Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008564.1 Hibiscus syriacus cultivar Beakdansim tig00111474_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: 58701
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6061 original size:21 final size:20
Alignment explanation
Indices: 6037--6095 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
6027 ATTTTCATAA
6037 TATTTATATGTATATTATTTT
1 TATTTATAT-TATATTATTTT
*
6058 TATTAATATT-T-TTA-TTT
1 TATTTATATTATATTATTTT
*
6075 TATTTAAATTTCATATTATTT
1 TATTTATA-TT-ATATTATTT
6096 GTTTGTCAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 9 0.30
18 5 0.17
19 1 0.03
20 2 0.07
21 11 0.37
22 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTTATATTATATTATTTT
Found at i:11367 original size:16 final size:16
Alignment explanation
Indices: 11338--11384 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
11328 CAGTAAAGAA
* *
11338 AGAAGAAAGAAAAAAG
1 AGAAAAAAGGAAAAAG
*
11354 ATG-AAAAAGGAAAATG
1 A-GAAAAAAGGAAAAAG
11370 AGAAAAAAGGAAAAA
1 AGAAAAAAGGAAAAA
11385 AAGGGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.04
Consensus pattern (16 bp):
AGAAAAAAGGAAAAAG
Found at i:15836 original size:22 final size:22
Alignment explanation
Indices: 15810--15889 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
15800 TACATCTACA
15810 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
15832 CTCTTCAAAGATAATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
15854 CTTTTTAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
15876 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
15890 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:16784 original size:76 final size:76
Alignment explanation
Indices: 16526--17314 Score: 1393
Period size: 76 Copynumber: 10.4 Consensus size: 76
16516 TATTTCCCAT
*
16526 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTGATGTTTTCAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-CTTTTTGATGTTTTCAA
* *
16591 TGCCGTAGGGTC
65 AGCCTTAGGGTC
*
16603 ATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
16667 -CTCTTAGGGTC
66 GC-CTTAGGGTC
*
16678 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
16743 GCCTTAGGGTC
66 GCCTTAGGGTC
*
16754 ATCTGTAAGTCCTACAGAGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
16819 GCCTTAGGGTC
66 GCCTTAGGGTC
* *
16830 ATTTGTAAGTACTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
16895 GCCTTAGGGTC
66 GCCTTAGGGTC
*
16906 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
16971 GCCTTAGGGTC
66 GCCTTAGGGTC
* * *
16982 ATCTGTAAGTTCTACAATGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
17047 GCCTTAGGGTC
66 GCCTTAGGGTC
*
17058 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
17123 GCCTTAGGGTC
66 GCCTTAGGGTC
*
17134 ATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
17199 GCCTTAGGGTC
66 GCCTTAGGGTC
*
17210 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
17275 GCCTTAGGGTC
66 GCCTTAGGGTC
* *
17286 ATCTGTAAGCCCTTCAGTGCATGATGTTT
1 ATCTGTAAGTCCTACAGTGCATGATGTTT
17315 TCAACATTTC
Statistics
Matches: 682, Mismatches: 27, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
74 1 0.00
75 70 0.10
76 564 0.83
77 47 0.07
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTAGGGTC
Found at i:17452 original size:3 final size:3
Alignment explanation
Indices: 17444--17494 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
17434 TTTTCATTTT
*
17444 TTA TTA TTA TTA TTA TTA TTA ATA TTA TATA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA
17490 TTA TT
1 TTA TT
17495 TAATAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:17504 original size:22 final size:22
Alignment explanation
Indices: 17460--17504 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17450 TTATTATTAT
* *
17460 TATTAATATTATATATTATATA
1 TATTAATATTATATAATAAATA
* *
17482 TATTATTATTATTTAATAAATA
1 TATTAATATTATATAATAAATA
17504 T
1 T
17505 TACAAACCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTAATATTATATAATAAATA
Found at i:34638 original size:23 final size:23
Alignment explanation
Indices: 34612--34660 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34602 ATAAAGAACC
*
34612 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
34635 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
34658 AAA
1 AAA
34661 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:39932 original size:19 final size:19
Alignment explanation
Indices: 39910--39972 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
39900 CACTAAACTT
*
39910 TGATATATGTTCTGATCTC
1 TGATATATATTCTGATCTC
* * *
39929 TGATTTCTATTATGATCTC
1 TGATATATATTCTGATCTC
* * *
39948 TGATATGTACTCTGATTTC
1 TGATATATATTCTGATCTC
39967 TGATAT
1 TGATAT
39973 CTCTATTTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (19 bp):
TGATATATATTCTGATCTC
Found at i:42368 original size:2 final size:2
Alignment explanation
Indices: 42358--42402 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
42348 AAAAAATTAA
42358 AT AT A- 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
42399 AT AT
1 AT AT
