Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006867.1 Hibiscus syriacus cultivar Beakdansim tig00017477_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: 63294
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:23204 original size:17 final size:17
Alignment explanation
Indices: 23154--23205 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
23144 TATTAAATTT
* *
23154 TATTTTATAATAATT-A
1 TATTTTAAAATTATTAA
*
23170 TATTCTAAAATT-TGTAA
1 TATTTTAAAATTAT-TAA
23187 TATTTTAAAATTATTAA
1 TATTTTAAAATTATTAA
23204 TA
1 TA
23206 AATATTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.03
16 10 0.34
17 17 0.59
18 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TATTTTAAAATTATTAA
Found at i:23342 original size:62 final size:57
Alignment explanation
Indices: 23268--23387 Score: 159
Period size: 62 Copynumber: 2.0 Consensus size: 57
23258 ACTATATTAG
* *
23268 TAGTAAAAACGAACGGCTATACCAAATAAAATTTAAGTTTAGATATAAATTTTAGGTCTAA
1 TAGTAAAAACGAACGGCTAGAACAAATAAAATTTAAGTTT---T-TAAATTTTAGGTCTAA
* *
23329 TAGTAAAAAACGAACGGCTAGAAGAAATAAATTTTAAGTTTTTAAATTTTAGGTCTAA
1 TAGT-AAAAACGAACGGCTAGAACAAATAAAATTTAAGTTTTTAAATTTTAGGTCTAA
23387 T
1 T
23388 GATATTTTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
58 17 0.31
59 1 0.02
61 4 0.07
62 32 0.59
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (57 bp):
TAGTAAAAACGAACGGCTAGAACAAATAAAATTTAAGTTTTTAAATTTTAGGTCTAA
Found at i:24405 original size:2 final size:2
Alignment explanation
Indices: 24400--24425 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24390 ATAAAAAATA
24400 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24426 TAAATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24742 original size:18 final size:18
Alignment explanation
Indices: 24719--24753 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24709 AATCTGACAC
24719 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
*
24737 AAAATAATATTTTTATT
1 AAAATAATATATTTATT
24754 CAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:25344 original size:22 final size:22
Alignment explanation
Indices: 25319--25360 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25309 ATTTTCATTT
*
25319 AATATATATAAATAGATAATTA
1 AATATATATAAATAAATAATTA
*
25341 AATATATATTAATAAATAAT
1 AATATATATAAATAAATAAT
25361 ATTTTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AATATATATAAATAAATAATTA
Found at i:27374 original size:13 final size:13
Alignment explanation
Indices: 27358--27384 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27348 CTTTTTCTTA
27358 TTTCATTTTAATT
1 TTTCATTTTAATT
27371 TTTCATTTTAATT
1 TTTCATTTTAATT
27384 T
1 T
27385 GTTTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCATTTTAATT
Found at i:28817 original size:133 final size:134
Alignment explanation
Indices: 28514--29086 Score: 747
Period size: 134 Copynumber: 4.3 Consensus size: 134
28504 TGTTGATCCA
* * * * * *
28514 TTCCACTGTCACTCAGGGAATATCAAATCTT-GAAAGAGAGGGATTTGTTTCACTTCTTTTGACG
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAA-AGAGGGACTTGTTCCACTTCTTCTAAAG
* *
28578 GGAATATCAGATCTTGAGGGAGTTGATCCATTCCTCTGTCACTCAGGGAAGATTGAATCGGGGCA
65 GGAATATCAGATCTGGA-GGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCA
28643 GACTTG
129 GACTTG
* * * ** *
28649 TTCCGCTGTCACTTAGGGAATATCAAATCTTGGAAAAGTGAGACTTAATCCACTTCTTCTAAAGA
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCACTTCTTCTAAAGG
* * * *
28714 GAATATTAGATCTGGATGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATTGAATC-GGGCATA
66 GAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGA
28778 CTTG
131 CTTG
* * ** * **
28782 TTCCGTTGTCACTCAGTGAATATCAAATCTTGGAAAAGTTGGACATGTTCTGCTTCTTCTAAAGG
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCACTTCTTCTAAAGG
* * *
28847 GAATATCAGATATGGGGGAGTTGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGCAGA
66 GAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGA
28912 CTTG
131 CTTG
*
28916 TTCCGCTGTCACTAAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCACTTCTTCTGAAA-
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCACTTCTTCT-AAAG
* * * * * *
28980 GGAGTATCATATCTGGAAGAGTTGATCCATTCCGCTGTCACTCAGTGAAGGTTTAATCGGGGCAG
65 GGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAG
*
29045 ACTTA
130 ACTTG
* * *
29050 TTCTGCTGTCACTCAAGGAATATCAAATATTGGAAAA
1 TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAA
29087 AAAAGGTTTG
Statistics
Matches: 377, Mismatches: 58, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
133 115 0.31
134 193 0.51
135 65 0.17
136 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (134 bp):
TTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCACTTCTTCTAAAGG
GAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGA
CTTG
Found at i:28996 original size:267 final size:268
Alignment explanation
Indices: 28513--29086 Score: 782
Period size: 267 Copynumber: 2.1 Consensus size: 268
28503 ATGTTGATCC
* ** * * *
28513 ATTCCACTGTCACTCAGGGAATATCAAATCTT-GAAAGAGAGGGATTTGTTTCACTTCTTTTGAC
1 ATTCCGCTGTCACTCA-GGAATATCAAATCTTGGAAA-AGAGGGACATGTTTCACTTCTTCTAAA
*
28577 GGGAATATCAGATCTTGAGGGAGTTGATCCATTCCTCTGTCACTCAGGGAAGATTGAATCGGGGC
64 GGGAATATCAGATCATGAGGGAGTTGATCCATTCCTCTGTCACTCAGGGAAGATTGAATCGGGGC
* *
28642 AGACTTGTTCCGCTGTCACTTAGGGAATATCAAATCTTGGAAAAGTGAGACTTAATCCACTTCTT
129 AGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGGAAAAGAGAGACTTAATCCACTTCTT
* *
28707 CTAAAGAGAATATTAGATCTGGATGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATTGAATC-
194 CTAAAGAGAATATCAGATCTGGAAGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATTGAATCG
*
28771 GGGCATACTT
259 GGGCAGACTT
* * ** *
28781 GTTCCGTTGTCACTCAGTGAATATCAAATCTTGGAAAAGTTGGACATG-TTCTGCTTCTTCTAAA
1 ATTCCGCTGTCACTCAG-GAATATCAAATCTTGGAAAAGAGGGACATGTTTC-ACTTCTTCTAAA
*
28845 GGGAATATCAGAT-ATGGGGGAGTTGATCCATT-CTGCTGTCACTCAGGGAAGATTGAATCGGGG
64 GGGAATATCAGATCATGAGGGAGTTGATCCATTCCT-CTGTCACTCAGGGAAGATTGAATCGGGG
* **
28908 CAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCACTTCT
128 CAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGGAAAAGAGAGACTTAATCCACTTCT
* * * * * *
28973 TCTGAAAG-GAGTATCATATCTGGAAGAGTTGATCCATTCCGCTGTCACTCAGTGAAGGTTTAAT
193 TCT-AAAGAGAATATCAGATCTGGAAGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATTGAAT
29037 CGGGGCAGACTT
257 CGGGGCAGACTT
* *
29049 ATTCTGCTGTCACTCAAGGAATATCAAATATTGGAAAA
1 ATTCCGCTGTCACTC-AGGAATATCAAATCTTGGAAAA
29087 AAAAGGTTTG
Statistics
Matches: 268, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
266 2 0.01
267 161 0.60
268 99 0.37
269 6 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (268 bp):
ATTCCGCTGTCACTCAGGAATATCAAATCTTGGAAAAGAGGGACATGTTTCACTTCTTCTAAAGG
GAATATCAGATCATGAGGGAGTTGATCCATTCCTCTGTCACTCAGGGAAGATTGAATCGGGGCAG
ACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGGAAAAGAGAGACTTAATCCACTTCTTCT
AAAGAGAATATCAGATCTGGAAGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATTGAATCGGG
GCAGACTT
Found at i:51285 original size:16 final size:16
Alignment explanation
Indices: 51261--51292 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51251 ATTTTCTTTT
*
51261 AATCGTAAAATTTATA
1 AATCATAAAATTTATA
51277 AATCATAAAATTTATA
1 AATCATAAAATTTATA
51293 TACCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATCATAAAATTTATA
Found at i:54363 original size:18 final size:18
Alignment explanation
Indices: 54340--54382 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54330 CTTTATATTA
* *
54340 TTTATTTATTTATTTTCT
1 TTTATTTAATTATTATCT
*
54358 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
54376 TTTATTT
1 TTTATTT
54383 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:54462 original size:35 final size:35
Alignment explanation
Indices: 54423--54512 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 35
54413 TCTTTAGTAC
*
54423 TATTATTTATTATTTTATT-ATTTTCCCTTTTT-ATT
1 TATTA-TTATTATTTTATTAATTTT-CCTTTTTAAAT
*
54458 TATTATTATTTATTTTATTAATTTTTCTTTTTAAAT
1 TATTATTA-TTATTTTATTAATTTTCCTTTTTAAAT
*
54494 TATAATTATCTATTTTATT
1 TATTATTAT-TATTTTATT
54513 TTATTAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
34 3 0.06
35 22 0.46
36 23 0.48
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (35 bp):
TATTATTATTATTTTATTAATTTTCCTTTTTAAAT
Found at i:54516 original size:20 final size:20
Alignment explanation
Indices: 54466--54516 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
54456 TTTATTATTA
*
54466 TTTATTTTATTAATTTTTCTT
1 TTTATTTTA-TAATTTATCTT
**
54487 TTTAAATTATAA-TTATCTAT
