595 AGAAAGAGAGGTGAGG
1 AGAAAGAGAGG-GAGG
57611 TGTTGAAGGC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
68 3 0.04
69 74 0.95
70 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (68 bp):
AGAAAGAGAGGGAGGAACGTCTTTTCCGGCATGGACTGAAGCTTCGGACAGTAGTTGATACCCAA
ATA
Found at i:62194 original size:21 final size:21
Alignment explanation
Indices: 62157--62196 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62147 ATATTTCTTC
*
62157 TTTATATGAAATATTTATCAA
1 TTTATATAAAATATTTATCAA
62178 TTTATCATAAAAT-TTTATC
1 TTTAT-ATAAAATATTTATC
62197 GTTTGATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTATATAAAATATTTATCAA
Found at i:63387 original size:27 final size:27
Alignment explanation
Indices: 63349--63405 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
63339 CATACATAAG
63349 TGTTTAAATTAATCTGTTATTGTTAAC
1 TGTTTAAATTAATCTGTTATTGTTAAC
*
63376 TGTTTAAATTAATTTGTTATTGTTAAC
1 TGTTTAAATTAATCTGTTATTGTTAAC
63403 TGT
1 TGT
63406 AATCATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.54
Consensus pattern (27 bp):
TGTTTAAATTAATCTGTTATTGTTAAC
Found at i:65477 original size:20 final size:20
Alignment explanation
Indices: 65452--65503 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
65442 CTCGGAGGGA
65452 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
65472 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
65492 ACCGATTCCCCC
1 ACCGATTCCCCC
65504 TGTGTAACGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.44, G:0.25, T:0.15
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:71305 original size:20 final size:22
Alignment explanation
Indices: 71277--71328 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
71267 TAGAGAAAAT
*
71277 CGATACCCCCATG-AG-GGAAC
1 CGATTCCCCCATGAAGAGGAAC
**
71297 CGATTCCCCTTTGAAGAGGAAC
1 CGATTCCCCCATGAAGAGGAAC
71319 CGATTCCCCC
1 CGATTCCCCC
71329 CACAGGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 2 0.08
22 14 0.54
ACGTcount: A:0.25, C:0.37, G:0.21, T:0.17
Consensus pattern (22 bp):
CGATTCCCCCATGAAGAGGAAC
Found at i:74592 original size:88 final size:89
Alignment explanation
Indices: 74485--74661 Score: 311
Period size: 88 Copynumber: 2.0 Consensus size: 89
74475 GAAGGATTTG
74485 GGTGAACTTAAAGTATTTCTTGGGAATTGAAGTATTGAGGTCAAAGGAATGTATACTTTTGAATA
1 GGTGAACTTAAAGTATTTCTTGGGAATTGAAGTATTGAGGTCAAAGGAATGTATACTTTTGAATA
* *
74550 AAATGAAGTATGCACTTCATTTAA
66 AAATGAAGTATACACTTCAGTTAA
* *
74574 GGTGAACTT-AAGTATTTCTTGGGAATTGAAGTATTGAGGTCAAAGGAATGTATATTTTTGAATC
1 GGTGAACTTAAAGTATTTCTTGGGAATTGAAGTATTGAGGTCAAAGGAATGTATACTTTTGAATA
74638 AAATGAAGTATACACTTCAGTTAA
66 AAATGAAGTATACACTTCAGTTAA
74662 TCAAAGATAC
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
88 75 0.89
89 9 0.11
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (89 bp):
GGTGAACTTAAAGTATTTCTTGGGAATTGAAGTATTGAGGTCAAAGGAATGTATACTTTTGAATA
AAATGAAGTATACACTTCAGTTAA
Found at i:75909 original size:17 final size:17
Alignment explanation
Indices: 75887--75936 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
75877 AAATTCTTCT
75887 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
75904 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
75918 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
75935 AA
1 AA
75937 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:76511 original size:2 final size:2
Alignment explanation
Indices: 76464--76495 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
76454 ACCTGCCATG
76464 TA TA -A TA TA TA 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 T
76496 GGATGGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.