Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005786.1 Hibiscus syriacus cultivar Beakdansim tig00013558_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: 46220
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5502 original size:5 final size:5
Alignment explanation
Indices: 5488--5517 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5478 GTGCTTAAAC
5488 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
5518 CTTTTGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:5559 original size:20 final size:21
Alignment explanation
Indices: 5516--5563 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
5506 TTTTCTTTTC
5516 TTCTTTTGAGTGCTTTCAATTT
1 TTCTTTTGAGTGCTTT-AATTT
5538 TTCTTTTGAGTGCTTT-ATTT
1 TTCTTTTGAGTGCTTTAATTT
5558 TTCTTT
1 TTCTTT
5564 GCTGGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (21 bp):
TTCTTTTGAGTGCTTTAATTT
Found at i:8220 original size:33 final size:35
Alignment explanation
Indices: 8155--8223 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 35
8145 TATGTGCAGG
* *
8155 GGGAACAGATTCCCTCTTGGATGGTATTGATTCCCC
1 GGGAACAGATT-CCTCTTGGAGGGTATCGATTCCCC
8191 GGGAACAGATT-CTCTTGG-GGGTATCGATTCCCC
1 GGGAACAGATTCCTCTTGGAGGGTATCGATTCCCC
8224 CTAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 13 0.42
34 7 0.23
36 11 0.35
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.29
Consensus pattern (35 bp):
GGGAACAGATTCCTCTTGGAGGGTATCGATTCCCC
Found at i:8794 original size:31 final size:31
Alignment explanation
Indices: 8756--8959 Score: 363
Period size: 31 Copynumber: 6.6 Consensus size: 31
8746 AGGGTCGAGG
8756 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
8787 GTTTACCTATGTTCTTCGAGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
8818 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
8849 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
8880 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
8911 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
8942 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
8960 AAATCTATAG
Statistics
Matches: 165, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 165 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:11219 original size:2 final size:2
Alignment explanation
Indices: 11212--11277 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
11202 AACTGAAATA
11212 AT AT AT AT AT AT 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 AT AT AT AT AT AT
11254 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
11278 GGATAGTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12610 original size:20 final size:19
Alignment explanation
Indices: 12585--12648 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 19
12575 AGGGAGAACA
12585 GATTCCCCCTGGGGGGTAT
1 GATTCCCCCTGGGGGGTAT
***
12604 CGATT-CCCC--GGGAACAT
1 -GATTCCCCCTGGGGGGTAT
12621 -ATTCCCCCTGGGGGGTATT
1 GATTCCCCCTGGGGGGTA-T
12640 GATTCCCCC
1 GATTCCCCC
12649 CTAAATGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
15 3 0.09
16 4 0.12
17 5 0.15
18 4 0.12
19 5 0.15
20 12 0.36
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.25
Consensus pattern (19 bp):
GATTCCCCCTGGGGGGTAT
Found at i:12626 original size:35 final size:35
Alignment explanation
Indices: 12580--12647 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
12570 TGTGCAGGGA
12580 GAACAGATTCCCCCTGGGGGGTATCGATTCCCCGG
1 GAACAGATTCCCCCTGGGGGGTATCGATTCCCCGG
* *
12615 GAACATATTCCCCCTGGGGGGTATTGATTCCCC
1 GAACAGATTCCCCCTGGGGGGTATCGATTCCCC
12648 CCTAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.24
Consensus pattern (35 bp):
GAACAGATTCCCCCTGGGGGGTATCGATTCCCCGG
Found at i:13250 original size:31 final size:31
Alignment explanation
Indices: 13212--13336 Score: 171
Period size: 31 Copynumber: 4.0 Consensus size: 31
13202 AGGGTCGAGG
13212 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
13243 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
13274 GTTTACCTATGTTCTTTGGGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
13305 GATTACCTAGGTTATTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
13336 G
