Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008233.1 Hibiscus syriacus cultivar Beakdansim tig00110873_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: 42965
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:3327 original size:31 final size:31
Alignment explanation
Indices: 3243--3348 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 31
3233 GTCGAGGGTT
*
3243 TACCTATGTTCTATGGAACATATGGAC-ATAA
1 TACCTATGTTCTAAGGAACATATGGACAAT-A
* *
3274 TTACCTATGCCTT-T-CGGGACATATGGACAATA
1 -TACCTATG--TTCTAAGGAACATATGGACAATA
* *
3306 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAATA
*
3337 TACCTAGGTTCT
1 TACCTATGTTCT
3349 TCAGGACCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.03
30 1 0.02
31 33 0.53
32 21 0.34
33 3 0.05
34 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAATA
Found at i:3361 original size:31 final size:31
Alignment explanation
Indices: 3290--3379 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
3280 ATGCCTTTCG
* * *
3290 GGACATATGGACAATATACCTATGTTC-TAA
1 GGACATATGGACAGTTTACCTAGGTTCTTAA
*
3320 GGAACATATGGACAGTTTACCTAGGTTCTTCA
1 GG-ACATATGGACAGTTTACCTAGGTTCTTAA
* *
3352 GGACCTATGGACAG-TTACCGAGGTTCTT
1 GGACATATGGACAGTTTACCTAGGTTCTT
3380 TATGACCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.29
31 33 0.63
32 4 0.08
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (31 bp):
GGACATATGGACAGTTTACCTAGGTTCTTAA
Found at i:6176 original size:3 final size:3
Alignment explanation
Indices: 6161--6201 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
6151 GTGTTTATAG
6161 TAT TAT ATAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6202 CAAATAATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9956 original size:8 final size:8
Alignment explanation
Indices: 9935--9975 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
9925 ATAATTTTCA
9935 TTCT-CAT
1 TTCTGCAT
9942 TTCTGCAT
1 TTCTGCAT
*
9950 TTTTGCAT
1 TTCTGCAT
9958 TTCTGCAT
1 TTCTGCAT
*
9966 TTTTGCAT
1 TTCTGCAT
9974 TT
1 TT
9976 GCATTACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 4 0.13
8 26 0.87
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.59
Consensus pattern (8 bp):
TTCTGCAT
Found at i:9960 original size:16 final size:16
Alignment explanation
Indices: 9939--9975 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
9929 TTTTCATTCT
9939 CATTTCTGCATTTTTG
1 CATTTCTGCATTTTTG
9955 CATTTCTGCATTTTTG
1 CATTTCTGCATTTTTG
9971 CATTT
1 CATTT
9976 GCATTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.57
Consensus pattern (16 bp):
CATTTCTGCATTTTTG
Found at i:12533 original size:7 final size:7
Alignment explanation
Indices: 12518--12663 Score: 94
Period size: 7 Copynumber: 21.4 Consensus size: 7
12508 TCCATCAGAA
12518 AAAAGAAG
1 AAAA-AAG
12526 AAAAAAG
1 AAAAAAG
12533 AGAAAAA-
1 A-AAAAAG
12540 AAGAAAGAG
1 AA-AAA-AG
12549 AAAAAA-
1 AAAAAAG
*
12555 AGAAAAG
1 AAAAAAG
12562 -AAAAAG
1 AAAAAAG
*
12568 -AAAGAG
1 AAAAAAG
12574 AAAAAA-
1 AAAAAAG
*
12580 AGAAAAG
1 AAAAAAG
12587 -AAAAAG
1 AAAAAAG
*
12593 -AAAGAG
1 AAAAAAG
12599 AAAAAA-
1 AAAAAAG
12605 AAGAAAAG
1 AA-AAAAG
*
12613 AGAAAAG
1 AAAAAAG
*
12620 AGAAAAG
1 AAAAAAG
*
12627 AGAAAAG
1 AAAAAAG
*
12634 AGAAAAG
1 AAAAAAG
*
12641 AGAAAAG
1 AAAAAAG
*
12648 AAAAGA-
1 AAAAAAG
12654 AAAAAAG
1 AAAAAAG
12661 AAA
1 AAA
12664 TTGAATCAAG
Statistics
Matches: 115, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
6 38 0.33
7 61 0.53
8 14 0.12
9 2 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12548 original size:14 final size:13
Alignment explanation
Indices: 12518--12663 Score: 151
Period size: 14 Copynumber: 11.2 Consensus size: 13
12508 TCCATCAGAA
*
12518 AAAAGAAGAAAA-
1 AAAAGAAAAAAAG
*
12530 AAGAGAAAAAAAG
1 AAAAGAAAAAAAG
12543 AAAGAGAAAAAAAG
1 AAA-AGAAAAAAAG
12557 AAAAG--AAAAAG
1 AAAAGAAAAAAAG
