Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000266.1 Hibiscus syriacus cultivar Beakdansim tig00000489_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: 63569
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8691 original size:20 final size:20
Alignment explanation
Indices: 8666--8705 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8656 GTAGAAGTTT
*
8666 ATTTTATGATTAATTGATTA
1 ATTTTATGATTAATTAATTA
*
8686 ATTTTATTATTAATTAATTA
1 ATTTTATGATTAATTAATTA
8706 TAGAAAGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTATGATTAATTAATTA
Found at i:9572 original size:21 final size:22
Alignment explanation
Indices: 9546--9589 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
9536 ATATATATAA
9546 TTTA-TTATAATAA-TATTTATT
1 TTTATTTAT-ATAATTATTTATT
9567 TTTATTTATATAATTATTTATT
1 TTTATTTATATAATTATTTATT
9589 T
1 T
9590 ATTTAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTTATATAATTATTTATT
Found at i:9586 original size:16 final size:16
Alignment explanation
Indices: 9567--9597 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9557 AATATTTATT
9567 TTTATTTATATAATTA
1 TTTATTTATATAATTA
*
9583 TTTATTTATTTAATT
1 TTTATTTATATAATT
9598 TCAGCTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTATATAATTA
Found at i:20139 original size:27 final size:27
Alignment explanation
Indices: 20108--20175 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
20098 TCTATTTACA
20108 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
20135 AAATCATATCACTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
20162 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
20176 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 8 0.21
27 31 0.79
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:23909 original size:27 final size:27
Alignment explanation
Indices: 23878--23945 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
23868 TCTATTTACA
*
23878 AAATCATATCTTTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
23905 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
23932 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
23946 ATTCCTACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:34691 original size:20 final size:23
Alignment explanation
Indices: 34651--34691 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
34641 TTAGAACTCA
34651 TCATGGCCACTTTGAGTTTAAGG
1 TCATGGCCACTTTGAGTTTAAGG
34674 TCAT-GCCA-TTTG-GTTTAA
1 TCATGGCCACTTTGAGTTTAA
34692 CAAATACACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 4 0.22
23 4 0.22
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (23 bp):
TCATGGCCACTTTGAGTTTAAGG
Found at i:42753 original size:24 final size:24
Alignment explanation
Indices: 42732--42781 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
42722 ACTAAAAAGG
42732 TAAACAAAAAT-AACAAGTAAAAC
1 TAAACAAAAATAAACAAGTAAAAC
* *
42755 TACACAAAAATAAAGAAGTAAAA-
1 TAAACAAAAATAAACAAGTAAAAC
42778 TAAA
1 TAAA
42782 AATGATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.70, C:0.10, G:0.06, T:0.14
Consensus pattern (24 bp):
TAAACAAAAATAAACAAGTAAAAC
Found at i:53107 original size:5 final size:5
Alignment explanation
Indices: 53093--53145 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
53083 CTCGGATAAC
* * * * *
53093 ACGCT ACGCT GCGCT ACGCT ACGCT ACGCT ACGTT ACGTT ACGTT ACGTT
1 ACGCT ACGCT ACGCT ACGCT ACGCT ACGCT ACGCT ACGCT ACGCT ACGCT
53143 ACG
1 ACG
53146 TTACCCAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (5 bp):
ACGCT
Found at i:53184 original size:5 final size:5
Alignment explanation
Indices: 53174--53671 Score: 771
Period size: 5 Copynumber: 99.6 Consensus size: 5
53164 TCTGTATATC
* * * *
53174 AACGT AACGT AACGT AACGT AACGT AGCGT AGCGT AGCGT AGCGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
* * *
53224 AGCGT AACGT AACGT AGCGT AACGT AACGT AACGT AACGT AACGT AGCGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
* * * *
53274 AACGT AGCGT AACAT AACGT AACGT AGCGT AACGT AGCGT AACGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
* * * *
53324 AACGT AGCGT AACGT AGCGT AACGT AACGT AGCGT AACGT AACGT AGCGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
* * *
53374 AGCGT AGCGT AACGT AACGT AACGT AACGT AACGT AAAGT AACGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
* * *
53424 AACGT AGCGT AGCGT AACGT AACGT AACGT AACGT AACGT AACGT AGCGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
* * * *
53474 AGCGT AACGT AGCGT AGCGT AGCGT AACGT AACGT AACGT AACGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
53524 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
53574 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT
53624 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AAC
1 AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AACGT AAC
53672 AGACAAACAT
Statistics
Matches: 461, Mismatches: 32, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 461 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (5 bp):
AACGT
Found at i:62641 original size:21 final size:21
Alignment explanation
Indices: 62612--62654 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62602 AATTCCTTGC
62612 AAGAATTCATGGCCTCGACAA
1 AAGAATTCATGGCCTCGACAA
* * *
62633 AAGATTTCATGGCGTCTACAA
1 AAGAATTCATGGCCTCGACAA
62654 A
1 A
62655 GACCTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (21 bp):
AAGAATTCATGGCCTCGACAA
Done.