Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003946.1 Hibiscus syriacus cultivar Beakdansim tig00008529_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: 53714
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7042 original size:21 final size:22
Alignment explanation
Indices: 7003--7046 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
6993 ATATTTGGGG
7003 TATAGACAGTTTAATAAACTGC
1 TATAGACAGTTTAATAAACTGC
7025 TATAGA-AG-TTAATGAAACTGC
1 TATAGACAGTTTAAT-AAACTGC
7046 T
1 T
7047 GCCTAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (22 bp):
TATAGACAGTTTAATAAACTGC
Found at i:7728 original size:90 final size:90
Alignment explanation
Indices: 7631--7816 Score: 363
Period size: 90 Copynumber: 2.1 Consensus size: 90
7621 ATTAGCCACA
7631 ACAACTTTGATTAAATAAATTTATTTATTTTGCTAATGATCTTATTAAGACCATAAACATCTATA
1 ACAACTTTGATTAAATAAATTTATTTATTTTGCTAATGATCTTATTAAGACCATAAACATCTATA
7696 AACATAAGATGTTGCATGATGAACT
66 AACATAAGATGTTGCATGATGAACT
7721 ACAACTTTGATTAAATAAATTTATTTATTTTGCTAATGATCTTATTAAGACCATAAACATCTATA
1 ACAACTTTGATTAAATAAATTTATTTATTTTGCTAATGATCTTATTAAGACCATAAACATCTATA
7786 AACATAAGATGTTGCATGATGAACT
66 AACATAAGATGTTGCATGATGAACT
7811 AGCAAC
1 A-CAAC
7817 AATTTTTGAT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 91 0.96
91 4 0.04
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (90 bp):
ACAACTTTGATTAAATAAATTTATTTATTTTGCTAATGATCTTATTAAGACCATAAACATCTATA
AACATAAGATGTTGCATGATGAACT
Found at i:16989 original size:28 final size:29
Alignment explanation
Indices: 16918--16990 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 29
16908 ACGGTAGCCG
*
16918 ATCGAACCAAA-TTATCATTAACCGAATTA
1 ATCGAACCAAATTTTTCATTAACCG-ATTA
**** *
16947 ATCGAACTTTTTTTTTCTTTAACCG-TTA
1 ATCGAACCAAATTTTTCATTAACCGATTA
16975 ATCGAACCAAATTTTT
1 ATCGAACCAAATTTTT
16991 TTTTTTTGAA
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
28 15 0.45
29 7 0.21
30 11 0.33
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (29 bp):
ATCGAACCAAATTTTTCATTAACCGATTA
Found at i:22714 original size:12 final size:12
Alignment explanation
Indices: 22699--22743 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
22689 CGGTTTTTTT
*
22699 ACCGGATAAAAA
1 ACCGGTTAAAAA
22711 ACCGGTTTGAAAAA
1 ACCGG-TT-AAAAA
22725 ACCGGTTAAAAA
1 ACCGGTTAAAAA
22737 ACCGGTT
1 ACCGGTT
22744 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.57
13 3 0.10
14 10 0.33
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:22725 original size:14 final size:13
Alignment explanation
Indices: 22705--22744 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
22695 TTTTACCGGA
22705 TAAAAAACCGGTT
1 TAAAAAACCGGTT
22718 TGAAAAAACCGG-T
1 T-AAAAAACCGGTT
22731 TAAAAAACCGGTT
1 TAAAAAACCGGTT
22744 T
1 T
22745 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:25060 original size:21 final size:21
Alignment explanation
Indices: 25036--25075 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25026 TTTATTTTAT
25036 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
25057 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
25076 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:25123 original size:33 final size:33
Alignment explanation
Indices: 25070--25168 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
25060 TTTGTTTCAA
25070 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
25102 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
25135 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
25168 T
1 T
25169 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:25197 original size:13 final size:13
Alignment explanation
Indices: 25154--25208 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
25144 TTGGAAGTAT
25154 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
25167 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
25181 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
25194 TTAAGTATTTGAA
1 TTAAGTATTTCAA
25207 TT
1 TT
25209 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:25656 original size:15 final size:15
Alignment explanation
Indices: 25604--25659 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
25594 ATCTAGAATA
*
25604 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
25619 TTATAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
25634 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
25651 TTAAAACCG
1 TTAAAACCG
25660 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 22 0.65
17 12 0.35
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:27067 original size:31 final size:31
