Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008922.1 Hibiscus syriacus cultivar Beakdansim tig00112226_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: 568381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:551490 original size:38 final size:33
Alignment explanation
Indices: 551403--551484 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
551393 CTTTATTTTG
*
551403 TTCGGGTCGGGTC-GGATTTGTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTGTTAAGTGTGATA
*
551435 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTGTTAAGTGTGATA
* *
551468 TTCGAGTCAGGTCGGGT
1 TTCGGGTCGGGTCGGGT
551485 CGGGTTCGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 13 0.29
33 32 0.71
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.38
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTGTTAAGTGTGATA
Found at i:553223 original size:14 final size:14
Alignment explanation
Indices: 553204--553277 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
553194 AACTTAATAT
553204 TATTATTTTTAAAA
1 TATTATTTTTAAAA
* **
553218 TATTA-TTATAATT
1 TATTATTTTTAAAA
*
553231 TATTTATTATT-AAA
1 TA-TTATTTTTAAAA
*
553245 TATTATTTTTATAA
1 TATTATTTTTAAAA
* **
553259 TTTTATTAATAAAA
1 TATTATTTTTAAAA
553273 TATTA
1 TATTA
553278 ATATTGGTAT
Statistics
Matches: 43, Mismatches: 14, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
13 14 0.33
14 27 0.63
15 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTTTTAAAA
Found at i:553233 original size:27 final size:29
Alignment explanation
Indices: 553198--553282 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 29
553188 TCATAAAACT
*
553198 TAATATTATTATTTTTAAA-A-TATTATTA
1 TAAT-TTATTATTATTAAATATTATTATTA
*
553226 TAATTTATTTATTATTAAATATTATTTTTA
1 TAATTTA-TTATTATTAAATATTATTATTA
* *
553256 TAA-TT-TTATTAATAAAATATTAATATT
1 TAATTTATTATT-ATTAAATATTATTATT
553283 GGTATATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 8 0.17
28 27 0.56
29 3 0.06
30 10 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATTTATTATTATTAAATATTATTATTA
Found at i:553238 original size:17 final size:17
Alignment explanation
Indices: 553218--553256 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
553208 ATTTTTAAAA
553218 TATTATTATAAT-TTATT
1 TATTATTA-AATATTATT
553235 TATTATTAAATATTATT
1 TATTATTAAATATTATT
553252 T-TTAT
1 TATTAT
553257 AATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTAAATATTATT
Found at i:553565 original size:23 final size:23
Alignment explanation
Indices: 553535--553604 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
553525 TTAAAATAAA
553535 AATATAATATATTATATTATTAT
1 AATATAATATATTATATTATTAT
*
553558 AATATAAT-TGATTATTTTATTAAT
1 AATATAATAT-ATTATATTATT-AT
* *
553582 ATTA-AAAATATTATATATATTAT
1 AATATAATATATTATAT-TATTAT
553605 TAGAAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 1 0.03
23 28 0.72
24 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:553626 original size:21 final size:20
Alignment explanation
Indices: 553580--553626 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
553570 TATTTTATTA
*
553580 ATATTAAAAATATTATATAT
1 ATATTAAAAATATTATAAAT
*
553600 ATTATTAGAAATATTAATAAAT
1 A-TATTAAAAATATT-ATAAAT
553622 ATATT
1 ATATT
553627 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 16 0.70
22 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATTAAAAATATTATAAAT
Found at i:553627 original size:53 final size:51
Alignment explanation
Indices: 553516--553688 Score: 144
Period size: 50 Copynumber: 3.4 Consensus size: 51
553506 AATAATTTAT
* * * **
553516 TATATATTATTAA-AATAAAAATATAATATATTATATTATTATAATATAATTGA
1 TATATTTTATTAATATTAAAAATAT--TATA-TATATTATTAAAATATAATAAA
553569 T-TATTTTATTAATATTAAAAATATTATATATATTATTAGAAATATTAATAAA
1 TATATTTTATTAATATTAAAAATATTATATATATTATTA-AAATA-TAATAAA
* * * *
553621 TATATTTTA--AAAATTTAAAA-ATTA-ATATTTTGATTAAAATGATATTAAA
1 TATATTTTATTAATATTAAAAATATTATATATATT-ATTAAAAT-ATAATAAA
*
553670 -CTATTTTATTAATATTAAA
1 TATATTTTATTAATATTAAA
553689 TTCATAAAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
48 7 0.07
49 16 0.16
50 26 0.26
51 17 0.17
52 16 0.16
53 18 0.18
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (51 bp):
TATATTTTATTAATATTAAAAATATTATATATATTATTAAAATATAATAAA
Found at i:553642 original size:21 final size:23
Alignment explanation
Indices: 553583--553651 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
553573 TTTATTAATA
553583 TTAAAAATATT-AT--ATATATT
1 TTAAAAATATTAATAAATATATT
*
553603 ATTAGAAATATTAATAAATATATT
1 -TTAAAAATATTAATAAATATATT
553627 TTAAAAAT-TTAA-AAATTAATATT
1 TTAAAAATATTAATAAA-T-ATATT
553650 TT
1 TT
553652 GATTAAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 13 0.32
22 7 0.17
23 14 0.34
24 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
TTAAAAATATTAATAAATATATT
Found at i:560217 original size:18 final size:18
Alignment explanation
Indices: 560194--560228 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
560184 ACTGAAAATT
560194 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
560212 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
560229 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Done.