1 TTTATTTTATAATTTATCT-T
54507 TTTATTTTAT
1 TTTATTTTAT
54517 TAAATCTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTTATAATTTATCTT
Found at i:59536 original size:14 final size:14
Alignment explanation
Indices: 59517--59543 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59507 ATTTCGTTCT
59517 ATTTTTTTTATTTC
1 ATTTTTTTTATTTC
59531 ATTTTTTTTATTT
1 ATTTTTTTTATTT
59544 TATTATTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTATTTC
Found at i:59544 original size:5 final size:5
Alignment explanation
Indices: 59516--59610 Score: 60
Period size: 5 Copynumber: 19.2 Consensus size: 5
59506 CATTTCGTTC
* *
59516 TATTT T-TTT TATTT CATTT T-TTT TATTT TA--T TATTT AGCAATCTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT ---TAT-TT
*
59561 TATTT TCATTC TA-TT TATTT TATTT T-TATT TA-TT TATTT TATTT TATTT
1 TATTT T-ATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT
59610 T
1 T
59611 TCTCTGAACA
Statistics
Matches: 71, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
3 3 0.04
4 16 0.23
5 42 0.59
6 6 0.08
8 2 0.03
9 2 0.03
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:61544 original size:19 final size:19
Alignment explanation
Indices: 61522--61623 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 19
61512 GTTTAAATAG
61522 GTTTTAGTATTTTAATTAA
1 GTTTTAGTATTTTAATTAA
*
61541 GTTTTAG-A--AT-ATT-A
1 GTTTTAGTATTTTAATTAA
* **
61555 TTTTTA-TATTTT-ATCTTT
1 GTTTTAGTATTTTAAT-TAA
61573 GTTTTAGGTATTTTAATTTAAATA
1 GTTTTA-GTATTTTAA-TT--A-A
61597 GGTTTTAGTATTTTAATTAA
1 -GTTTTAGTATTTTAATTAA
61617 GTTTTAG
1 GTTTTAG
61624 GATATTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
14 7 0.11
15 3 0.05
16 4 0.06
17 1 0.02
18 6 0.10
19 14 0.22
20 7 0.11
21 3 0.05
22 1 0.02
23 2 0.03
24 9 0.14
25 6 0.10
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (19 bp):
GTTTTAGTATTTTAATTAA
Found at i:61564 original size:76 final size:76
Alignment explanation
Indices: 61466--61691 Score: 384
Period size: 76 Copynumber: 3.0 Consensus size: 76
61456 TAAGATAATA
61466 TTTTA-AATATTATATTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
1 TTTTAGAATATTAT-TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
61530 ATTTTAATTAAG
65 ATTTTAATTAAG
*
61542 TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTA
1 TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
61607 TTTTAATTAAG
66 TTTTAATTAAG
* *
61618 TTTTAGGATATTATTTTTACATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGT
1 TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGT
*
61682 GTTTTAATTA
65 ATTTTAATTA
61692 GGATTTAAGA
Statistics
Matches: 143, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
75 5 0.03
76 130 0.91
77 8 0.06
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (76 bp):
TTTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
TTTTAATTAAG
Found at i:61988 original size:100 final size:100
Alignment explanation
Indices: 61861--62067 Score: 387
Period size: 100 Copynumber: 2.1 Consensus size: 100
61851 TGTTTACAAC
61861 AATTGCTAAGTATGACTTTGCTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
1 AATTGCTAAGTATGACTTTGCTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
61926 GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
66 GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
* *
61961 AATTGCTAAGTATGACTTTGGTCATGCTTAGTTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
1 AATTGCTAAGTATGACTTTGCTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
*
62026 GCTCAATTCCAAATGTGAGAATTGTAAGGTACTTA
66 GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
62061 AATTGCT
1 AATTGCT
62068 TCGGATTTTT
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 104 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (100 bp):
AATTGCTAAGTATGACTTTGCTCATGCTTAGCTAATTTTCTTTCAAGCCGAAGACTAAATCGAAG
GCTCAATTCCAAACGTGAGAATTGTAAGGTACTTA
Found at i:62421 original size:18 final size:18
Alignment explanation
Indices: 62398--62439 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
62388 CTTATATTAC
62398 TTATTTAATTATTTTCTT
1 TTATTTAATTATTTTCTT
62416 TTATTTAATTATTTTCTT
1 TTATTTAATTATTTTCTT
62434 TTATTT
1 TTATTT
62440 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTAATTATTTTCTT
Done.