Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002045.1 Hibiscus syriacus cultivar Beakdansim tig00004167_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: 83967
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:347 original size:29 final size:29
Alignment explanation
Indices: 305--376 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
295 TTTTCTGCAT
**
305 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
334 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
363 ATTCATGTCATGTA
1 ATTCATGTCATGTA
377 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:844 original size:67 final size:67
Alignment explanation
Indices: 675--823 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 67
665 TTTTTCTCAT
* * * *
675 GGGGGAATC-GTTCCCCCCTGGGGGTATCGATTCCTCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
739 GA
66 GA
* * * *
741 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
805 GA
66 GA
807 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
824 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 31 0.42
67 43 0.58
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:6820 original size:22 final size:22
Alignment explanation
Indices: 6792--6836 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6782 GCTCGATAAA
6792 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
6814 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
6836 T
1 T
6837 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:7172 original size:29 final size:29
Alignment explanation
Indices: 7130--7201 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
7120 TTTTCTGCAT
**
7130 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
7159 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
7188 ATTCATGTCATGTA
1 ATTCATGTCATGTA
7202 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:7641 original size:67 final size:68
Alignment explanation
Indices: 7502--7651 Score: 214
Period size: 68 Copynumber: 2.2 Consensus size: 68
7492 TCTTTTTCAT
* * * *
7502 GGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCTCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
7566 GAG
66 GAG
* * * *
7569 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
7633 GAG
66 GAG
7636 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
7652 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
67 34 0.46
68 40 0.54
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GAG
Found at i:7663 original size:67 final size:67
Alignment explanation
Indices: 7502--7673 Score: 213
Period size: 67 Copynumber: 2.6 Consensus size: 67
7492 TCTTTTTCAT
* * * *
7502 GGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCTCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
7567 AG
66 AG
* * * *
7569 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
7633 GAG
65 GAG
* *
7636 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
7674 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 6 0.07
67 46 0.50
68 40 0.43
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AG
Found at i:16906 original size:19 final size:18
Alignment explanation
Indices: 16878--16928 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
16868 CTCAAATTTT
*
16878 TTTTAATTTAAAATATATA
1 TTTTATTTTAAAATAT-TA
16897 TTTTATTTT--AATATTA
1 TTTTATTTTAAAATATTA
16913 TTTATATTTTAAAATA
1 TTT-TATTTTAAAATA
16929 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 5 0.18
17 11 0.39
19 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATTTTAAAATATTA
Found at i:16909 original size:17 final size:17
Alignment explanation
Indices: 16889--16924 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
16879 TTTAATTTAA
16889 AATATATATTT-TATTTT
1 AATAT-TATTTATATTTT
16906 AATATTATTTATATTTT
1 AATATTATTTATATTTT
16923 AA
1 AA
16925 AATAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATTATTTATATTTT
Found at i:16932 original size:17 final size:17
Alignment explanation
Indices: 16884--16933 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
16874 TTTTTTTTAA
*
16884 TTTAAAATATATATTTTAT
1 TTTAAAATA-AT-TTATAT
* *
16903 TTTAATATTATTTATAT
1 TTTAAAATAATTTATAT
16920 TTTAAAATAATTTA
1 TTTAAAATAATTTA
16934 AAAATAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 17 0.65
18 2 0.08
19 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAAATAATTTATAT
Found at i:27653 original size:2 final size:2
