Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003995.1 Hibiscus syriacus cultivar Beakdansim tig00008705_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: 73388
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:447 original size:39 final size:39
Alignment explanation
Indices: 374--448 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
364 TCATGTGTTA
* ***
374 GTTAATTGATGCGGAGCTTTAAATTTATTTTTTATTATC
1 GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATTATC
413 GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATT
1 GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATT
449 TTATTATCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (39 bp):
GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATTATC
Found at i:4918 original size:41 final size:41
Alignment explanation
Indices: 4862--4944 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
4852 GATTAGACAT
4862 ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
1 ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
*
4903 ATATGAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
1 ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
4944 A
1 A
4945 CTCTTGGGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (41 bp):
ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
Found at i:13086 original size:18 final size:18
Alignment explanation
Indices: 13042--13080 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
13032 CCTCTGAAAT
13042 TTTTAAA-TTTTCTTATA
1 TTTTAAATTTTTCTTATA
*
13059 TTTTAAATTTTTTTTATA
1 TTTTAAATTTTTCTTATA
13077 TTTT
1 TTTT
13081 CTATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTAAATTTTTCTTATA
Found at i:14106 original size:31 final size:31
Alignment explanation
Indices: 14068--14195 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
14058 GAACCTCGGC
* *
14068 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
14099 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
14130 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * *
14161 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAGAACATAGGTA
14193 AAC
1 AAC
14196 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 51 0.65
32 25 0.32
33 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:14184 original size:63 final size:62
Alignment explanation
Indices: 14069--14192 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
14059 AACCTCGGCA
* *
14069 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
14131 ACTGTCCATATGTCTCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTA
14193 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 26 0.47
63 28 0.51
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:14333 original size:30 final size:31
Alignment explanation
Indices: 14297--14354 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
14287 TATCACATGT
* *
14297 CATATAAGCTCATAGTTTC-TTTCATATATA
1 CATATAAGCACATAGCTTCTTTTCATATATA
*
14327 CATATAATCACATAGCTTCTTTTCATAT
1 CATATAAGCACATAGCTTCTTTTCATAT
14355 TCTCATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (31 bp):
CATATAAGCACATAGCTTCTTTTCATATATA
Found at i:14478 original size:2 final size:2
Alignment explanation
Indices: 14471--14495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14461 ACATATGTTC
14471 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 A
14496 CATCACATAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18371 original size:31 final size:31
Alignment explanation
Indices: 18333--18461 Score: 116
Period size: 31 Copynumber: 4.1 Consensus size: 31
18323 GAACCTCGAC
* *
18333 AACTGTCCATAGGTCTCGAAAAACCTAGGTA
1 AACTGTCCATATGTCTCGAAAAACATAGGTA
* ** *
18364 AACTGTCCATATGTTTCTTAGAACATAGGTA
1 AACTGTCCATATGTCTCGAAAAACATAGGTA
* * *
18395 TACTGTCCATATGTCTCGAAAGATATAGGTA
1 AACTGTCCATATGTCTCGAAAAACATAGGTA
* * *
18426 AATTCTATCCATATGT-TCCGTAGAACATAGGTA
1 AA--CTGTCCATATGTCT-CGAAAAACATAGGTA
18459 AAC
1 AAC
18462 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
31 51 0.67
32 1 0.01
33 24 0.32
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTCTCGAAAAACATAGGTA
Found at i:18456 original size:33 final size:33
Alignment explanation
Indices: 18369--18460 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 33
18359 AGGTAAACTG
* * *
18369 TCCATATGTTTCTTAGAACATAGGT--ATACTG
1 TCCATATGTTCCGTAGAACATAGGTAAATACTA
* * *
18400 TCCATATG-TCTCG-AAAGATATAGGTAAATTCTA
1 TCCATATGTTC-CGTAGA-ACATAGGTAAATACTA
18433 TCCATATGTTCCGTAGAACATAGGTAAA
1 TCCATATGTTCCGTAGAACATAGGTAAA
18461 CCCTCGACCC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
30 3 0.06
31 16 0.34
33 24 0.51
34 4 0.09
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (33 bp):
TCCATATGTTCCGTAGAACATAGGTAAATACTA
Found at i:18994 original size:2 final size:2
Alignment explanation
Indices: 18987--19015 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18977 TATCTTATTC
18987 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19016 CCGCAAATAC
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:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19619 original size:64 final size:63
Alignment explanation
Indices: 19535--19688 Score: 161
Period size: 64 Copynumber: 2.4 Consensus size: 63
19525 ATGTGCATAA
* * *
19535 ATGCACTACCCATGCATCGATACACAA-AGCACCTTCGATATTTT-AATCTTAAGGGGGTGTATC
1 ATGCACTTCCTATGCATCGATACACAATAGCA--TTCGATATTTTCAATCTTAA-GGGGTGCATC
19598 G
63 G
* * * *
19599 ATGCAC-TCCTTATGCATCGATGCACTAATTGCATTCGATATTTTCATTTTTAAGGGGTGCATCG
