Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007191.1 Hibiscus syriacus cultivar Beakdansim tig00018953_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: 29467
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:118 original size:23 final size:23
Alignment explanation
Indices: 92--139 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
82 ATTTTGTATG
92 GTATGCGCCTTTAATGGATGCTT
1 GTATGCGCCTTTAATGGATGCTT
*
115 GTATGTGCCTTTAATGGATGCTT
1 GTATGCGCCTTTAATGGATGCTT
138 GT
1 GT
140 GTAGATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.42
Consensus pattern (23 bp):
GTATGCGCCTTTAATGGATGCTT
Found at i:389 original size:45 final size:45
Alignment explanation
Indices: 331--687 Score: 583
Period size: 45 Copynumber: 8.0 Consensus size: 45
321 ATTTAATATA
* *
331 ATAACGGTTCATTAAAGGCATGAAAGGATGCCATAAATAATATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* *
376 ATAACGGTGCATTAAAGGCATGAAAGGGTGACATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
** *
421 ATAACGGTGCATTAAAGAAATGAAAGGATGACATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
*
466 ATAACAGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAA-GC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
*
510 ATAACGGTTCATTAAAGGCATGAAAGGATGCCA-AAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
554 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* *
599 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAATTGT
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
*
644 ATAACGGTGCATTAAAGGCATGAAAGGATGACATAAATGAAAAT
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAAT-AAAAT
688 AATGAATAAT
Statistics
Matches: 291, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
43 8 0.03
44 67 0.23
45 212 0.73
46 4 0.01
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.21
Consensus pattern (45 bp):
ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
Found at i:636 original size:178 final size:180
Alignment explanation
Indices: 331--686 Score: 608
Period size: 178 Copynumber: 2.0 Consensus size: 180
321 ATTTAATATA
*
331 ATAACGGTTCATTAAAGGCATGAAAGGATGCCATAAATAATATGCATAACGGTGCATTAAAGGCA
1 ATAACGGTTCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTGCATTAAAGGCA
*
396 TGAAAGGGTGACATAAATAAAATGCATAACGGTGCATTAAAGAAATGAAAGGATGACATAAATAA
66 TGAAAGGATGACATAAATAAAATGCATAACGGTGCATTAAAGAAATGAAAGGATGACATAAATAA
*
461 AATGCATAACAGTGCATTAAAGGCATGAAAGGATGCCATAAAT-AAAAGC
131 AATGCATAACAGTGCATTAAAGGCATGAAAGGATGACATAAATGAAAAGC
510 ATAACGGTTCATTAAAGGCATGAAAGGATGCCA-AAATAAAATGCATAACGGTGCATTAAAGGCA
1 ATAACGGTTCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTGCATTAAAGGCA
* ** *
574 TGAAAGGATGCCATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAA
66 TGAAAGGATGACATAAATAAAATGCATAACGGTGCATTAAAGAAATGAAAGGATGACATAAATAA
* * *
639 ATTGTATAACGGTGCATTAAAGGCATGAAAGGATGACATAAATGAAAA
131 AATGCATAACAGTGCATTAAAGGCATGAAAGGATGACATAAATGAAAA
687 TAATGAATAA
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
178 129 0.78
179 37 0.22
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.21
Consensus pattern (180 bp):
ATAACGGTTCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTGCATTAAAGGCA
TGAAAGGATGACATAAATAAAATGCATAACGGTGCATTAAAGAAATGAAAGGATGACATAAATAA
AATGCATAACAGTGCATTAAAGGCATGAAAGGATGACATAAATGAAAAGC
Found at i:4017 original size:16 final size:16
Alignment explanation
Indices: 3988--4029 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3978 TTTTTGAATT
3988 AATTAAA-A-TTTATA
1 AATTAAATATTTTATA
*
4002 AATTATATATTTTATA
1 AATTAAATATTTTATA
*
4018 TATTAAATATTT
1 AATTAAATATTT
4030 ATTTTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 1 0.04
16 16 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAAATATTTTATA
Found at i:4103 original size:2 final size:2
Alignment explanation
Indices: 4096--4128 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4086 CTAAGTAGTG
