Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002476.1 Hibiscus syriacus cultivar Beakdansim tig00005058_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: 137035
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6494 original size:2 final size:2
Alignment explanation
Indices: 6487--6531 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6477 TTATTACAAT
6487 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
6529 TA T
1 TA T
6532 TCTGGGTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22985 original size:6 final size:6
Alignment explanation
Indices: 22974--23005 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
22964 GTCGTTTACT
22974 CGTTTC CGTTTC CGTTTC CGTTTC CGTTTC CG
1 CGTTTC CGTTTC CGTTTC CGTTTC CGTTTC CG
23006 AAAGGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.19, T:0.47
Consensus pattern (6 bp):
CGTTTC
Found at i:30613 original size:97 final size:95
Alignment explanation
Indices: 30448--30638 Score: 276
Period size: 97 Copynumber: 2.0 Consensus size: 95
30438 GCTACTGGGA
* *
30448 TTATCTTTCGAGTTTTGAATGTGACAAAGTTTGTCTTTAGTCCAAAAGTAACATAAAAATAAATG
1 TTATCTTTCGAGTTTTGAATGTGACAAAGTTTGTCTTTAGTCCAAAAATAACATAAAAAGAAATG
**
30513 TATGCACTATGCACTGTGAATAAAGTTGGT
66 TATGCACTATGCACCATGAATAAAGTTGGT
* * * *
30543 TTATCTTTTGTGTTTT-AGATGTGACAAAGTTTGTGTTTTTAGTCCAAAAATAGCATAAAAAGAA
1 TTATCTTTCGAGTTTTGA-ATGTGACAAAG-TT-TGTCTTTAGTCCAAAAATAACATAAAAAGAA
30607 ATGTATGCACTATGCACCATGAATAAAGTTGG
63 ATGTATGCACTATGCACCATGAATAAAGTTGG
30639 ATTTGTCATC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 1 0.01
95 25 0.29
96 2 0.02
97 57 0.67
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (95 bp):
TTATCTTTCGAGTTTTGAATGTGACAAAGTTTGTCTTTAGTCCAAAAATAACATAAAAAGAAATG
TATGCACTATGCACCATGAATAAAGTTGGT
Found at i:31943 original size:30 final size:30
Alignment explanation
Indices: 31909--31966 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
31899 ATACATGACG
31909 TATGAGAATAACACGA-CAAATATGACAACT
1 TATGAGAATAACAC-ACCAAATATGACAACT
31939 TATGAGAATAACACACCAAATATGACAA
1 TATGAGAATAACACACCAAATATGACAA
31967 GTTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (30 bp):
TATGAGAATAACACACCAAATATGACAACT
Found at i:36362 original size:283 final size:284
Alignment explanation
Indices: 35813--36382 Score: 778
Period size: 283 Copynumber: 2.0 Consensus size: 284
35803 TAACTCTCTG
* * * *
35813 TAAGGATCAATTCAACTTGTGAGTGTTGAGGTATTGTTTCAATTTGGCCATTGGGTTTATTGATT
1 TAAGGATCAATTCAACTTGGGAGTGTTGAGGTATTGATTCAATTTGGCCATTGGATTTATTGAGT
*
35878 TTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGATTCCCT
66 TTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGACTCCCT
* * *
35943 ACTGTCTATCTGATGCGGGATACTTTTAGGGTTGATATCTCCTATGTCATCCTGTTGTCTTCACC
131 ACTGTCTATCTGATGCGGGA-ACTTTTAAGGTTGATATCTCCTATGGCATCCTGCTGTCTTCACC
* * * * *
36008 AGGAAGCCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTGTTGTACTCCCCTTATCT
195 AGGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAAGTGTTGTACTCCACTTATCT
36073 GACCTGCAGAAGTTCATTGGACGCA
260 GACCTGCAGAAGTTCATTGGACGCA
* ** *
36098 TAAGGATCAATTGAACTTGGGAGT-TCTGATTTATTGATTCAATTTGTCCATTGGATTTCA-TGA
1 TAAGGATCAATTCAACTTGGGAGTGT-TGAGGTATTGATTCAATTTGGCCATTGGATTT-ATTGA
* *
36161 GTTTCTTCTCAAAATTCATCTGAAAAGTTGGGTTCAAGGTCCAT-A-AAA-TAAGACTGGACTCC
64 GTTTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGACTCC
* *
36223 CTACTG-CGTATCTGATGTGGG-ACTGTTTAAGGTTGGA-GTCTCCTATGGCATACTCTGCTGTC
129 CTACTGTC-TATCTGATGCGGGAACT-TTTAAGGTT-GATATCTCCTATGGCAT-C-CTGCTGTC
*
36285 TTCACCAGGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAATTGTTGTACTCCAC
189 TTCACCAGGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAAGTGTTGTACTCCAC
* * * *
36350 TTATTTGACCTGCGGTAGTTCATTGGATGCA
