Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000620.1 Hibiscus syriacus cultivar Beakdansim tig00001198_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: 38247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:406 original size:64 final size:64
Alignment explanation
Indices: 245--424 Score: 278
Period size: 64 Copynumber: 2.9 Consensus size: 64
235 TTTTTGACAT
* * *
245 GGTACATGAGTCATATGAGTGATCTGTACTATA--CCATTATCACTCCACCTCATGCACCACAA
1 GGTACATGAGTCATATGAGTGATATGTACTATATTCAATTATCACTCCACCTCATGCACAACAA
* *
307 GGTACATGAGT-ATATGAGTGATTTGTATTATATTCAATTATCACTCCACCTCATGCACAACAAA
1 GGTACATGAGTCATATGAGTGATATGTACTATATTCAATTATCACTCCACCTCATGCACAAC-AA
371 GGTACATGAGTCATATGAGTGATATGTA-TATATTCAATTATCACTCCACCTCAT
1 GGTACATGAGTCATATGAGTGATATGTACTATATTCAATTATCACTCCACCTCAT
425 ACCATGCCTA
Statistics
Matches: 109, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
61 19 0.17
62 11 0.10
63 25 0.23
64 39 0.36
65 15 0.14
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (64 bp):
GGTACATGAGTCATATGAGTGATATGTACTATATTCAATTATCACTCCACCTCATGCACAACAA
Found at i:1699 original size:21 final size:21
Alignment explanation
Indices: 1659--1699 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1649 TCTGGGCTAG
*
1659 GGGAATCGATACCCATTCAAT
1 GGGAATCGATACCCACTCAAT
* *
1680 GGGAATCGATTCCCCCTCAA
1 GGGAATCGATACCCACTCAA
1700 ACGAATATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
GGGAATCGATACCCACTCAAT
Found at i:2351 original size:103 final size:98
Alignment explanation
Indices: 2209--2421 Score: 329
Period size: 103 Copynumber: 2.1 Consensus size: 98
2199 AGGTAGGGTC
* *
2209 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACACATATGTATTCTTTGGAACATGTGTGA-GTCTGGT--GACACATAC
*
2274 TTGATCCTTGG-TTATGTATGATGATTCTTAAGGAATGA
63 TTGATCCTTGGCATATGTAT-A--ATTCTTAAGGAATGA
*
2312 TATGTGGTCTTTCGAGACACATATGTATTCTTTGGAACATGTGTGAGTCTGGTGACACATACTTG
1 TATGTGGTCCTTCGAGACACATATGTATTCTTTGGAACATGTGTGAGTCTGGTGACACATACTTG
2377 ATCCTTGGCATATGTATAATTCTTAAGGAATGA
66 ATCCTTGGCATATGTATAATTCTTAAGGAATGA
2410 TATGTGGTCCTT
1 TATGTGGTCCTT
2422 ATGGACATTA
Statistics
Matches: 104, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
98 26 0.25
100 21 0.20
101 7 0.07
102 7 0.07
103 43 0.41
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (98 bp):
TATGTGGTCCTTCGAGACACATATGTATTCTTTGGAACATGTGTGAGTCTGGTGACACATACTTG
ATCCTTGGCATATGTATAATTCTTAAGGAATGA
Found at i:8535 original size:21 final size:21
Alignment explanation
Indices: 8493--8535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8483 TTTCTGGGCT
*
8493 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
8514 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
8535 A
1 A
8536 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:8588 original size:20 final size:20
Alignment explanation
Indices: 8563--8600 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8553 GAATGCTAGA
*
8563 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
8583 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
8601 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:9297 original size:102 final size:103
Alignment explanation
Indices: 9073--9289 Score: 409
Period size: 102 Copynumber: 2.1 Consensus size: 103
9063 GTAGAGGGTC
9073 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
*
9138 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
9176 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGA-GTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
9240 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
9278 TATGTGGTCCTT
1 TATGTGGTCCTT
9290 ATGGACATTA
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 67 0.60
103 45 0.40
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:9344 original size:23 final size:23
Alignment explanation
Indices: 9314--9368 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
9304 ATGGCACTAT
*
9314 GGTGCAATTCTACGCGGAACTTC
1 GGTGCAATTCTACGCGGAACTTA
* *
9337 GGTGCAATTCTACGTGGCACTTA
1 GGTGCAATTCTACGCGGAACTTA
9360 GGTGCAATT
1 GGTGCAATT
9369 ATATGAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGAACTTA
Found at i:13555 original size:31 final size:31
Alignment explanation
Indices: 13502--13561 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
13492 GTGCAATTAG
* * *
13502 AAATTTCAATTTTGATATTTGATTTTTATAA
1 AAATATCAAATTTGATATTTGATATTTATAA
