Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009446.1 Corchorus capsularis cultivar CVL-1 contig09467, 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: 44257
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3674 original size:13 final size:13
Alignment explanation
Indices: 3656--3685 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3646 AAAGACAAGT
*
3656 AGTTACTTACGCA
1 AGTTACTTACACA
3669 AGTTACTTACACA
1 AGTTACTTACACA
3682 AGTT
1 AGTT
3686 TGTGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (13 bp):
AGTTACTTACACA
Found at i:6411 original size:29 final size:29
Alignment explanation
Indices: 6327--6411 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
6317 TTAATGCCCT
* *
6327 TTTTGCCTC-CTGAACTTGTATGATTTTGACG
1 TTTTGCC-CACTGAACTTGTA--ATTTGGACA
*
6358 TTTTGCCCACTAAACTT-TAATTTTGGACA
1 TTTTGCCCACTGAACTTGTAA-TTTGGACA
*
6387 TTTTGCCCATTGAACTTGTAATTTG
1 TTTTGCCCACTGAACTTGTAATTTG
6412 AAGTCATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.02
29 25 0.54
30 6 0.13
31 14 0.30
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (29 bp):
TTTTGCCCACTGAACTTGTAATTTGGACA
Found at i:9164 original size:13 final size:13
Alignment explanation
Indices: 9146--9170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9136 ACTTAGATCT
9146 CTCTCCATATAAG
1 CTCTCCATATAAG
9159 CTCTCCATATAA
1 CTCTCCATATAA
9171 AGAGAGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (13 bp):
CTCTCCATATAAG
Found at i:16058 original size:30 final size:30
Alignment explanation
Indices: 16022--16084 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
16012 TTCAAGACCC
*
16022 GGAACACCCACTGGACGCCCTACATTGAGT
1 GGAACACCCACGGGACGCCCTACATTGAGT
16052 GGAACACCCACGGGACGCCCTACATTGAGT
1 GGAACACCCACGGGACGCCCTACATTGAGT
16082 GGA
1 GGA
16085 GCATCTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (30 bp):
GGAACACCCACGGGACGCCCTACATTGAGT
Found at i:16178 original size:21 final size:21
Alignment explanation
Indices: 16154--16202 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
16144 GCCCTCAATC
*
16154 TCTGCAACCAAGCCTGTAACT-
1 TCTGCAACAAAGCCTGTAA-TA
**
16175 TCTGCTGCAAAGCCTGTAATA
1 TCTGCAACAAAGCCTGTAATA
16196 TCTGCAA
1 TCTGCAA
16203 ATAGGTCTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
TCTGCAACAAAGCCTGTAATA
Found at i:30893 original size:19 final size:19
Alignment explanation
Indices: 30842--30894 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
30832 AAAGAAATAA
30842 TTGTTTTTTGTTT-TTTGTT
1 TTGTTTTTT-TTTGTTTGTT
* *
30861 TTGCTTTGTTTTGTTTG-T
1 TTGTTTTTTTTTGTTTGTT
30879 TTGTTTTTTTATTGTT
1 TTGTTTTTTT-TTGTT
30895 GTTAAAGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.02, C:0.02, G:0.17, T:0.79
Consensus pattern (19 bp):
TTGTTTTTTTTTGTTTGTT
Found at i:30896 original size:22 final size:21
Alignment explanation
Indices: 30847--30897 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
30837 AATAATTGTT
*
30847 TTTTGTTTTTTGTTTTGCTTTG
1 TTTTGTTTTTTGTTTT-CTTTA
30869 TTTTGTTTGTTTGTTTT-TTTA
1 TTTTGTTT-TTTGTTTTCTTTA
30890 TTGTTGTT
1 TT-TTGTT
30898 AAAGATCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 13 0.50
23 8 0.31
ACGTcount: A:0.02, C:0.02, G:0.18, T:0.78
Consensus pattern (21 bp):
TTTTGTTTTTTGTTTTCTTTA
Found at i:33179 original size:18 final size:17
Alignment explanation
Indices: 33149--33182 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33139 CGTAACATTA
33149 TTAAATTGAATCAAACT
1 TTAAATTGAATCAAACT
*
33166 TTAACATTGGATCAAAC
1 TTAA-ATTGAATCAAAC
33183 GAGAAAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (17 bp):
TTAAATTGAATCAAACT
Done.