Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006541.1 Hibiscus syriacus cultivar Beakdansim tig00015968_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: 41339
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:2470 original size:40 final size:40
Alignment explanation
Indices: 2412--2573 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
2402 TTCGGGTTTA
* * *
2412 TAATACAGTTTGGTGTATATGGTGGGCACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
2452 TAATACACTTCGGCGTATATAGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
2492 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
2532 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
2572 TA
1 TA
2574 GCACTACGGT
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:2728 original size:44 final size:44
Alignment explanation
Indices: 2678--2838 Score: 198
Period size: 44 Copynumber: 3.6 Consensus size: 44
2668 GTAAGCATGC
*
2678 AAATAAGCTTCCGAGCTTATGGAATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
* * **
2722 AAATAAGCTCACGAGCTTATGGAACAAATGGTAAGTATATTATTA
1 AAATAAGCTTACGAGCTTATGGAA-TAATGGTAAGTATATTGGTA
* ** *
2767 AAAT-AGCTTACGAGTTTATGGGTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
* *
2811 AAATAAGCTTACAAGCTTATGGGATAAT
1 AAATAAGCTTACGAGCTTATGGAATAAT
2839 TGATACAAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
44 60 0.61
45 38 0.39
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
Found at i:12108 original size:45 final size:45
Alignment explanation
Indices: 12040--12178 Score: 219
Period size: 45 Copynumber: 3.1 Consensus size: 45
12030 TTTTGTGTAC
12040 GTTTATGATGTTAATGAAA-CATGTTCTTAGGCCATTCTTGGGTAA
1 GTTTATGATGTTAAT-AAACCATGTTCTTAGGCCATTCTTGGGTAA
* *
12085 GTTTATGATGTTAATTAACCATGTTCTTAGGCCATTCTTGGATAA
1 GTTTATGATGTTAATAAACCATGTTCTTAGGCCATTCTTGGGTAA
*
12130 GTTTATG-TAGTTAATAAACAATGTTCTTAGGCCATTCTTGGGTAA
1 GTTTATGAT-GTTAATAAACCATGTTCTTAGGCCATTCTTGGGTAA
12175 GTTT
1 GTTT
12179 TGCGTGTTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
44 3 0.03
45 84 0.97
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (45 bp):
GTTTATGATGTTAATAAACCATGTTCTTAGGCCATTCTTGGGTAA
Found at i:23260 original size:23 final size:20
Alignment explanation
Indices: 23210--23260 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
23200 AAAATAAAAG
*
23210 AAAAGAAAATAAAGAATATT
1 AAAAGAAAATAAAGAAGATT
23230 AAAGAGAAAAGTGAAAGAAGATT
1 AAA-AGAAAA-T-AAAGAAGATT
23253 AAGAAGAA
1 AA-AAGAA
23261 GATTTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 6 0.23
22 1 0.04
23 15 0.58
24 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14
Consensus pattern (20 bp):
AAAAGAAAATAAAGAAGATT
Found at i:26981 original size:40 final size:40
Alignment explanation
Indices: 26926--27161 Score: 368
Period size: 40 Copynumber: 6.0 Consensus size: 40
26916 TATACACCGT
* *
26926 AGTGCATTACACATAAGGTTGTTCCCACCATATGCACCTA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTA
26966 AGTGCATTACACATAAGGTCGTGCCCACCATATG--CCTA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTA
* * *
27004 AGTGCATTACATATAAGGTCGTGCCCACAATATGCACCGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTA
* *
27044 AGTGCATTACACATAAGGTCATGCCCACCATATGCACCTG
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTA
*
27084 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTG
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTA
* *
27124 AGTGCATTATACATAAGGTCATGCCCACCATATGCACC
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACC
27162 AATTGTCCTT
Statistics
Matches: 181, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
38 36 0.20
40 145 0.80
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (40 bp):
AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCTA
Found at i:32350 original size:28 final size:28
Alignment explanation
Indices: 32318--32378 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
32308 GTATAAGGTT
32318 GAATCGAAGTTGATTTTATGCTTGAATC
1 GAATCGAAGTTGATTTTATGCTTGAATC
32346 GAATCGAAGTTGATTTTATGCTTGAATC
1 GAATCGAAGTTGATTTTATGCTTGAATC
32374 GAATC
1 GAATC
32379 AAAACCGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (28 bp):
GAATCGAAGTTGATTTTATGCTTGAATC
Found at i:34196 original size:40 final size:40
Alignment explanation
Indices: 34085--34198 Score: 138
Period size: 40 Copynumber: 2.9 Consensus size: 40
34075 TCGATTAAGC
* ** *
34085 ACTTCAGTGCATATGGTGGGCACGACCTTATATGTGATGC
1 ACTTCAGTGCATATGGTGGGCACGACCTTATGTGCAATGA
* ***
34125 ACTTCTGTGCATATGGTGGGCTTAACCTTATGTGCAATGA
1 ACTTCAGTGCATATGGTGGGCACGACCTTATGTGCAATGA
* *
34165 ACTTCGGTGCAAATGGTGGGCACGACCTTATGTG
1 ACTTCAGTGCATATGGTGGGCACGACCTTATGTG
34199 TAAGAACCAT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
ACTTCAGTGCATATGGTGGGCACGACCTTATGTGCAATGA
Found at i:36951 original size:67 final size:67
Alignment explanation
Indices: 36843--36973 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
36833 TGGCAATAGT
*
36843 AGTGTTTACTTTGTTGATATAACACAACTATCTATATGGTGAGTGACGTTATATATATGTGAATA
1 AGTGTTTACTTTATTGATATAACACAACTATCTATATGGTGAGTGACGTTATATATATGTGAATA
36908 AG
66 AG
* *
36910 AGTGTTTACTTTATTGATATAACACCACTATCTATATGGTGAGTGATGTTATATATATGTGAAT
1 AGTGTTTACTTTATTGATATAACACAACTATCTATATGGTGAGTGACGTTATATATATGTGAAT
36974 CTCAAAAGTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (67 bp):
AGTGTTTACTTTATTGATATAACACAACTATCTATATGGTGAGTGACGTTATATATATGTGAATA
AG
Found at i:41339 original size:40 final size:40
Alignment explanation
Indices: 41240--41339 Score: 139
Period size: 40 Copynumber: 2.5 Consensus size: 40
41230 CGATTAAGCA
* *
41240 CTTCGGTGCATATGGTGGGAACGACCGTATATGTAATGCT
1 CTTCGGTGCATATGGTGGGCACGACCGTATATGCAATGCT
* * *
41280 CTTCGGTGCATATGGTGGGCACGAGCTTATGTGCAATGCAT
1 CTTCGGTGCATATGGTGGGCACGACCGTATATGCAATGC-T
41321 -TTCGGTGCATATGGTGGGC
1 CTTCGGTGCATATGGTGGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (40 bp):
CTTCGGTGCATATGGTGGGCACGACCGTATATGCAATGCT
Done.