Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008849.1 Hibiscus syriacus cultivar Beakdansim tig00112059_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: 43675
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:15505 original size:29 final size:29
Alignment explanation
Indices: 15471--15531 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
15461 TTCTTTTATT
* *
15471 TAAGTACCTAAAATATTTCTTGGTTAAAA
1 TAAGTACCTAAAATATTTCTTGATCAAAA
* * *
15500 TAAGTACTTAAATTATTTTTTGATCAAAA
1 TAAGTACCTAAAATATTTCTTGATCAAAA
15529 TAA
1 TAA
15532 ATATGTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
TAAGTACCTAAAATATTTCTTGATCAAAA
Found at i:15684 original size:30 final size:29
Alignment explanation
Indices: 15628--15699 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
15618 AAAAAAATTG
*
15628 AATACTTTAAGTATATATTTTGACCAAAA
1 AATACTTTAGGTATATATTTTGACCAAAA
* * *
15657 AATAACTTTAGGTATTTTTTTTTACCAAAA
1 AAT-ACTTTAGGTATATATTTTGACCAAAA
* *
15687 TATATTTTAGGTA
1 AATACTTTAGGTA
15700 CTTAGATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (29 bp):
AATACTTTAGGTATATATTTTGACCAAAA
Found at i:25517 original size:177 final size:177
Alignment explanation
Indices: 25221--25578 Score: 698
Period size: 177 Copynumber: 2.0 Consensus size: 177
25211 AATAAACATC
25221 TATTTACCACTAAGATAGCTTGGTTTGAACGCTAGAGATTGTAAGAATATTTGAATTTTCATTGT
1 TATTTACCACTAAGATAGCTTGGTTTGAACGCTAGAGATTGTAAGAATATTTGAATTTTCATTGT
25286 CAAATTATTATGAATCTTTAGAAAAATATCTTTTATTGCTACTGAAACATGACACAAATAACTAT
66 CAAATTATTATGAATCTTTAGAAAAATATCTTTTATTGCTACTGAAACATGACACAAATAACTAT
25351 TAAGCAATATTCTATACGTACAATTAATTCCTCGTATTATTATTTAT
131 TAAGCAATATTCTATACGTACAATTAATTCCTCGTATTATTATTTAT
*
25398 TATTTACCACTAAGATTGCTTGGTTTGAACGCTAGAGATTGTAAGAATATTTGAATTTTCATTGT
1 TATTTACCACTAAGATAGCTTGGTTTGAACGCTAGAGATTGTAAGAATATTTGAATTTTCATTGT
25463 CAAATTATTATGAATCTTTAGAAAAATATCTTTTATTGCTACTGAAACATGACACAAATAACTAT
66 CAAATTATTATGAATCTTTAGAAAAATATCTTTTATTGCTACTGAAACATGACACAAATAACTAT
*
25528 TAAGCAATATTCTATACGTACAATTAATTCCTCGTATTATTATTTGT
131 TAAGCAATATTCTATACGTACAATTAATTCCTCGTATTATTATTTAT
25575 TATT
1 TATT
25579 CAATACTAAT
Statistics
Matches: 179, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 179 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (177 bp):
TATTTACCACTAAGATAGCTTGGTTTGAACGCTAGAGATTGTAAGAATATTTGAATTTTCATTGT
CAAATTATTATGAATCTTTAGAAAAATATCTTTTATTGCTACTGAAACATGACACAAATAACTAT
TAAGCAATATTCTATACGTACAATTAATTCCTCGTATTATTATTTAT
Found at i:28628 original size:21 final size:21
Alignment explanation
Indices: 28595--28646 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
28585 TATAAATAAA
*
28595 AATATTATGAATATTATTTTAT
1 AATATTAT-AATATAATTTTAT
*
28617 AATTTTATAATATAATTTTAT
1 AATATTATAATATAATTTTAT
*
28638 TATATTATA
1 AATATTATA
28647 CCAATAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATATTATAATATAATTTTAT
Found at i:28792 original size:20 final size:21
Alignment explanation
Indices: 28728--28784 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
28718 ATTGCGAGAG
28728 ATTCTTAATCACACCGATATGA
1 ATTCTTAATCAC-CCGATATGA
*
28750 ATTCTTAATCA-TCGATATGA
1 ATTCTTAATCACCCGATATGA
28770 ATTCTTAATCACCCG
1 ATTCTTAATCACCCG
28785 TTGCAATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 19 0.59
21 2 0.06
22 11 0.34
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (21 bp):
ATTCTTAATCACCCGATATGA
Found at i:29004 original size:15 final size:15
Alignment explanation
Indices: 28984--29033 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
28974 CACTATTAAA
28984 AATATTTATTAAAAT
1 AATATTTATTAAAAT
**
28999 AATA-TTATTTATCAT
1 AATATTTA-TTAAAAT
*
29014 -TTATTTATTAAAAT
1 AATATTTATTAAAAT
29028 AATATT
1 AATATT
29034 ATTTTGTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTTATTAAAAT
Found at i:29035 original size:25 final size:23
Alignment explanation
Indices: 28986--29064 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 23
28976 CTATTAAAAA
28986 TATTTATTAAAATAATATTATTTATCATT
1 TATTTATTAAAAT-A-A-TA-TTAT--TT
29015 TATTTATTAAAATAATATTATTT
1 TATTTATTAAAATAATATTATTT
* *
29038 TGTATTACTTAAAATAAAATTATTT
1 TAT-TTA-TTAAAATAATATTATTT
29063 TA
1 TA
29065 CATCTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 4 0.09
24 3 0.07
25 21 0.47
26 2 0.04
27 1 0.02
28 1 0.02
29 13 0.29
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (23 bp):
TATTTATTAAAATAATATTATTT
Found at i:29324 original size:22 final size:21
Alignment explanation
Indices: 29298--29338 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
29288 TAAAGTTTAT
29298 TTCTT-TTTTTCATTCTCTTCTC
1 TTCTTCTTTTT-ATTC-CTTCTC
29320 TTCTTCTTTTTATTCCTTC
1 TTCTTCTTTTTATTCCTTC
29339 CATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCTTCTTTTTATTCCTTCTC
Found at i:31186 original size:21 final size:23
Alignment explanation
Indices: 31144--31186 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
31134 GAAAGTAAAA
*
31144 AGTAATTTTAGTTTTTACTTAAGT
1 AGTAATTTTAGTTATTA-TTAAGT
31168 AGTAATTTTA-TTATT-TTAA
1 AGTAATTTTAGTTATTATTAA
31187 AATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
23 4 0.22
24 10 0.56
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (23 bp):
AGTAATTTTAGTTATTATTAAGT
Found at i:31343 original size:2 final size:2
Alignment explanation
Indices: 31338--31421 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
31328 AATTTAATGA
31338 AT AT 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 AT AT
31380 AT AT 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 AT AT
31422 GTGTGTGTGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32112 original size:22 final size:21
Alignment explanation
Indices: 32079--32121 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
32069 TCTGAAAATC
32079 TAAAATTACTATATATATTTT
1 TAAAATTACTATATATATTTT
*
32100 TAAAGATTTCTATATATATTTT
1 TAAA-ATTACTATATATATTTT
32122 CTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (21 bp):
TAAAATTACTATATATATTTT
Done.