Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008792.1 Hibiscus syriacus cultivar Beakdansim tig00111936_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: 28534
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Found at i:8553 original size:16 final size:16
Alignment explanation
Indices: 8528--8570 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
8518 AACGTCTTTT
8528 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
8544 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
8561 ACAAAAATTT
1 AAAAAAATTT
8571 GGTCTGCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:11337 original size:25 final size:25
Alignment explanation
Indices: 11240--11338 Score: 157
Period size: 25 Copynumber: 4.0 Consensus size: 25
11230 AGTTAGGGGA
*
11240 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
11264 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
11289 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
11314 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
11339 GGGTTGGTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.13
25 61 0.87
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:11511 original size:15 final size:15
Alignment explanation
Indices: 11466--11511 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
11456 AATATATAAT
11466 TTAATAATAATAATAA
1 TTAATAATAATAA-AA
11482 -TAATAATTAATAAAA
1 TTAATAA-TAATAAAA
11497 TTAAATAAT-ATAAAA
1 TT-AATAATAATAAAA
11512 AAGACCCGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 14 0.52
16 8 0.30
17 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAATAATAATAAAA
Found at i:11849 original size:3 final size:3
Alignment explanation
Indices: 11841--11868 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11831 AGTGTAGTTT
11841 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11869 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16397 original size:21 final size:21
Alignment explanation
Indices: 16367--16420 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
16357 TGTTGAGCCT
*
16367 GTCGGGTTACATCCCAAGCTC
1 GTCGGTTTACATCCCAAGCTC
** *
16388 GTCGGTTTACATGTCAAGCTT
1 GTCGGTTTACATCCCAAGCTC
*
16409 GTTGGTTTACAT
1 GTCGGTTTACAT
16421 TTCGAGCACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (21 bp):
GTCGGTTTACATCCCAAGCTC
Found at i:24197 original size:22 final size:20
Alignment explanation
Indices: 24172--24211 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
24162 ATTTCTCTTG
24172 ATATCATGTATCTCTATCACTC
1 ATATCATGT-TCTC-ATCACTC
24194 ATATCATGTTCTCATCAC
1 ATATCATGTTCTCATCAC
24212 ATGTCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATCATGTTCTCATCACTC
Found at i:24221 original size:11 final size:12
Alignment explanation
Indices: 24207--24240 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
24197 TCATGTTCTC
*
24207 ATCACATGTCA-
1 ATCACATATCAT
24218 ATCACATATCAT
1 ATCACATATCAT
24230 ATCACATATCA
1 ATCACATATCA
24241 CATGAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
ATCACATATCAT
Found at i:24625 original size:12 final size:12
Alignment explanation
Indices: 24608--24632 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24598 TATTGCTGGG
24608 ATGCATCGATGC
1 ATGCATCGATGC
24620 ATGCATCGATGC
1 ATGCATCGATGC
24632 A
1 A
24633 CCAATTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGCATCGATGC
Done.