Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006656.1 Hibiscus syriacus cultivar Beakdansim tig00016432_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: 61676
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:20602 original size:24 final size:23
Alignment explanation
Indices: 20577--20661 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
20567 TCGTATACAT
20577 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
20600 TTTGTC-CCGGAG-GACCACGTAGAA
1 -TTG-CACCGAAGTG-CCACGTAGAA
* * * *
20624 ATGAACTGAAGTACCACGTAG-A
1 TTGCACCGAAGTGCCACGTAGAA
*
20646 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
20662 TATATATGTC
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
22 12 0.26
23 15 0.33
24 18 0.39
25 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:26438 original size:17 final size:17
Alignment explanation
Indices: 26416--26462 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
26406 TATGGAATTG
26416 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
26433 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
* *
26450 GGTTCTAATTCCT
1 GATTCCAATTCCT
26463 TCACAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:27648 original size:23 final size:22
Alignment explanation
Indices: 27613--27655 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
27603 ATAATTATTT
27613 AAAAAATTAAATAAAAAATACA
1 AAAAAATTAAATAAAAAATACA
*
27635 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
27656 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACA
Found at i:33469 original size:121 final size:121
Alignment explanation
Indices: 33255--33475 Score: 433
Period size: 121 Copynumber: 1.8 Consensus size: 121
33245 TACCATAACA
33255 AAAACACATACAATTCAAATCTCTCTGATCTAATAATCTTCACCAGTATGCTGCCCTTTTTTTTG
1 AAAACACATACAATTCAAATCTCTCTGATCTAATAATCTTCACCAGTATGCTGCCCTTTTTTTTG
33320 CTTACTCGGCTTGCACCTCGAATCTCTTTAGACCTTTATAGTACGATTTAAACATG
66 CTTACTCGGCTTGCACCTCGAATCTCTTTAGACCTTTATAGTACGATTTAAACATG
*
33376 AAAACACATACAATTCAAATCTCTCTGATCTAATAATCTTCACCAGTATGCTGCCTTTTTTTTTG
1 AAAACACATACAATTCAAATCTCTCTGATCTAATAATCTTCACCAGTATGCTGCCCTTTTTTTTG
33441 CTTACTCGGCTTGCACCTCGAATCTCTTTAGACCT
66 CTTACTCGGCTTGCACCTCGAATCTCTTTAGACCT
33476 ACGTGTGAAA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 99 1.00
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (121 bp):
AAAACACATACAATTCAAATCTCTCTGATCTAATAATCTTCACCAGTATGCTGCCCTTTTTTTTG
CTTACTCGGCTTGCACCTCGAATCTCTTTAGACCTTTATAGTACGATTTAAACATG
Found at i:41129 original size:20 final size:20
Alignment explanation
Indices: 41084--41134 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
41074 TCTTTACTTA
*
41084 CAGTATTGATACCTTATCCT
1 CAGTATTGATACCTTATCAT
**
41104 TGGTATTGATACCTTCA-CAT
1 CAGTATTGATACCTT-ATCAT
*
41124 CAGTATCGATA
1 CAGTATTGATA
41135 TTTCTTCAAC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (20 bp):
CAGTATTGATACCTTATCAT
Found at i:45701 original size:3 final size:3
Alignment explanation
Indices: 45693--45725 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
45683 AATTTTTTCA
45693 TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
45726 AAAAAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:47088 original size:12 final size:11
Alignment explanation
Indices: 47068--47132 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
47058 TTATTTGCAA
47068 TATTATTTTAT
1 TATTATTTTAT
47079 TATTACTTTTGA-
1 TATTA-TTTT-AT
47091 TA-TATTTTAAAT
1 TATTATTTT--AT
*
47103 TATTACTTTCAT
1 TATTA-TTTTAT
*
47115 TATTATTTTAG
1 TATTATTTTAT
47126 TATTATT
1 TATTATT
47133 GTAGTCATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.09
11 19 0.43
12 15 0.34
13 3 0.07
14 3 0.07
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:47575 original size:2 final size:2
Alignment explanation
Indices: 47563--47601 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
47553 ATATCTTATT
*
47563 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47602 TTCTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47618 original size:148 final size:146
Alignment explanation
Indices: 47322--47621 Score: 387
