Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002692.1 Hibiscus syriacus cultivar Beakdansim tig00005559_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: 49315
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--89 Score: 169
Period size: 31 Copynumber: 2.9 Consensus size: 31
*
1 TGGATGAATGGTTGATTCTTTAATTCCGTTT
1 TGGATGAATGGTTGATTCTTTAATTCCATTT
32 TGGATGAATGGTTGATTCTTTAATTCCATTT
1 TGGATGAATGGTTGATTCTTTAATTCCATTT
63 TGGATGAATGGTTGATTCTTTAATTCC
1 TGGATGAATGGTTGATTCTTTAATTCC
90 TTCTTTAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.47
Consensus pattern (31 bp):
TGGATGAATGGTTGATTCTTTAATTCCATTT
Found at i:3411 original size:18 final size:18
Alignment explanation
Indices: 3384--3424 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3374 TATAACCTCA
* *
3384 TTATCCTTATTATTATTC
1 TTATCATTATTATCATTC
3402 TTATCATTATTATCATTC
1 TTATCATTATTATCATTC
*
3420 ATATC
1 TTATC
3425 TCTTAGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATCATTATTATCATTC
Found at i:3685 original size:22 final size:22
Alignment explanation
Indices: 3660--3701 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3650 ATATGAAATT
3660 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
*
3682 TGTCCTGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
3702 ACCCTCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:4530 original size:275 final size:275
Alignment explanation
Indices: 4034--4595 Score: 1079
Period size: 275 Copynumber: 2.0 Consensus size: 275
4024 ATATATCATT
4034 TATATCAATTCACATGGTTTATCAGACAACATATATTCCCATGGATCATGTAACATATAACACAT
1 TATA-CAATTCACATGGTTTATCAGACAACATATATTCCCATGGATCATGTAACATATAACACAT
4099 ATACTCATATCAAACACATGCCTACATTCATGAATTCATGCATTATAATATAGGAAATAGACTCA
65 ATACTCATATCAAACACATGCCTACATTCATGAATTCATGCATTATAATATAGGAAATAGACTCA
4164 TCACAAGTATTATTTCCATTAAACATCATATATCAACTAGTATGCACTCACCTAGACCTCACTAG
130 TCACAAGTATTATTTCCATTAAACATCATATATCAACTAGTATGCACTCACCTAGACCTCACTAG
*
4229 CCATTCCTATACGTACAACTCTTATACACTCTTATAACTTCAAACCATCTTGGACTTGTATTTGA
195 CCATTCCTATACGTACAACTCTTATACACTCTTATAACTTCAAACCATCTTGGACTTGTATTCGA
4294 TCGATATCTACACGAA
260 TCGATATCTACACGAA
4310 TATACAATTCACATGGTTTATCAGACAACATATATTCCCATGGATCATGTAACATATAACACATA
1 TATACAATTCACATGGTTTATCAGACAACATATATTCCCATGGATCATGTAACATATAACACATA
*
4375 TACTCATATCAAATACATGCCTACATTCATGAATTCATGCATTATAATATAGGAAATAGACTCAT
66 TACTCATATCAAACACATGCCTACATTCATGAATTCATGCATTATAATATAGGAAATAGACTCAT
*
4440 CGCAAGTATTATTTCCATTAAACATCATATATCAACTAGTATGCACTCACCTAGACCTCACTAGC
131 CACAAGTATTATTTCCATTAAACATCATATATCAACTAGTATGCACTCACCTAGACCTCACTAGC
*
4505 CATTCCTATACGTACAACTCTTATACACTCTTATAACTTCAAACCATCTTGGACTTGTCTTCGAT
196 CATTCCTATACGTACAACTCTTATACACTCTTATAACTTCAAACCATCTTGGACTTGTATTCGAT
4570 CGATATCTACACGAA
261 CGATATCTACACGAA
4585 TATACAATTCA
1 TATACAATTCA
4596 ATGAATATCG
Statistics
Matches: 282, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
275 278 0.99
276 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (275 bp):
TATACAATTCACATGGTTTATCAGACAACATATATTCCCATGGATCATGTAACATATAACACATA
TACTCATATCAAACACATGCCTACATTCATGAATTCATGCATTATAATATAGGAAATAGACTCAT
CACAAGTATTATTTCCATTAAACATCATATATCAACTAGTATGCACTCACCTAGACCTCACTAGC
CATTCCTATACGTACAACTCTTATACACTCTTATAACTTCAAACCATCTTGGACTTGTATTCGAT
CGATATCTACACGAA
Found at i:6393 original size:55 final size:55
Alignment explanation
Indices: 6309--6547 Score: 365
Period size: 55 Copynumber: 4.4 Consensus size: 55
6299 TAAACTTAAG
* *
6309 AAGTGGATGAGTTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACT
1 AAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACT
6364 AAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACT
1 AAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACT
* * *
6419 ATGTTGATGAATTTCCGTATGGGCACTTTATGAGTAAACTTAAGAAATTCATACT
1 AAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACT
* * * *
6474 AGGTGGATGAATTTCTGTATGGGTACTTTATGTGTAAAAC-TAGGAAATTCATACT
1 AAGTGGATGAATTTCCGTATGGGCACTTTATGTGT-AAACTTAAGAAATTCATACT
*
6529 AAGTGTAT-AATTTCCGTAT
1 AAGTGGATGAATTTCCGTAT
6548 TGGTAGTGGG
Statistics
Matches: 169, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
54 10 0.06
55 155 0.92
56 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (55 bp):
AAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACT
Found at i:15922 original size:3 final size:3
Alignment explanation
Indices: 15914--15980 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
15904 GCAAAAATTG
* **
15914 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15958 TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