12568 AAAGAGAAAAAAAG
1 AAA-AGAAAAAAAG
12582 AAAAG--AAAAAG
1 AAAAGAAAAAAAG
12593 AAAGAGAAAAAAAAG
1 AAA-AG-AAAAAAAG
*
12608 AAAAGAGAAAAGAG
1 AAAAGA-AAAAAAG
*
12622 AAAAGAGAAAAGAG
1 AAAAGA-AAAAAAG
*
12636 AAAAG-AGAAAAG
1 AAAAGAAAAAAAG
12648 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
12661 AAA
1 AAA
12664 TTGAATCAAG
Statistics
Matches: 116, Mismatches: 7, Indels: 21
0.81 0.05 0.15
Matches are distributed among these distances:
11 18 0.16
12 24 0.21
13 16 0.14
14 49 0.42
15 9 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:12565 original size:25 final size:25
Alignment explanation
Indices: 12526--12663 Score: 190
Period size: 25 Copynumber: 5.4 Consensus size: 25
12516 AAAAAAGAAG
*
12526 AAAAAAGAGAA-AAAAAGAAAGAGA
1 AAAAAAGAAAAGAAAAAGAAAGAGA
12550 AAAAAAGAAAAGAAAAAGAAAGAGA
1 AAAAAAGAAAAGAAAAAGAAAGAGA
12575 AAAAAAGAAAAGAAAAAGAAAGAGAA
1 AAAAAAGAAAAGAAAAAGAAAGAG-A
*
12601 AAAAAAGAAAAGAGAAAAGAGAAAAGA
1 AAAAAAGAAAAGA-AAAAGA-AAGAGA
*
12628 GAAAAGAGAAAAGAGAAAAGAAA-AGA
1 -AAAAAAGAAAAGA-AAAAGAAAGAGA
12654 AAAAAAGAAA
1 AAAAAAGAAA
12664 TTGAATCAAG
Statistics
Matches: 105, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
24 10 0.10
25 46 0.44
26 17 0.16
27 9 0.09
28 23 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAGAAAAAGAAAGAGA
Found at i:13391 original size:90 final size:91
Alignment explanation
Indices: 13236--13408 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 91
13226 ATTTTCAAAG
*
13236 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTGAACATCGAATCCATT
1 TGATGCACCGATGCACCAAACCATGCATCGATGCACCATGGAATAAATTGAACATCGAATCCATT
13301 TTATGCATCGATGCACTCAATGCATT
66 TTATGCATCGATGCACTCAATGCATT
* * * ** *
13327 TGATGCATCGATGCA-CAAACTATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCA
1 TGATGCACCGATGCACCAAACCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATCCA
*
13389 TTTTATGCATCGATGTACTC
64 TTTTATGCATCGATGCACTC
13409 TTAGTGCACC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 5 0.07
90 52 0.72
91 15 0.21
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (91 bp):
TGATGCACCGATGCACCAAACCATGCATCGATGCACCATGGAATAAATTGAACATCGAATCCATT
TTATGCATCGATGCACTCAATGCATT
Found at i:13396 original size:45 final size:42
Alignment explanation
Indices: 13286--13409 Score: 115
Period size: 45 Copynumber: 2.8 Consensus size: 42
13276 GAATAAATTG
*
13286 AACATCGAATCCATTTTATGCATCGATGCACTCAATGCATTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACTC--TGCATTTGA
** ***
13330 TGCATCG-ATGCACAAACTATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATG--CATTTTATGCATCGATGCACTCT-GC-A-TTTGA
*
13376 AACATCGAATGCATTTTATGCATCGATGTACTCT
1 AACATCGAATGCATTTTATGCATCGATGCACTCT
13410 TAGTGCACCG
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
43 3 0.05
44 7 0.11
45 39 0.63
46 10 0.16
47 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCTGCATTTGA
Found at i:23252 original size:20 final size:21
Alignment explanation
Indices: 23229--23311 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
23219 TTGGTGCAGA
*
23229 GGGAATCGATTCCCCCCTGA-
1 GGGAACCGATTCCCCCCTGAG
*
23249 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CTG-AG
**
23272 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCTGAG
* *
23293 GGGAATCGATACCCCCCTG
1 GGGAACCGATTCCCCCCTG
23312 GGGTTCTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.29
21 19 0.37
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTGAG
Found at i:30295 original size:19 final size:22
Alignment explanation
Indices: 30271--30318 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
30261 TTCCTTCAAA
30271 ACATGTCG-AA-ATTA-TTTAT
1 ACATGTCGAAACATTATTTTAT
30290 ACATGTCGAAACATTATTTTAT
1 ACATGTCGAAACATTATTTTAT
30312 ACATGTC
1 ACATGTC
30319 TTCTTAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.31
20 2 0.08
21 4 0.15