Alignment explanation
Indices: 27032--27124 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
27022 GGTGAAAAGG
27032 TTGGAATGCAATGAGTAAATCGATTGGTTTT
1 TTGGAATGCAATGAGTAAATCGATTGGTTTT
27063 TTGGAATGCAATGAGTAAATCGATTGGTTTT
1 TTGGAATGCAATGAGTAAATCGATTGGTTTT
*
27094 TTGGAATGCAATGAGTAAATCGATTGATTTT
1 TTGGAATGCAATGAGTAAATCGATTGGTTTT
27125 CGCTAAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (31 bp):
TTGGAATGCAATGAGTAAATCGATTGGTTTT
Found at i:34425 original size:197 final size:198
Alignment explanation
Indices: 34089--34484 Score: 670
Period size: 197 Copynumber: 2.0 Consensus size: 198
34079 GGTAAGACCA
*
34089 TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTCTTGGTCCATAA
1 TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
*
34154 ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTTTAAGTTTC
66 ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
* *
34219 ATAGAGTTTTTTATATGATTTTTA-GGCT-TTGAAACATTAAAGCCTAGTATCTTAAAGATTAAT
131 ATAGAGTTTTTTATATGATTTTTATGG-TATTGAAACATTAAAGCCTAATACCTTAAAGATTAAT
34282 ATTT
195 ATTT
** *
34286 TAATCTTAGTTTTCTTTTGGTACTAATTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
1 TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
* *
34351 ACCCTAACTTAAAATGTTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
66 ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
* *
34416 ATGGAGTTTTTTCTATGATTTTTATGGTATTGAAACATTAAAGCCTAATACCTTAAAGATTAATA
131 ATAGAGTTTTTTATATGATTTTTATGGTATTGAAACATTAAAGCCTAATACCTTAAAGATTAATA
34481 TTT
196 TTT
34484 T
1 T
34485 CATGTTTATT
Statistics
Matches: 186, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
197 146 0.78
198 40 0.22
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (198 bp):
TAATCTTAAATTTCTTTTGGTACTAACTTCTTTAAGTTTTGAACACATGTATTATTGGTCCATAA
ACCCTAACTTAAAAGGCTTATGTAATTAGAGATCCTAAGTTGTTATAAAATTGATTATAAGTTTC
ATAGAGTTTTTTATATGATTTTTATGGTATTGAAACATTAAAGCCTAATACCTTAAAGATTAATA
TTT
Found at i:35441 original size:23 final size:23
Alignment explanation
Indices: 35396--35473 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
35386 CACCGAAGTC
* * *
35396 CCACATAGAATTTGTCCCGAAGGA
1 CCACATAG-GTTTGTCTCAAAGGA
35420 CCACATAGGTTTGTCTCAAAGGA
1 CCACATAGGTTTGTCTCAAAGGA
*
35443 CTACATAGGTTTGTCTCAAAGGA
1 CCACATAGGTTTGTCTCAAAGGA
*
35466 CTACATAG
1 CCACATAG
35474 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 42 0.84
24 8 0.16
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CCACATAGGTTTGTCTCAAAGGA
Found at i:41614 original size:20 final size:20
Alignment explanation
Indices: 41589--41633 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
41579 GATTTTTAAC
41589 TTTTAGTTGGCATGCACACT
1 TTTTAGTTGGCATGCACACT
*
41609 TTTTAGTTGGCATGTACACT
1 TTTTAGTTGGCATGCACACT
41629 TTTTA
1 TTTTA
41634 AAACAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (20 bp):
TTTTAGTTGGCATGCACACT
Found at i:42385 original size:23 final size:22
Alignment explanation
Indices: 42353--42414 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 22
42343 AGAATATGTC
42353 CCGAAGGACCACATAGGTTTGTT
1 CCGAAGGACCACATAGGTTTG-T
*
42376 CCGAATGACCACATAGGTTTGT
1 CCGAAGGACCACATAGGTTTGT
42398 CTCGAAGGACCACATAG
1 C-CGAAGGACCACATAG
42415 AACCCTCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (22 bp):
CCGAAGGACCACATAGGTTTGT
Found at i:43112 original size:20 final size:20
Alignment explanation
Indices: 43068--43118 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
43058 TTTTCGATAA
*
43068 CAGTATCGATACCTTCCTCT
1 CAGTATCGATACCTTCCTAT
*
43088 TAGTATCGATACC-TCCATAT
1 CAGTATCGATACCTTCC-TAT
43108 CAGTATCGATA
1 CAGTATCGATA
43119 TTACTTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (20 bp):
CAGTATCGATACCTTCCTAT
Found at i:51164 original size:21 final size:22
Alignment explanation
Indices: 51138--51193 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
51128 AAACCATTCA
51138 GGGGGGAATCGGTACCCCCTTG
1 GGGGGGAATCGGTACCCCCTTG
* *
51160 GGGGGGAATCGGTA-CCCTTTT
1 GGGGGGAATCGGTACCCCCTTG
51181 GGGGGGAATCGGT
1 GGGGGGAATCGGT
51194 TCCCTCTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.14, C:0.20, G:0.45, T:0.21
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCCCTTG
Found at i:53017 original size:21 final size:22
Alignment explanation
Indices: 52987--53027 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52977 TTAGGATCAA
*
52987 TGGGATTAGGAATAGGATTTAG
1 TGGGATTAGGAAGAGGATTTAG
*
53009 TGGGA-TAGGAGGAGGATTT
1 TGGGATTAGGAAGAGGATTT
53028 GGAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTAG
Done.