1 G
13337 GTCCTTCGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 82 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:15438 original size:47 final size:45
Alignment explanation
Indices: 15368--15477 Score: 150
Period size: 47 Copynumber: 2.4 Consensus size: 45
15358 TATAAAATCT
15368 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
15413 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
15460 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATCCCATAA
15478 CCATATACCA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
44 9 0.15
45 10 0.17
46 2 0.03
47 38 0.64
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:15510 original size:20 final size:20
Alignment explanation
Indices: 15474--15511 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15464 CCATTATTCC
* *
15474 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
15494 ATAACCATAAACAATAGA
1 ATAACCATAAACAATAGA
15512 CAATTGCCCA
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:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:16402 original size:11 final size:11
Alignment explanation
Indices: 16388--16415 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16378 CATCAATTAT
16388 ACAACACTTAC
1 ACAACACTTAC
16399 ACAACACTTAC
1 ACAACACTTAC
16410 ACAACA
1 ACAACA
16416 ACCATCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (11 bp):
ACAACACTTAC
Found at i:21670 original size:16 final size:15
Alignment explanation
Indices: 21651--21694 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
21641 AAAAATAAAG
21651 ATTGAAATAAATGGAA
1 ATTGAAATAAAT-GAA
*
21667 ATTGATATAGAATGAA
1 ATTGAAATA-AATGAA
*
21683 ATGGAAATAAAT
1 ATTGAAATAAAT
21695 TATATCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
ATTGAAATAAATGAA
Found at i:25717 original size:15 final size:14
Alignment explanation
Indices: 25697--25736 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
25687 GTTGTAGGAG
25697 TCTTTTCTTTTCTTT
1 TCTTTT-TTTTCTTT
*
25712 TCTTTTTGTTTTTTT
1 TCTTTTT-TTTCTTT
25727 TCTTTTTTTT
1 TCTTTTTTTT
25737 TTGTTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TCTTTTTTTTCTTT
Found at i:25729 original size:20 final size:20
Alignment explanation
Indices: 25699--25744 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
25689 TGTAGGAGTC
25699 TTTTCTTTTCTTTTCTTTTTG
1 TTTT-TTTTCTTTTCTTTTTG
*
25720 TTTTTTTTCTTTTTTTTTTG
1 TTTTTTTTCTTTTCTTTTTG
25740 TTTTT
1 TTTTT
25745 GTTTGATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (20 bp):
TTTTTTTTCTTTTCTTTTTG
Found at i:25743 original size:10 final size:10
Alignment explanation
Indices: 25699--25749 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
25689 TGTAGGAGTC
* *
25699 TTTTCTTTTC
1 TTTTTTTTTG
25709 TTTTCTTTTTG
1 TTTT-TTTTTG
25720 TTTTTTTTCT-
1 TTTTTTTT-TG
25730 TTTTTTTTTG
1 TTTTTTTTTG
*
25740 TTTTTGTTTG
1 TTTTTTTTTG
25750 ATCACTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 1 0.03
10 25 0.71
11 9 0.26
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:26148 original size:13 final size:13
Alignment explanation
Indices: 26130--26187 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
26120 TAGGTATGCA
26130 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
26143 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
26156 A-GGCG-T-GAAA
1 ATGGTGATGGAAG
26166 ATGGTGATGGAAG
1 ATGGTGATGGAAG
26179 ATGGTGATG
1 ATGGTGATG
26188 AACAGATAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.29, C:0.02, G:0.41, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:26169 original size:36 final size:35
Alignment explanation
Indices: 26093--26188 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 35
26083 AGAATGATTT
* * * *
26093 AATGGTGAATAGAAGATGGTGATAATATAGGTATGC
1 AATGGTG-ATGGAAGATGGTGATGATATAGGCATGA
* *
26129 AATGGTGATGGAAGATGGTGATGTTATAGGCGTGAA
1 AATGGTGATGGAAGATGGTGATGATATAGGCATG-A
26165 AATGGTGATGGAAGATGGTGATGA
1 AATGGTGATGGAAGATGGTGATGA
26189 ACAGATAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
35 22 0.42
36 30 0.58
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.27
Consensus pattern (35 bp):
