Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006198.1 Hibiscus syriacus cultivar Beakdansim tig00014754_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: 55238
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:663 original size:2 final size:2
Alignment explanation
Indices: 656--686 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
646 CCTATGAAGG
*
656 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
687 GGTCGGGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:25130 original size:38 final size:37
Alignment explanation
Indices: 25045--25292 Score: 133
Period size: 38 Copynumber: 7.0 Consensus size: 37
25035 GGTTTCCGAA
* *
25045 AAAATATATATACAATATAGT-TTTTTAAAACGTTTTTG
1 AAAAT-TATATACAATATA-TAGTTTTAAAACATTTTTG
25083 AAAACTTATATACAATATATAAGTTTTAAAACATTTTTG
1 AAAA-TTATATACAATATAT-AGTTTTAAAACATTTTTG
**
25122 AAAATTATAT--AATATATAGTTTTGAAGTCA-TTTTG
1 AAAATTATATACAATATATAGTTTT-AAAACATTTTTG
* **
25157 AAAA-TATAT--AGT-T-T--TTAAAAAACATTTTTGG
1 AAAATTATATACAATATATAGTTTTAAAACATTTTT-G
* **
25188 AAAATT-TATATAATATATAGCTTAAAAAACA-TTTTG
1 AAAATTATATACAATATATAG-TTTTAAAACATTTTTG
* *
25224 AAAAACTTGTAT----TATAT--TTTTAAAATCATTTTTA
1 -AAAA-TTATATACAATATATAGTTTTAAAA-CATTTTTG
*
25258 AAAACTATAT--AATATATAGTTTTAAAAACATTTTT
1 AAAATTATATACAATATATAGTTTT-AAAACATTTTT
25293 AAATATAATA
Statistics
Matches: 171, Mismatches: 15, Indels: 50
0.72 0.06 0.21
Matches are distributed among these distances:
29 4 0.02
30 6 0.04
31 8 0.05
32 12 0.07
33 9 0.05
34 17 0.10
35 21 0.12
36 23 0.13
37 13 0.08
38 35 0.20
39 23 0.13
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATTATATACAATATATAGTTTTAAAACATTTTTG
Found at i:25154 original size:36 final size:36
Alignment explanation
Indices: 25067--25292 Score: 142
Period size: 36 Copynumber: 6.4 Consensus size: 36
25057 CAATATAGTT
*
25067 TTTTAAAACGTTTTTGAAAACTTATATACAATATATAAG
1 TTTTAAAACATTTTTGAAAA-TTATAT--AATATATAAG
25106 TTTTAAAACATTTTTGAAAATTATATAATATAT-AG
1 TTTTAAAACATTTTTGAAAATTATATAATATATAAG
** *
25141 TTTTGAAGTCA-TTTTGAAAA-TATATAGT-T-T---
1 TTTT-AAAACATTTTTGAAAATTATATAATATATAAG
**
25171 TTAAAAAACATTTTTGGAAAATTTATATAATATAT-AG
1 TTTTAAAACATTTTT-GAAAA-TTATATAATATATAAG
** *
25208 CTTAAAAAACA-TTTTGAAAAACTTGTAT--TATAT---
1 -TTTTAAAACATTTTTG-AAAA-TTATATAATATATAAG
* *
25241 TTTTAAAATCATTTTTAAAAACTATATAATATAT-AG
1 TTTTAAAA-CATTTTTGAAAATTATATAATATATAAG
25277 TTTTAAAAACATTTTT
1 TTTT-AAAACATTTTT
25293 AAATATAATA
Statistics
Matches: 153, Mismatches: 16, Indels: 39
0.74 0.08 0.19
Matches are distributed among these distances:
29 4 0.03
30 6 0.04
31 5 0.03
32 11 0.07
33 14 0.09
34 17 0.11
35 21 0.14
36 23 0.15
37 17 0.11
38 16 0.10
39 19 0.12
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (36 bp):
TTTTAAAACATTTTTGAAAATTATATAATATATAAG
Found at i:25325 original size:33 final size:31
Alignment explanation
Indices: 25195--25314 Score: 96
Period size: 31 Copynumber: 3.6 Consensus size: 31
25185 TGGAAAATTT
* *
25195 ATATAATATATAGCTTAAAAAACATTTTGAA
1 ATATAATATATAGTTTAAAAAACATTTTTAA
* ** * * *
25226 AAACTTGTATTATATTTTTAAAATCATTTTTAAAAA
1 ATA-TAATA-TATAGTTTAAAAAACATTTTT---AA
*
25262 CTATATAATATATAGTTTTAAAAACATTTTTAA
1 --ATATAATATATAGTTTAAAAAACATTTTTAA
25295 ATATAATATATAGTTTAAAA
1 ATATAATATATAGTTTAAAA
25315 GAAATATTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
31 21 0.31
32 3 0.04
33 18 0.26
36 21 0.31
37 3 0.04
38 2 0.03
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (31 bp):
ATATAATATATAGTTTAAAAAACATTTTTAA
Found at i:25332 original size:33 final size:31
Alignment explanation
