Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001010.1 Hibiscus syriacus cultivar Beakdansim tig00002016_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: 69894
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2165 original size:20 final size:20
Alignment explanation
Indices: 2140--2187 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2130 GTCAGAGTGT
*
2140 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
2160 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
2180 GGCAGCGG
1 GGCGGCGG
2188 CCAGCAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:2177 original size:17 final size:16
Alignment explanation
Indices: 2157--2188 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2147 GACGGCTGAC
2157 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
2174 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
2189 CAGCAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:3822 original size:19 final size:19
Alignment explanation
Indices: 3798--3845 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
3788 TATTTATTAT
*
3798 GTTTTATTAGATAGGATCA
1 GTTTTATTAGATAGAATCA
*
3817 GTTTTAATCAGATAGAATCA
1 GTTTT-ATTAGATAGAATCA
3837 GTTTATATT
1 GTTT-TATT
3846 CTGTTAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (19 bp):
GTTTTATTAGATAGAATCA
Found at i:8389 original size:52 final size:52
Alignment explanation
Indices: 8325--8432 Score: 198
Period size: 52 Copynumber: 2.1 Consensus size: 52
8315 TAACTAGATA
8325 TTTTATTATGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAGT
1 TTTTATTATGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAGT
* *
8377 TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCATT
1 TTTTATTATGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAGT
8429 TTTT
1 TTTT
8433 TTTGTTGCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.49
Consensus pattern (52 bp):
TTTTATTATGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAGT
Found at i:8431 original size:20 final size:20
Alignment explanation
Indices: 8341--8430 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
8331 TATGTTAGTT
*
8341 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
8361 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
8381 ATT--CT-G--TTAG--TT-
1 ATTAGATAGAATCAGTTTTA
*
8393 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
8413 ATTAGATAGAATCA-TTTT
1 ATTAGATAGAATCAGTTTT
8431 TTTTTGTTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
12 3 0.05
13 2 0.04
14 1 0.02
15 4 0.07
17 4 0.07
18 1 0.02
19 6 0.11
20 34 0.62
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:22355 original size:8 final size:8
Alignment explanation
Indices: 22342--22370 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
22332 AAATTATTTG
22342 AATTGTAA
1 AATTGTAA
22350 AATTGTAA
1 AATTGTAA
22358 AATTGTAA
1 AATTGTAA
22366 AATTG
1 AATTG
22371 CTGTCTTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (8 bp):
AATTGTAA
Found at i:23907 original size:33 final size:34
Alignment explanation
Indices: 23838--23910 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
23828 AAACAGTAAT
* *
23838 AAATTACTAAAATAAGTAAATAGGCAGGCTCTTG
1 AAATTACTAAAATAAGTAAATAGACAGGCTCGTG
*
23872 AAATTACTAAACT-AG-AAGATAGACAGGCTCGTG
1 AAATTACTAAAATAAGTAA-ATAGACAGGCTCGTG
23905 AAATTA
1 AAATTA
23911 TAATCTATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 2 0.06
33 21 0.60
34 12 0.34
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (34 bp):
AAATTACTAAAATAAGTAAATAGACAGGCTCGTG
Found at i:34273 original size:51 final size:52
Alignment explanation
Indices: 34183--34285 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 52
34173 ATAAGAAAGC
* * **
34183 ATAGTTTTCATTCACAAAATGGCCAATCAGACCCACTAATTGCTGGTTATTG
1 ATAGTTTTCATTCACAAAATGGCCAATCACACACACTAATTGAAGGTTATTG
*
34235 ATAGTTTTCATTCAC-AAGTGGCCAATCACACACACTAATTGAAGGTTATTG
1 ATAGTTTTCATTCACAAAATGGCCAATCACACACACTAATTGAAGGTTATTG
34286 CATGAGAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 31 0.67
52 15 0.33
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (52 bp):
ATAGTTTTCATTCACAAAATGGCCAATCACACACACTAATTGAAGGTTATTG
Found at i:36419 original size:10 final size:10
Alignment explanation
Indices: 36404--36438 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
36394 TTTATCACAC
36404 CAAATTCTCT
1 CAAATTCTCT
36414 CAAATTCTCT
1 CAAATTCTCT
36424 -AAATTTCTCT
1 CAAA-TTCTCT
36434 CAAAT
1 CAAAT
36439 ACTATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:36794 original size:112 final size:111
Alignment explanation
Indices: 36570--36903 Score: 587
Period size: 111 Copynumber: 3.0 Consensus size: 111
36560 TATAAATCAT
*
36570 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
36635 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
36681 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAATTTTTTTAGTA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAA-ATTATTAGTA
36746 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
36793 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
36858 CAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
36904 TTTTTGCAAT
Statistics
Matches: 212, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
111 106 0.50
112 106 0.50
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:38439 original size:18 final size:18
Alignment explanation
Indices: 38408--38447 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38398 CCAGTAGCCA
*
38408 CCGCAACCATATATGATG
1 CCGCAACCACATATGATG
*
38426 CCGCAGCCACATATGATG
1 CCGCAACCACATATGATG
38444 CCGC
1 CCGC
38448 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (18 bp):
CCGCAACCACATATGATG
Found at i:41862 original size:2 final size:2
Alignment explanation
Indices: 41855--41904 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
41845 TCGGGCCGGG
* *
41855 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
41896 AA TA TA TA T
1 TA TA TA TA T
41905 TTTTTATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:50529 original size:20 final size:21
Alignment explanation
Indices: 50487--50533 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
50477 TACTTGGCAC
50487 ATTTTTTAAAGGTGATATGTA
1 ATTTTTTAAAGGTGATATGTA
* * *
50508 ATTTTTTAAGGGTTA-ATTTA
1 ATTTTTTAAAGGTGATATGTA
50528 ATTTTT
1 ATTTTT
50534 GATCCCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
ATTTTTTAAAGGTGATATGTA
Found at i:60583 original size:12 final size:12
Alignment explanation
Indices: 60566--60593 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
60556 TTTCCTCCTT
60566 TGCACATGATCA
1 TGCACATGATCA
60578 TGCACATGATCA
1 TGCACATGATCA
60590 TGCA
1 TGCA
60594 ATTCTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (12 bp):
TGCACATGATCA
Found at i:65383 original size:34 final size:33
Alignment explanation
Indices: 65323--65388 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
65313 TGGAACTATA
* * *
65323 ATATTGTATTCTAATCGAATATAAATTTATAAT
1 ATATTGTATTCTAATCAAATAAAAATTCATAAT
* *
65356 ATATTCGTATTTTAATTAAATAAAAATTCATAA
1 ATATT-GTATTCTAATCAAATAAAAATTCATAA
65389 ATAACACATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (33 bp):
ATATTGTATTCTAATCAAATAAAAATTCATAAT
Done.