Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021745.1 Corchorus olitorius cultivar O-4 contig21778, 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: 9356
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2414 original size:45 final size:45
Alignment explanation
Indices: 2350--2464 Score: 194
Period size: 45 Copynumber: 2.6 Consensus size: 45
2340 GGCCATGGCT
* *
2350 CGGCCATCATCGAGCCATGCCGAGGTTGAGTGCCCACGAGACTGC
1 CGGCCATCATCGAGCCATGCCGAGGTCGAGTGCCCACGAGACAGC
*
2395 CGGCCATCATCGAGCCATGCCGAGGTCGAGTGCCCGCGAGACAGC
1 CGGCCATCATCGAGCCATGCCGAGGTCGAGTGCCCACGAGACAGC
*
2440 AGGCCATCATCGAGCCATGCCGAGG
1 CGGCCATCATCGAGCCATGCCGAGG
2465 CCATGGCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (45 bp):
CGGCCATCATCGAGCCATGCCGAGGTCGAGTGCCCACGAGACAGC
Found at i:3925 original size:21 final size:21
Alignment explanation
Indices: 3882--3925 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3872 CCAATTTAGG
*
3882 TTTAGATTTAAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
3903 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
3924 TT
1 TT
3926 ATGCATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:9066 original size:303 final size:302
Alignment explanation
Indices: 8515--9119 Score: 865
Period size: 303 Copynumber: 2.0 Consensus size: 302
8505 GCTTCTCAAG
* *
8515 CAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTTTGTACTCTACTTT
1 CAGAAGAAGATGGTGAAATGTCGACGACTGAGGCACAGGTGTTCCAC-TTTTTGTACTCTACTTC
* * *
8580 GCAATTGCTGACTCACTTAAGTTTTTATATATAGGGTCTTCAAGAGTCGTCTTAACAAATGCATC
65 GCAATTGCTGACTCACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCGTCTTAACAAATGCATC
* * *
8645 GTGACAAAATTTACCCAATAACTTGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTGA
130 GTGACAAAATTTACCCAATAACATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGA
* * * * * *
8710 ATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCCATTTTTGTTTTGCAATTATTTTCCTTA
195 ATATACTTGTGAAAACCTCCCTAGAACAGGCCAGCTCCATTTTTGTCTTGCAATTATTTTCCTTA
* *
8775 ATAATCAAGTCGGGGCTTTTC-GCAGGTGAAATGACTCCGCTTA
260 ATAATCAAGTCGGGG-TTTTCTGCAGCTGAAACGACTCCGCTTA
* * *
8818 CAGAAGAAGATGGTGCAATGTCGACGACTGAGGCACATGTGTTCCA-TTTTTGAATACTCTTCTT
1 CAGAAGAAGATGGTGAAATGTCGACGACTGAGGCACAGGTGTTCCACTTTTTG--TACTCTACTT
* ** *
8882 CGCAATTGTTGACTTGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
64 CGCAATTGCTGACTCACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCGTCTTAACAAATGCAT
* * * * *
8947 CGTGACAAACTTTACCGAATACCATGAGTTCATCGCAACACTTCTTTGTGACAGCTCCGGTATAG
129 CGTGACAAAATTTACCCAATAACATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAG
* *
9012 AATATACTTTTGAAAACCTCCCTAGAACAGGCCAGACT-CATTTTTGTCTTGCAATTATTTTGCT
194 AATATACTTGTGAAAACCTCCCTAGAACAGGCCAG-CTCCATTTTTGTCTTGCAATTATTTTCCT
*
9076 TAATAATCAAGTCTGGGTTTTCTGCAGCTGAAACGACTCCGCTT
258 TAATAATCAAGTCGGGGTTTTCTGCAGCTGAAACGACTCCGCTT
9120 GTTAAAACAA
Statistics
Matches: 267, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
301 6 0.02
302 5 0.02
303 255 0.96
304 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (302 bp):
CAGAAGAAGATGGTGAAATGTCGACGACTGAGGCACAGGTGTTCCACTTTTTGTACTCTACTTCG
CAATTGCTGACTCACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCGTCTTAACAAATGCATCG
TGACAAAATTTACCCAATAACATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAA
TATACTTGTGAAAACCTCCCTAGAACAGGCCAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAA
TAATCAAGTCGGGGTTTTCTGCAGCTGAAACGACTCCGCTTA
Done.