Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007202.1 Hibiscus syriacus cultivar Beakdansim tig00019018_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: 43947
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:4003 original size:16 final size:15
Alignment explanation
Indices: 3958--4010 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
3948 CTAAATTTTT
3958 TTAAAAAATA-GAAA
1 TTAAAAAATATGAAA
3972 TTAAAAAATCAT--AA
1 TTAAAAAAT-ATGAAA
3986 TTAAAAAATATGGAAA
1 TTAAAAAATAT-GAAA
4002 TTAATAAAA
1 TTAA-AAAA
4011 ATATCCTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.06
14 20 0.61
15 1 0.03
16 6 0.18
17 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (15 bp):
TTAAAAAATATGAAA
Found at i:6981 original size:40 final size:40
Alignment explanation
Indices: 6855--6981 Score: 145
Period size: 41 Copynumber: 3.2 Consensus size: 40
6845 AAGGGGGTTG
**
6855 AAACCCCTAAAG-AGTGT-AAAAATGCACTTATGGTTTTG
1 AAACCCCTAAAGTAGTGTCAAAAATGCACTTATGGTTTCA
* * *
6893 AAACTCCTAAGGTAGAGTCCAAAAA-GCACTTATGGTTTCA
1 AAACCCCTAAAGTAGTGT-CAAAAATGCACTTATGGTTTCA
*
6933 AAACCCCCTAAAGTAGTGTCAAAAATG-ATCATATGGTTTCA
1 AAA-CCCCTAAAGTAGTGTCAAAAATGCA-CTTATGGTTTCA
6974 AAACCCCT
1 AAACCCCT
6982 CCCATGGTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
38 10 0.14
39 4 0.05
40 28 0.38
41 32 0.43
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (40 bp):
AAACCCCTAAAGTAGTGTCAAAAATGCACTTATGGTTTCA
Found at i:12329 original size:20 final size:20
Alignment explanation
Indices: 12292--12330 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12282 AGATTGAGTG
* * *
12292 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
12312 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
12331 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:12550 original size:20 final size:21
Alignment explanation
Indices: 12504--12564 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
12494 TTCCCCTGTG
*
12504 GGGGGAATCGGATCCCCTTCAAA
1 GGGGGAATCGG-TTCCC-TCAAA
12527 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
12547 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
12565 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 4 0.11
23 11 0.31
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:19834 original size:75 final size:76
Alignment explanation
Indices: 19629--19844 Score: 314
Period size: 76 Copynumber: 2.9 Consensus size: 76
19619 ATTTTAAACA
***
19629 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAATTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
*
19694 GGATATTATTT
66 GAATATTATTT
19705 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
19770 GAATATTA-TT
66 GAATATTATTT
* **
19780 TTA-ATTATTAT-TATTTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGCTTTAATTAGGAT
1 TTATATT-TTATCT-TTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGAT
19842 TTA
63 TTA
19845 AGATGTTTTA
Statistics
Matches: 130, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
74 9 0.07
75 52 0.40
76 69 0.53
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
GAATATTATTT
Found at i:20442 original size:13 final size:13
Alignment explanation
Indices: 20420--20469 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
20410 CTTTATCCCA
*
20420 ATTTAATTATTTT
1 ATTTATTTATTTT
20433 ATTTATTTATTTT
1 ATTTATTTATTTT
*
20446 ATTTAATTTTATTTC
1 ATTT-A-TTTATTTT
20461 ATTATATTT
1 ATT-TATTT
20470 CTTTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 16 0.50
14 4 0.12
15 11 0.34
16 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:24672 original size:21 final size:21
Alignment explanation
Indices: 24648--24687 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
24638 GATATTGATG
24648 TGTCATCA-TAAAATAATATCA
1 TGTCATCATTAAAA-AATATCA
24669 TGTCATCATTAAAAAATAT
1 TGTCATCATTAAAAAATAT
24688 AAATATCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (21 bp):
TGTCATCATTAAAAAATATCA
Found at i:25431 original size:2 final size:2
Alignment explanation
Indices: 25424--25450 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25414 CATCACTGTA
25424 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
25451 CCAATCATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34862 original size:13 final size:13
Alignment explanation
Indices: 34844--34882 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
34834 ACATTGACAT
34844 TGATATAAGAATA
1 TGATATAAGAATA
34857 TGATATAA-AATA
1 TGATATAAGAATA
34869 T-ATAATAAGAATA
1 TGAT-ATAAGAATA
34882 T
1 T
34883 ATGTGTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 9 0.38
13 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (13 bp):
TGATATAAGAATA
Found at i:35174 original size:21 final size:21
Alignment explanation
Indices: 35150--35227 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
35140 CCTTCGGGAT
35150 ATATATGTAATCCTTTGGAAC
1 ATATATGTAATCCTTTGGAAC
** * * *
35171 ATATATGTGGTTCTTCGAAAC
1 ATATATGTAATCCTTTGGAAC
* * ** *
35192 ACATATTTGGTCCTTTGGAAT
1 ATATATGTAATCCTTTGGAAC
35213 ATATATGTAATCCTT
1 ATATATGTAATCCTT
35228 AAGGAGTGAT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (21 bp):
ATATATGTAATCCTTTGGAAC
Found at i:36894 original size:13 final size:13
Alignment explanation
Indices: 36833--36893 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
36823 TGCGTCATAA
*
36833 ATTTATGACACGC
1 ATTTATGACACAC
36846 ATTTATGACACAC
1 ATTTATGACACAC
36859 ATTTATGACACAC
1 ATTTATGACACAC
* *
36872 ATTTATGACGCGC
1 ATTTATGACACAC
36885 ATTTATGAC
1 ATTTATGAC
36894 GTTCATTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:37022 original size:85 final size:85
Alignment explanation
Indices: 36872--37037 Score: 192
Period size: 85 Copynumber: 2.0 Consensus size: 85
36862 TATGACACAC
* * * * * *
36872 ATTTATGACGCGCATTTATGACGTTCATTGAGCGTCATTGAAGCCCTCGTCATAAATTAAGATGA
1 ATTTATGACACGCATGTATGACGTTCATTGAGCGTCATTGAAGCACACGCCATAAATAAAGATGA
* * *
36937 CATATATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
* * *
36957 ATTTATGACACGCATGTATGAC-TTACATTGCGTGTCATTGAAGCACACGCCATTAAA-AAATAT
1 ATTTATGACACGCATGTATGACGTT-CATTGAGCGTCATTGAAGCACACGCCA-TAAATAAAGAT
37020 GACACACATTCGTGTGTC
64 GACACACATTCGTGTGTC
37038 GTGATTGTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 2 0.03
85 61 0.91
86 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACGTTCATTGAGCGTCATTGAAGCACACGCCATAAATAAAGATGA
CACACATTCGTGTGTCATAA
Done.