Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002881.1 Hibiscus syriacus cultivar Beakdansim tig00005939_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: 1746118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1740658 original size:9 final size:9
Alignment explanation
Indices: 1740608--1740672 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
1740598 TCTTTGCATG
1740608 TTTTTTTGTC
1 TTTTTTT-TC
* *
1740618 CTTTTTTCC
1 TTTTTTTTC
1740627 TTTGTTTTT-
1 TTT-TTTTTC
*
1740636 TCTTTTGTTC
1 T-TTTTTTTC
*
1740646 TTTTTTTTG
1 TTTTTTTTC
1740655 TTTTTTTTC
1 TTTTTTTTC
1740664 TTTATTTTT
1 TTT-TTTTT
1740673 TTCCCTTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
9 25 0.58
10 18 0.42
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1740662 original size:39 final size:39
Alignment explanation
Indices: 1740608--1740693 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
1740598 TCTTTGCATG
*
1740608 TTTTTTTGTCCTTTTTTCCTTT-GTTTTTT-CTTTTGTTCT
1 TTTTTTTG-CCTTTTTT-CTTTAGTTTTTTCCCTTTGTTCT
** *
1740647 TTTTTTTGTTTTTTTTCTTTATTTTTTTCCCTTTGTTCT
1 TTTTTTTGCCTTTTTTCTTTAGTTTTTTCCCTTTGTTCT
1740686 TTGTTTTT
1 TT-TTTTT
1740694 CTTTGCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 4 0.10
38 12 0.30
39 19 0.47
40 5 0.12
ACGTcount: A:0.01, C:0.13, G:0.07, T:0.79
Consensus pattern (39 bp):
TTTTTTTGCCTTTTTTCTTTAGTTTTTTCCCTTTGTTCT
Found at i:1741326 original size:20 final size:20
Alignment explanation
Indices: 1741287--1741327 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1741277 GGATAAATGC
*
1741287 AATGTTTCAAGGTCGGAAAG
1 AATGTTTCAAGGTCGCAAAG
*
1741307 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCGCAAAG
1741327 A
1 A
1741328 GAGGGAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (20 bp):
AATGTTTCAAGGTCGCAAAG
Found at i:1742747 original size:32 final size:32
Alignment explanation
Indices: 1742706--1742767 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1742696 ATGAAAAATG
* *
1742706 ACACAAACAAAATAAACGAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
*
1742738 ACACAAACAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
1742768 ACAGGTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
Found at i:1743338 original size:19 final size:19
Alignment explanation
Indices: 1743314--1743353 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1743304 TCATACGAAG
1743314 AATATATTCTTACGAGAGT
1 AATATATTCTTACGAGAGT
1743333 AATATATTCTTACGAGAGT
1 AATATATTCTTACGAGAGT
1743352 AA
1 AA
1743354 AGCATTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
AATATATTCTTACGAGAGT
Found at i:1744236 original size:23 final size:23
Alignment explanation
Indices: 1744209--1744256 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1744199 CCGTTAGACA
1744209 GGGGGAATCGGTACCCCCTGGGG
1 GGGGGAATCGGTACCCCCTGGGG
*
1744232 GGGGGAATCTGTACCCCCTGGGG
1 GGGGGAATCGGTACCCCCTGGGG
1744255 GG
1 GG
1744257 AATCTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.48, T:0.15
Consensus pattern (23 bp):
GGGGGAATCGGTACCCCCTGGGG
Found at i:1744256 original size:20 final size:21
Alignment explanation
Indices: 1744209--1744262 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 21
1744199 CCGTTAGACA
*
1744209 GGGGGAATCGGTACCCCCTGGGG
1 GGGGGAATCTGTACCCCCT--GG
1744232 GGGGGAATCTGTACCCCCT-G
1 GGGGGAATCTGTACCCCCTGG
1744252 GGGGGAATCTG
1 GGGGGAATCTG
1744263 ATTTTTCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.40
23 18 0.60
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:1745724 original size:19 final size:20
Alignment explanation
Indices: 1745681--1745728 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1745671 TCTAAATCCT
*
1745681 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1745701 GTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1745720 TTTTCAAAA
1 TTTTCAAAA
1745729 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Done.