Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008281.1 Hibiscus syriacus cultivar Beakdansim tig00110943_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: 2054746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2032335 original size:89 final size:88
Alignment explanation
Indices: 2032162--2032384 Score: 213
Period size: 89 Copynumber: 2.5 Consensus size: 88
2032152 TTAAAACCAT
* *
2032162 TTTAGTCTCTTAAGTTTCTATTTTTTTTATTTTAGTTCCTTT-AATGTCTATTTTTGCTATTTTG
1 TTTAGTCCCTTAAGTTTCTA-TTTTTTTATTTTAG-TCCTTTAAATGTCTATTTTTGCTATTTTA
* ** * * *
2032226 GTCCTTTGATTTTTTGTTTTAGCT-A
64 GACAATTAAGTTTATGTTTTA-CTAA
* * *
2032251 TTTAGTCCCTTAAGTTTTTGTTTTTGTTATTTTAGTCCTTTAAATGTCTGTATTTT-CTA-TTTA
1 TTTAGTCCCTTAAGTTTCTATTTTT-TTATTTTAGTCCTTTAAATGTCTAT-TTTTGCTATTTTA
2032314 GACAATTAAGTTTATGTTTTTACTAA
64 GACAATTAAGTTTATG-TTTTACTAA
* * *
2032340 TTTAG-CCATTTAAGTTTCTATTTTTTCCATTTTAATCCTTTAAAT
1 TTTAGTCC-CTTAAGTTTCTATTTTTT-TATTTTAGTCCTTTAAAT
2032385 TCTTAATTCC
Statistics
Matches: 111, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
88 29 0.26
89 78 0.70
90 4 0.04
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (88 bp):
TTTAGTCCCTTAAGTTTCTATTTTTTTATTTTAGTCCTTTAAATGTCTATTTTTGCTATTTTAGA
CAATTAAGTTTATGTTTTACTAA
Found at i:2034169 original size:22 final size:21
Alignment explanation
Indices: 2034130--2034171 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2034120 GATCAATATT
*
2034130 TTTGCATCTGCATTTGCATTC
1 TTTGCATCTGCATCTGCATTC
*
2034151 TTTGCATTTTGCATCTGCATT
1 TTTGCA-TCTGCATCTGCATT
2034172 TCATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTGCATCTGCATCTGCATTC
Found at i:2044476 original size:22 final size:22
Alignment explanation
Indices: 2044448--2044490 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2044438 AATATGAATC
2044448 TATCCATATAAAGAACTCCTTA
1 TATCCATATAAAGAACTCCTTA
*
2044470 TATCCATATAAATAACTCCTT
1 TATCCATATAAAGAACTCCTT
2044491 CTAATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (22 bp):
TATCCATATAAAGAACTCCTTA
Found at i:2046264 original size:19 final size:18
Alignment explanation
Indices: 2046220--2046319 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 18
2046210 GAGGGCTGGA
2046220 AACCGGTTTGACCGGTTTT
1 AACCGGTTTGACCGG-TTT
*
2046239 CAACCGGTTCTGATCGGTTT
1 -AACCGGTT-TGACCGGTTT
*
2046259 AACCGGTTTCGACCGGTTCG
1 AACCGGTTT-GACCGGTT-T
*
2046279 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGT-TT
* *
2046298 AACCGGTTTGATCGGTCT
1 AACCGGTTTGACCGGTTT
2046316 AACC
1 AACC
2046320 CGACCCAACC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
18 5 0.07
19 38 0.54
20 21 0.30
21 6 0.09
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTT
Found at i:2046283 original size:39 final size:38
Alignment explanation
Indices: 2046220--2046313 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 38
2046210 GAGGGCTGGA
* *
2046220 AACCGGTTTGACCGGTTTTCAACCGGTTCTGATCGGT-TT
1 AACCGGTTTGACCGG-TTTCAACCGGTT-TGACCGGTCTG
2046259 AACCGGTTTCGACCGG-TTCGAACCGGTTTGACCGGTCTG
1 AACCGGTTT-GACCGGTTTC-AACCGGTTTGACCGGTCTG
*
2046298 AACCGGTTTGATCGGT
1 AACCGGTTTGACCGGT
2046314 CTAACCCGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 15 0.31
39 27 0.56
40 6 0.12
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (38 bp):
AACCGGTTTGACCGGTTTCAACCGGTTTGACCGGTCTG
Found at i:2046285 original size:29 final size:30
Alignment explanation
Indices: 2046220--2046305 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
2046210 GAGGGCTGGA
2046220 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
* * *
2046251 -ATCGGTTTAACCGGTTTCGACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
2046279 AACCGGTTTGACCGGTCTGAACCGGTT
1 AACCGGTTTGACCGGTTTCAACCGGTT
