Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018358.1 Corchorus olitorius cultivar O-4 contig18391, 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: 19935
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2541 original size:27 final size:27
Alignment explanation
Indices: 2480--2541 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
2470 GGAGAGTTTG
* * * * *
2480 TGGGTTTAAGAGGGGTTTTTGAGTTGT
1 TGGGTTTGAGAAGGGTCTTTAAGTTGC
2507 TGGGTTTGAGAAGGGTCTTTAAGTTGC
1 TGGGTTTGAGAAGGGTCTTTAAGTTGC
2534 TGGGTTTG
1 TGGGTTTG
2542 GGACACAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.15, C:0.03, G:0.40, T:0.42
Consensus pattern (27 bp):
TGGGTTTGAGAAGGGTCTTTAAGTTGC
Found at i:19612 original size:330 final size:332
Alignment explanation
Indices: 18989--19802 Score: 1164
Period size: 330 Copynumber: 2.5 Consensus size: 332
18979 CCATTGCCCA
* * * * * *
18989 TTCAAGGCATCTTGACGCCAAAAATGATGGAAAACTGAGCCGGCACCCCGCAATGCGTTTTTAGC
1 TTCAAGGAATCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAAGCGTTTTTAGC
* * * ** *
19054 CAAAAACTGTGATGGTTAGTATACGATTTTAGCTAAAATTTTGCAAAGAATAACCGTG-AAAATA
66 CAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCACGAAAAATT
* * *
19118 TTTCCTCAATTTTTGGATAAAATACTCATATAATTTATATAATTTAACGCCAAAAATATTGGACG
131 TTTCCTCAATTTTTGGATAAAATACTCATATAATATATATAATTTAACACCAAAAAGATTGGACG
*
19183 ACTTGTCACGCTTTTAATATCGTTTTTCAGATTTCTTCTAAATTAATTCTAATTAAATCGAAACA
196 ACTTGTCACGCTTTTAATATCGTTTTTCAAATTTCTTCTAAATTAATTCTAATTAAATCGAAACA
* * * *
19248 AGATTCAAATGCTTGTAAAACCAAATCGTTAAATGCAAGGTGACAAAGTTTTTATTAGATCAATA
261 AGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAGGAGACAAAGTTTTTATTAGATCAATA
19313 TAGATAG
326 TAGATAG
* * *
19320 TTCAAGGAATCTTGACGCTAAAATTCATGCAAAACTGAGCCGGGACCCCGAAAAGCATTTTTAGC
1 TTCAAGGAATCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAAGCGTTTTTAGC
19385 CAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCACGAAAAATT
66 CAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCACGAAAAATT
*
19450 TTTCCTCAATTTTTGGATAAAATACTCATA-AA-ATATATAATTTAACACCAAAAAGATTGGAGG
131 TTTCCTCAATTTTTGGATAAAATACTCATATAATATATATAATTTAACACCAAAAAGATTGGACG
* * *
19513 ACTTTTCACGCTTTTAATATCGTTTTTCATAATTT-TTCTGAATTAATTCTAATTAAATTGAAAC
196 ACTTGTCACGCTTTTAATATCGTTTTTCA-AATTTCTTCTAAATTAATTCTAATTAAATCGAAAC
* * * * * *
19577 AAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGAGGCTAATTTTTTATTTGATGAAT
260 AAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAGGAGACAAAGTTTTTATTAGATCAAT
*
19642 ATAGATAT
325 ATAGATAG
* * * * * *
19650 TTCAAGCAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCAGAAACGCGTTTTTAGC
1 TTCAAGGAATCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAAGCGTTTTTAGC
19715 C-AAAA----GATGGTTAGTACACGATTTT-GCCTAAAATTTTGCAAAAAATGACCAC-AAAAAT
66 CAAAAACTGTGATGGTTAGTACACGATTTTAG-CTAAAATTTTGCAAAAAATGACCACGAAAAAT
*
19773 TTTTCCTCAAGTTTTGGATAAAATACTCAT
130 TTTTCCTCAATTTTTGGATAAAATACTCAT
19803 TTTGGCTAAA
Statistics
Matches: 436, Mismatches: 44, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
324 36 0.08
325 45 0.10
329 4 0.01
330 201 0.46
331 115 0.26
332 35 0.08
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (332 bp):
TTCAAGGAATCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAAAGCGTTTTTAGC
CAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAAATGACCACGAAAAATT
TTTCCTCAATTTTTGGATAAAATACTCATATAATATATATAATTTAACACCAAAAAGATTGGACG
ACTTGTCACGCTTTTAATATCGTTTTTCAAATTTCTTCTAAATTAATTCTAATTAAATCGAAACA
AGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAAGGAGACAAAGTTTTTATTAGATCAATA
TAGATAG
Done.