4096 TA TA TA TA -A TA T- 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 T
4129 TTAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4113 original size:12 final size:13
Alignment explanation
Indices: 4096--4135 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
4086 CTAAGTAGTG
4096 TATATATAATATTA
1 TATATATAATA-TA
4110 TATATATATATATA
1 TATATATA-ATATA
*
4124 TATATTTAATAT
1 TATATATAATAT
4136 TTTGATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATAATATA
Found at i:4285 original size:433 final size:425
Alignment explanation
Indices: 3449--4300 Score: 1083
Period size: 433 Copynumber: 2.0 Consensus size: 425
3439 GCTACTCAAA
* *
3449 ATTCATTAATTGATTTTTCCTTTTAATCGTTAACTGAATTAAATTTTTTTCAGAAATTTTTAACG
1 ATTCATTAATTGATTTTTCCTTTTAATCGTTAACTGAATTAAATCTTTTTCAGAAAGTTTTAACG
* *
3514 TAATCGAATAAAGTTTGGTTAATTCGATCAATTTTTGAATTAATTGAAATTTTTAAATAATATAT
66 TAATCGAATAAAGTTTGGTTAATTCGATCAATTTTTGAATTAATTAAAATTTATAAATAATATAT
*
3579 TTTATATATTAAATATTTAATATTTTTGGTTAATTCGATTAATTTGGTTAAAATCAAAGTTTGAA
131 TTTATATATTAAATATTTAATATTTTTGGTTAATTCGATTAATTTGGTTAAAAACAAAGTTTGAA
* *
3644 TACTCCTAAGACTAAGTAGTATTTAAATAATATATATAATATATATATTTTAACATTTCGATTAA
196 TACCCCTAAGACTAAGTAGTATATAAATAATATATATAATATATATATTTTAACATTTCGATTAA
* * * * * * *
3709 TCAGTTCATTCGATTAATTAACAGATTTCAAATCGAATTAGCAAAGCCAAGTTTGAAAAATCATT
261 TCAGTTAAGTCGATTAATTAACAGATTTCAAATCGAATTAACAAAACCAAATTTAAAAAATCACT
* * * * *
3774 AATTGTTAAACAATCAAACTTCAAATTAAAAAATTGATAACCAAAAAACTTCAGTTCGATTGGTT
326 AATGGTTAAACAATCAAACTTCAAATCAAAAAACTAATAACCAAAAAA---CAGTTCGATTCG-T
3839 AATTCAATAAAACCCAAAATTTAAACACCCTTAACTCATAG
387 -ATTCAATAAAA-CCAAAATTTAAACACCCTTAACTCATAG
* * *
3880 ATTCATTAATTTACTTTTTTTCTTTTAATCGTTAACTGAATTGAAA-CTTTTTCATAAAGTTTTA
1 ATTCATTAATTGA--TTTTTCCTTTTAATCGTTAACTGAATT-AAATCTTTTTCAGAAAGTTTTA
* * *
3944 ACGTAATCGAATAAAGTTTGGTTAATTCGGTCGATTTTTGAATTAATTAAAATTTATAAATTATA
63 ACGTAATCGAATAAAGTTTGGTTAATTCGATCAATTTTTGAATTAATTAAAATTTATAAATAATA
* * *
4009 TATTTTATATATTAAATATTT-AT-TTTTTTGTTAATTTGATTAATTTGGTTAAAAACGAAGTTT
128 TATTTTATATATTAAATATTTAATATTTTTGGTTAATTCGATTAATTTGGTTAAAAACAAAGTTT
* *
4072 GAATACCCCTAAGACTAAGTAGTGTATATATAATATTATATATATATATATATATATTTAATATT
193 GAATACCCCTAAGACTAAGTA--GTATATA-AATAATATATATA-ATATATATAT-TTTAACATT
* * * *
4137 TTGATTAATCAG-TAAGTCGGTTAATTAATC-GGTTTCGAATCGAATTAACTAATAACCGAAATT
253 TCGATTAATCAGTTAAGTCGATTAATTAA-CAGATTTCAAATCGAATTAAC-AA-AACC-AAATT
* * *
4200 TAAAAAAAAATCACTAATGGTTAACCAATCGAACTTCAAATCAATAAACTAATTAACCAAAAAA-
314 T---AAAAAATCACTAATGGTTAAACAATCAAACTTCAAATCAAAAAACTAA-TAACCAAAAAAC
* * *
4264 AG-TCGGTTCG-ATT-ATTAAAACCTAAATTTAAACACCC
375 AGTTCGATTCGTATTCAATAAAACCAAAATTTAAACACCC
4301 CTAATTCTCT
Statistics
Matches: 365, Mismatches: 40, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
431 68 0.19
432 18 0.05
433 134 0.37
434 18 0.05
435 39 0.11
436 22 0.06
437 9 0.02
438 7 0.02
441 39 0.11
442 11 0.03
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (425 bp):
ATTCATTAATTGATTTTTCCTTTTAATCGTTAACTGAATTAAATCTTTTTCAGAAAGTTTTAACG
TAATCGAATAAAGTTTGGTTAATTCGATCAATTTTTGAATTAATTAAAATTTATAAATAATATAT
TTTATATATTAAATATTTAATATTTTTGGTTAATTCGATTAATTTGGTTAAAAACAAAGTTTGAA
TACCCCTAAGACTAAGTAGTATATAAATAATATATATAATATATATATTTTAACATTTCGATTAA
TCAGTTAAGTCGATTAATTAACAGATTTCAAATCGAATTAACAAAACCAAATTTAAAAAATCACT
AATGGTTAAACAATCAAACTTCAAATCAAAAAACTAATAACCAAAAAACAGTTCGATTCGTATTC
AATAAAACCAAAATTTAAACACCCTTAACTCATAG
Found at i:10969 original size:23 final size:22
Alignment explanation
Indices: 10943--11006 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
10933 CAGCTCATAT
10943 AATTGCACCTAAGTGCCACGTAA
1 AATTGCACCT-AGTGCCACGTAA
* * * * *
10966 AATTGAACCGGAGTGTCGCGTAG
1 AATTGCACC-TAGTGCCACGTAA
10989 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
11007 TATAATAATG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAA
Found at i:11293 original size:103 final size:103
Alignment explanation
Indices: 11022--11341 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
11012 TAATGTCCAT
*
11022 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
11087 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
11125 AAGGACCACATAACATT-TTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
11189 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
11227 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGTTCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
11292 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
11330 AAGGACCACATA
1 AAGGACCACATA
11342 GACCCTCTAC
Statistics
Matches: 205, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
102 96 0.47
103 109 0.53
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:11862 original size:18 final size:19
Alignment explanation
Indices: 11825--11861 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11815 TTTTTTATTA
*
11825 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
11844 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
11862 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:11913 original size:21 final size:21
Alignment explanation
Indices: 11889--11931 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11879 TCATATTCGT
* *
11889 TTGAGGGGGTATTGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
**
11910 TTGAATTGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
11931 T
1 T
11932 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:18008 original size:23 final size:23
Alignment explanation
Indices: 17982--18034 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
17972 CAGCTCATAT
*
17982 AATTGCACCTAAGTGCCACGTAA
1 AATTGCACCGAAGTGCCACGTAA
* * *
18005 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAA
18028 AATTGCA
1 AATTGCA
18035 TAGTAGTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAA
Found at i:18042 original size:23 final size:23
Alignment explanation
Indices: 17993--18045 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
17983 ATTGCACCTA
*
17993 AGTGCCACGTAAAATTGCACCGG
1 AGTGCCACGTAAAATTGCACAGG
* * * *
18016 AGTGCCGCGTAGAATTGCATAGT
1 AGTGCCACGTAAAATTGCACAGG
18039 AGTGCCA
1 AGTGCCA
18046 TATAATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAAAATTGCACAGG
Found at i:18237 original size:103 final size:103
Alignment explanation
Indices: 18061--18381 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
18051 TAATGTCCAT
*
18061 AAGGACCACATATCATTCCTTAAGAATCATATACATATTCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
18126 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
18164 AAGGACCACATATCATTCCTTAATAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* * *
18229 GACCTCACACATGTTCTAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
18267 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
18332 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
18370 AAGGACCACATA
1 AAGGACCACATA
18382 GACCCTCTAC
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:18899 original size:19 final size:20
Alignment explanation
Indices: 18862--18899 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18852 TTTTTTATTA
*
18862 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
18882 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
18900 TCTAGCGTTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:18951 original size:21 final size:21
Alignment explanation
Indices: 18927--18969 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18917 TCATATTCGT
* *
18927 TTGAGGGGGTCTCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
18948 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
18969 T
1 T
18970 AGCCCAGAAA
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:0.14, C:0.26, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Done.