Indices: 25263--25339 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 31
25253 TTTTAAAAAC
*
25263 TATATAATATATAGTTTTAAAAACATTTTTA
1 TATATAATATATAGTTTAAAAAACATTTTTA
* * *
25294 AATATAATATATAGTTTAAAAGAAATATTTTTT
1 TATATAATATATAGTTT-AAA-AAACATTTTTA
*
25327 TATATATTATATA
1 TATATAATATATA
25340 CGCTATATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 16 0.42
32 2 0.05
33 20 0.53
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (31 bp):
TATATAATATATAGTTTAAAAAACATTTTTA
Found at i:26886 original size:29 final size:30
Alignment explanation
Indices: 26840--26906 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
26830 TAAACCTTTT
*
26840 TTTATTTATTTACTTTTTTCCTTTTCTTTTGA
1 TTTA-TTATTTACTTTTTTCCTTTTC-TATGA
*
26872 TTTATTATTT-CTTTTTTTCTTTTCTATGA
1 TTTATTATTTACTTTTTTCCTTTTCTATGA
26901 TTTATT
1 TTTATT
26907 TAATATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 10 0.30
30 13 0.39
31 6 0.18
32 4 0.12
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (30 bp):
TTTATTATTTACTTTTTTCCTTTTCTATGA
Found at i:26923 original size:3 final size:3
Alignment explanation
Indices: 26910--26948 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
26900 ATTTATTTAA
26910 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26949 CTAACATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30269 original size:27 final size:27
Alignment explanation
Indices: 30235--30327 Score: 177
Period size: 27 Copynumber: 3.4 Consensus size: 27
30225 GATAATGGCT
30235 CTGAATCATTCATAATGTACTTCTGTG
1 CTGAATCATTCATAATGTACTTCTGTG
30262 CTGAATCATTCATAATGTACTTCTGTG
1 CTGAATCATTCATAATGTACTTCTGTG
30289 CTGAATCATTCATAATGTACTTCTGTG
1 CTGAATCATTCATAATGTACTTCTGTG
*
30316 TTGAATCATTCA
1 CTGAATCATTCA
30328 ACACTGTTTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (27 bp):
CTGAATCATTCATAATGTACTTCTGTG
Found at i:46002 original size:12 final size:12
Alignment explanation
Indices: 45987--46013 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
45977 TGATAATCTC
45987 ATTGCTATTATT
1 ATTGCTATTATT
45999 ATTGCTATTATT
1 ATTGCTATTATT
46011 ATT
1 ATT
46014 TTGTCCGGTC
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:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (12 bp):
ATTGCTATTATT
Found at i:46151 original size:34 final size:30
Alignment explanation
Indices: 46077--46152 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
46067 TACTCGATTC
* * *
46077 GTGCTTGTTAAAAAAATTGTTGCTCGACTT
1 GTGCTCGTTAAAAAAATTCTTGCTCGACGT
46107 GTGCTCGTTAAAAAAACTTCTTCGACTCGACGT
1 GTGCTCGTTAAAAAAA-TTCTT-G-CTCGACGT
46140 GTTGCTCGTTAAA
1 G-TGCTCGTTAAA
46153 CTTACTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 15 0.38
31 4 0.10
32 1 0.03
33 8 0.21
34 11 0.28
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (30 bp):
GTGCTCGTTAAAAAAATTCTTGCTCGACGT
Found at i:52401 original size:2 final size:2
Alignment explanation
Indices: 52394--52431 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52384 CAGAAAAGTG
52394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52432 TTGTGGTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53577 original size:41 final size:42
Alignment explanation
Indices: 53528--53606 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
53518 AATATTATTA
*
53528 ATTAATAATCAATATTTTTT-TTATTTATTAAAAATTAATAG
1 ATTAATAATCAATATTTTTTATTATCTATTAAAAATTAATAG
** *
53569 ATTAATAATTTATCTTTTTTATTATCTATTAAAAATTA
1 ATTAATAATCAATATTTTTTATTATCTATTAAAAATTA
53607 GTATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (42 bp):
ATTAATAATCAATATTTTTTATTATCTATTAAAAATTAATAG
Done.