Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003323.1 Hibiscus syriacus cultivar Beakdansim tig00007001_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: 66579
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4751 original size:32 final size:32
Alignment explanation
Indices: 4691--4751 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4681 TGACATGATT
* *
4691 GAAATTAAAATCAAAATTTAATGTTATAATTA
1 GAAAATAAAATCAAAATTTAATGATATAATTA
4723 GAAAATAAAAT-AAAATTTGAATGATATAA
1 GAAAATAAAATCAAAATTT-AATGATATAA
4752 ACAATGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (32 bp):
GAAAATAAAATCAAAATTTAATGATATAATTA
Found at i:4846 original size:80 final size:82
Alignment explanation
Indices: 4683--4846 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 82
4673 TAGCACAATG
* * *
4683 ACATGATTGAAATTAAAATCAAAATTTAATGTTATAATTAGAAAATAAAATAAAATTTGAATGAT
1 ACATAATTGAAATTAAAATCAAAATTTAATGCTACAATTA-AAAATAAAATAAAATTTGAATGAT
4748 ATAAACAATGTATCATCT
65 ATAAACAATGTATCATCT
* * * * *
4766 ACATAATTGAAGTTAAAATTAAAATTTAATGCTACAATT-AAAA-AAATTGAAGTTTGAATGATA
1 ACATAATTGAAATTAAAATCAAAATTTAATGCTACAATTAAAAATAAAATAAAATTTGAATGATA
4829 TAAACAATGTATCATCT
66 TAAACAATGTATCATCT
4846 A
1 A
4847 AAATTCAACG
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
80 35 0.48
81 4 0.05
83 34 0.47
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.34
Consensus pattern (82 bp):
ACATAATTGAAATTAAAATCAAAATTTAATGCTACAATTAAAAATAAAATAAAATTTGAATGATA
TAAACAATGTATCATCT
Found at i:10354 original size:12 final size:12
Alignment explanation
Indices: 10337--10363 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10327 AGTAAAATAC
10337 TCACTAACATTA
1 TCACTAACATTA
10349 TCACTAACATTA
1 TCACTAACATTA
10361 TCA
1 TCA
10364 ACTTTAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (12 bp):
TCACTAACATTA
Found at i:11696 original size:20 final size:21
Alignment explanation
Indices: 11663--11703 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
11653 ATAATTCAAA
*
11663 ATATTTTATAAATTTATTATT
1 ATATTTAATAAATTTATTATT
11684 ATATTTAAT-AATTTATTATT
1 ATATTTAATAAATTTATTATT
11704 TTTAGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTAATAAATTTATTATT
Found at i:13072 original size:23 final size:23
Alignment explanation
Indices: 13046--13094 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
13036 AAATTATGTA
13046 AAGTGTAAACCGTATCACATATG
1 AAGTGTAAACCGTATCACATATG
13069 AAGTGTAAACCGTATCACATATG
1 AAGTGTAAACCGTATCACATATG
13092 AAG
1 AAG
13095 GGTTGGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (23 bp):
AAGTGTAAACCGTATCACATATG
Found at i:13247 original size:67 final size:67
Alignment explanation
Indices: 13139--13290 Score: 207
Period size: 67 Copynumber: 2.3 Consensus size: 67
13129 ATTCATATAA
* * * * *
13139 GAATATTATTACCTCCATTTGGTAATGTACGATTACTAATAGTGAATTTTTTA-AGATATATTAT
1 GAATATCATTACCTCCATATGGTAATGTAAGATTACCAATAGTGAATTTTTTAGAG-TATATTAC
13203 TGG
65 TGG
* * *
13206 GAATATCATTACCTCCCTATGGTAATGTAAGATTACCAATAGTGGATTTTTTGGAGTATATTACT
1 GAATATCATTACCTCCATATGGTAATGTAAGATTACCAATAGTGAATTTTTTAGAGTATATTACT
13271 GG
66 GG
*
13273 GAATGTCATTACCTCCAT
1 GAATATCATTACCTCCAT
13291 TAAGTATTGT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 72 0.97
68 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (67 bp):
GAATATCATTACCTCCATATGGTAATGTAAGATTACCAATAGTGAATTTTTTAGAGTATATTACT
GG
Found at i:25151 original size:42 final size:43
Alignment explanation
Indices: 25092--25201 Score: 213
Period size: 42 Copynumber: 2.6 Consensus size: 43
25082 TAGTTTGCAA
25092 CTTCAGAAATATCAGGTTCATCATACACTTCCTA-TTTCTTAT
1 CTTCAGAAATATCAGGTTCATCATACACTTCCTATTTTCTTAT
25134 CTTCAGAAATATCAGGTTCATCATACACTTCCTATTTTCTTAT
1 CTTCAGAAATATCAGGTTCATCATACACTTCCTATTTTCTTAT
25177 CTTCAGAAATATCAGGTTCATCATA
1 CTTCAGAAATATCAGGTTCATCATA
25202 TTATTTATGT
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
42 34 0.51
43 33 0.49
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (43 bp):
CTTCAGAAATATCAGGTTCATCATACACTTCCTATTTTCTTAT
Found at i:29203 original size:2 final size:2
Alignment explanation
Indices: 29196--29235 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29186 TGCTCAAAGA
29196 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
29236 GGAAAATTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32482 original size:60 final size:60
Alignment explanation
Indices: 32428--32547 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
32418 TGGTCCTCTG
32428 ACTATA-AGATAATGCTTTGTTAAATCACCAGACTATTAAAAGTTACAAAATGGTCCCCCA
1 ACTATAGAGA-AATGCTTTGTTAAATCACCAGACTATTAAAAGTTACAAAATGGTCCCCCA
* * * * ** * *
32488 ACTATAGAGAATTGCTTTGTTGAGTCTCTTGACTATTGAAAGTTACAAAATGGTCACCCA
1 ACTATAGAGAAATGCTTTGTTAAATCACCAGACTATTAAAAGTTACAAAATGGTCCCCCA
32548 TTTATTCATT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 48 0.94
61 3 0.06
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (60 bp):
ACTATAGAGAAATGCTTTGTTAAATCACCAGACTATTAAAAGTTACAAAATGGTCCCCCA
Found at i:32885 original size:60 final size:60
Alignment explanation
Indices: 32765--32897 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
32755 TCAAGTGACT
* * * *
32765 ATTTTGTAACTTTTAATAGTCGAGGGACTCATCAAAGCAACTCTCTATAATCGAGAGACC
1 ATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAAATCTCTATAATCGAGAGACC
* * * *
32825 ATTTTATAACTTTTAATAGTCG-GGAGACTCAACAAAATAATATC-CTATTATCGGGGGACC
1 ATTTTATAACTTTTAATAGTCGAGG-GACTCAACAAAACAA-ATCTCTATAATCGAGAGACC
32885 ATTTGTAT-ACTTT
1 ATTT-TATAACTTT
32898 ACCCTGAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
59 2 0.03
60 55 0.89
61 5 0.08
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAAATCTCTATAATCGAGAGACC
Found at i:49533 original size:29 final size:26
Alignment explanation
Indices: 49464--49525 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
49454 CTGTAAAAGC
49464 TAGATTGAATAATACCTCTTCTTTTT
1 TAGATTGAATAATACCTCTTCTTTTT
49490 TAGATTGAATAATACCTCTTCTTTTT
1 TAGATTGAATAATACCTCTTCTTTTT
49516 TA-ATATGAAT
1 TAGAT-TGAAT
49526 GGGAATACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 2 0.06
26 33 0.94
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (26 bp):
TAGATTGAATAATACCTCTTCTTTTT
Done.