13533 AAATATCAAATTTGA-ATATTGATATTTAT
1 AAATATCAAATTTGATAT-TTGATATTTAT
13562 CTTGAGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (31 bp):
AAATATCAAATTTGATATTTGATATTTATAA
Found at i:14014 original size:14 final size:14
Alignment explanation
Indices: 13997--14024 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13987 ATTCAGTTTG
13997 ATCAAAATTTCAGT
1 ATCAAAATTTCAGT
14011 ATCAAAATTTCAGT
1 ATCAAAATTTCAGT
14025 TTTGATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATCAAAATTTCAGT
Found at i:19497 original size:2 final size:2
Alignment explanation
Indices: 19454--19478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19444 TGTTATTAGT
19454 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 T
19479 GTACAAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19712 original size:15 final size:15
Alignment explanation
Indices: 19692--19721 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19682 TGCATGTGTC
19692 ATTATTATATATTAT
1 ATTATTATATATTAT
*
19707 ATTATTATTTATTAT
1 ATTATTATATATTAT
19722 TTGCATGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATATATTAT
Found at i:25490 original size:15 final size:15
Alignment explanation
Indices: 25470--25520 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
25460 TTTAGTAAGT
25470 AAGAAAATCTAAGAA
1 AAGAAAATCTAAGAA
* **
25485 AAGAAAA-GTACTAA
1 AAGAAAATCTAAGAA
*
25499 AGGAAAATCTAAGAA
1 AAGAAAATCTAAGAA
25514 AAGAAAA
1 AAGAAAA
25521 GTACTAAAGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.67, C:0.06, G:0.16, T:0.12
Consensus pattern (15 bp):
AAGAAAATCTAAGAA
Found at i:25505 original size:29 final size:29
Alignment explanation
Indices: 25472--25539 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
25462 TAGTAAGTAA
25472 GAAAATCTAAGAAAAGAAAAGTACTAAAG
1 GAAAATCTAAGAAAAGAAAAGTACTAAAG
25501 GAAAATCTAAGAAAAGAAAAGTACTAAAG
1 GAAAATCTAAGAAAAGAAAAGTACTAAAG
25530 GAAAATCTAA
1 GAAAATCTAA
25540 TCACATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.62, C:0.07, G:0.16, T:0.15
Consensus pattern (29 bp):
GAAAATCTAAGAAAAGAAAAGTACTAAAG
Found at i:28866 original size:31 final size:31
Alignment explanation
Indices: 28828--28886 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28818 CTATGTAACA
28828 GTCCATATATTCCAAAGAACATAGGTAAATT
1 GTCCATATATTCCAAAGAACATAGGTAAATT
* **
28859 GTCCATATGTTCCGTAGAACATAGGTAA
1 GTCCATATATTCCAAAGAACATAGGTAA
28887 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (31 bp):
GTCCATATATTCCAAAGAACATAGGTAAATT
Found at i:30704 original size:8 final size:8
Alignment explanation
Indices: 30691--30717 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
30681 TGTATTCATC
30691 ATATCTAT
1 ATATCTAT
30699 ATATCTAT
1 ATATCTAT
30707 ATATCTAT
1 ATATCTAT
30715 ATA
1 ATA
30718 ATCCAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATCTAT
Found at i:33002 original size:31 final size:31
Alignment explanation
Indices: 32966--33025 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
32956 CCTATGTAAC
32966 TGTCCATATGTTCCGAAGAACATAGGTAAAT
1 TGTCCATATGTTCCGAAGAACATAGGTAAAT
*
32997 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTTCCGAAGAACATAGGTAA
33026 CCCTCGACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (31 bp):
TGTCCATATGTTCCGAAGAACATAGGTAAAT
Found at i:35099 original size:34 final size:34
Alignment explanation
Indices: 35025--35099 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
35015 CACCGTCAAG
* * *
35025 TCCAA-TAAGGCCCTGAGCACAAGGCGAGGAGTC
1 TCCAAGTAAGGCCCTGAACACAAAGCGAGGAGCC
*** *
35058 GGTAAGTAAGGTCCTGAACACAAAGCGAGGAGCC
1 TCCAAGTAAGGCCCTGAACACAAAGCGAGGAGCC
35092 TCCAAGTA
1 TCCAAGTA
35100 TACTTTCTCC
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.13
Consensus pattern (34 bp):
TCCAAGTAAGGCCCTGAACACAAAGCGAGGAGCC
Found at i:35189 original size:24 final size:24
Alignment explanation
Indices: 35162--35245 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
35152 TATATCAAAA
*
35162 ATCAAAACATAATCCAGGTCAAGT
1 ATCATAACATAATCCAGGTCAAGT
* *
35186 ATCATATCAAAATCCAGGTCAAGT
1 ATCATAACATAATCCAGGTCAAGT
* * *
35210 AT-ATGATCAGAATCCAGGTCAGGT
1 ATCAT-AACATAATCCAGGTCAAGT
35234 ATCATAACATAA
1 ATCATAACATAA
35246 ATCAAATCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
23 2 0.04
24 47 0.92
25 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCATAACATAATCCAGGTCAAGT
Done.