Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004282.1 Hibiscus syriacus cultivar Beakdansim tig00009386_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: 87077
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17998 original size:10 final size:10
Alignment explanation
Indices: 17960--17996 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
17950 AGTGAAACAA
17960 CTCAGCCCAG
1 CTCAGCCCAG
17970 CTCAGCCCAG
1 CTCAGCCCAG
17980 CTCAGCCGC-G
1 CTCAGCC-CAG
17990 CTCAGCC
1 CTCAGCC
17997 GCACCTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 25 0.96
11 1 0.04
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (10 bp):
CTCAGCCCAG
Found at i:20810 original size:21 final size:21
Alignment explanation
Indices: 20768--20810 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20758 GCACCTTACC
** *
20768 CTATCGCAACACGATTTTCAA
1 CTATCGCAACACGAAATGCAA
*
20789 CTATCGCAACGCGAAATGCAA
1 CTATCGCAACACGAAATGCAA
20810 C
1 C
20811 GCGAATTTGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.21
Consensus pattern (21 bp):
CTATCGCAACACGAAATGCAA
Found at i:24279 original size:30 final size:30
Alignment explanation
Indices: 24244--24306 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
24234 TTCAACATAG
24244 TATAAGGACATAATACAATCAAACATAAAT
1 TATAAGGACATAATACAATCAAACATAAAT
* *
24274 TATAAGGACATACTACAATTAAACATAAAT
1 TATAAGGACATAATACAATCAAACATAAAT
24304 TAT
1 TAT
24307 CAATAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (30 bp):
TATAAGGACATAATACAATCAAACATAAAT
Found at i:24974 original size:2 final size:2
Alignment explanation
Indices: 24967--24993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24957 ATCTTATCTC
24967 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 A
24994 GGTTTCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36486 original size:24 final size:24
Alignment explanation
Indices: 36459--36558 Score: 78
Period size: 24 Copynumber: 4.2 Consensus size: 24
36449 TATATCAAAA
36459 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
36483 ATCATATCAAAATCCAGGTTAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
36507 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * *
36531 ATCAAATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
36555 ATCA
1 ATCA
36559 GATCAGAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.09
24 57 0.88
25 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:36563 original size:24 final size:24
Alignment explanation
Indices: 36476--36567 Score: 123
Period size: 24 Copynumber: 3.8 Consensus size: 24
36466 CATAAATCAG
* * *
36476 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
36500 GTTAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
36524 GTC-AGATATCAAATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
36548 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
36568 TCAAATCGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.03
24 55 0.93
25 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:41292 original size:24 final size:24
Alignment explanation
Indices: 41265--41366 Score: 73
Period size: 24 Copynumber: 4.2 Consensus size: 24
41255 TATATCAAAA
41265 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
41289 ATCATATCAAAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
41313 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
41337 ATCATATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
41361 ATCAAA
1 ATCAAA
41367 TCAGAATTCA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
23 6 0.09
24 60 0.88
25 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:41369 original size:24 final size:24
Alignment explanation
Indices: 41282--41373 Score: 141
Period size: 24 Copynumber: 3.8 Consensus size: 24
41272 CATAAATCAG
*
41282 GTCAAGTATCATATCAAAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
*
41306 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
41330 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
*
41354 GTCAAGTATCAAATCAGAAT
1 GTCAAGTATCATATCAGAAT
41374 TCAAATCGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
23 2 0.03
24 58 0.94
25 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:44625 original size:13 final size:13
Alignment explanation
Indices: 44609--44633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44599 ATAGAATTGA
44609 TAAGTTGAATTTT
1 TAAGTTGAATTTT
44622 TAAGTTGAATTT
1 TAAGTTGAATTT
44634 GACTTGTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TAAGTTGAATTTT
Found at i:44899 original size:21 final size:21
Alignment explanation
Indices: 44873--44917 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
44863 GATTTCTGGG
* *
44873 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
44894 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
44915 CAA
1 CAA
44918 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:45629 original size:31 final size:31
Alignment explanation
Indices: 45591--45713 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
45581 GGGTCGAGGG
45591 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
45622 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
45653 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
45684 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
45714 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:49418 original size:21 final size:21
Alignment explanation
Indices: 49392--49436 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49382 GATTTCTGGG
* *
49392 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
49413 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
49434 CAA
1 CAA
49437 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:50150 original size:31 final size:31
Alignment explanation
Indices: 50112--50234 Score: 203
Period size: 31 Copynumber: 4.0 Consensus size: 31
50102 GGGTCGAGGG
*
50112 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
50143 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
50174 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
50205 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
50235 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:54395 original size:14 final size:15
Alignment explanation
Indices: 54376--54413 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
54366 GAATCAATAC
*
54376 ATATATATAT-ATAT
1 ATATATATATGATAA
54390 ATATATATATGATAA
1 ATATATATATGATAA
54405 ACTATATAT
1 A-TATATAT
54414 TTAGTCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
ATATATATATGATAA
Found at i:61954 original size:22 final size:22
Alignment explanation
Indices: 61926--61975 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
61916 CACCAGTGGG
61926 TCCTTCGGATTGGAATCCTTAT
1 TCCTTCGGATTGGAATCCTTAT
61948 TCCTTCGGATTGGAATCCTTAT
1 TCCTTCGGATTGGAATCCTTAT
61970 TCCTTC
1 TCCTTC
61976 ATGTCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (22 bp):
TCCTTCGGATTGGAATCCTTAT
Found at i:62145 original size:22 final size:21
Alignment explanation
Indices: 62109--62150 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
62099 TGCATGACAT
62109 ATAAAATTTTAAAATCTTTTAA
1 ATAAAATTTTAAAAT-TTTTAA
62131 ATAAAATATTT-AAATTTTTA
1 ATAAAAT-TTTAAAATTTTTA
62151 TAAGCCTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 11 0.58
23 3 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAAATTTTAAAATTTTTAA
Done.