Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003396.1 Hibiscus syriacus cultivar Beakdansim tig00007144_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: 58247
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:8506 original size:21 final size:21
Alignment explanation
Indices: 8459--8511 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
8449 TTAATGAAAC
8459 CTCGG-AATGGATATCCGGGTG
1 CTCGGAAAT-GATATCCGGGTG
* *
8480 CCCGGAAATGATATCCGGGTT
1 CTCGGAAATGATATCCGGGTG
8501 CTCGGAAATGA
1 CTCGGAAATGA
8512 AGAAACCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (21 bp):
CTCGGAAATGATATCCGGGTG
Found at i:11506 original size:2 final size:2
Alignment explanation
Indices: 11499--11569 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
11489 AAACATAATC
11499 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
11541 AT 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 AT A
11570 ATTAAAATCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30387 original size:2 final size:2
Alignment explanation
Indices: 30380--30410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30370 TTAAATTTAA
30380 AT AT 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 AT AT A
30411 ATTAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32656 original size:61 final size:60
Alignment explanation
Indices: 32576--32730 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 60
32566 TTTGGGGTTG
* * ** * * *
32576 AATTGGAATATACAAAAGTTTGGGGACTAATTTAGAAAGAGGGTCAGAGTTTAGGGGGTGA
1 AATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTAAGAGTTTA-GGGATGA
* ** * *
32637 AATTAGAAT-TTCCAAAAGTTTAAGGATTGGTTTAGAATGAGAGTAATAGTTTAGGGATGA
1 AATTAGAATATT-CAAAAGTTTAAGGACTAATTTAGAAAGAGAGTAAGAGTTTAGGGATGA
32697 AATTAGAATATTCAAAAGTTTAAGGA-TAAATTTA
1 AATTAGAATATTCAAAAGTTTAAGGACT-AATTTA
32731 AAATGAGGGT
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 34 0.44
61 42 0.55
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (60 bp):
AATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTAAGAGTTTAGGGATGA
Found at i:32736 original size:60 final size:61
Alignment explanation
Indices: 32623--32737 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
32613 AGAGGGTCAG
* *** *
32623 AGTTTAGGGGGTGAAATTAGAATTTCCAAAAGTTTAAGGATTGGTTTAGAATGAGAGTAAT
1 AGTTTAGGGGATGAAATTAGAATTTCCAAAAGTTTAAGGATAAATTTAAAATGAGAGTAAT
32684 AGTTTA-GGGATGAAATTAGAATATT-CAAAAGTTTAAGGATAAATTTAAAATGAG
1 AGTTTAGGGGATGAAATTAGAAT-TTCCAAAAGTTTAAGGATAAATTTAAAATGAG
32738 GGTTATAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 40 0.83
61 8 0.17
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (61 bp):
AGTTTAGGGGATGAAATTAGAATTTCCAAAAGTTTAAGGATAAATTTAAAATGAGAGTAAT
Found at i:34585 original size:60 final size:60
Alignment explanation
Indices: 34471--34603 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
34461 ATAGTCTGGT
* * * * * *
34471 GACCATTTTGTATCTTTTAATAGTTGAGGGACTCAATAAAGCAATACTTTATAGTCGATG
1 GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAACAATACTTCATAGTCGAAG
* * *
34531 GATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAATAATA-TTCCATAGTCGAAG
1 GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAACAATACTT-CATAGTCGAAG
34591 GACCATTTGTGTA
1 GACCATTT-TGTA
34604 CTTAACCCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.03
60 55 0.90
61 4 0.07
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAACAATACTTCATAGTCGAAG
Found at i:37731 original size:18 final size:19
Alignment explanation
Indices: 37708--37743 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
37698 TTTTTTGAAA
*
37708 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
37726 AACCGAAAAACCCGAACC
1 AACCGAAAAACCCGAACC
37744 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.36, G:0.14, T:0.03
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:45633 original size:28 final size:28
Alignment explanation
Indices: 45578--45633 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
45568 TCCATCATTA
* * *
45578 TAAATTCATATTTTATTCATTACTTAAT
1 TAAATTAATATTTTATTAATTACATAAT
45606 TAAATTAATATTTATATTAATTA-ATAAT
1 TAAATTAATATTT-TATTAATTACATAAT
45634 ACTAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TAAATTAATATTTTATTAATTACATAAT
Found at i:45925 original size:19 final size:20
Alignment explanation
Indices: 45891--45928 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
45881 AATGATTTTT
45891 TTACAAATTCTTTTTTCTAG
1 TTACAAATTCTTTTTTCTAG
*
45911 TTACACATT-TTTTTTCTA
1 TTACAAATTCTTTTTTCTA
45929 TAAGTTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.58
Consensus pattern (20 bp):
TTACAAATTCTTTTTTCTAG
Done.