Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008821.1 Hibiscus syriacus cultivar Beakdansim tig00111989_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: 1271541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1271037 original size:14 final size:14
Alignment explanation
Indices: 1271018--1271107 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1271008 TTGAAATGAA
1271018 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1271032 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1271049 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1271065 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1271084 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1271098 AATCGCAACG
1 AATCGCAACG
1271108 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1271055 original size:33 final size:33
Alignment explanation
Indices: 1271010--1271124 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1271000 TCTTTTGGTT
1271010 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1271043 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1271076 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1271109 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1271125 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1271056 original size:19 final size:18
Alignment explanation
Indices: 1271017--1271129 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1271007 GTTGAAATGA
1271017 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1271032 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1271049 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1271065 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1271082 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1271098 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1271115 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1271130 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1271160 original size:14 final size:14
Alignment explanation
Indices: 1271141--1271195 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1271131 TTTGGTTTCG
1271141 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1271155 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1271174 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1271188 CGTTGCGA
1 CGTTGCGA
1271196 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1271358 original size:33 final size:33
Alignment explanation
Indices: 1271316--1271386 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1271306 AATACTAACT
*
1271316 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1271349 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1271382 TGAAA
1 TGAAA
1271387 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Done.