254 TTATCTGACCTGCAGAAGTTCATTGGACGCA
36381 TA
1 TA
36383 TTAGGTTCAA
Statistics
Matches: 252, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
280 3 0.01
281 21 0.08
282 34 0.13
283 98 0.39
284 2 0.01
285 93 0.37
286 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (284 bp):
TAAGGATCAATTCAACTTGGGAGTGTTGAGGTATTGATTCAATTTGGCCATTGGATTTATTGAGT
TTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGACTCCCT
ACTGTCTATCTGATGCGGGAACTTTTAAGGTTGATATCTCCTATGGCATCCTGCTGTCTTCACCA
GGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAAGTGTTGTACTCCACTTATCTG
ACCTGCAGAAGTTCATTGGACGCA
Found at i:42778 original size:2 final size:2
Alignment explanation
Indices: 42773--42811 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42763 AGAAAAAAAT
42773 TA TA TA TA TA 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 TA TA TA TA TA T
42812 TGATGTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44192 original size:21 final size:21
Alignment explanation
Indices: 44166--44212 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
44156 AGGAGTAGAA
44166 GCAGGAGCGCCAGTCCACGCC
1 GCAGGAGCGCCAGTCCACGCC
*
44187 GCAGGAGTGCCAGTCCACGCC
1 GCAGGAGCGCCAGTCCACGCC
*
44208 ACAGG
1 GCAGG
44213 CGTGACAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.34, T:0.06
Consensus pattern (21 bp):
GCAGGAGCGCCAGTCCACGCC
Found at i:46548 original size:11 final size:11
Alignment explanation
Indices: 46532--46556 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46522 AATATTGATT
46532 TGGGTTTTAAA
1 TGGGTTTTAAA
46543 TGGGTTTTAAA
1 TGGGTTTTAAA
46554 TGG
1 TGG
46557 ATTGGGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:56930 original size:11 final size:11
Alignment explanation
Indices: 56914--56943 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
56904 GTCAATTAAG
56914 TCATTTAATTT
1 TCATTTAATTT
56925 TCATTTAATTT
1 TCATTTAATTT
*
56936 TCAATTAA
1 TCATTTAA
56944 GTCATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (11 bp):
TCATTTAATTT
Found at i:62778 original size:15 final size:16
Alignment explanation
Indices: 62758--62787 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
62748 CGTCGGAAGA
62758 GGGCTTCTGG-ATTTG
1 GGGCTTCTGGCATTTG
62773 GGGCTTCTGGCATTT
1 GGGCTTCTGGCATTT
62788 CTCCTCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.17, G:0.37, T:0.40
Consensus pattern (16 bp):
GGGCTTCTGGCATTTG
Found at i:63454 original size:24 final size:24
Alignment explanation
Indices: 63420--63468 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
63410 TCTCGCTAGC
63420 CACTTCCTATTGTTAATCCACCTT
1 CACTTCCTATTGTTAATCCACCTT
* *
63444 CACTTCTTATTGTTAATCCATCTT
1 CACTTCCTATTGTTAATCCACCTT
63468 C
1 C
63469 TATCCACTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.31, G:0.04, T:0.45
Consensus pattern (24 bp):
CACTTCCTATTGTTAATCCACCTT
Found at i:63597 original size:16 final size:16
Alignment explanation
Indices: 63576--63607 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
63566 TTTCTACTTC
63576 AACTCAAATCATCTGG
1 AACTCAAATCATCTGG
63592 AACTCAAATCATCTGG
1 AACTCAAATCATCTGG
63608 GCATGCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
AACTCAAATCATCTGG
Found at i:66122 original size:37 final size:36
Alignment explanation
Indices: 66047--66122 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
66037 TTTTTATTTT
* *
66047 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAAATATATAAATATTATCAA
*
66083 TTTAATTTT-TAAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTATAAAA-AAAATATATAAATATTAT-CAA
66120 TTT
1 TTT
66123 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 5 0.14
36 25 0.71
37 5 0.14
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAAATATATAAATATTATCAA
Found at i:66345 original size:20 final size:20
