Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005271.1 Hibiscus syriacus cultivar Beakdansim tig00011917_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: 54439
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3419 original size:20 final size:18
Alignment explanation
Indices: 3375--3410 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3365 ATTAAAAAAA
* *
3375 TGTTTTTGATTTAATTGT
1 TGTTTTTGATATAATTAT
3393 TGTTTTTGATATAATTAT
1 TGTTTTTGATATAATTAT
3411 ATTGTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (18 bp):
TGTTTTTGATATAATTAT
Found at i:12785 original size:20 final size:21
Alignment explanation
Indices: 12748--12808 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 21
12738 TTTTGGTGCA
*
12748 GAGGGAATCGA-TCGCCCC-AT
1 GAGGGAACCGATTC-CCCCTAT
*
12768 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTAT
*
12789 GAAGGGGAACTGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
12809 CACTGTGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 14 0.41
21 4 0.12
22 1 0.03
23 15 0.44
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTAT
Found at i:13544 original size:21 final size:21
Alignment explanation
Indices: 13520--13559 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13510 ACCGTCAACC
*
13520 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
13541 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
13560 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:14427 original size:17 final size:17
Alignment explanation
Indices: 14405--14439 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14395 AAAAGTTTTC
*
14405 TCTTTTCCTTTTCAAGT
1 TCTTTTCATTTTCAAGT
*
14422 TCTTTTTATTTTCAAGT
1 TCTTTTCATTTTCAAGT
14439 T
1 T
14440 TTATGTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.06, T:0.63
Consensus pattern (17 bp):
TCTTTTCATTTTCAAGT
Found at i:22164 original size:24 final size:23
Alignment explanation
Indices: 22114--22186 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
22104 GCTTCAACTT
* *
22114 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
22137 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
22161 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
22184 TTT
1 TTT
22187 CTTTGGATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 2 0.05
23 12 0.28
24 12 0.28
25 12 0.28
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.26, T:0.56
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:28495 original size:21 final size:21
Alignment explanation
Indices: 28454--28495 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28444 GACATTGGCG
* *
28454 CTGTTGTAACTATTGTTGAAA
1 CTGTTATAACTATTATTGAAA
28475 CTGTTATAAC-ATTATTAGAAA
1 CTGTTATAACTATTATT-GAAA
28496 AAGAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (21 bp):
CTGTTATAACTATTATTGAAA
Found at i:29063 original size:25 final size:24
Alignment explanation
Indices: 29028--29079 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
29018 ATCTTTTGAA
29028 AAATGACTTTTAAAAGTGAAGTAC
1 AAATGACTTTTAAAAGTGAAGTAC
**
29052 AAATGAACTTTTAAAAGTGTCGTAC
1 AAATG-ACTTTTAAAAGTGAAGTAC
29077 AAA
1 AAA
29080 AGTGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (24 bp):
AAATGACTTTTAAAAGTGAAGTAC
Found at i:29425 original size:17 final size:15
Alignment explanation
Indices: 29391--29440 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
29381 ACAAAAAGAA
