Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006014.1 Hibiscus syriacus cultivar Beakdansim tig00014182_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: 70747
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2769 original size:12 final size:12
Alignment explanation
Indices: 2752--2778 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2742 CATCTTGATG
2752 ACATGAGCTCCT
1 ACATGAGCTCCT
2764 ACATGAGCTCCT
1 ACATGAGCTCCT
2776 ACA
1 ACA
2779 AGAGTTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (12 bp):
ACATGAGCTCCT
Found at i:4093 original size:2 final size:2
Alignment explanation
Indices: 4086--4122 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4076 AAACATATCC
4086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4123 CACGTCCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6950 original size:18 final size:17
Alignment explanation
Indices: 6919--6952 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6909 TTCTTGTGTT
6919 TTAAGGATTATAAAGAG
1 TTAAGGATTATAAAGAG
*
6936 TTAAGTGATTTTAAAGA
1 TTAAG-GATTATAAAGA
6953 ATTGGTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (17 bp):
TTAAGGATTATAAAGAG
Found at i:7904 original size:59 final size:59
Alignment explanation
Indices: 7807--7935 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
7797 CAGCAGGCTG
** *
7807 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
* * * *
7866 TATATTCGGGACTATACTTAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
*
7925 CATACTCGGGA
1 CATATTCGGGA
7936 TTGCACTACG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
Found at i:8105 original size:43 final size:44
Alignment explanation
Indices: 8036--8164 Score: 217
Period size: 43 Copynumber: 2.9 Consensus size: 44
8026 ATGGAAAATG
8036 TATTGGTAAAATAAGCTTAC-AGGCTTATGGATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGA-GCTTATGGATAAATGGTAAGTA
8080 TATTGGT-AAATAAGCTTACGAGCTTATGGATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTA
*
8123 TATTGGTAAAATAAGCTTACGAGCTTTTGGGATAAATGGTAA
1 TATTGGTAAAATAAGCTTACGAGCTTAT-GGATAAATGGTAA
8165 AAGATTTTAT
Statistics
Matches: 81, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
43 41 0.51
44 27 0.33
45 13 0.16
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (44 bp):
TATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTA
Found at i:9166 original size:45 final size:45
Alignment explanation
Indices: 9117--9265 Score: 176
Period size: 45 Copynumber: 3.3 Consensus size: 45
9107 CATACTCTAA
* *
9117 CATATGGGTGCATTATCATCATGAAAGGATGCCAAAAGAATAATG
1 CATATGGGTGCATTATCAGCATGAAATGATGCCAAAAGAATAATG
* *
9162 CATATGGGTGCATTATCAGCATAAAATGATGCCAGAAGAATAATG
1 CATATGGGTGCATTATCAGCATGAAATGATGCCAAAAGAATAATG
* * ** * *
9207 AATATGGATGCATTATTGGCATGAAATGATGCC-ATAG-CTGAAATG
1 CATATGGGTGCATTATCAGCATGAAATGATGCCAAAAGAAT--AATG
9252 CATATGGGTGCATT
1 CATATGGGTGCATT
9266 TTCACATAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 85 0.97
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (45 bp):
CATATGGGTGCATTATCAGCATGAAATGATGCCAAAAGAATAATG
Found at i:16295 original size:45 final size:45
Alignment explanation
Indices: 16246--16351 Score: 158
Period size: 45 Copynumber: 2.4 Consensus size: 45
16236 GAATCAACAT
* * * *
16246 CTCCCAAGTATCTTAGGCGAGGTCTGGGTCACACATCATCGGCCC
1 CTCCCAAATACCTTAGGCGAGGTATGGGTCACACATCATCGGCAC
* *
16291 CTCCCAAATACCTTAGGCTAGGTATGGGTCACACATCATTGGCAC
1 CTCCCAAATACCTTAGGCGAGGTATGGGTCACACATCATCGGCAC
16336 CTCCCAAATACCTTAG
1 CTCCCAAATACCTTAG
16352 TCTACTCCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (45 bp):
CTCCCAAATACCTTAGGCGAGGTATGGGTCACACATCATCGGCAC
Found at i:17307 original size:20 final size:20
Alignment explanation
Indices: 17284--17326 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17274 GGTTTTGAAC
17284 CCACCATAGGGGTTTCAAAA
1 CCACCATAGGGGTTTCAAAA
* *
17304 CCACCCTAGGGGTTTCGAAA
1 CCACCATAGGGGTTTCAAAA
17324 CCA
1 CCA
17327 TAATGTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (20 bp):
CCACCATAGGGGTTTCAAAA
Found at i:19217 original size:18 final size:18
Alignment explanation
Indices: 19194--19231 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19184 TTTTAAGATT
19194 TTATATTCGAATT-AATTA
1 TTATATTCG-ATTAAATTA
*
19212 TTATATTTGATTAAATTA
1 TTATATTCGATTAAATTA
19230 TT
1 TT
19232 CGAATATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATTCGATTAAATTA
Found at i:20095 original size:16 final size:16
Alignment explanation
Indices: 20074--20111 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
20064 TTAGTGAATT
20074 TGTGGAAAATCCTTAG
1 TGTGGAAAATCCTTAG
20090 TGTGGAAAATCCTTAG
1 TGTGGAAAATCCTTAG
20106 TGTGGA
1 TGTGGA
20112 TAGCTAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (16 bp):
TGTGGAAAATCCTTAG
Found at i:23263 original size:20 final size:18
Alignment explanation
Indices: 23234--23273 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
23224 AATAAAGTGT
23234 TAATTAATTTTAATATTTTA
1 TAATTAA-TTTAA-ATTTTA
*
23254 TAATTGATTTAAATTTTA
1 TAATTAATTTAAATTTTA
23272 TA
1 TA
23274 TTCGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TAATTAATTTAAATTTTA
Found at i:23284 original size:17 final size:18
Alignment explanation
Indices: 23242--23285 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
23232 GTTAATTAAT
23242 TTTAATATTTTATAATTGA
1 TTTAA-ATTTTATAATTGA
23261 TTTAAATTTTAT-ATTCGA
1 TTTAAATTTTATAATT-GA
23279 -TTAAATT
1 TTTAAATT
23286 ATTCAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.42
18 9 0.38
19 5 0.21
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTAAATTTTATAATTGA
Found at i:23654 original size:24 final size:23
Alignment explanation
Indices: 23622--23698 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 23
23612 ACCGTGTTAG
23622 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTAC-TTACATAGTA
*
23646 GTATCGATACT-C--AC-TAGAA
1 GTATCGATACTACTTACATAGTA
*
23665 GGTATTGATACTACTTCACATAGTA
1 -GTATCGATACTACTT-ACATAGTA
*
23690 ATATCGATA
1 GTATCGATA
23699 ATCTCTTGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
19 4 0.10
20 12 0.29
21 1 0.02
23 1 0.02
24 20 0.48
25 4 0.10
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (23 bp):
GTATCGATACTACTTACATAGTA
Found at i:34946 original size:20 final size:20
Alignment explanation
Indices: 34903--34946 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
34893 TTAACTTTTT
*
34903 CTTTTTTCTTTCTTTATTAA
1 CTTTTTTCTTTCATTATTAA
34923 -TTTTTCTCTTTCATT-TTAA
1 CTTTTT-TCTTTCATTATTAA
34942 CTTTT
1 CTTTT
34947 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (20 bp):
CTTTTTTCTTTCATTATTAA
Found at i:45162 original size:19 final size:21
Alignment explanation
Indices: 45125--45167 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
45115 TAACTTTTTC
*
45125 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
45145 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
45165 TTT
1 TTT
45168 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Done.