Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003084.1 Hibiscus syriacus cultivar Beakdansim tig00006438_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: 56678
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3592 original size:23 final size:23
Alignment explanation
Indices: 3549--3592 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3539 AACACAATTT
* **
3549 AATTTGCCATGACATTTCCATCC
1 AATTTACCATGACATACCCATCC
3572 AATTTACCATGACATACCCAT
1 AATTTACCATGACATACCCAT
3593 TTACTACCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (23 bp):
AATTTACCATGACATACCCATCC
Found at i:6950 original size:11 final size:11
Alignment explanation
Indices: 6934--6966 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
6924 TTTCTAAAAA
6934 TAAAATGAAAT
1 TAAAATGAAAT
*
6945 TAAAATGAAAA
1 TAAAATGAAAT
6956 TAAAATGAAAT
1 TAAAATGAAAT
6967 GAGTTGCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (11 bp):
TAAAATGAAAT
Found at i:9270 original size:19 final size:19
Alignment explanation
Indices: 9246--9285 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9236 TCATATTTTC
*
9246 TTTTTAGTTAGCTTAATTT
1 TTTTTAGTTACCTTAATTT
* *
9265 TTTTTATTTTCCTTAATTT
1 TTTTTAGTTACCTTAATTT
9284 TT
1 TT
9286 CTTCATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTTAGTTACCTTAATTT
Found at i:29328 original size:26 final size:25
Alignment explanation
Indices: 29299--29381 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
29289 TCAGATAAAG
29299 ATAAAAAGATAAGAATATTAAAATAA
1 ATAAAAAGATAA-AATATTAAAATAA
*
29325 ATAATTAA-ATATAAATAATTAAAATAGA
1 ATAA-AAAGATA-AAAT-ATTAAAATA-A
* * * *
29353 AGATAAGGATAAAATAATAAAATAA
1 ATAAAAAGATAAAATATTAAAATAA
29378 ATAA
1 ATAA
29382 TTAAATATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
25 3 0.07
26 18 0.41
27 17 0.39
28 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (25 bp):
ATAAAAAGATAAAATATTAAAATAA
Found at i:29350 original size:27 final size:27
Alignment explanation
Indices: 29315--29389 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
29305 AGATAAGAAT
29315 ATTAAAATAAATAATTAAATATAAATA
1 ATTAAAATAAATAATTAAATATAAATA
*
29342 ATTAAAATAGAA-GA-TAAGGATA-AAATA
1 ATTAAAATA-AATAATTAA--ATATAAATA
29369 A-TAAAATAAATAATTAAATAT
1 ATTAAAATAAATAATTAAATAT
29390 TTATAAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
25 5 0.12
26 11 0.28
27 19 0.47
28 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (27 bp):
ATTAAAATAAATAATTAAATATAAATA
Found at i:29372 original size:48 final size:48
Alignment explanation
Indices: 29291--29415 Score: 124
Period size: 53 Copynumber: 2.4 Consensus size: 48
29281 ATAGAATTTC
* *
29291 AGATAAAGATAAAAAGATAAGAATATTAAAATAAATAATTAAATATAAATAATTA
1 AGATAAAGAT--AAAGATAA-AATAATAAAATAAATAATT-AA-AT-AATTA-TA
* * *
29346 AAATAGAAGATAAGGATAAAATAATAAAATAAATAATTAAATATTTATA
1 AGATA-AAGATAAAGATAAAATAATAAAATAAATAATTAAATAATTATA
*
29395 AGATAAGGATAAAGATAAAAT
1 AGATAAAGATAAAGATAAAAT
29416 GGGGGAGTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
48 14 0.23
49 6 0.10
50 3 0.05
51 2 0.03
52 2 0.03
53 18 0.30
54 7 0.11
55 4 0.07
56 5 0.08
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (48 bp):
AGATAAAGATAAAGATAAAATAATAAAATAAATAATTAAATAATTATA