AATGGTGATGGAAGATGGTGATGATATAGGCATGA
Found at i:34526 original size:14 final size:14
Alignment explanation
Indices: 34506--34545 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
34496 TTTTTTTATG
34506 ACCCGTGAACAGTT
1 ACCCGTGAACAGTT
*
34520 CCCCGTGAACAG-T
1 ACCCGTGAACAGTT
34533 ACCCGTGAACAGT
1 ACCCGTGAACAGT
34546 GGGGGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.17
Consensus pattern (14 bp):
ACCCGTGAACAGTT
Found at i:35147 original size:45 final size:45
Alignment explanation
Indices: 35054--35195 Score: 191
Period size: 45 Copynumber: 3.2 Consensus size: 45
35044 AAGTTTGTAC
* *
35054 GCTTATTTTACCAACATGCTTACCATTTA-TTCATAAGT-ACGTAA
1 GCTTATTTTACCAACATACTTACCATTTATTTCATAA-TCTCGTAA
* *
35098 GCTTATTTAACTAACATACTTACCATTTATTTCATAATCTCGTAA
1 GCTTATTTTACCAACATACTTACCATTTATTTCATAATCTCGTAA
* *
35143 GCTTATTTTACCAACATACTTATCC-TTTATTCCATAAACTCGTAA
1 GCTTATTTTACCAACATACTTA-CCATTTATTTCATAATCTCGTAA
35188 GCTTATTT
1 GCTTATTT
35196 GCCAGTTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
44 27 0.31
45 58 0.67
46 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (45 bp):
GCTTATTTTACCAACATACTTACCATTTATTTCATAATCTCGTAA
Found at i:40087 original size:18 final size:17
Alignment explanation
Indices: 40064--40104 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40054 ACATCCATTA
40064 CATTTAAATAATCTAGTT
1 CATTTAAATAA-CTAGTT
**
40082 CATTTAGGTAACTAGTT
1 CATTTAAATAACTAGTT
40099 CATTTA
1 CATTTA
40105 TGCATTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (17 bp):
CATTTAAATAACTAGTT
Found at i:40151 original size:17 final size:17
Alignment explanation
Indices: 40074--40155 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
40064 CATTTAAATA
* *
40074 ATCTAGTTCATTTAGGT
1 ATCTAGTTCATTTATGC
*
40091 AACTAGTTCATTTATGC
1 ATCTAGTTCATTTATGC
* *
40108 ATTTAGATT-ATTTA-GTA
1 ATCTAG-TTCATTTATG-C
* *
40125 AGCTATTTCATTTATGC
1 ATCTAGTTCATTTATGC
40142 ATCTAGTTCATTTA
1 ATCTAGTTCATTTA
40156 ATAAAGTTAG
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
16 3 0.06
17 43 0.88
18 3 0.06
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (17 bp):
ATCTAGTTCATTTATGC
Found at i:40155 original size:34 final size:34
Alignment explanation
Indices: 40074--40155 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
40064 CATTTAAATA
40074 ATCTAGTTCATTTAGGTAACTAGTTCATTTATGC
1 ATCTAGTTCATTTAGGTAACTAGTTCATTTATGC
* *
40108 ATTTAGATT-ATTTA-GTAAGCTATTTCATTTATGC
1 ATCTAG-TTCATTTAGGTAA-CTAGTTCATTTATGC
40142 ATCTAGTTCATTTA
1 ATCTAGTTCATTTA
40156 ATAAAGTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.14
34 34 0.81
35 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (34 bp):
ATCTAGTTCATTTAGGTAACTAGTTCATTTATGC
Found at i:40187 original size:17 final size:17
Alignment explanation
Indices: 40144--40224 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
40134 ATTTATGCAT
40144 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
* *
40161 GTTAGCTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
40179 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
40196 CTATTTCATTTA-TAAA
1 CTAGTTCATTAATTAAA
*
40212 CTAATTC-TTAATT
1 CTAGTTCATTAATT
40225 GTTTCATGCG
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
15 3 0.06
16 10 0.20
17 27 0.54
18 10 0.20
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:40642 original size:25 final size:25
Alignment explanation
Indices: 40614--40668 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
40604 AAGCATTCAA
40614 GGCTGATTTAATAATCCAAACCAAG
1 GGCTGATTTAATAATCCAAACCAAG
* *
40639 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATAATCCAAACCAAG
40664 GGCTG
1 GGCTG
40669 TTCATATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATAATCCAAACCAAG
Found at i:44802 original size:18 final size:19
Alignment explanation
Indices: 44771--44809 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
44761 CCAAAGTTTT
44771 AATATATAAACTAA-TTAA
1 AATATATAAACTAACTTAA
44789 AATAT-TAAACCTAACTTAA
1 AATATATAAA-CTAACTTAA
44808 AA
1 AA
44810 CTGAAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATATAAACTAACTTAA
Done.