Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001214.1 Hibiscus syriacus cultivar Beakdansim tig00002396_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: 15952
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:52 original size:14 final size:14
Alignment explanation
Indices: 33--59 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23 TACATTGCGT
33 GTCATTGAAGCCCG
1 GTCATTGAAGCCCG
47 GTCATTGAAGCCC
1 GTCATTGAAGCCC
60 CTGTCATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (14 bp):
GTCATTGAAGCCCG
Found at i:5940 original size:3 final size:3
Alignment explanation
Indices: 5934--5995 Score: 74
Period size: 3 Copynumber: 21.3 Consensus size: 3
5924 ATTAATAAAG
* * * *
5934 TAA TAA TAA TAA GAA TAA TAA -AG TAA AAA TAA TAA TAA TAA TAA -AG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5980 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
5996 TAAAATCCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5969 original size:17 final size:19
Alignment explanation
Indices: 5934--5995 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 19
5924 ATTAATAAAG
* *
5934 TAATAAT-AATAAGAATAA
1 TAATAATAAAGAATAATAA
*
5952 TAA-AGTAAA-AATAATAA
1 TAATAATAAAGAATAATAA
5969 TAATAATAAAGTAATAATAA
1 TAATAATAAAG-AATAATAA
5989 TAATAAT
1 TAATAAT
5996 TAAAATCCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.32
18 10 0.27
20 15 0.41
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAATAATAAAGAATAATAA
Found at i:5992 original size:23 final size:23
Alignment explanation
Indices: 5926--5995 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
5916 AAAATATTAT
*
5926 TAATAAAGTAATAATAATAAGAA
1 TAATAAAGTAATAATAATAATAA
*
5949 TAATAAAGTAAAAATAATAATAA
1 TAATAAAGTAATAATAATAATAA
5972 TAATAAAGTAATAATAATAATAA
1 TAATAAAGTAATAATAATAATAA
5995 T
1 T
5996 TAAAATCCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (23 bp):
TAATAAAGTAATAATAATAATAA
Found at i:13553 original size:3 final size:3
Alignment explanation
Indices: 13545--13681 Score: 122
Period size: 3 Copynumber: 45.0 Consensus size: 3
13535 TAAACCCCAA
13545 TCT TCT TCT TCT TCT TCCT TCT T-T CTCT TCT T-T TCT TCT T-T T-T
1 TCT TCT TCT TCT TCT T-CT TCT TCT -TCT TCT TCT TCT TCT TCT TCT
* * * * *
13588 TCT TCTT TCTT TCT TCT TTT TCT TCT TTT TTT TTT TCT TCT T-T TTT
1 TCT TC-T TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
13634 TCT TCT TCT TCTT TCT TCT TCT TCT TCTT TCAC TCT TCT TCT TCT TCT
1 TCT TCT TCT TC-T TCT TCT TCT TCT TC-T TC-T TCT TCT TCT TCT TCT
13682 CTCACATCCA
Statistics
Matches: 117, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
2 9 0.08
3 89 0.76
4 19 0.16
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:13581 original size:30 final size:30
Alignment explanation
Indices: 13547--13681 Score: 144
Period size: 30 Copynumber: 4.6 Consensus size: 30
13537 AACCCCAATC
13547 TTCTTCTTCTTCTTCCTTCTTTC-TCTTCTT
1 TTCTTCTTCTTCTT-CTTCTTTCTTCTTCTT
13577 TTCTTCTT-TT-TTCTTCTTTCTTTCTTCTTT
1 TTCTTCTTCTTCTTCTTCTTTC-TTCTTC-TT
*
13607 TTCTTCTT-TT-TT-TT-TTTCTTCTTTTT
1 TTCTTCTTCTTCTTCTTCTTTCTTCTTCTT
13633 TTCTTCTTCTTCTTTCTTC-TTCTTCTTC-T
1 TTCTTCTTCTTC-TTCTTCTTTCTTCTTCTT
*
13662 TTCACTCTTCTTCTTCTTCT
1 TTC-TTCTTCTTCTTCTTCT
13682 CTCACATCCA
Statistics
Matches: 92, Mismatches: 3, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
26 10 0.11
27 15 0.16
28 6 0.07
29 21 0.23
30 40 0.43
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (30 bp):
TTCTTCTTCTTCTTCTTCTTTCTTCTTCTT
Found at i:13686 original size:20 final size:19
Alignment explanation
Indices: 13633--13686 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
13623 TCTTCTTTTT
**
13633 TTCTTCTTCTTCTTTCTTC
1 TTCTTCTTCTTCACTCTTC
13652 TTCTTCTTCTTTCACTCTTC
1 TTCTTCTTC-TTCACTCTTC
13672 TTCTTCTTCTCTCAC
1 TTCTTCTTCT-TCAC
13687 ATCCATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.61
Consensus pattern (19 bp):
TTCTTCTTCTTCACTCTTC
Found at i:15341 original size:20 final size:20
Alignment explanation
Indices: 15316--15353 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15306 GACCCCGAGT
15316 CGATCCGAGCCGTGCCGTAC
1 CGATCCGAGCCGTGCCGTAC
15336 CGATCCGAGCCGTGCCGT
1 CGATCCGAGCCGTGCCGT
15354 GCCATGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.39, G:0.32, T:0.16
Consensus pattern (20 bp):
CGATCCGAGCCGTGCCGTAC
Done.