22 12 0.46
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
ACATGTCGAAACATTATTTTAT
Found at i:31684 original size:26 final size:26
Alignment explanation
Indices: 31654--31703 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
31644 TTGAACATCG
*
31654 AATGCATTTTATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACTC
31680 AATGCATTTGATGCATCGATGCAC
1 AATGCATTTGATGCATCGATGCAC
31704 AAGCTATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (26 bp):
AATGCATTTGATGCATCGATGCACTC
Found at i:31757 original size:45 final size:42
Alignment explanation
Indices: 31647--31770 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 42
31637 GAATAAATTG
31647 AACATCGAATGCATTTTATGCATCGATGCACTCAATGCATTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACTC--TGCATTTGA
** ***
31691 TGCATCG-ATGCACAAGCTATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATG--CATTTTATGCATCGATGCACTCT-GC-A-TTTGA
*
31737 AACATCGAATGCATTTTATGCATCGGTGCACTCT
1 AACATCGAATGCATTTTATGCATCGATGCACTCT
31771 TAGTGCACCG
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 4 0.06
44 7 0.11
45 39 0.62
46 10 0.16
47 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (42 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCTGCATTTGA
Found at i:40477 original size:31 final size:31
Alignment explanation
Indices: 40442--40502 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
40432 AAACTTAAAA
*
40442 TAGTTTTGCAATACTGAAATTTAAATAATTT
1 TAGTTTTACAATACTGAAATTTAAATAATTT
40473 TAGTTTTACAATACTGAAATTTAAATAATT
1 TAGTTTTACAATACTGAAATTTAAATAATT
40503 CATACAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (31 bp):
TAGTTTTACAATACTGAAATTTAAATAATTT
Found at i:40680 original size:31 final size:31
Alignment explanation
Indices: 40644--40702 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
40634 AACTTAAAAG
* * *
40644 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
40675 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
40703 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:41553 original size:20 final size:20
Alignment explanation
Indices: 41505--41566 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
41495 AACTTAAATC
*
41505 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
41525 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
41543 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
41562 AAAAT
1 AAAAT
41567 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:41599 original size:14 final size:14
Alignment explanation
Indices: 41582--41630 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
41572 ATCTATAATA
41582 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
41596 TAATATT---TAAT
1 TAATATTAAAAAAT
*
41607 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
41620 TAATATTAAAA
1 TAATATTAAAA
41631 TTAATATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 6 0.22
13 6 0.22
14 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:41600 original size:64 final size:59
Alignment explanation
Indices: 41531--41668 Score: 134
Period size: 64 Copynumber: 2.2 Consensus size: 59
41521 ATATAAAATT
*
41531 TTAATAATATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATA-TTAAAAAA
1 TTAATAATATATAAAA-AA-TTA-AT-AT-TAAAATT-AATATCTATAATATAAAACTTAAAAAA
* *
41595 TTAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAAAACTTATAAAA
1 TT-A-A--TAA--TATATAAAAAATTAATATTAAAATTAATATCTATAATATAAAACTTAAAAAA
41660 TTAATAATA
1 TTAATAATA
41669 CATGTGATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 19
0.74 0.03 0.22
Matches are distributed among these distances:
59 2 0.03
61 3 0.05
63 1 0.02
64 20 0.31
65 17 0.27
66 3 0.05
67 2 0.03
68 6 0.09
69 2 0.03
70 8 0.12
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (59 bp):
TTAATAATATATAAAAAATTAATATTAAAATTAATATCTATAATATAAAACTTAAAAAA
Done.