Period size: 148 Copynumber: 2.0 Consensus size: 146
47312 TAATCATATT
*** *
47322 TTAATATTTATTTTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGTCATTTTCTG
1 TTAATATTTATTTTTTTTAATATTAAGAAATGAACTGTCTTAAAGCACCTAAAAGTCATTTTCTG
* * *
47387 ATATTCTTAAATAAATAAATATTCTATTTTTATAAATTATATATATTAATTTATTTTAATTATTT
66 ATATTCTTAAATAAATAAATATTCTATATTTATAAATTATATATATTAATTTATATTAATTATAT
*
47452 TTACAGAAATATTTTA
131 TTACAGAAATATTATA
47468 TTAATATTTATTTATTTTTTAATATTAAGAAATGAACTGTCTTAAAGCACCTAAAAGTCATTTTC
1 TTAATATTTA-TT-TTTTTTAATATTAAGAAATGAACTGTCTTAAAGCACCTAAAAGTCATTTTC
*
47533 TGATATT-TCTAAGTAAATAAATA-TCT-TATTTATAAATATATATATATATATATATATATATT
64 TGATATTCT-TAAATAAATAAATATTCTATATTTATAAAT-TATATATAT-TA-AT-T-TATATT
**
47595 AA-TATATTT-CTTAAA-ATTATA
123 AATTATATTTACAGAAATATTATA
47616 TTAATA
1 TTAATA
47622 AATTTGAAAT
Statistics
Matches: 135, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
146 20 0.15
147 15 0.11
148 80 0.59
149 6 0.04
150 7 0.05
151 7 0.05
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (146 bp):
TTAATATTTATTTTTTTTAATATTAAGAAATGAACTGTCTTAAAGCACCTAAAAGTCATTTTCTG
ATATTCTTAAATAAATAAATATTCTATATTTATAAATTATATATATTAATTTATATTAATTATAT
TTACAGAAATATTATA
Found at i:53087 original size:7 final size:7
Alignment explanation
Indices: 53077--53172 Score: 160
Period size: 7 Copynumber: 13.7 Consensus size: 7
53067 AAAAAAAAAA
53077 AAAAAGG
1 AAAAAGG
53084 AAAAAGG
1 AAAAAGG
53091 -AAAAGG
1 AAAAAGG
53097 -AAAAGG
1 AAAAAGG
53103 AAAAAGG
1 AAAAAGG
53110 AAAAAGG
1 AAAAAGG
53117 AAAAAGG
1 AAAAAGG
53124 AAAAAGG
1 AAAAAGG
53131 AAAAAGG
1 AAAAAGG
53138 AAAAAGG
1 AAAAAGG
53145 AAAAAAGG
1 -AAAAAGG
53153 AAAAAGG
1 AAAAAGG
53160 AAAAAAGG
1 -AAAAAGG
53168 AAAAA
1 AAAAA
53173 ATGAATCAAG
Statistics
Matches: 86, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.14
7 60 0.70
8 14 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:56496 original size:75 final size:75
Alignment explanation
Indices: 56359--56539 Score: 200
Period size: 75 Copynumber: 2.4 Consensus size: 75
56349 ATTAACAAGA
* * * *
56359 AGCAAATGATGGAGGCATGTTGAAAGCCCATTTCAATCATAATCAGGAATATTGACACATTTTGA
1 AGCAAATGATGG-GGCATGCTGAAAGCCCATTTCAATAAGAATCAGAAATATTGACACATTTTGA
* *
56424 ACATTTGTATT
65 ACACTTGTATC
* * * * ***
56435 AGCCAATGCTGGGGCATGCTGAAAGCCCCTTTCAATAAGAATCAGAAATGTTGATGTATTTTGAA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATAAGAATCAGAAATATTGACACATTTTGAA
*
56500 CGCTTGTATC
66 CACTTGTATC
* * *
56510 AGCAAATGTTGGGGCATACTGAAGGCCCAT
1 AGCAAATGATGGGGCATGCTGAAAGCCCAT
56540 ATCTTATGAA
Statistics
Matches: 86, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
75 76 0.88
76 10 0.12
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (75 bp):
AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATAAGAATCAGAAATATTGACACATTTTGAA
CACTTGTATC
Found at i:58648 original size:76 final size:74
Alignment explanation
Indices: 58522--58828 Score: 262
Period size: 76 Copynumber: 4.3 Consensus size: 74
58512 CCCACATCTG
*
58522 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTC
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA-TTT-AAAGCCTC
* *
58587 CGTGTCATCCA
64 AGGGTCATCCA
* *
58598 TAAGACCTACAGTGTAGGATGTTTTCTAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCAG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCAG
**
58663 GGTCATCTG
66 GGTCATCCA
* * * ** ** *
58672 TAAGACCTACAGTGCAAGATG--AT--AAGA-CC-TCGGG-GC-CATCCATA---AGA-CCTACA
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCT-CA
* *
58725 GTGCCATCCA
65 GGGTCATCCA
* * * * *
58735 TAAGACCTACAGTGCATGATGTTTTC-TAAAGCCTTCGGAAGTTTTTTTATATTTAAAGCCTCAG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCAG
* **
58799 GGTTATCTG
66 GGTCATCCA
*
58808 TAAGACCTACAGTGCAAGATG
1 TAAGACCTACAGTGCAGGATG
58829 ATAAGACCTC
Statistics
Matches: 182, Mismatches: 37, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
62 3 0.02
63 30 0.16
65 1 0.01
66 6 0.03
67 4 0.02
68 9 0.05
69 3 0.02
70 7 0.04
72 1 0.01
73 29 0.16
74 37 0.20
75 3 0.02
76 49 0.27
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (74 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCAG
GGTCATCCA
Found at i:58732 original size:21 final size:21
Alignment explanation
Indices: 58693--58749 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
58683 GTGCAAGATG
* *
58693 ATAAGACCT-CGGGGCCATCC
1 ATAAGACCTACAGTGCCATCC
58713 ATAAGACCTACAGTGCCATCC
1 ATAAGACCTACAGTGCCATCC
58734 ATAAGACCTACAGTGC
1 ATAAGACCTACAGTGC
58750 ATGATGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (21 bp):
ATAAGACCTACAGTGCCATCC
Found at i:58837 original size:136 final size:137
Alignment explanation
Indices: 58592--58864 Score: 476
Period size: 136 Copynumber: 2.0 Consensus size: 137
58582 GCCTCCGTGT
* *
58592 CATCCATAAGACCTACAGTGTAGGATGTTTTCTAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
1 CATCCATAAGACCTACAGTGCAGGATGTTTTCTAAAAGCCTTCGGAAGCTTTTTGATATTTAAAG
*
58657 CCTCAGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCGGGGCCATCCATAAGACCT
66 CCTCAGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCGGGGCCATCCATAAAACCT
58722 ACAGTGC
131 ACAGTGC
* * *
58729 CATCCATAAGACCTACAGTGCATGATGTTTTCT-AAAGCCTTCGGAAGTTTTTTTATATTTAAAG
1 CATCCATAAGACCTACAGTGCAGGATGTTTTCTAAAAGCCTTCGGAAGCTTTTTGATATTTAAAG
*
58793 CCTCAGGGTTATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCGGGGCCATCCATAAAACCT
66 CCTCAGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCGGGGCCATCCATAAAACCT
58858 ACAGTGC
131 ACAGTGC
58865 AGGATGTTTT
Statistics
Matches: 129, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
136 98 0.76
137 31 0.24
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (137 bp):
CATCCATAAGACCTACAGTGCAGGATGTTTTCTAAAAGCCTTCGGAAGCTTTTTGATATTTAAAG
CCTCAGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCGGGGCCATCCATAAAACCT
ACAGTGC
Found at i:58863 original size:115 final size:118
Alignment explanation
Indices: 58713--58996 Score: 412
Period size: 118 Copynumber: 2.4 Consensus size: 118
58703 GGGGCCATCC
* *
58713 ATAAGACCTACAGTGCCATCCATAAGACCTACAGTGCATGATGTTTTC-TAAAGCCTTCGGAAG-
1 ATAAGACCT-CAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGC
* * *
58776 TTTTT-TTATATTTAAAGCCTCAGGGTTATCTGTAAGACCTACAGTGCAAGATG
65 TTTTTGATATATTTAAAGCCCCAGGGTCATCTGTAAGACCTACAGTGCAAGATG
* * * * *
58829 ATAAGACCTCGGGGCCATCCATAAAACCTACAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCT
1 ATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCT
* *
58894 TTTTGATATTTTTAAAGCCCCAGGGTCGTCTGTAAGACCTACAGTGCAAGATG
66 TTTTGATATATTTAAAGCCCCAGGGTCATCTGTAAGACCTACAGTGCAAGATG
* *
58947 ATAAGACCTCAGGGCCATCCTTAAGACCTACAGTACATGATGTTTTCAAA
1 ATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAA
58997 TGAGATTTTA
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
115 34 0.23
116 21 0.14
117 5 0.03
118 88 0.59
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (118 bp):
ATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCT
TTTTGATATATTTAAAGCCCCAGGGTCATCTGTAAGACCTACAGTGCAAGATG
Found at i:59266 original size:3 final size:3
Alignment explanation
Indices: 59245--59299 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
59235 AATTTTTTCA
* * *
59245 TAT TA- TAT TAT TAA AAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59292 TAT TAT TA
1 TAT TAT TA
59300 AAAAAAATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:60533 original size:19 final size:19
Alignment explanation
Indices: 60511--60548 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
60501 AATTATGTAC
60511 ATTAAT-ATTATATTTTATA
1 ATTAATCATTA-ATTTTATA
*
60530 ATTAATCCTTAATTTTATA
1 ATTAATCATTAATTTTATA
60549 TATTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAATCATTAATTTTATA
Found at i:60688 original size:22 final size:21
Alignment explanation
Indices: 60639--60688 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
60629 TATTTGCAAT
*
60639 ATTATTTTATTATTACTTTTG
1 ATTATTTTATTATTACTTTTC
60660 ATATATTTTAAATTATTAC-TTTC
1 AT-TATTTT--ATTATTACTTTTC
60683 ATTATT
1 ATTATT
60689 ATTTTAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 10 0.40
23 5 0.20
24 8 0.32
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATTTTATTATTACTTTTC
Done.