1 ATGCACTTCC-TATGCATCGATACAC-AATAGCATTCGATATTTTCAATCTTAAGGGGTGCATCG
* *
19663 ATGCACTTCCTGTGCATAGATACACA
1 ATGCACTTCCTATGCATCGATACACA
19689 CTGAACAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
63 3 0.04
64 58 0.77
65 11 0.15
66 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (63 bp):
ATGCACTTCCTATGCATCGATACACAATAGCATTCGATATTTTCAATCTTAAGGGGTGCATCG
Found at i:28934 original size:17 final size:16
Alignment explanation
Indices: 28912--28945 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28902 TAAAAACAGT
28912 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
28929 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
28945 A
1 A
28946 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:29465 original size:25 final size:25
Alignment explanation
Indices: 29420--29467 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
29410 ATAAAGAGCC
*
29420 AAAATAAACTTAAATATACCATTAA
1 AAAATAAACTTAAACATACCATTAA
*
29445 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
29468 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATAAACTTAAACATACCATTAA
Found at i:32782 original size:19 final size:20
Alignment explanation
Indices: 32760--32803 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
32750 GAGAAAAGGT
32760 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
32779 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
32799 AAAAG
1 AAAAG
32804 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:37746 original size:17 final size:16
Alignment explanation
Indices: 37724--37757 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
37714 TAAAAACAGT
37724 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
37741 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
37757 A
1 A
37758 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:38276 original size:24 final size:24
Alignment explanation
Indices: 38232--38278 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38222 ATAAAGAGCC
*
38232 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
38256 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
38279 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:42200 original size:18 final size:16
Alignment explanation
Indices: 42168--42203 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
42158 TAAAAATATT
42168 TTATTTTTAAAATAAA
1 TTATTTTTAAAATAAA
42184 TTATTTTATAGAAATAAA
1 TTATTTT-TA-AAATAAA
42202 TT
1 TT
42204 TTATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATTTTTAAAATAAA
Found at i:51106 original size:63 final size:63
Alignment explanation
Indices: 51033--51161 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 63
51023 GGTTGCACTC
* * *
51033 TTTGATGTATCTGTTTCAAGGCATTGTTTCTTTGCTGATGGCTCCTCCAATTTATCTACTTGA
1 TTTGATGTATCTGTTTCAAGGCATTGTTCCTTTGCTGATGGATCCTCCAACTTATCTACTTGA
* *
51096 TTTGATGTATCTGTTTCAAGGCATTGTTCCTTTGCTGGTGGATCCTCCGACTTATCTACTTGA
1 TTTGATGTATCTGTTTCAAGGCATTGTTCCTTTGCTGATGGATCCTCCAACTTATCTACTTGA
51159 TTT
1 TTT
51162 TCAATATTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (63 bp):
TTTGATGTATCTGTTTCAAGGCATTGTTCCTTTGCTGATGGATCCTCCAACTTATCTACTTGA
Found at i:53635 original size:30 final size:30
Alignment explanation
Indices: 53599--53681 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 30
53589 ATGTTAATCG
* *
53599 AAATATTAATTTGACCTTATATTTTATATA
1 AAATATTAATTTAACCTTATATTTTACATA
* *
53629 AAATATTAATTTAATCTTA-A-ATTACATA
1 AAATATTAATTTAACCTTATATTTTACATA
53657 AAATATTAATTTAACCCTTATATTT
1 AAATATTAATTTAA-CCTTATATTT
53682 AATCAAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 20 0.45
29 5 0.11
30 18 0.41
31 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (30 bp):
AAATATTAATTTAACCTTATATTTTACATA
Found at i:54295 original size:2 final size:2
Alignment explanation
Indices: 54288--54315 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54278 ATTCTCTATG
54288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54316 GCTTTTGTTT
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):
TA
Found at i:54950 original size:6 final size:6
Alignment explanation
Indices: 54939--54976 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
54929 TAAAGGAAGA
* *
54939 GATTGT GATTGT GATTGT GATCGT GATTGT GATCGT GA
1 GATTGT GATTGT GATTGT GATTGT GATTGT GATTGT GA
54977 GAGTTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.05, G:0.34, T:0.42
Consensus pattern (6 bp):
GATTGT
Found at i:54956 original size:12 final size:12
Alignment explanation
Indices: 54939--54976 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
54929 TAAAGGAAGA
*
54939 GATTGTGATTGT
1 GATTGTGATCGT
54951 GATTGTGATCGT
1 GATTGTGATCGT
54963 GATTGTGATCGT
1 GATTGTGATCGT
54975 GA
1 GA
54977 GAGTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.18, C:0.05, G:0.34, T:0.42
Consensus pattern (12 bp):
GATTGTGATCGT
Found at i:65463 original size:47 final size:46
Alignment explanation
Indices: 65391--65483 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 46
65381 GAGTACTCTA
*
65391 TTGAAAGAGATATGAAATGAAGATAAGGTATCACCCTTTCCAAGAGC
1 TTGAAAGAGATATGAAATGAAGATAAGGTAT-ACCCTTACCAAGAGC
* *
65438 TTGAAAGAGATATGAACT-AAGGATAAGGTATATCCTTACCAAGAGC
1 TTGAAAGAGATATGAAATGAA-GATAAGGTATACCCTTACCAAGAGC
65484 AAAAGTGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 15 0.36
47 27 0.64
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (46 bp):
TTGAAAGAGATATGAAATGAAGATAAGGTATACCCTTACCAAGAGC
Done.