Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004134.1 Hibiscus syriacus cultivar Beakdansim tig00009042_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: 55578
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:375 original size:17 final size:19
Alignment explanation
Indices: 343--378 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
333 TACGAGCGAA
343 TTTTAATTTATCATCAATT
1 TTTTAATTTATCATCAATT
362 TTTTAATTT-T-ATCAATT
1 TTTTAATTTATCATCAATT
379 AAACCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAATTTATCATCAATT
Found at i:20445 original size:20 final size:22
Alignment explanation
Indices: 20408--20447 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20398 ATGAAAATGA
*
20408 TTTTTTGATAAGATAAAATTAT
1 TTTTTTGATAACATAAAATTAT
20430 TTTTTTGAT-ACA-AAAATT
1 TTTTTTGATAACATAAAATT
20448 TTAGGTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTTTGATAACATAAAATTAT
Found at i:27248 original size:17 final size:18
Alignment explanation
Indices: 27226--27265 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
27216 TATTTTATGC
27226 ACTTGATC-ATGA-AAGTG
1 ACTTGATCAATGATAA-TG
27243 ACTTGATCAATGATAATG
1 ACTTGATCAATGATAATG
27261 ACTTG
1 ACTTG
27266 GTCTCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 11 0.52
19 2 0.10
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (18 bp):
ACTTGATCAATGATAATG
Found at i:37731 original size:20 final size:20
Alignment explanation
Indices: 37695--37742 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
37685 TCAAAATCCT
* *
37695 TTTTCAAAATTTCATTTTTC
1 TTTTCAAAATTCCATTTTAC
37715 TTTTCAAAA-TCCAATTTTAC
1 TTTTCAAAATTCC-ATTTTAC
37735 -TTTCAAAA
1 TTTTCAAAA
37743 GAAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAC
Found at i:38182 original size:3 final size:3
Alignment explanation
Indices: 38174--38246 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
38164 ATTTTTCTCG
*
38174 TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
38221 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
38247 TTTTCCTTTG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:39643 original size:24 final size:24
Alignment explanation
Indices: 39616--39676 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
39606 ACTGAGATCA
*
39616 TAGTATTGATACTACTATATAAAG
1 TAGTATCGATACTACTATATAAAG
39640 TAGTATCGATACTACTATATAAAG
1 TAGTATCGATACTACTATATAAAG
39664 TAGTATCGATACT
1 TAGTATCGATACT
39677 CCTTATAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (24 bp):
TAGTATCGATACTACTATATAAAG
Found at i:39787 original size:20 final size:20
Alignment explanation
Indices: 39762--39809 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39752 CATGAGAGTG
*
39762 TCGATATTACAAGAACAATA
1 TCGATACTACAAGAACAATA
** *
39782 TCGATACTGTAAGAATAATA
1 TCGATACTACAAGAACAATA
39802 TCGATACT
1 TCGATACT
39810 TCTTGCCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TCGATACTACAAGAACAATA
Found at i:42209 original size:23 final size:23
Alignment explanation
Indices: 42179--42231 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
42169 CAAATTACAA
*
42179 GAAAAGATACATAGGATTGGTTT
1 GAAAAGATACATAGGATTGGATT
42202 GAAAAGATACATAGGATTGGATT
1 GAAAAGATACATAGGATTGGATT
42225 GAAAAGA
1 GAAAAGA
42232 AATTACCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.26, T:0.25
Consensus pattern (23 bp):
GAAAAGATACATAGGATTGGATT
Found at i:43637 original size:32 final size:31
Alignment explanation
Indices: 43537--43643 Score: 126
Period size: 31 Copynumber: 3.4 Consensus size: 31
43527 AAGGTGACCA
* *
43537 TTGGGTAGGCTCCGAGGCCCCGAGAACTTTC
1 TTGGGTAGGCTCTGCGGCCCCGAGAACTTTC
* *
43568 TTGGGTAGGCTCTGCGGCCCCGAGATCCTTC
1 TTGGGTAGGCTCTGCGGCCCCGAGAACTTTC
* * *
43599 TTGGGTAGGTTCTGTGGCCTCG-GTTAACTTTC
1 TTGGGTAGGCTCTGCGGCCCCGAG--AACTTTC
43631 TTGGGTAGGCTCT
1 TTGGGTAGGCTCT
43644 CAGGCCCTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.02
31 46 0.72
32 17 0.27
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (31 bp):
TTGGGTAGGCTCTGCGGCCCCGAGAACTTTC
Found at i:44253 original size:21 final size:23
Alignment explanation
Indices: 44210--44256 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
44200 ATGAAATTTG
44210 TTTTATTTTTTGAATATTGATAAA
1 TTTTATTTTTTG-ATATTGATAAA
*
44234 TTTTA-TTTTTG-TATTTATAAA
1 TTTTATTTTTTGATATTGATAAA
44255 TT
1 TT
44257 ATTTTATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
23 6 0.27
24 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTTATTTTTTGATATTGATAAA
Found at i:45523 original size:31 final size:29
Alignment explanation
Indices: 45488--45571 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 29
45478 AAATTACGTG
* *
45488 TTTAGTATTTAAATTATTAATTTTTATTTAT
1 TTTAGTATCTAAACTATTAATTTTTA-TT-T
*
45519 TTTAGTATCTAAGCTATTAATTTTTATTT
1 TTTAGTATCTAAACTATTAATTTTTATTT
* *
45548 TTTAGTACCTAAACT-TTCATTTTT
1 TTTAGTATCTAAACTATTAATTTTT
45572 TTTCAAAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.17
29 14 0.30
30 2 0.04
31 23 0.49
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (29 bp):
TTTAGTATCTAAACTATTAATTTTTATTT
Done.