Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001103.1 Hibiscus syriacus cultivar Beakdansim tig00002184_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: 58976
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:11071 original size:16 final size:16
Alignment explanation
Indices: 11033--11063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11023 CTGACCCGTT
*
11033 GACTTTAACCAGAGTA
1 GACTTTGACCAGAGTA
11049 GACTTTGACCAGAGT
1 GACTTTGACCAGAGT
11064 TAACTTTGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (16 bp):
GACTTTGACCAGAGTA
Found at i:15312 original size:16 final size:16
Alignment explanation
Indices: 15276--15318 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
15266 GACCTGACCC
*
15276 GTTGACTTTGACCATA
1 GTTGACTTTGACCAGA
* *
15292 TTTGACCTTGACCAGA
1 GTTGACTTTGACCAGA
15308 GTTGACTTTGA
1 GTTGACTTTGA
15319 ACTGAAAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (16 bp):
GTTGACTTTGACCAGA
Found at i:15342 original size:17 final size:17
Alignment explanation
Indices: 15320--15353 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15310 TGACTTTGAA
15320 CTGAAAAGTCAAATTTT
1 CTGAAAAGTCAAATTTT
*
15337 CTGAAAAGTCATATTTT
1 CTGAAAAGTCAAATTTT
15354 ATATGTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
CTGAAAAGTCAAATTTT
Found at i:18266 original size:131 final size:130
Alignment explanation
Indices: 17912--18268 Score: 450
Period size: 131 Copynumber: 2.7 Consensus size: 130
17902 GAAAATAATA
*
17912 ATATCTCTTCATTTTGGTTGGAGTAATAAATAACTGC-TTAAGGCAGGAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTTGGTTGGAGTAATAAATAACTGCTTTAAGGCATGAGAGGTCATTTATTCTC
* * * *
17976 GATTGGAAATAACTAGATATAATGTTTTCTCTCGAATCAATATTGATTTGTAAGACGAAATAGTG
66 GATTGGAAATAATTAGATATTATGTTTTCTCTCAAATCAATATTGATTTGTAAGACGAAAGAGTG
* *** * * * * * *
18041 ATATCTTTTCATTTCAATTAGAATAATAAATTATTGTTTTAACGG-ATGAGAGGTCATTTATTAT
1 ATATCTCTTCATTTTGGTTGGAGTAATAAATAACTGCTTTAA-GGCATGAGAGGTCATTTATTCT
* * *
18105 CGATTGGAAATAATTAGATATTTTTGTTTTCTTTCAAATCAATATTGAATTT-TAAGACTAAAGA
65 CGATTGGAAATAATTAGATA-TTATGTTTTCTCTCAAATCAATATTG-ATTTGTAAGACGAAAGA
18169 GTG
128 GTG
* * * *
18172 ATATCTCGTCATTTTGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGCTCACTTATTCTC
1 ATATCTCTTCATTTTGGTTGGAGTAATAAATAACTGCTTTAAGGCATGAGAGGTCATTTATTCTC
*
18237 GATTGGAAATAATTAGATATTATCATTTTCTC
66 GATTGGAAATAATTAGATATTAT-GTTTTCTC
18269 CCTTAAAATT
Statistics
Matches: 188, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
129 28 0.15
130 45 0.24
131 111 0.59
132 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (130 bp):
ATATCTCTTCATTTTGGTTGGAGTAATAAATAACTGCTTTAAGGCATGAGAGGTCATTTATTCTC
GATTGGAAATAATTAGATATTATGTTTTCTCTCAAATCAATATTGATTTGTAAGACGAAAGAGTG
Found at i:19543 original size:6 final size:6
Alignment explanation
Indices: 19532--19558 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19522 TACCTTGTTT
19532 ATTTGC ATTTGC ATTTGC ATTTGC ATT
1 ATTTGC ATTTGC ATTTGC ATTTGC ATT
19559 CTTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (6 bp):
ATTTGC
Found at i:25317 original size:133 final size:133
Alignment explanation
Indices: 25029--25481 Score: 521
Period size: 135 Copynumber: 3.4 Consensus size: 133
25019 AATTGAACTT
* * * * * * *
25029 GATTCAATCTTCCCTGAAGGACAATGGAAAGAATTAATATTTCCAGATCTGTTTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTTAAGA
* *** * * * * *
25094 AGGAGGGGAACATATCCCTATTTATTCCAAATTTGATCTTCTATGAGGAACAGTGGAACATGTAT
66 AGCAACAGAACATATCCCT-TTT-TTCTAAATTTGATCTTCCATGAGGAATAGTGGAACAAGTCT
25159 GCCTC
129 GCCTC
* * * *
25164 AATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGACCTGATTTTCTCTTAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTTAAGA
* * * * * *
25229 AGCAACATAACATATCCCTTTTTTCTAGATTTGACCTTCCCTGAGGAATAATGAAACAAGTCTGC
66 AGCAACAGAACATATCCCTTTTTTCTAAATTTGATCTTCCATGAGGAATAGTGGAACAAGTCTGC
25294 CTC
131 CTC
* * * *
25297 GATTCAATCTTCCCTGAAGAACAGTTGAATGAATCAACATTACCAGATCTAATATTCCCTTAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTTAAGA
* *
25362 AGCAACAGAACAAATCCCTTTTTTTTTCAAATTTGATCTTCCATGAGGAATAGTGGAACAAGTCT
