Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005969.1 Hibiscus syriacus cultivar Beakdansim tig00014027_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: 67756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14744 original size:12 final size:12
Alignment explanation
Indices: 14729--14783 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
14719 GTTATTTAAA
*
14729 CGGGTATTGAGC
1 CGGGTATTGGGC
*
14741 CGGGTATTGGGT
1 CGGGTATTGGGC
14753 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
14765 CGAGAATCGGGC
1 CGGGTATTGGGC
14777 CGGGTAT
1 CGGGTAT
14784 ATATATATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.15, C:0.16, G:0.45, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:14831 original size:33 final size:33
Alignment explanation
Indices: 14791--14856 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14781 TATATATATA
14791 TATTTAAATTAAATATATAAAAT-ATATATTTTT
1 TATTTAAATTAAATATATAAAATAAT-TATTTTT
* *
14824 TATTTAAATTAAATTTATTAAATAATTATTTTT
1 TATTTAAATTAAATATATAAAATAATTATTTTT
14857 AATATTTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTTAAATTAAATATATAAAATAATTATTTTT
Found at i:14894 original size:13 final size:12
Alignment explanation
Indices: 14863--14899 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
14853 TTTTAATATT
*
14863 TATCGGGTCGGG
1 TATCGGGGCGGG
14875 TATCGGGGCGGG
1 TATCGGGGCGGG
14887 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
14900 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:25344 original size:20 final size:20
Alignment explanation
Indices: 25319--25389 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
25309 GGTAACAAAT
25319 TTGACAAAACCGATTGGAAA
1 TTGACAAAACCGATTGGAAA
*
25339 TTGACAAAATCGATTGGAAA
1 TTGACAAAACCGATTGGAAA
*
25359 TTGACAAAACCAATT-GAAA
1 TTGACAAAACCGATTGGAAA
25378 TTTGACAAAACC
1 -TTGACAAAACC
25390 AGTTTCAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 4 0.09
20 43 0.91
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (20 bp):
TTGACAAAACCGATTGGAAA
Found at i:25399 original size:20 final size:20
Alignment explanation
Indices: 25270--25407 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 20
25260 AATATAACAG
* * *
25270 GTTGAAATTTGAGAAATCCA
1 GTTGCAATTTGACAAAACCA
* *
25290 GTTTCAATTTGACAAAA-GA
1 GTTGCAATTTGACAAAACCA
**
25309 GGTAACAAATTTGACAAAACC-
1 -GTTGC-AATTTGACAAAACCA
* * *
25330 GATTGGAAATTGACAAAATC-
1 G-TTGCAATTTGACAAAACCA
* *
25350 GATTGGAAATTGACAAAACCA
1 G-TTGCAATTTGACAAAACCA
* *
25371 ATTGAAATTTGACAAAACCA
1 GTTGCAATTTGACAAAACCA
* *
25391 GTTTCAATTTGAGAAAA
1 GTTGCAATTTGACAAAA
25408 TTGATAAAGA
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.01
20 78 0.85
21 13 0.14
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (20 bp):
GTTGCAATTTGACAAAACCA
Found at i:36119 original size:3 final size:3
Alignment explanation
Indices: 36111--36139 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
36101 ATCACCGAGC
36111 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36140 TCCAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41774 original size:16 final size:16
Alignment explanation
Indices: 41723--41775 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
41713 ATTTATAGTC
*
41723 TAAAATATCTTAAAGA
1 TAAAATATCTTAAAAA
* * *
41739 TAGAAGAAATATTCAAAA
1 TA-AA-ATATCTTAAAAA
41757 TAAAATATCTTAAAAA
1 TAAAATATCTTAAAAA
41773 TAA
1 TAA
41776 TCCAAAAGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (16 bp):
TAAAATATCTTAAAAA
Found at i:52593 original size:12 final size:12
Alignment explanation
Indices: 52578--52603 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52568 GATTATCAAT
52578 AAAAATATCTAA
1 AAAAATATCTAA
52590 AAAAATATCTAA
1 AAAAATATCTAA
52602 AA
1 AA
52604 TATAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATATCTAA
Found at i:59811 original size:2 final size:2
Alignment explanation
Indices: 59804--59831 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59794 TATTATTTTG
59804 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
59832 TTGGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.