Found at i:31428 original size:3 final size:3
Alignment explanation
Indices: 31416--31450 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
31406 AATTGGTTTA
31416 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31451 TCTCTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:31927 original size:21 final size:20
Alignment explanation
Indices: 31903--31970 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
31893 GAACATTTTT
31903 GATACTGAT-TGAAGTAGTATC
1 GATACTGATGTGAAG--GTATC
* *
31924 GATATTGATGTGGAGGTATC
1 GATACTGATGTGAAGGTATC
*
31944 GATACCAAGA-G-GAAGGTATC
1 GATA-C-TGATGTGAAGGTATC
31964 GATACTG
1 GATACTG
31971 TAATTGAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 21 0.55
21 9 0.24
22 6 0.16
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.28
Consensus pattern (20 bp):
GATACTGATGTGAAGGTATC
Found at i:37215 original size:32 final size:32
Alignment explanation
Indices: 37170--37286 Score: 182
Period size: 32 Copynumber: 3.7 Consensus size: 32
37160 CAACAAAGGG
* *
37170 GGCCAACCTAAGGGTATGCCTTGGGGCCTATA
1 GGCCTACCCAAGGGTATGCCTTGGGGCCTATA
* *
37202 GGCCTACCCAAGGGTAAGTCTTGGGGCCTATA
1 GGCCTACCCAAGGGTATGCCTTGGGGCCTATA
*
37234 GGCCTACACAAGGGTATGCCTTGGGGCCTATA
1 GGCCTACCCAAGGGTATGCCTTGGGGCCTATA
37266 GGCCTACCCAAGGGTAT-CCTT
1 GGCCTACCCAAGGGTATGCCTT
37287 AGGTCCTTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 4 0.05
32 73 0.95
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.22
Consensus pattern (32 bp):
GGCCTACCCAAGGGTATGCCTTGGGGCCTATA
Found at i:39666 original size:116 final size:115
Alignment explanation
Indices: 39514--39735 Score: 320
Period size: 116 Copynumber: 1.9 Consensus size: 115
39504 GGCTTACCAA
** * *
39514 GTGCGAATTTAGCAAAACAGACTTTGGATTTGGACTCAGGACGTCGAGAAACATAAAATGAGACC
1 GTGCGAATTTAGCAAAACAGACTTTGGATTCAGACTCAGGACGTAGAAAAACATAAAATGAGACC
*
39579 TTTTCAAAAAAGTTGGCTTTTTGGTAAACAGTCAATAGTCAAAGTCAACTT
66 TTCTCAAAAAAGTTGGCTTTTTGGTAAACAGTCAA-AGTCAAAGTCAACTT
* * *
39630 GTGCGAATTTGGCAAAA-TGAACTTTGGATTCAGACTCAGGACGTAGAAAAACATAAAATGGGAC
1 GTGCGAATTTAGCAAAACAG-ACTTTGGATTCAGACTCAGGACGTAGAAAAACATAAAATGAGAC
* * *
39694 CTTCTCGAAAAAGTTGGGTTTTTGGTCAACAGTCAAAGTCAA
65 CTTCTCAAAAAAGTTGGCTTTTTGGTAAACAGTCAAAGTCAA
39736 CATGTCAAAG
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
115 7 0.07
116 87 0.93
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (115 bp):
GTGCGAATTTAGCAAAACAGACTTTGGATTCAGACTCAGGACGTAGAAAAACATAAAATGAGACC
TTCTCAAAAAAGTTGGCTTTTTGGTAAACAGTCAAAGTCAAAGTCAACTT
Found at i:39736 original size:13 final size:14
Alignment explanation
Indices: 39718--39750 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39708 TGGGTTTTTG
39718 GTCAACA-GTCAAA
1 GTCAACATGTCAAA
39731 GTCAACATGTCAAA
1 GTCAACATGTCAAA
39745 GTCAAC
1 GTCAAC
39751 GGGTTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (14 bp):
GTCAACATGTCAAA
Found at i:55060 original size:19 final size:19
Alignment explanation
Indices: 55036--55077 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
55026 AAATTCCATG
55036 ATTCCATAAATCATGAACA
1 ATTCCATAAATCATGAACA
*
55055 ATTCCATAAATCATGAATA
1 ATTCCATAAATCATGAACA
55074 ATTC
1 ATTC
55078 ATAGTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (19 bp):
ATTCCATAAATCATGAACA
Done.