66 AGCAACAGAACATATCCC-TTTTTTCT-AAATTTGATCTTCCATGAGGAATAGTGGAACAAGTCT
*
25427 TCCTC
129 GCCTC
* * * *
25432 GATTCAATCTTTCTTGTAGAGA-AGTGGAATGAATCAATATTTCCAGATCT
1 GATTCAATCTTCCCTGAAGA-ACAGTGGAATGAATCAACATTTCCAGATCT
25482 CTTCTCATAC
Statistics
Matches: 266, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
133 109 0.41
134 10 0.04
135 146 0.55
136 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (133 bp):
GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTTAAGA
AGCAACAGAACATATCCCTTTTTTCTAAATTTGATCTTCCATGAGGAATAGTGGAACAAGTCTGC
CTC
Found at i:25680 original size:3 final size:3
Alignment explanation
Indices: 25672--25729 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
25662 TGGGGTCCAC
* * *
25672 TAT TAT TAT TAT TAT TAT CAT TA- TAT TAT TAT TAT TAT TA- TAC TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25718 TAT T-T TAT TAT T
1 TAT TAT TAT TAT T
25730 TTGTTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:25702 original size:23 final size:23
Alignment explanation
Indices: 25672--25729 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
25662 TGGGGTCCAC
*
25672 TATTATTATTATTATTAT-CATTA
1 TATTATTATTATTATTATAC-TAA
25695 TATTATTATTATTATTATACTAA
1 TATTATTATTATTATTATACTAA
25718 TATT-TTATTATT
1 TATTATTATTATT
25730 TTGTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 8 0.24
23 24 0.73
24 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATTATTATTATTATACTAA
Found at i:27238 original size:15 final size:17
Alignment explanation
Indices: 27200--27238 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
27190 ATTGTGATTA
*
27200 TATTTTATATCATATAC
1 TATTGTATATCATATAC
27217 TATTGTATAT-ATATAC
1 TATTGTATATCATATAC
27233 -ATTGTA
1 TATTGTA
27239 CGCATGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 9 0.43
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (17 bp):
TATTGTATATCATATAC
Found at i:28458 original size:20 final size:20
Alignment explanation
Indices: 28430--28474 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28420 ATTAATGTTT
*
28430 CTTTCTTTTAAAAAATTAAA
1 CTTTATTTTAAAAAATTAAA
* * *
28450 CTTTATTTTTAAAACTTCAA
1 CTTTATTTTAAAAAATTAAA
28470 CTTTA
1 CTTTA
28475 ATATTTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (20 bp):
CTTTATTTTAAAAAATTAAA
Found at i:40477 original size:21 final size:21
Alignment explanation
Indices: 40453--40503 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
40443 GTTGAAGGAC
40453 AGGGTATAGTTGGCATGCCAT
1 AGGGTATAGTTGGCATGCCAT
40474 AGGGTATAGTTGGCATGCCAT
1 AGGGTATAGTTGGCATGCCAT
*
40495 AGAGTATAG
1 AGGGTATAG
40504 CAGCTGCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (21 bp):
AGGGTATAGTTGGCATGCCAT
Found at i:40818 original size:10 final size:10
Alignment explanation
Indices: 40803--40827 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40793 TGCACAACAT
40803 TTTAGTTGCA
1 TTTAGTTGCA
40813 TTTAGTTGCA
1 TTTAGTTGCA
40823 TTTAG
1 TTTAG
40828 GTTATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:41622 original size:19 final size:21
Alignment explanation
Indices: 41582--41622 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41572 GACAATTATT
*
41582 TTATGTTTTATGAATGATGAA
1 TTATGTTTTATGAATCATGAA
41603 TTATGTTTT-TG-ATCATGAA
1 TTATGTTTTATGAATCATGAA
41622 T
1 T
41623 GTTTTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.51
Consensus pattern (21 bp):
TTATGTTTTATGAATCATGAA
Found at i:43830 original size:21 final size:20
Alignment explanation
Indices: 43802--43840 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
43792 CATTGCAAGA
43802 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
**
43822 ATTTCATGGGTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
43841 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:55623 original size:13 final size:13
Alignment explanation
Indices: 55602--55636 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55592 CCCACTTACT
55602 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
55615 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
55628 TTTCACTTT
1 TTTCACTTT
55637 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Done.