Alignment explanation
Indices: 27646--27674 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27636 ATTATTTTAT
27646 TA 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 T
27675 CACCTAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35602 original size:92 final size:93
Alignment explanation
Indices: 35416--35603 Score: 247
Period size: 92 Copynumber: 2.0 Consensus size: 93
35406 ACAAAAATGT
* *
35416 GCTTAATGAGGTTTACTTAATAAATACTTTTATTCAAAACATCCATTACTGACCCGAAATCGGCA
1 GCTTAATGAGCTTTACTTAATAAATAC-TTTATTCAAAACATCCATTACTGACCCGAAATCAGCA
* *
35481 TTTACTTGCACAGGAAGGTTCACCCATCG
65 TTTACTTGAACAGGAAGGTTCACCAATCG
* * *
35510 GCTTAATGAGCTTTTCTTGATAAATAC-TTCTTCAAAACATCCATTACTGACCCGAAATCAGC-T
1 GCTTAATGAGCTTTACTTAATAAATACTTTATTCAAAACATCCATTACTGACCCGAAATCAGCAT
* *
35573 CTTACTTGAACCGG-AGGATTCGCCAATCG
66 -TTACTTGAACAGGAAGG-TTCACCAATCG
35602 GC
1 GC
35604 AGGCCATGTC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
91 4 0.05
92 55 0.66
94 24 0.29
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (93 bp):
GCTTAATGAGCTTTACTTAATAAATACTTTATTCAAAACATCCATTACTGACCCGAAATCAGCAT
TTACTTGAACAGGAAGGTTCACCAATCG
Found at i:56270 original size:14 final size:14
Alignment explanation
Indices: 56251--56280 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56241 CTAATTAGCA
56251 TATTTATTTAGAAT
1 TATTTATTTAGAAT
56265 TATTTATTTAGAAT
1 TATTTATTTAGAAT
56279 TA
1 TA
56281 GAAGAAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTATTTAGAAT
Found at i:64055 original size:23 final size:23
Alignment explanation
Indices: 64029--64089 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
64019 CACCATAACT
*
64029 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
64052 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
64075 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
64090 TAGTATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:64335 original size:30 final size:30
Alignment explanation
Indices: 64301--64369 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
64291 ACATAATTTG
* * *
64301 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCAATTTCATACCTT
*
64331 TATCACATAGACATATCAATTTCATACTTT
1 TATCACATAGACATATCAATTTCATACCTT
64361 TATCACATA
1 TATCACATA
64370 ACTCATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (30 bp):
TATCACATAGACATATCAATTTCATACCTT
Found at i:64735 original size:20 final size:20
Alignment explanation
Indices: 64712--64804 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
64702 TAATGGAGAT
*
64712 ATGCATCGATGCATTACACC
1 ATGCATCGATGCACTACACC
*
64732 ATGCATCGGTGCACTACACC
1 ATGCATCGATGCACTACACC
64752 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
64772 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
64792 ATGCATCGATGCA
1 ATGCATCGATGCA
64805 TAAATCTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (20 bp):
ATGCATCGATGCACTACACC
Found at i:64915 original size:56 final size:54
Alignment explanation
Indices: 64813--64917 Score: 129
Period size: 56 Copynumber: 1.9 Consensus size: 54
64803 CATAAATCTT
** * * *
64813 ATTCGATTTTGTATTTAATGGGGTGCATCGATGCACTCCTTATGCATCGATGGC
1 ATTCGATTTTGTATTTAAAAGAGTGCATCAATGCACTCCATATGCATCGATGGC
* *
64867 ATTCGATGTTTGTATTTTAAAAGAGTGCATCAATGCACTTCATGTGCATCG
1 ATTCGAT-TTTGTA-TTTAAAAGAGTGCATCAATGCACTCCATATGCATCG
64918 GTACACCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 7 0.17
55 6 0.14
56 29 0.69
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (54 bp):
ATTCGATTTTGTATTTAAAAGAGTGCATCAATGCACTCCATATGCATCGATGGC
Found at i:72904 original size:20 final size:22
Alignment explanation
Indices: 72864--72920 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
72854 TGAATATGTG
*
72864 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
72886 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
72906 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
72921 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:73485 original size:31 final size:31
Alignment explanation
Indices: 73447--73540 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
73437 AGGGTCGAGG
73447 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
73478 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
73509 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
73540 G
1 G
73541 GTCCTTCGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Done.