Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005679.1 Hibiscus syriacus cultivar Beakdansim tig00013278_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: 141915
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:120432 original size:12 final size:11
Alignment explanation
Indices: 120405--120467 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
120395 GTAATTTTTA
120405 TTATTTTGT-T
1 TTATTTTGTAT
*
120415 TAATTTTAGTAT
1 TTATTTT-GTAT
*
120427 TTA-TTT-AAT
1 TTATTTTGTAT
120436 TTATTTTGTAAT
1 TTATTTTGT-AT
120448 TTATTTTGTAATT
1 TTATTTTGT-A-T
120461 TTATTTT
1 TTATTTT
120468 TAATTAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.12
10 9 0.21
11 5 0.12
12 16 0.37
13 8 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTATTTTGTAT
Found at i:120471 original size:12 final size:12
Alignment explanation
Indices: 120432--120472 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
120422 AGTATTTATT
120432 TAATTTATTTTG
1 TAATTTATTTTG
120444 TAATTTATTTTG
1 TAATTTATTTTG
120456 TAATTTTATTTT-
1 TAA-TTTATTTTG
120468 TAATT
1 TAATT
120473 AAGATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 2 0.07
12 18 0.64
13 8 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (12 bp):
TAATTTATTTTG
Found at i:131988 original size:6 final size:6
Alignment explanation
Indices: 131977--132027 Score: 79
Period size: 6 Copynumber: 8.7 Consensus size: 6
131967 ACTACGCCTG
131977 AAAAGA AAAAGA AAAAGAA AAAAGA AAAAGA AAAAG- AAAAG- AAAAGA
1 AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
132024 AAAA
1 AAAA
132028 AAAGGAGAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.23
6 27 0.63
7 6 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:131994 original size:12 final size:12
Alignment explanation
Indices: 131977--132027 Score: 79
Period size: 13 Copynumber: 4.3 Consensus size: 12
131967 ACTACGCCTG
131977 AAAAGAAAAAGA
1 AAAAGAAAAAGA
131989 AAAAGAAAAAAGA
1 AAAAG-AAAAAGA
132002 AAAAGAAAAAG-
1 AAAAGAAAAAGA
132013 AAAAG-AAAAGA
1 AAAAGAAAAAGA
132024 AAAA
1 AAAA
132028 AAAGGAGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.14
11 9 0.24
12 11 0.30
13 12 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:131999 original size:19 final size:17
Alignment explanation
Indices: 131976--132027 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 17
131966 TACTACGCCT
131976 GAAAAGAAAAAGAAAAA
1 GAAAAGAAAAAGAAAAA
131993 GAAAAAAGAAAAAGAAAAA
1 G--AAAAGAAAAAGAAAAA
132012 GAAAAG-AAAAGAAAAA
1 GAAAAGAAAAAGAAAAA
132028 AAAGGAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.30
17 6 0.18
19 17 0.52
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAGAAAAA
Found at i:132005 original size:25 final size:25
Alignment explanation
Indices: 131978--132031 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
131968 CTACGCCTGA
*
131978 AAAGAAAAAGAAAAAGAAAA-AAGAA
1 AAAGAAAAAG-AAAAGAAAAGAAAAA
132003 AAAGAAAAAGAAAAGAAAAGAAAAA
1 AAAGAAAAAGAAAAGAAAAGAAAAA
132028 AAAG
1 AAAG
132032 GAGAGGTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAGAAAAAGAAAAGAAAAGAAAAA
Found at i:132939 original size:44 final size:44
Alignment explanation
Indices: 132891--133356 Score: 230
Period size: 44 Copynumber: 10.6 Consensus size: 44
132881 TACTTTTTGC
* * * *
132891 TCGATTCTATCACAGAAGAAGGTAGATCAGCATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* ****
132935 TCGATTTCATCACAGAAGGAGGTGGATC-GACATTTTTATTTTCGCT
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATCGACA-TTTCG-T
* * * * * * * * * *
132981 T-AAATCCATCTCAGAAGAAGTTGGATCAGCGTCAACTTTTTGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* * * *
133024 TCGATTCTATCACAGAAGGAGATAGATCAGCATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* **** *
133068 TCGATTCCATCACTGAAGGAGGTGGATC-GACATTTTTATTTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATCGACA-TTTCGT
* * * * * * * * * *
133113 TCAAATCCATCGCAGAAGGAGTTGGATCAACTTCAACTTTTTGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* * * *