15981 CGGAAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:15972 original size:35 final size:35
Alignment explanation
Indices: 15914--15982 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
15904 GCAAAAATTG
*
15914 TAATAATAAATAATAATAAAATAATAAGATAACGA
1 TAATAATAAATAATAATAAAATAATAAAATAACGA
15949 TAATAAT-AATAATAATAATAATAATAAAATAACG
1 TAATAATAAATAATAATAA-AATAATAAAATAACG
15983 GAAAAAAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (35 bp):
TAATAATAAATAATAATAAAATAATAAAATAACGA
Found at i:16241 original size:46 final size:43
Alignment explanation
Indices: 16156--16303 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 43
16146 CTCATACGCA
* * * * * *
16156 ATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCTCCTACGTG
1 ATGAGGAGATCTGGTCATCTATGGTTAACACGGCTCCTACGTG
* *
16199 ATGAGGAGATCTGGTCATCTTTAGGTGATAACACGGTTCCTACGTG
1 ATGAGGAGATCTGGTCATCTAT-GGT--TAACACGGCTCCTACGTG
* * * *
16245 ATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCATACGTG
1 ATGAGGA-GATCTGGTCATCTATGGTTAACACGGCTCCTACGTG
*
16288 ATGAAGAGATCTGGTC
1 ATGAGGAGATCTGGTC
16304 TGGGGATGAC
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 43 0.52
44 2 0.02
45 3 0.04
46 33 0.40
47 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (43 bp):
ATGAGGAGATCTGGTCATCTATGGTTAACACGGCTCCTACGTG
Found at i:30993 original size:3 final size:3
Alignment explanation
Indices: 30985--31048 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
30975 GCAAAAATTG
* **
30985 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31029 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
31049 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:31040 original size:32 final size:32
Alignment explanation
Indices: 30987--31050 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
30977 AAAAATTGTA
*
30987 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
31019 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
31051 GAAAAAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:32545 original size:55 final size:55
Alignment explanation
Indices: 32182--32535 Score: 575
Period size: 55 Copynumber: 6.4 Consensus size: 55
32172 AAGTGTGTAA
* *
32182 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGCCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* *
32237 AAACTTAAGAAATTCATACTAAGTGGAAGAATTTTTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
*
32292 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGACACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* *
32347 AAACTTAAGAAATTCATACTAAGTAGATGAATTTCTGTATGGGCACTTTATATGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* *
32402 AAACTTAAGAAATTCATACTAAGTGGATAAATTTCCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* *
32457 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTAATGTGCA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTG-T
* *
32513 AAAC-TAGGAAATTCATATTAAGT
1 AAACTTAAGAAATTCATACTAAGT
32536 ATATAAATTT
Statistics
Matches: 280, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 276 0.99
56 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
Found at i:41126 original size:13 final size:13
Alignment explanation
Indices: 41108--41159 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
41098 GTCATAAATC
41108 TATGACGCGCATT
1 TATGACGCGCATT
* *
41121 TATGACACGTATT
1 TATGACGCGCATT
*
41134 TATGACGCGTATT
1 TATGACGCGCATT
*
41147 TATGATGCGCATT
1 TATGACGCGCATT
41160 GCGCATCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:46598 original size:48 final size:47
Alignment explanation
Indices: 46528--46623 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 47
46518 AATTTGGTTA
*
46528 ACTTAAAATATTTACGAATAGGTTTTGTACTTTCAGAAAATATTAAT
1 ACTTAAAATATTTACGAATAGGTTCTGTACTTTCAGAAAATATTAAT
*
46575 ACTTAAGATTATTTACGAATAGGTTCTGTACTTTCAGAAAATATTAAT
1 ACTTAA-AATATTTACGAATAGGTTCTGTACTTTCAGAAAATATTAAT
46623 A
1 A
46624 AGGTCCCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 6 0.13
48 40 0.87
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (47 bp):
ACTTAAAATATTTACGAATAGGTTCTGTACTTTCAGAAAATATTAAT
Found at i:47732 original size:24 final size:26
Alignment explanation
Indices: 47696--47758 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
47686 TATTAAGGTA
*
47696 TATTTTATATATTTAAT-TTTTAT-T
1 TATTTTATATATTTAATATTTAATAT
47720 TATTTTA-AGTATTTAATATTTAATAT
1 TATTTTATA-TATTTAATATTTAATAT
*
47746 TATTTAATA-ATTT
1 TATTTTATATATTT
47759 TTTTTGCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 15 0.45
25 9 0.27
26 7 0.21
27 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTTTATATATTTAATATTTAATAT
Done.