42403 TAAGGGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47369 original size:26 final size:26
Alignment explanation
Indices: 47291--47369 Score: 61
Period size: 29 Copynumber: 2.9 Consensus size: 26
47281 ATTTTTTTGG
* * *
47291 AATTTTGATATATTTTTAAAATTAAT
1 AATTATGATATATTTTAAAAATTAAA
* * *
47317 CATAATTATA-ATTTCATAAATAGATTAAA
1 AATTATGATATATTT--TAAA-A-ATTAAA
47346 AATTATGATATATTTTAAAAATTA
1 AATTATGATATATTTTAAAAATTA
47370 CATGATATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
25 4 0.10
26 10 0.26
27 4 0.10
28 5 0.13
29 12 0.31
30 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (26 bp):
AATTATGATATATTTTAAAAATTAAA
Found at i:47376 original size:21 final size:20
Alignment explanation
Indices: 47341--47382 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
47331 CATAAATAGA
47341 TTAAAAATTATGATA-TATT
1 TTAAAAATTATGATATTATT
47360 TTAAAAATTACATGATATTATT
1 TTAAAAATT--ATGATATTATT
47382 T
1 T
47383 CTATAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TTAAAAATTATGATATTATT
Found at i:48456 original size:7 final size:8
Alignment explanation
Indices: 48415--48453 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
48405 TGTATTCTAC
48415 ATTTTAAT
1 ATTTTAAT
48423 ATATTTAAT
1 AT-TTTAAT
48432 -TTTTAAAT
1 ATTTT-AAT
48440 ATTTTAAT
1 ATTTTAAT
48448 ATTTTA
1 ATTTTA
48454 TATAAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.11
8 15 0.54
9 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:50157 original size:18 final size:18
Alignment explanation
Indices: 50136--50254 Score: 111
Period size: 18 Copynumber: 6.7 Consensus size: 18
50126 AATCTACGTT
* *
50136 TGATAATTGTAAAACATT
1 TGATAACTGTAAAACATC
50154 TGATAACTGT-AAACATC
1 TGATAACTGTAAAACATC
*
50171 TGATGACTG-AAAATCATC
1 TGATAACTGTAAAA-CATC
*
50189 TGATAACTGT-AAATATC
1 TGATAACTGTAAAACATC
*
50206 TGATAACT-AAAAATCATC
1 TGATAACTGTAAAA-CATC
* ** *
50224 TGATAACTGTGAAATGTT
1 TGATAACTGTAAAACATC
50242 TGATAACTGTAAA
1 TGATAACTGTAAA
50255 CATTTAGAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
17 31 0.38
18 48 0.59
19 3 0.04
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (18 bp):
TGATAACTGTAAAACATC
Found at i:50200 original size:35 final size:35
Alignment explanation
Indices: 50146--50233 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 35
50136 TGATAATTGT
* * *
50146 AAAA-CATTTGATAACTGTAAACATCTGATGACTG
1 AAAATCATCTGATAACTGTAAACATCTGATAACTA
*
50180 AAAATCATCTGATAACTGTAAATATCTGATAACTA
1 AAAATCATCTGATAACTGTAAACATCTGATAACTA
50215 AAAATCATCTGATAACTGT
1 AAAATCATCTGATAACTGT
50234 GAAATGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 4 0.08
35 45 0.92
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (35 bp):
AAAATCATCTGATAACTGTAAACATCTGATAACTA
Found at i:50224 original size:53 final size:52
Alignment explanation
Indices: 50136--50257 Score: 129
Period size: 53 Copynumber: 2.3 Consensus size: 52
50126 AATCTACGTT
* * ** *
50136 TGATAATTGTAAAACATTTGATAACTGTAAACATCTGATGACTG-AAAATCATC
1 TGATAACTGT-AAACATCTGATAACTAAAAACATCTGATAACTGTAAAAT-ATC
* * * *
50189 TGATAACTGTAAATATCTGATAACTAAAAATCATCTGATAACTGTGAAATGTT
1 TGATAACTGTAAACATCTGATAACTAAAAA-CATCTGATAACTGTAAAATATC
50242 TGATAACTGTAAACAT
1 TGATAACTGTAAACAT
50258 TTAGAATTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
52 16 0.28
53 37 0.65
54 4 0.07
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (52 bp):
TGATAACTGTAAACATCTGATAACTAAAAACATCTGATAACTGTAAAATATC
Found at i:51632 original size:9 final size:9
Alignment explanation
Indices: 51618--51642 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
51608 TCAACCATAC
51618 AACTTGATA
1 AACTTGATA
51627 AACTTGATA
1 AACTTGATA
51636 AACTTGA
1 AACTTGA
51643 AATTAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (9 bp):
AACTTGATA
Found at i:56798 original size:19 final size:19
Alignment explanation
Indices: 56763--56799 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56753 TCATGTGTTA
*
56763 GGTCAAAGTCAATGGGTCG
1 GGTCAAAGTCAACGGGTCG
*
56782 GGTCAAAGTTAACGGGTC
1 GGTCAAAGTCAACGGGTC
56800 AGACCGGTTC
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:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
GGTCAAAGTCAACGGGTCG
Found at i:56894 original size:20 final size:20
Alignment explanation
Indices: 56808--56881 Score: 132
Period size: 20 Copynumber: 3.7 Consensus size: 20
56798 TCAGACCGGT
56808 TCAGGTTGACTCAGATCAGA
1 TCAGGTTGACTCAGATCAGA
56828 TCAGGTTGACTCAGATCAGA
1 TCAGGTTGACTCAGATCAGA
56848 TCAGGTTGACTCAGATCAGA
1 TCAGGTTGACTCAGATCAGA
56868 TC-GAGTTGACTCAG
1 TCAG-GTTGACTCAG
56882 TTCGATCTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 1 0.02
20 52 0.98
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (20 bp):
TCAGGTTGACTCAGATCAGA
Found at i:57755 original size:11 final size:11
Alignment explanation
Indices: 57739--57764 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57729 AATTAATCAA
57739 TTTTAAATAAT
1 TTTTAAATAAT
57750 TTTTAAATAAT
1 TTTTAAATAAT
57761 TTTT
1 TTTT
57765 GGGGTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAATAAT
Done.