133157 TCGATTCTATCAAAGAAGGAGGTAGATCAGCATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* **** *
133201 TCGATTCCATCACTGAAGGAGGTGGATC-GACATTTTTATTTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATCGACA-TTTCGT
* * * * ** * *
133246 TCAAATCCATCGCAGAAGGAGTTGGATCA--A-C--TTTTTTGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* * * *
133285 TCGATTCTATCACAGAATGAGGTAGATCAGCATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
* * *
133329 TCGAATCCATTACAGAAAGAGGTGGATC
1 TCGATTCCATCACAGAAGGAGGTGGATC
133357 GACATCATAA
Statistics
Matches: 298, Mismatches: 108, Indels: 32
0.68 0.25 0.07
Matches are distributed among these distances:
39 27 0.09
40 1 0.00
41 1 0.00
42 1 0.00
43 5 0.02
44 178 0.60
45 82 0.28
46 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACATTTCGT
Found at i:133098 original size:133 final size:133
Alignment explanation
Indices: 132860--133361 Score: 798
Period size: 133 Copynumber: 3.8 Consensus size: 133
132850 TCACAGAAGG
* ** * *
132860 AGAAGGAGTTAGATCAGTGTCTACTTTTTGCTCGATTCTATCACAGAAGAAGGTAGATCAGCATC
1 AGAAGGAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
* *
132925 GACATCTCGTTCGATTTCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTTAAATCCAT
66 GACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT
*
132990 CTC
131 CGC
* * *
132993 AGAAGAAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCATC
1 AGAAGGAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
*
133058 GACATCTCGTTCGATTCCATCACTGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT
66 GACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT
133123 CGC
131 CGC
* *
133126 AGAAGGAGTTGGATCAACTTCAACTTTTTGCTCGATTCTATCAAAGAAGGAGGTAGATCAGCATC
1 AGAAGGAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
*
133191 GACATCTCGTTCGATTCCATCACTGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT
66 GACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT
133256 CGC
131 CGC
*
133259 AGAAGGAGTTGGATCAAC-T----TTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCATC
1 AGAAGGAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
* * *
133319 GACATCTCGTTCGAATCCATTACAGAAAGAGGTGGATCGACAT
66 GACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACAT
133362 CATAATATAT
Statistics
Matches: 348, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
128 78 0.22
132 1 0.00
133 269 0.77
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (133 bp):
AGAAGGAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
GACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT
CGC
Found at i:133393 original size:33 final size:33
Alignment explanation
Indices: 133350--133428 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
133340 ACAGAAAGAG
*
133350 GTGGATCGACATCATAATAT-ATCACATGAGG-A
1 GTGGATCGACATCATAAT-TCATCACATAAGGAA
**
133382 GCTGGATCGACATTTTAATTCATCACATAAGGAA
1 G-TGGATCGACATCATAATTCATCACATAAGGAA
*
133416 GTGGATTGACATC
1 GTGGATCGACATC
133429 TCCAACGAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 2 0.05
33 35 0.90
34 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (33 bp):
GTGGATCGACATCATAATTCATCACATAAGGAA
Found at i:134710 original size:18 final size:16
Alignment explanation
Indices: 134687--134726 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
134677 ATTTGTAATT
*
134687 TTTATTATTTTGTTTAAA
1 TTTATTA-TTTATTT-AA
134705 TTTATTATTTATTTAA
1 TTTATTATTTATTTAA
134721 TTTATT
1 TTTATT
134727 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTATTATTTATTTAA
Found at i:134735 original size:17 final size:16
Alignment explanation
Indices: 134691--134731 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
134681 GTAATTTTTA
*
134691 TTATTTTGT-TTAAAT
1 TTATTTTGTATTTAAT
134706 TTATTATT-TATTTAAT
1 TTATT-TTGTATTTAAT
134722 TTATTTTGTA
1 TTATTTTGTA
134732 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
TTATTTTGTATTTAAT
Done.