2046306 TGATCGGTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.02
29 33 0.72
30 12 0.26
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:2046377 original size:5 final size:5
Alignment explanation
Indices: 2046317--2046358 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
2046307 GATCGGTCTA
* **
2046317 ACCCG ACCCA ACCCG ACCCG ACCCG A-CTA ACCCG ACCCG ACC
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACC
2046359 GTTGACCTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
4 2 0.07
5 28 0.93
ACGTcount: A:0.26, C:0.57, G:0.14, T:0.02
Consensus pattern (5 bp):
ACCCG
Found at i:2046401 original size:6 final size:7
Alignment explanation
Indices: 2046377--2046406 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2046367 GGCCCGACCC
2046377 GACCGTT
1 GACCGTT
2046384 GACCGTT
1 GACCGTT
2046391 GACCG-T
1 GACCGTT
2046397 GACCGTT
1 GACCGTT
2046404 GAC
1 GAC
2046407 TTCCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:2046401 original size:13 final size:14
Alignment explanation
Indices: 2046377--2046406 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2046367 GGCCCGACCC
2046377 GACCGTTGACCGTT
1 GACCGTTGACCGTT
2046391 GACCG-TGACCGTT
1 GACCGTTGACCGTT
2046404 GAC
1 GAC
2046407 TTCCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:2051702 original size:18 final size:20
Alignment explanation
Indices: 2051668--2051713 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
2051658 AGTCAGTTAA
2051668 TTTATAA-ATGTTATATA-T
1 TTTATAATATGTTATATACT
*
2051686 TTTATAATAT-TTTTATACT
1 TTTATAATATGTTATATACT
2051705 TTTAATAAT
1 TTT-ATAAT
2051714 TAAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.54
19 6 0.25
20 5 0.21
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTATAATATGTTATATACT
Found at i:2051977 original size:60 final size:60
Alignment explanation
Indices: 2051847--2052009 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 60
2051837 ATTATCACTT
* * * *
2051847 ATCCTCAAAGTATGACTCTCATTTTAAATTAGTCCCTAAACTTTTAAATGTTATAATTAC
1 ATCCTCAAACTATGACTATCATTCTAAATTAGTCCCTAAACTTTTAAATATTATAATTAC
* * * *
2051907 ATGCTTAAACTATGACTATCATTCTAAATTAGT-CCTCAAACTTTTGAATATT-TCAATTTC
1 ATCCTCAAACTATGACTATCATTCTAAATTAGTCCCT-AAACTTTTAAATATTAT-AATTAC
* * *
2051967 ATCCCCAAAC--TGACTTTCATTCTAAATTGGTCCCTAAACTTTT
1 ATCCTCAAACTATGACTATCATTCTAAATTAGTCCCTAAACTTTT
2052010 TCAGCATTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
58 27 0.31
59 7 0.08
60 53 0.61
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (60 bp):
ATCCTCAAACTATGACTATCATTCTAAATTAGTCCCTAAACTTTTAAATATTATAATTAC
Found at i:2052032 original size:58 final size:58
Alignment explanation
Indices: 2051919--2052035 Score: 132
Period size: 58 Copynumber: 2.0 Consensus size: 58
2051909 GCTTAAACTA
* *
2051919 TGACTATCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAATTTCATCCCCAAAC
1 TGACTATCATTCTAAATTAGTCCTCAAACTTTTCAACATTTCAATTTCATCCCCAAAC
* * * *
2051977 TGACTTTCATTCTAAATTGGTCC-CTAAACTTTTTCAGCATTAT-AATTTC-TTCCCAAAC
1 TGACTATCATTCTAAATTAGTCCTC-AAAC-TTTTCAACATT-TCAATTTCATCCCCAAAC
2052035 T
1 T
2052036 ATACATAGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
57 1 0.02
58 34 0.68
59 14 0.28
60 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (58 bp):
TGACTATCATTCTAAATTAGTCCTCAAACTTTTCAACATTTCAATTTCATCCCCAAAC
Found at i:2054633 original size:21 final size:21
Alignment explanation
Indices: 2054609--2054650 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2054599 AAGGTACATG
2054609 TATTAATCAAATCAAATAAAT
1 TATTAATCAAATCAAATAAAT
2054630 TATTAATCAAATCAAATAAAT
1 TATTAATCAAATCAAATAAAT
2054651 GAATTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
TATTAATCAAATCAAATAAAT
Done.