Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004902.1 Hibiscus syriacus cultivar Beakdansim tig00011029_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: 63875
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:449 original size:20 final size:21
Alignment explanation
Indices: 417--455 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
407 TTTATTACCC
417 TTGTTTCCATTGTCTTAATCT
1 TTGTTTCCATTGTCTTAATCT
438 TTGTTT-CATTGTCTTAAT
1 TTGTTTCCATTGTCTTAAT
456 TTCCAACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (21 bp):
TTGTTTCCATTGTCTTAATCT
Found at i:820 original size:31 final size:31
Alignment explanation
Indices: 762--825 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
752 GTAGAGTGAT
** *
762 CATTTTGTTACAAATTGATAACGTTAGTAAC
1 CATTTTGTTACAAATCAATAACATTAGTAAC
*
793 CATTTTGTTACAAATCAAT-ACTATTAGTGAC
1 CATTTTGTTACAAATCAATAAC-ATTAGTAAC
824 CA
1 CA
826 ATGTCACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (31 bp):
CATTTTGTTACAAATCAATAACATTAGTAAC
Found at i:19309 original size:18 final size:18
Alignment explanation
Indices: 19286--19344 Score: 91
Period size: 18 Copynumber: 3.2 Consensus size: 18
19276 TTTGCACACA
* *
19286 AAAGTTTCGAAACTCTGG
1 AAAGTTTCAAAACTCTCG
19304 AAAGTTTCAAAACTCTCG
1 AAAGTTTCAAAACTCTCG
19322 AAAGTTTCAAAACTCTTCG
1 AAAGTTTCAAAACTC-TCG
19341 AAAG
1 AAAG
19345 AGTTGCCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 31 0.82
19 7 0.18
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (18 bp):
AAAGTTTCAAAACTCTCG
Found at i:19397 original size:20 final size:20
Alignment explanation
Indices: 19374--19425 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
19364 CTTTAGGGAA
*
19374 AGTTTCTAAACTCTTGAGAT
1 AGTTTCAAAACTCTTGAGAT
19394 AGTTTCAAAACTCTTGAGAT
1 AGTTTCAAAACTCTTGAGAT
19414 AGTTTCAAAACT
1 AGTTTCAAAACT
19426 TTTACACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
AGTTTCAAAACTCTTGAGAT
Found at i:20572 original size:19 final size:19
Alignment explanation
Indices: 20535--20576 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
20525 TCTAAATCAT
*
20535 TTTTCAAAGTTTCATTTTG
1 TTTTCAAAGTCTCATTTTG
20554 ATTTTCAAAGTCT-ATTTTG
1 -TTTTCAAAGTCTCATTTTG
20573 TTTT
1 TTTT
20577 AAAAAATCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTTCAAAGTCTCATTTTG
Found at i:28534 original size:6 final size:6
Alignment explanation
Indices: 28523--28563 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
28513 ATTCCATTAC
*
28523 ATTTTT ATTTTTT ATTTTT ATTTTT -GTTTT A-TTTT ATTTTT
1 ATTTTT A-TTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
28564 TTCGTTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
5 9 0.29
6 16 0.52
7 6 0.19
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:28541 original size:13 final size:13
Alignment explanation
Indices: 28523--28547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28513 ATTCCATTAC
28523 ATTTTTATTTTTT
1 ATTTTTATTTTTT
28536 ATTTTTATTTTT
1 ATTTTTATTTTT
28548 GTTTTATTTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:28564 original size:17 final size:17
Alignment explanation
Indices: 28532--28563 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28522 CATTTTTATT
28532 TTTTATTTTTATTTTTG
1 TTTTATTTTTATTTTTG
28549 TTTTA-TTTTATTTTT
1 TTTTATTTTTATTTTT
28564 TTCGTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTATTTTTATTTTTG
Found at i:39985 original size:7 final size:7
Alignment explanation
Indices: 39973--39998 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39963 GAAATAAATG
39973 TATAAAA
1 TATAAAA
39980 TATAAAA
1 TATAAAA
39987 TATAAAA
1 TATAAAA
39994 TATAA
1 TATAA
39999 TATTCAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TATAAAA
Found at i:52174 original size:42 final size:42
Alignment explanation
Indices: 52115--52199 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
52105 CAAATAACTA
* *
52115 ACCTCTATGCATCTAATCCTATTAGACTAACCTAGCTAAGCT
1 ACCTCTAGGCATCTAATCCTATTAGACTAACCAAGCTAAGCT
* * *
52157 ACCTCTAGGTATCTAATCCTATTAGAGTGACCAAGCTAAGCT
1 ACCTCTAGGCATCTAATCCTATTAGACTAACCAAGCTAAGCT
52199 A
1 A
52200 TTAACCAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (42 bp):
ACCTCTAGGCATCTAATCCTATTAGACTAACCAAGCTAAGCT
Found at i:55105 original size:30 final size:30
Alignment explanation
Indices: 55071--55148 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
55061 TCTAGCAAAT
55071 GTAATTCATTTTACGTAAAATAGTTTTCAG
1 GTAATTCATTTTACGTAAAATAGTTTTCAG
*
55101 GTAATTCATTTTACGTAAAATAGTTTTTAG
1 GTAATTCATTTTACGTAAAATAGTTTTCAG
* *
55131 GCAATT-AATTTACGTAAA
1 GTAATTCATTTTACGTAAA
55149 TTATTTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 11 0.24
30 34 0.76
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAATAGTTTTCAG
Found at i:55156 original size:29 final size:30
Alignment explanation
Indices: 55073--55159 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
55063 TAGCAAATGT
* * *
55073 AATTCATTTTACGTAAAATAGTTTTCAGGT
1 AATTCAATTTACGTAAAATAGTTTTTAGGC
*
55103 AATTCATTTTACGTAAAATAGTTTTTAGGC
1 AATTCAATTTACGTAAAATAGTTTTTAGGC
* *
55133 AATT-AATTTACGTAAATTATTTTTTAG
1 AATTCAATTTACGTAAAATAGTTTTTAG
55160 AAAACCAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
29 20 0.38
30 32 0.62
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (30 bp):
AATTCAATTTACGTAAAATAGTTTTTAGGC
Found at i:55169 original size:29 final size:29
Alignment explanation
Indices: 55080--55169 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 29
55070 TGTAATTCAT
* * ** *
55080 TTTACGTAAAATAGTTTTCAGGTAATTCAT
1 TTTACGTAAAATAGTTTTTA-GAAAACCAA
** **
55110 TTTACGTAAAATAGTTTTTAGGCAATTAA
1 TTTACGTAAAATAGTTTTTAGAAAACCAA
* *
55139 TTTACGTAAATTATTTTTTAGAAAACCAA
1 TTTACGTAAAATAGTTTTTAGAAAACCAA
55168 TT
1 TT
55170 ACAACCTATC
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
29 29 0.60
30 19 0.40
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (29 bp):
TTTACGTAAAATAGTTTTTAGAAAACCAA
Found at i:63759 original size:49 final size:49
Alignment explanation
Indices: 63703--63875 Score: 238
Period size: 49 Copynumber: 3.5 Consensus size: 49
63693 TGTTGCAAAA
* ** * * *
63703 TAAATGCACAACGGTGCATTTTGGCATAAATGGTGTCACTAATGAAAGT
1 TAAATGCATAACATTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
* *
63752 TGAATGCATAACAATGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACATTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
* *
63801 TAAATGCATAACATTGCATTTCAGTATAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACATTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
**
63850 TAAATGCATAATGTTGCATTTCGGCA
1 TAAATGCATAACATTGCATTTCGGCA
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (49 bp):
TAAATGCATAACATTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
Done.