Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005099.1 Hibiscus syriacus cultivar Beakdansim tig00011465_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: 73246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:13502 original size:2 final size:2
Alignment explanation
Indices: 13495--13521 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13485 ACATCAGGGA
13495 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
13522 AACTTACCAG
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:14624 original size:61 final size:62
Alignment explanation
Indices: 14507--14645 Score: 253
Period size: 61 Copynumber: 2.3 Consensus size: 62
14497 TTTTTGGTAC
14507 CCAGGGGAGGCTACTACAATATAAAAAACACGAAATAAAAAAAATGAACGAAACTTATGTAA
1 CCAGGGGAGGCTACTACAATATAAAAAACACGAAATAAAAAAAATGAACGAAACTTATGTAA
*
14569 CCAGGGGAGGCTACTACAATAT-AAAAACACGAAATAAAAAAAATGAACGAAACTTATGTAC
1 CCAGGGGAGGCTACTACAATATAAAAAACACGAAATAAAAAAAATGAACGAAACTTATGTAA
*
14630 CCAGGGGAGGCAACTA
1 CCAGGGGAGGCTACTA
14646 GCGACTACAA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 53 0.71
62 22 0.29
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.15
Consensus pattern (62 bp):
CCAGGGGAGGCTACTACAATATAAAAAACACGAAATAAAAAAAATGAACGAAACTTATGTAA
Found at i:15884 original size:11 final size:11
Alignment explanation
Indices: 15868--15895 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
15858 ACAAAGCTTG
15868 AAAAAAAAAGA
1 AAAAAAAAAGA
15879 AAAAAAAAAGA
1 AAAAAAAAAGA
15890 AAAAAA
1 AAAAAA
15896 CTTGAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:18438 original size:30 final size:30
Alignment explanation
Indices: 18398--18467 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
18388 ATTTTCATAT
* *
18398 GGGTTTTGCTAACATGC-GCTGACCTTCAAA
1 GGGTTGTGCTAACATGCATC-GACCTTCAAA
*
18428 GGGTTGTGCTAACGTGCATCGACCTTCAAA
1 GGGTTGTGCTAACATGCATCGACCTTCAAA
18458 GGGTTGTGCT
1 GGGTTGTGCT
18468 GACGTGCGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (30 bp):
GGGTTGTGCTAACATGCATCGACCTTCAAA
Found at i:18473 original size:30 final size:30
Alignment explanation
Indices: 18418--18474 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
18408 AACATGCGCT
18418 GACCTTCAAAGGGTTGTGCTAACGTGCATC
1 GACCTTCAAAGGGTTGTGCTAACGTGCATC
*
18448 GACCTTCAAAGGGTTGTGCTGACGTGC
1 GACCTTCAAAGGGTTGTGCTAACGTGC
18475 GTCGTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (30 bp):
GACCTTCAAAGGGTTGTGCTAACGTGCATC
Found at i:32527 original size:3 final size:3
Alignment explanation
Indices: 32521--32552 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
32511 TTCATCATCA
*
32521 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
32553 AATAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:33823 original size:11 final size:10
Alignment explanation
Indices: 33801--33834 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
33791 AATCTTTTTG
*
33801 TTTAATTTTA
1 TTTAATTATA
33811 TTTAATTACTA
1 TTTAATTA-TA
33822 TTTAATTATA
1 TTTAATTATA
33832 TTT
1 TTT
33835 TTTTAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTAATTATA
Found at i:34166 original size:2 final size:2
Alignment explanation
Indices: 34159--34183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34149 ATCCTGCTTT
34159 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34184 TTACTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44158 original size:31 final size:30
Alignment explanation
Indices: 44122--44184 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
44112 AATATAAACA
44122 AACATTAATTTAA-GATAAAAATACATATAAT
1 AACATTAATTTAATGAT-AAAA-ACATATAAT
*
44153 AACATTAATTTAATGATAATAACATATAAT
1 AACATTAATTTAATGATAAAAACATATAAT
44183 AA
1 AA
44185 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.37
31 16 0.53
32 3 0.10
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.33
Consensus pattern (30 bp):
AACATTAATTTAATGATAAAAACATATAAT
Found at i:45087 original size:15 final size:15
Alignment explanation
Indices: 45069--45098 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45059 TAATAGTTTA
*
45069 TTATTTTATTATATT
1 TTATTTTACTATATT
45084 TTATTTTACTATATT
1 TTATTTTACTATATT
45099 ACTTTTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTACTATATT
Found at i:62610 original size:15 final size:15
Alignment explanation
Indices: 62580--62626 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
62570 TTTTCTATCA
* *
62580 AACAACAACAACAAC
1 AACAACAATAATAAC
*
62595 AACAATAATAATAAC
1 AACAACAATAATAAC
*
62610 AATAACAATAATAAC
1 AACAACAATAATAAC
62625 AA
1 AA
62627 TAGCACGAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (15 bp):
AACAACAATAATAAC
Found at i:62613 original size:9 final size:9
Alignment explanation
Indices: 62595--62628 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
62585 CAACAACAAC
62595 AACAATAAT
1 AACAATAAT
* *
62604 AATAACAAT
1 AACAATAAT
62613 AACAATAAT
1 AACAATAAT
62622 AACAATA
1 AACAATA
62629 GCACGAACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (9 bp):
AACAATAAT
Found at i:62616 original size:18 final size:18
Alignment explanation
Indices: 62589--62623 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
62579 AAACAACAAC
62589 AACAACAACAATAATAAT
1 AACAACAACAATAATAAT
*
62607 AACAATAACAATAATAA
1 AACAACAACAATAATAA
62624 CAATAGCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (18 bp):
AACAACAACAATAATAAT
Found at i:66722 original size:24 final size:23
Alignment explanation
Indices: 66689--66737 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
66679 TTTATTAGTT
*
66689 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
* *
66713 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAAAATTATAA
66736 TA
1 TA
66738 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:70399 original size:40 final size:42
Alignment explanation
Indices: 70326--70418 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 42
70316 TATTAATGGT
* * * *
70326 GTGGCGTTTTTTGATAAACGCCGCAATATTATT-G-TATCTA
1 GTGGCGTTTTATGACAAACGCCGCAATATTATTGGACATATA
*
70366 GTGGCGTTTTATGTACAAACGCTGCAATA-TATTGGACATATA
1 GTGGCGTTTTATG-ACAAACGCCGCAATATTATTGGACATATA
70408 GTGGCGTTTTA
1 GTGGCGTTTTA
70419 ACAAAAAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
40 16 0.36
41 14 0.31
42 15 0.33
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (42 bp):
GTGGCGTTTTATGACAAACGCCGCAATATTATTGGACATATA
Found at i:70648 original size:39 final size:39
Alignment explanation
Indices: 70545--70648 Score: 95
Period size: 39 Copynumber: 2.6 Consensus size: 39
70535 GTTTTTAGAC
* * * *
70545 AAACGCCACAATAGTATTAATCAATAGTGGCGTTTTTTTAT
1 AAACGCCGCAAAAGTATAAAT--ATAGTGGCGTTTTCTTAT
* **
70586 AAACGCCGTAAAAGTATGTATATAGTGGCGTTTTGCTTA-
1 AAACGCCGCAAAAGTATAAATATAGTGGCGTTTT-CTTAT
70625 AAACGCCGCAAAATGT-TAAATATA
1 AAACGCCGCAAAA-GTATAAATATA
70649 TGGTCCTCCT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
39 31 0.60
40 5 0.10
41 16 0.31
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (39 bp):
AAACGCCGCAAAAGTATAAATATAGTGGCGTTTTCTTAT
Done.