Alignment explanation
Indices: 66272--66338 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
66262 TATTCTCTGG
*
66272 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGA
66292 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
*
66312 TAATCTTTTATTCCCACTAA
1 TAATCTTTTATTCCCACTGA
66332 TAATCTT
1 TAATCTT
66339 ACATTCCGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.46
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGA
Found at i:70093 original size:2 final size:2
Alignment explanation
Indices: 70086--70114 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70076 AAGTGAAAGC
70086 AT AT 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 AT AT A
70115 AATGAGAGGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85804 original size:68 final size:68
Alignment explanation
Indices: 85695--85831 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
85685 GAGCTATTTT
* **
85695 ATGGATTGCCAAATAAATGCCTGAAACCGGCAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
1 ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
85760 TGC
66 TGC
*
85763 ATGGATTGCCAAATAAGGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
1 ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
85828 TGC
66 TGC
85831 A
1 A
85832 AGGAAGGGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (68 bp):
ATGGATTGCCAAATAAAGGCCTGAAACCAACAGTTGTAACTTATTCTATAATGATCCAGTTTCTG
TGC
Found at i:87215 original size:2 final size:2
Alignment explanation
Indices: 87204--87248 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
87194 TAGAATTCTT
87204 TA TA -A TA TA TA TA 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 TA TA TA TA TA TA TA
87245 -A TA T
1 TA TA T
87249 TGCCGAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:87831 original size:2 final size:2
Alignment explanation
Indices: 87824--87860 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
87814 TAAGCTGATA
87824 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
87861 AAACCAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:93465 original size:34 final size:34
Alignment explanation
Indices: 93419--93488 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
93409 ATTTTTAAAA
*
93419 AAATGTTTGCATTTACTTTCAAAAGTCATGCATT
1 AAATGTTAGCATTTACTTTCAAAAGTCATGCATT
*
93453 AAATGTTAGCATTTACTTTCAAAAGTCGTGCATT
1 AAATGTTAGCATTTACTTTCAAAAGTCATGCATT
93487 AA
1 AA
93489 GAACTGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (34 bp):
AAATGTTAGCATTTACTTTCAAAAGTCATGCATT
Found at i:96646 original size:41 final size:41
Alignment explanation
Indices: 96601--96683 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
96591 CCGGTGAAAG
*
96601 GGTCCGGTCACAATCCGTGCACGTACATCCCTGGAAGAGAA
1 GGTCCGGTCACAATCCGTGCACGAACATCCCTGGAAGAGAA
*
96642 GGTCCGGTCACAATTCGTGCACGAACATCCCTGGAAGAGAA
1 GGTCCGGTCACAATCCGTGCACGAACATCCCTGGAAGAGAA
96683 G
1 G
96684 CCGGCGTCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (41 bp):
GGTCCGGTCACAATCCGTGCACGAACATCCCTGGAAGAGAA
Found at i:111553 original size:15 final size:14
Alignment explanation
Indices: 111519--111549 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
111509 AATTGAACCT
*
111519 ATTAAATTATTCAA
1 ATTAAAATATTCAA
111533 ATTAAAATATTCAA
1 ATTAAAATATTCAA
111547 ATT
1 ATT
111550 TAAACAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAAAATATTCAA
Found at i:119682 original size:3 final size:3
Alignment explanation
Indices: 119674--119754 Score: 135
Period size: 3 Copynumber: 27.0 Consensus size: 3
119664 TCTCTACTTG
119674 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
119722 AAT GAT AAT AAT GAT AAT AAA AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
119755 CCATATTCTC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Done.