29391 TATTACAAAAAT--AT
1 TATTA-AAAAATAAAT
29405 TATTAATTAAAATAAAT
1 TATTAA--AAAATAAAT
*
29422 TATTAAATAATAAAT
1 TATTAAAAAATAAAT
29437 TATT
1 TATT
29441 TTCTAAGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 17 0.55
17 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTAAAAAATAAAT
Found at i:29771 original size:22 final size:22
Alignment explanation
Indices: 29743--29788 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29733 ATAATACACC
29743 ACTTTTCATTTTTGGGTTAACT
1 ACTTTTCATTTTTGGGTTAACT
29765 ACTTTTCATTTTTGGGTTAACT
1 ACTTTTCATTTTTGGGTTAACT
29787 AC
1 AC
29789 ATGATTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (22 bp):
ACTTTTCATTTTTGGGTTAACT
Found at i:30347 original size:248 final size:248
Alignment explanation
Indices: 29865--30359 Score: 715
Period size: 248 Copynumber: 2.0 Consensus size: 248
29855 GATATCTTTC
* * **
29865 GTTTTTATTTAATTAAGATGTAGTCACCACTAGTTAATTGTTGTTAACAATTAACTTATTAGATG
1 GTTTTTATTTAATTAAGATGTAGCCACCACGAGTTAATTGTTGTTAACAATTAACAGATTAGATG
* * * *
29930 ACATGGTATTTTGGTATAATCACATATTTAGTCTCTGTTATTTACATATTCTCTTAATTTAGCCC
66 ACATGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTACATATTCTCTCAATTTAGCCA
* * *
29995 TACATTTAATAAATTAAAATAAATGTAATGTATAGTTGAATGATGATACGTTTCACCATTCGGTT
131 TACATTTAACAAATTAAAATAAATGTAATGCATAATTGAATGATGATACGTTTCACCATTCGGTT
* * * *
30060 GGAGGACTAACTTTATTTTAATTTGTTAAAATAAAACAAAACAAGTCAAATTA
196 GAAGGACTAAATTCATTTTAATTTGTTAAAATAAAACAAAACAAATCAAATTA
* * *
30113 GTTTTTATTTAATTAAGATGTGGCCACCACGAGTTAATTGTTGTTAACATTTAACAGATTAGGTG
1 GTTTTTATTTAATTAAGATGTAGCCACCACGAGTTAATTGTTGTTAACAATTAACAGATTAGATG
* * * *
30178 ACGTGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTATATATTGTCTCAATTTAGTCA
66 ACATGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTACATATTCTCTCAATTTAGCCA
* *
30243 TACATTTAACAAATTAAAATAAATTTAAT-CATCCAATTGAATGATGATACTTTTCACCATTCGG
131 TACATTTAACAAATTAAAATAAATGTAATGCAT--AATTGAATGATGATACGTTTCACCATTCGG
* **
30307 TTGAAGGACTAAATTCATTTTTATTTGTTGTAAT-AAACAAAACAAATCAAATT
194 TTGAAGGACTAAATTCATTTTAATTTGTTAAAATAAAACAAAACAAATCAAATT
30360 GAGGCTAAAG
Statistics
Matches: 218, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
247 2 0.01
248 160 0.73
249 56 0.26
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (248 bp):
GTTTTTATTTAATTAAGATGTAGCCACCACGAGTTAATTGTTGTTAACAATTAACAGATTAGATG
ACATGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTACATATTCTCTCAATTTAGCCA
TACATTTAACAAATTAAAATAAATGTAATGCATAATTGAATGATGATACGTTTCACCATTCGGTT
GAAGGACTAAATTCATTTTAATTTGTTAAAATAAAACAAAACAAATCAAATTA
Found at i:33348 original size:15 final size:16
Alignment explanation
Indices: 33314--33356 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
33304 GGTGAGTGCA
33314 ATACATGCATGACATT
1 ATACATGCATGACATT
* *
33330 ATACATGGATG-CTTT
1 ATACATGCATGACATT
33345 ATACATGCATGA
1 ATACATGCATGA
33357 TGTGTTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (16 bp):
ATACATGCATGACATT
Found at i:38463 original size:32 final size:32
Alignment explanation
Indices: 38427--38493 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
38417 TTTCGTAGAT
38427 AGATGCCACTCTAGTTATTTTAGAGGCAAATC
1 AGATGCCACTCTAGTTATTTTAGAGGCAAATC
38459 AGATGCCACTCTAGTTATTTTAGAGGCAAATC
1 AGATGCCACTCTAGTTATTTTAGAGGCAAATC
38491 AGA
1 AGA
38494 CACCAGATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (32 bp):
AGATGCCACTCTAGTTATTTTAGAGGCAAATC
Done.