Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001955.1 Hibiscus syriacus cultivar Beakdansim tig00003957_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: 52825
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:836 original size:37 final size:38
Alignment explanation
Indices: 795--877 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
785 TTTAACAGAG
* *
795 TAATATTTAAGTTG-AA-ATAGAAATATTATATTTTTTA
1 TAATATTTAAGTTGTAACA-AAAAATATTATATTTTTCA
**
832 TAATATTTTTGTTGTAACAAAAAATATTATATTTTTCA
1 TAATATTTAAGTTGTAACAAAAAATATTATATTTTTCA
870 TAATATTT
1 TAATATTT
878 TTTGTTGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 12 0.30
38 27 0.68
39 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (38 bp):
TAATATTTAAGTTGTAACAAAAAATATTATATTTTTCA
Found at i:1263 original size:29 final size:30
Alignment explanation
Indices: 1221--1289 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
1211 GGATTTGAAG
*
1221 AGAATTAGGCTTGTAACCTTGG-AAAAAAA
1 AGAATTAGGCTTGTAACCCTGGAAAAAAAA
1250 AGAATTAGGCTTGTAACCCTGGAAAAAAAA
1 AGAATTAGGCTTGTAACCCTGGAAAAAAAA
1280 AGAATTAGGC
1 AGAATTAGGC
1290 CTAATTGCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (30 bp):
AGAATTAGGCTTGTAACCCTGGAAAAAAAA
Found at i:2379 original size:19 final size:20
Alignment explanation
Indices: 2345--2385 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
2335 AAACTCAAAT
2345 TGATATAGACTACCAAGAGA
1 TGATATAGACTACCAAGAGA
*
2365 TGATATA-AGTACCAAGAGA
1 TGATATAGACTACCAAGAGA
2384 TG
1 TG
2386 GTACCAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
TGATATAGACTACCAAGAGA
Found at i:5432 original size:20 final size:20
Alignment explanation
Indices: 5387--5444 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
5377 GCATGGGTAG
5387 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
5411 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
5431 TGCATCGATGCACT
1 TGCATCGATGCACT
5445 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:9438 original size:20 final size:22
Alignment explanation
Indices: 9393--9450 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
9383 GCATGGGTAG
9393 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
9417 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
9437 TGCATCGATGCACT
1 TGCATCGATGCACT
9451 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:12822 original size:41 final size:41
Alignment explanation
Indices: 12768--12851 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
12758 ATTCGTGTTG
* * *
12768 CATTTCGCATTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCACATTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
12809 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCACATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
12850 CA
1 CA
12852 AATTCGTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (41 bp):
CATTTCACATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:12955 original size:6 final size:6
Alignment explanation
Indices: 12944--12972 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12934 AGACACGTAT
12944 GACCAC GACCAC GACCAC GACCAC GACCA
1 GACCAC GACCAC GACCAC GACCAC GACCA
12973 TTAGGGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.48, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:13195 original size:21 final size:20
Alignment explanation
Indices: 13083--13175 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
13073 TTGGCTTACT
13083 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
13103 ATCGCAACGCGATTTTTAACT
1 ATCGCAACGCGAAATGGAA-A
13124 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
13144 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
13164 ATCGCAACGCGA
1 ATCGCAACGCGA
13176 TTTTCAACTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:13231 original size:61 final size:61
Alignment explanation
Indices: 13083--13200 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
13073 TTGGCTTACT
*
13083 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTTAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
13144 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
13201 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (61 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:25188 original size:19 final size:19
Alignment explanation
Indices: 25164--25203 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
25154 GTTTTTTTCC
25164 TATTTT-TTTCATTTATTAT
1 TATTTTATTTCATTT-TTAT
*
25183 TATTTTATTTTATTTTTAT
1 TATTTTATTTCATTTTTAT
25202 TA
1 TA
25204 ATAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTTTATTTCATTTTTAT
Found at i:26579 original size:12 final size:11
Alignment explanation
Indices: 26556--26605 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
26546 TTTCAAAATG
26556 TTTAATTTATTA
1 TTTAA-TTATTA
26568 CTTTAATTATTA
1 -TTTAATTATTA
26580 TTTAAATTATTA
1 TTT-AATTATTA
*
26592 TTTTATT-TTA
1 TTTAATTATTA
26602 TTTA
1 TTTA
26606 TATAAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 6 0.18
11 6 0.18
12 17 0.50
13 5 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:26589 original size:24 final size:22
Alignment explanation
Indices: 26556--26605 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
26546 TTTCAAAATG
*
26556 TTTAATTTATTACTTTAATTATTA
1 TTTAAATTATTA-TTTAATT-TTA
*
26580 TTTAAATTATTATTTTATTTTA
1 TTTAAATTATTATTTAATTTTA
26602 TTTA
1 TTTA
26606 TATAAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTAAATTATTATTTAATTTTA
Found at i:29256 original size:21 final size:21
Alignment explanation
Indices: 29230--29274 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29220 GATTTCTGGG
* *
29230 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
29251 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
29272 CAA
1 CAA
29275 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:31026 original size:23 final size:22
Alignment explanation
Indices: 30967--31033 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
30957 TATGGACATC
*
30967 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
30989 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
31011 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
31034 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:46508 original size:20 final size:19
Alignment explanation
Indices: 46479--46518 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
46469 ATGAGCAAAG
46479 AGATGAAGAG-AAGATGTGA
1 AGATGAAGAGCAAGAT-TGA
46498 AGATAGAAGAGCAAGATTGA
1 AGAT-GAAGAGCAAGATTGA
46518 A
1 A
46519 AGGAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.15
Consensus pattern (19 bp):
AGATGAAGAGCAAGATTGA
Found at i:51574 original size:123 final size:123
Alignment explanation
Indices: 51412--51913 Score: 738
Period size: 123 Copynumber: 4.1 Consensus size: 123
51402 TCACTTGATA
*
51412 GATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATATAAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
* * * * *
51477 AATTTGAAGAACGTATTCAACCTTTTGCTTGATTCTATCTCAGAAAGATATAGAGCAG
66 AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAG
* *
51535 GATCAACATTTCCAGAAGAAGTTCGTAATAAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
*
51600 AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAATGAGATAGAGCAG
66 AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAG
* * * *
51658 CATCAACGTTTCCAGAAGAAGTTTGCAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
* *
51723 AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGTAG
66 AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAG
* * * *
51781 AATCAACGTTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATTTAAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
* * ** * * * *
51846 AATCTGAAGAACTTGTTCAACC-TTAGCTCAATTC-ATCGCAGAAGGAGATAGATCAA
66 AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAG
*
51902 CATCAACATTTC
1 GATCAACATTTC
51914 TATCTTAATC
Statistics
Matches: 347, Mismatches: 32, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 29 0.08
122 8 0.02
123 310 0.89
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
GATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCAT
AATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAG
Found at i:52051 original size:3 final size:3
Alignment explanation
Indices: 52043--52101 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
52033 ATTTTTTCAT
* * *
52043 TTA TTA TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA ATA -AA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
52088 TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TT
52102 GCATACCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
2 5 0.10
3 43 0.90
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:52061 original size:16 final size:17
Alignment explanation
Indices: 52042--52075 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
52032 CATTTTTTCA
52042 TTTATTATTATT-TTAT
1 TTTATTATTATTATTAT
52058 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
52075 T
1 T
52076 ATTAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTATTATTATTAT
Done.